U.S. patent application number 17/313742 was filed with the patent office on 2021-12-23 for methods of identifying risk of bevacizumab-induced proteinuria and hypertension.
The applicant listed for this patent is Duke University, The University of North Carolina at Chapel Hill. Invention is credited to Federico Innocenti, Danyu Lin, Kouros Owzar, Julia Quintanilha, Jin Wang.
Application Number | 20210395833 17/313742 |
Document ID | / |
Family ID | 1000005826074 |
Filed Date | 2021-12-23 |
United States Patent
Application |
20210395833 |
Kind Code |
A1 |
Innocenti; Federico ; et
al. |
December 23, 2021 |
METHODS OF IDENTIFYING RISK OF BEVACIZUMAB-INDUCED PROTEINURIA AND
HYPERTENSION
Abstract
The disclosure relates to methods of identifying subjects at
risk of developing bevacizumab-induced toxicities such as
proteinuria and/or hypertension involving measuring nucleic acid or
gene mutations in a sample obtained from the subject.
Inventors: |
Innocenti; Federico; (Chapel
Hill, NC) ; Quintanilha; Julia; (Chapel Hill, NC)
; Lin; Danyu; (Chapel Hill, NC) ; Owzar;
Kouros; (Durham, NC) ; Wang; Jin; (Chapel
Hill, NC) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The University of North Carolina at Chapel Hill
Duke University |
Chapel Hill
Durham |
NC
NC |
US
US |
|
|
Family ID: |
1000005826074 |
Appl. No.: |
17/313742 |
Filed: |
May 6, 2021 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
16932002 |
Jul 17, 2020 |
11028448 |
|
|
17313742 |
|
|
|
|
62903442 |
Sep 20, 2019 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 2600/106 20130101;
C12Q 1/6883 20130101; C12Q 2600/156 20130101; C12Q 1/6886
20130101 |
International
Class: |
C12Q 1/6886 20060101
C12Q001/6886; C12Q 1/6883 20060101 C12Q001/6883 |
Goverment Interests
STATEMENT OF GOVERNMENTAL INTEREST
[0002] This invention was made with government support under Grant
Numbers CA180821, CA180882, CA196171, CA233327, CA233253, CA233373,
CA139280 and CA140390 awarded by the National Institutes of Health.
The government has certain rights in the invention.
Claims
1. A method of treating a subject, the method comprising the steps
of: a. determining the risk of developing one or more VEGF-pathway
inhibitor-induced toxicities in the subject based upon the presence
or absence of a mutation in one or more nucleic acids in a sample
obtained from a subject, wherein the subject is undergoing therapy
or is a candidate for therapy with a VEGF-pathway inhibitor; and b.
modulating therapy with a VEGF-pathway inhibitor and/or providing
the subject with one or more supportive therapies based upon the
determined risk of developing one or more VEGF-pathway
inhibitor-induced toxicities in the subject.
2. The method of claim 1, wherein the method further comprises
detecting the mutation in the one or more nucleic acids in a sample
obtained from the subject.
3. The method of claim 1, wherein the detecting of the mutation in
one or more nucleic acids in the sample comprises detecting a
single nucleotide polymorphism (SNP) in the one or more nucleic
acids in the sample.
4. The method of claim 3, wherein the SNP is located in a gene
provided in Table 8 or Table 9.
5. The method of claim 4, wherein the gene is KCNAB1, PIK3R5, DNAH5
TRIO, or TTMA.
6. The method of claim 4, wherein the mutation in the gene is a
mutation that lowers expression of KCNAB1 relative to wildtype.
7. The method of claim 3, wherein the SNP is selected from the SNPs
provided in Table 4, Table 5, Table 6, Table 7, Table 10, Table 11,
Table 12, Table 13, rs444904, and rs427554.
8. The method of claim 3, wherein the SNP is selected from the
group consisting of rs339947, rs12482855, rs13135230, rs2350620,
rs11662763, rs6770663, rs408130, rs418173, rs12482855, rs444904,
and rs427554.
9. The method of claim 8, wherein a. the mutation is SNP rs6770663
and wherein the base identified at rs6770663 is a guanine, b. the
mutation is SNP rs444904 and wherein the base identified at
rs444904 is a an adenine, c. the mutation is rs427554 and wherein
the base identified at rs427554 is an adenine, d. the mutation is
SNP rs339947 and wherein the base identified at rs339947 is an
adenine, and/or e. the mutation is SNP rs11662763 and the base
identified at rs11662763 is an adenine.
10. The method of claim 1, wherein the one or more VEGF-pathway
inhibitor-induced toxicities are selected from proteinuria,
hypertension, or both.
11. The method of claim 10, comprising providing the subject with
one or more supportive therapies when the subject is determined to
have a high risk of developing proteinuria, hypertension, or
both.
12. The method of claim 11, wherein the one or more supportive
therapies include one or more anti-hypertensive agents, one or more
proteinuria medications, or a combination thereof.
13. The method of claim 12, wherein the anti-hypertensive agent or
proteinuria medication is in a class of drug selected from the
group consisting of diuretics, beta blockers, alpha and beta
blockers, calcium channel blockers, Angiotensin-converting enzyme
(ACE) inhibitors, angiotensin II receptor antagonists (ARBs),
adrenergic receptor antagonists, vasodilators, renin inhibitors,
aldosterone receptor antagonists, alpha-2 adrenergic receptor
agonists, central alpha-2 agonists and other centrally acting
drugs, and endothelin receptor blockers.
14. (canceled)
15. The method of claim 11, wherein the supportive therapy
comprises blood pressure monitoring and/or monitoring for
proteinuria.
16. The method of claim 11, wherein the subject is treated with the
supportive therapy prior to or concurrently with the VEGF pathway
inhibitor.
17. (canceled)
18. (canceled)
19. (canceled)
20. (canceled)
21. The method of claim 1, wherein modulating therapy with the VEGF
pathway inhibitor comprises reducing the total number of doses of
the VEGF inhibitor.
22. The method of claim 1, wherein modulating therapy with the VEGF
pathway inhibitor comprises reducing the dosing frequency of the
VEGF inhibitor.
23. (canceled)
24. (canceled)
25. (canceled)
26. The method of claim 1, wherein the VEGF-pathway inhibitor is
selected from the group consisting of bevacizumab,
bevacizumab-awwb, bevacizumab-bvzr, ranibizumab, aflibercept,
ziv-aflibercept, lenalidomide, lenvatinib, ramucirumab,
cabozantinib, pazopanib, sunitinib malate, regorafenib, axitinib,
tipiracil and trifluridine, ponatinib, vandetanib, sorafenib,
everolimus, thalidomide, temsirolimus, interferon alfa, interferon
alfa-2B, interferon alfa-N3, peginterferon alfa-2B, peginterferon
alfa-2A, rhEndostatin, cediranib, semaxanib, pomalidomide,
alitretinoin, imiquimod, sinecatechins, vismodegib, sonidegib,
pegaptanib sodium, dexamethasone intravitreal implant, fluocinolone
acetonide, conbercept, brolucizumab-dbll, selpercatinib,
nintedanib, apatinib, and motesanib.
27. (canceled)
28. A method for treating or preventing a VEGF pathway
inhibitor-induced toxicity in a subject in need of treatment with a
VEGF pathway inhibitor, the method comprising (i) identifying the
subject as having a mutation in the gene KCNAB1 and (ii) treating
the subject with one or more prophylactic therapies for the
toxicity.
29. A method for treating a subject having a disease or disorder
associated with neovascularization or angiogenesis, the method
comprising (i) identifying the subject as having a mutation in the
gene KCNAB1; (ii) treating the subject with an anti-hypertensive
agent; and (iii) treating the subject with a VEGF pathway
inhibitor.
30. (canceled)
Description
CROSS REFERENCE TO RELATED APPLICATION
[0001] This application is a continuation of U.S. application Ser.
No. 16/932,002, filed Jul. 17, 2020, which claims priority to U.S.
Provisional Application No. 62/903,442, filed Sep. 20, 2019, which
are hereby incorporated by reference in its entirety.
FIELD
[0003] The present disclosure relates to methods of identifying
patients at risk of developing bevacizumab-induced toxicities. In
particular, the disclosure relates methods of identifying patients
at risk of developing bevacizumab-induced proteinuria and/or
hypertension involving measuring nucleic acid mutations in a sample
obtained from the patient.
BACKGROUND
[0004] Bevacizumab is a recombinant humanized monoclonal antibody
that targets vascular endothelial growth factor (VEGF), inhibiting
its binding to its receptors VEGFR1 and VEGFR2. It was approved by
the U.S. Food and Drug Administration (FDA) in 2004 and by the
European Medicines Agency in 2005 for the treatment of metastatic
colorectal cancer. The FDA has also approved its use for the
treatment of advanced non-squamous lung cancer, metastatic renal
cell carcinoma, recurrent glioblastoma, advanced cervical cancer
and platinum-resistant ovarian cancer..sup.1 Bevacizumab antitumor
efficacy relies on its inhibition of the VEGF-signaling pathway
involved in endothelial survival, vascular permeability and
therefore angiogenesis..sup.2
[0005] Despite the demonstrated efficacy of bevacizumab in
combination with other therapies, patients frequently experience
toxicity that limits the duration of therapy with bevacizumab and
the efficacy of the regimen. The most frequent toxicities are
hypertension and proteinuria, with a prevalence that varies in
different studies (proteinuria 21%-41%, hypertension
3%-43)..sup.3-5 Although hypertension and proteinuria are usually
asymptomatic, they can be occasionally life
threatening..sup.4,5
[0006] The underlying mechanisms of how bevacizumab induces
hypertension and proteinuria are not well understood, but they are
postulated to involve nitric oxide (NO) inhibition and increases in
peripheral vascular resistance, renal dysfunction and glomerular
damage by inhibition of VEGF produced by podocytes. It is not clear
whether the occurrence of proteinuria shares the same mechanism
responsible for hypertension, or whether the kidney damage is a
secondary effect..sup.6
[0007] Currently, there are no validated biomarkers to predict
bevacizumab-induced hypertension or proteinuria. Previous genetic
studies of bevacizumab-induced hypertension focused on a few
single-nucleotide polymorphisms (SNPs) in genes of the VEGF
pathway..sup.7-14
[0008] Despite the reported associations, none of the studies
generated robust enough evidence to use these markers in the
clinic, mostly because the biomarker signal was not concordant
across multiple studies..sup.16 Accordingly, what is needed are
robust biomarkers and methods of identifying patients at risk of
bevacizumab-induced hypertension and/or proteinuria that can be
reproduced in different studies.
SUMMARY
[0009] Provided herein are methods for determining risk and/or
treating a subject.
[0010] In one aspect, provided herein is a method including
detecting a mutation in one or more nucleic acids in a sample
obtained from a subject who is undergoing therapy or is a candidate
for therapy with a VEGF-pathway inhibitor.
[0011] In another aspect, provided herein is a method of predicting
the risk of developing one or more VEGF-pathway inhibitor-induced
toxicities in a subject, including detecting a mutation in one or
more nucleic acids in a sample obtained from the subject who is
undergoing therapy or is a candidate for therapy with a
VEGF-pathway inhibitor, and determining the risk of developing one
or more VEGF-pathway inhibitor-induced toxicities in the subject
based upon the presence or absence of the mutation in the one or
more nucleic acids in the sample.
[0012] In another aspect, provided herein is a method of treating a
subject, comprising detecting a mutation in one or more nucleic
acids in a sample obtained from a subject who is undergoing therapy
or is a candidate for therapy with a VEGF-pathway inhibitor;
determining the risk of developing one or more VEGF-pathway
inhibitor-induced toxicities in the subject based upon the presence
or absence of the mutation in the one or more nucleic acids in the
sample; and modulating therapy with a VEGF-pathway inhibitor and/or
providing the subject with one or more supportive therapies based
upon the determined risk of developing one or more VEGF-pathway
inhibitor-induced toxicities in the subject.
[0013] In another aspect, provided herein is a method for treating
or preventing a VEGF pathway inhibitor-induced toxicity in a
subject in need of treatment with a VEGF-pathway inhibitor, the
method comprising identifying the subject as having a genetic
mutation that confers a risk of developing the VEGF pathway
inhibitor-induced toxicity, and treating the subject with a
supportive and/or prophylactic therapy for the toxicity in addition
to the VEGF-pathway inhibitor.
[0014] In another aspect, provided herein is a method for treating
a subject having a disease or disorder, wherein the disease or
disorder is indicated for treatment with a VEGF pathway inhibitor,
the method comprising identifying the subject as having a genetic
mutation that confers a risk of developing a VEGF pathway
inhibitor-induced toxicity, treating the subject with a supportive
and/or prophylactic therapy to prevent or reduce the toxicity, and
treating the subject with the VEGF-pathway inhibitor.
[0015] In embodiments, the mutation is in a gene selected from the
group consisting of KCNAB1, DNAH5, TRIO, RIPK4, IL17F, ASPH, TTMA,
EPB41L3 and SLC25A24. In embodiments, the genetic mutation is a
SNP. In embodiments, the genetic mutation is a mutation that lowers
expression of KCNAB1 relative to wild type.
[0016] In embodiments, the SNP is selected from the group
consisting of rs339947, rs12482855, rs13135230, rs2350620,
rs11662763, rs6770663, rs408130, rs418173, rs12482855, rs444904,
and rs427554. In embodiments, the base identified at rs339947 is an
adenine, the base identified at rs12482855 is an adenine, the base
identified at rs11662763 is an adenine, the base identified at
rs408130 is an adenine, the base identified at rs418173 is an
adenine, the base identified at rs12482855 is an adenine, the base
identified at rs13135230 is an adenine, the base identified at
rs11662763 is an adenine, the base identified at rs6770663 is a
guanine, the base identified at rs444904 is an adenine, the base
identified at rs427554 is an adenine, the base identified at
rs2350620 is a guanine, or the base identified at rs11662763 is an
adenine. In embodiments, the toxicity comprises hypertension and
the SNP is rs677063, wherein the base identified at rs6770663 is a
guanine.
[0017] In embodiments, the toxicity comprises hypertension,
proteinuria, or both. In embodiments, the methods provided herein
comprise administering a prophylactic and/or supportive therapy to
prevent or reduce the toxicity. In embodiments, the prophylactic
and/or supportive therapy is administered to the patient prior to
and/or concurrently with administration of the VEGF pathway
inhibitor. In embodiments, the methods comprise delaying the
initiation of treatment with the VEGF pathway inhibitor until the
prophylactic and/or supportive therapy has been administered to the
subject for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
or more days, and/or until the subject's hypertension or
proteinuria or other condition associated with the toxicity is
reduced and/or resolved and/or under control. In embodiments, the
methods comprise adding one or more prophylactic and/or supportive
therapy to the subject's treatment regimen; switching the subject
to a different prophylactic and/or supportive therapy; and/or
increasing the dose and/or frequency of dosing of an
anti-hypertensive agent relative to the dose administered to the
subject prior to treatment with the VEGF pathway inhibitor. For
example, in embodiments, a subject may have already been undergoing
a treatment regimen with a prophylactic and/or supportive therapy
for the condition associated with the toxicity risk. In such
situations, the methods may comprise adding one or more additional
prophylactic and/or supportive therapy, switching to a different
class of drug for the prophylactic and/or supportive therapy,
switching to a different drug within the same class for the
prophylactic and/or supportive therapy, and/or increasing the dose
and/or frequency of dosing with the prophylactic and/or supportive
therapy, when the subject is identified as being at risk of
developing the toxicity upon treatment with a VEGF pathway
inhibitor.
[0018] In embodiments, the methods provided herein comprise
modulating the dose of the VEGF pathway inhibitor. For example, in
embodiments, the methods comprise reducing the total dosing amount,
mg/kg dosing amount, or frequency of dosing of the VEGF pathway
inhibitor. In embodiments, modulating the dose of the VEGF pathway
inhibitor comprises starting at a dose lower than the recommended
starting dose and maintaining the low dose or increasing the dose
as appropriate with close monitoring for signs of the toxicity. In
embodiments, the dose modulation is for the duration of treatment
of the VEGF pathway inhibitor. In embodiments, the dose modulation
is for a portion of the treatment with the VEGF pathway inhibitor,
for example while symptoms of the toxicity persist. In embodiments,
the methods comprise monitoring the subject for signs and symptoms
of the toxicity or for worsening severity of the toxicity.
[0019] In embodiments, the toxicity comprises hypertension. In
embodiments, the methods comprise monitoring the blood pressure of
the subject, and/or monitoring the blood pressure of the subject
more frequently than the blood pressure would be monitored in a
patient who does not have the risk factor for the toxicity as
provided herein. In embodiments, the toxicity comprises
proteinuria. In embodiments, the toxicity comprises monitoring for
proteinuria. In embodiments, monitoring for proteinuria comprises a
urine dipstick and sulfosalicyclic acid test, a 24 hour urine
collection test assay, or a spot albumin or protein-to-creatinine
ratio test. In embodiments, the prophylactic and/or supportive
therapy is an anti-hypertensive agent and/or an agent that treats
or prevents proteinuria (e.g., a proteinuria medication). In
embodiments, the anti-hypertensive agent or proteinuria medication
is selected from the group consisting of loop diuretics, thiazide
diuretics, thiazide-like diuretics, potassium-sparing diuretics,
calcium channel blockers, ACE inhibitors, angiotensin II receptor
antagonists, adrenergic receptor antagonists, vasodilators, renin
inhibitors, aldosterone receptor antagonists, alpha-2 adrenergic
receptor agonists, and endothelium receptor blockers.
[0020] In embodiments, the VEGF pathway inhibitor is any drug or
therapeutic agent that inhibits, interferes with, or alters the
VEGF pathway. For example, the VEGF pathway inhibitor may be an
antibody, an antibody-like molecule, a small molecule, a soluble
protein, a peptide, or the like that interferes with the VEGF-VEGFR
interaction. In embodiments, the VEGF pathway inhibitor is selected
from the group consisting of bevacizumab, bevacizumab-awwb,
bevacizumab-bvzr, ranibizumab, aflibercept, ziv-aflibercept,
lenalidomide, lenvatinib, ramucirumab, cabozantinib, pazopanib,
sunitinib malate, regorafenib, axitinib, tipiracil and
trifluridine, ponatinib, vandetanib, sorafenib, everolimus,
thalidomide, temsirolimus, interferon alfa, interferon alfa-2B,
interferon alfa-N3, peginterferon alfa-2B, peginterferon alfa-2A,
rhEndostatin, cediranib, semaxanib, pomalidomide, alitretinoin,
imiquimod, sinecatechins, vismodegib, sonidegib, pegaptanib sodium,
dexamethasone intravitreal implant, fluocinolone acetonide,
conbercept, brolucizumab-dbll, selpercatinib, nintedanib, apatinib,
and motesanib. In embodiments, the VEGF pathway inhibitor is any
biosimilar, generic, salt, ester, ether, isomer, mixture of
isomers, complex, prodrug, or derivative of any VEGF pathway
inhibitor provided herein or otherwise known in the art.
[0021] In embodiments, treating the subject with the VEGF pathway
inhibitor comprises reducing exposure of the subject to the VEGF
pathway inhibitor relative to the exposure of a subject treated as
provided on prescribing information (e.g., the package insert or
label) for the VEGF pathway inhibitor. For example, in embodiments,
the methods provided herein comprise delaying initiation of
treatment with the VEGF inhibitor, reducing the dose of the VEGF
inhibitor, reducing the total number of doses of the VEGF
inhibitor, reducing the dosing frequency of the VEGF inhibitor,
and/or selecting a different VEGF pathway inhibitor (e.g., a VEGF
pathway inhibitor that is less likely to be associated with the
toxicity) or a non-VEGF pathway inhibitor therapy in the method of
treating the subject, wherein the subject has been identified as
being at risk of developing the toxicity. In embodiments, reducing
the dose of the VEGF inhibitor comprises reducing the dose by about
5%, about 10%, about 25%, about 33%, about 50%, about 75%, or more
relative to a reference dose, wherein the reference dose is the
dose provided in prescribing information for the VEGF inhibitor. In
embodiments, reducing the total number of doses of the VEGF
inhibitor comprises reducing the total number of doses by about 5%,
about 10%, about 25%, about 33%, about 50%, about 75%, or more
relative to a reference total number of doses, wherein the
reference total number of doses are total number of doses provided
in prescribing information for the VEGF inhibitor. In embodiments,
the methods comprise starting the subject on a lower dose and/or
dosing frequency than the starting dose and/or dosing frequency
recommended on the package insert for the VEGF pathway inhibitor,
and titrating the dose upward to the dose and/or dosing frequency
recommended on the package insert. In embodiments, such dosing
comprising upward titrating is performed in combination with close
monitoring of the subject for the toxicity. In embodiments,
reducing the dosing frequency of the VEGF inhibitor comprises
reducing the dosing frequency to about one third, about half, or
about three quarters as often as the dosing frequency provided in
prescribing information for the VEGF inhibitor.
Definitions
[0022] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art. In case of conflict, the present
document, including definitions, will control. Preferred methods
and materials are described below, although methods and materials
similar or equivalent to those described herein can be used in
practice or testing of the present disclosure. All publications,
patent applications, patents and other references mentioned herein
are incorporated by reference in their entirety. The materials,
methods, and examples disclosed herein are illustrative only and
not intended to be limiting.
[0023] The terms "comprise(s)," "include(s)," "having," "has,"
"can," "contain(s)," and variants thereof, as used herein, are
intended to be open-ended transitional phrases, terms, or words
that do not preclude the possibility of additional acts or
structures. The singular forms "a," "and" and "the" include plural
references unless the context clearly dictates otherwise. The
present disclosure also contemplates other embodiments
"comprising," "consisting of and "consisting essentially of," the
embodiments or elements presented herein, whether explicitly set
forth or not.
[0024] For the recitation of numeric ranges herein, each
intervening number there between with the same degree of precision
is explicitly contemplated. For example, for the range of 6-9, the
numbers 7 and 8 are contemplated in addition to 6 and 9, and for
the range 6.0-7.0, the number 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6,
6.7, 6.8, 6.9, and 7.0 are explicitly contemplated. Recitation of
ranges of values herein are merely intended to serve as a shorthand
method of referring individually to each separate value falling
within the range, unless otherwise-Indicated herein, and each
separate value is incorporated into the specification as if it were
individually recited herein. For example, if a concentration range
is stated as 1% to 50%, it is intended that values such as 2% to
40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in
this specification. These are only examples of what is specifically
intended, and all possible combinations of numerical values between
and including the lowest value and the highest value enumerated are
to be considered to be expressly stated in this disclosure.
[0025] The term "single nucleotide polymorphism" or "SNP" as used
interchangeably herein refer to a DNA sequence variation occurring
when a single nucleotide (adenine (A), thymine (T), cytosine (C),
or guanine (G)) in the genome differs between members of a species.
Single nucleotides may be changed (substitution), removed
(deletions) or added (insertion) to a polynucleotide sequence.
Single nucleotide polymorphisms may fall within coding sequences of
genes, non-coding regions of genes, or in the intergenic regions
between genes. SNPs within a coding sequence may not necessarily
change the amino acid sequence of the protein that is produced, due
to degeneracy of the genetic code.
[0026] "Subject" and "patient" as used herein interchangeably
refers to any vertebrate, including, but not limited to, a mammal
(e.g., cow, pig, camel, llama, horse, goat, rabbit, sheep,
hamsters, guinea pig, cat, dog, rat, and mouse, a non-human primate
(e.g., a monkey, such as a cynomolgus or rhesus monkey, chimpanzee,
etc.) and a human). In some embodiments, the subject may be a human
or a non-human. In one embodiment, the subject is a human. The
subject or patient may be undergoing various forms of treatment,
such as with a VEGF-pathway inhibitor. The subject may be male or
female. The subject may be of any ancestry. In some embodiments,
the subject is of European ancestry.
[0027] "Treat," "treating" or "treatment" are each used
interchangeably herein to describe reversing, alleviating, or
inhibiting the progress of a disease and/or injury, or one or more
symptoms of such disease, to which such term applies. Depending on
the condition of the subject, the term also refers to preventing a
disease, and includes preventing the onset of a disease, or
preventing the symptoms associated with a disease. A treatment may
be either performed in an acute or chronic way. The term also
refers to reducing the severity of a disease or symptoms associated
with such disease prior to affliction with the disease. Such
prevention or reduction of the severity of a disease prior to
affliction refers to administration of a treatment to a subject
that is not at the time of administration afflicted with the
disease. "Preventing" also refers to preventing the recurrence of a
disease or of one or more symptoms associated with such
disease.
[0028] "Therapy" and/or "therapy regimen" generally refer to the
clinical intervention made in response to a disease, disorder or
physiological condition manifested by a patient or to which a
patient may be susceptible. The aim of treatment includes the
alleviation or prevention of symptoms, slowing or stopping the
progression or worsening of a disease, disorder, or condition
and/or the remission of the disease, disorder or condition. The
term "providing" or "administering" as used herein with relation to
a therapy (e.g. a VEGF-pathway inhibitor or a supportive therapy)
may refer to providing to the subject the therapy or modulating the
dose of a therapy currently being provided to the patient. For
example, providing a supportive therapy may refer to increasing the
dose of a supportive therapy currently being administered to the
subject. The term "supportive therapies" and the like may be used
interchangeably herein with "prophylactic therapies" and the like
and refers to a therapy other than the therapy with the VEGF
pathway inhibitor that prevents or controls (e.g., reduces the
severity of or resolves) an adverse event such as hypertension or
proteinuria. For example, the supportive therapy may be an
anti-hypertensive agent.
DESCRIPTION OF THE DRAWINGS
[0029] These and other features, aspects, and advantages of the
present disclosure will become better understood with regard to the
following drawings:
[0030] FIG. 1 shows CONSORT and quality control flowchart for CALGB
80303, 40503, 90401, and 40502. MAF minor allele frequency, HWE
Hardy-Weinberg Equilibrium.
[0031] FIG. 2 shows Manhattan plots (left) and quantile-quantile
(Q-Q) plots (right) from the SNP-based association results for
proteinuria, hypertension, and composite toxicity grade.gtoreq.2.
Composite toxicity is defined as the occurrence of either
proteinuria or hypertension or both.
[0032] FIG. 3 shows effect of genotypes of rs339947 and rs12482855
associated with proteinuria grade.gtoreq.2, rs13135230 and
rs2350620 associated with hypertension grade.gtoreq.2, and
rs11662763 associated with composite toxicity grade.gtoreq.2.
Composite toxicity is defined as the occurrence of either
proteinuria or hypertension or both.
[0033] FIG. 4A-4C shows LocusZoom plots using 400 kb window left
and right from the variant limits associated with
bevacizumab-induced grade.gtoreq.2 proteinuria (FIG. 4A, top panel
and FIG. 4C., top panel), composite toxicity (FIG. 4A, bottom
panel), and hypertension (FIGS. 4B and 4C., bottom panel) in
SNP-based analysis. Each circle represents the p-value for one SNP,
with the top SNP shown in purple and the SNPs in the region colored
depending on their degree of linkage disequilibrium (LD) (R.sup.2).
X-axis denotes the position of the SNP in the region on chromosome;
Y-axis denotes the p-value of the association.
[0034] FIG. 5 shows Manhattan plots (left) and quantile-quantile
(Q-Q) plots (right) from the SNP-based association results for
proteinuria, hypertension, and composite toxicity grade.gtoreq.3.
Composite toxicity is defined as the occurrence of either
proteinuria or hypertension or both.
[0035] FIG. 6 shows LocusZoom plots using 400 kb window left and
right from the variant limits associated with bevacizumab-induced
grade.gtoreq.3 proteinuria, hypertension, and composite toxicity in
SNP-based analysis. Each circle represents the p-value for one SNP,
with the top SNP shown in purple and the SNPs in the region colored
depending on their degree of linkage disequilibrium (LD) (R.sup.2).
X-axis denotes the position of the SNP in the region on chromosome;
Y-axis denotes the p-value of the association.
[0036] FIG. 7 shows quantile-quantile (Q-Q) plot from gene-based
association results for grade.gtoreq.3 proteinuria, hypertension,
and composite toxicity. Composite toxicity is defined as the
occurrence of either proteinuria or hypertension or both.
[0037] FIG. 8 shows LocusZoom plots using 400 kb window left and
right from the IL17F and SLC25A24 limits associated with
bevacizumab-induced proteinuria and composite toxicity,
respectively, in gene-based analysis of grade.gtoreq.3. Each circle
represents the p-value for one SNP, with the top SNP shown in
purple and the SNPs in the region colored depending on their degree
of linkage disequilibrium (LD) (R.sup.2). X-axis denotes the
position of the SNP in the region on chromosome; Y-axis denotes the
p-value of the association. Composite toxicity is defined as the
occurrence of either proteinuria or hypertension or both.
[0038] FIG. 9A provides a quality control flowchart for the TARGET
study. Abbreviations: IBS: identical by state, MAF: minor allele
frequency, HWE: Hardy-Weinberg Equilibrium, QC: quality control,
SNP: single nucleotide polymorphism.
[0039] FIG. 9B is a bar graph showing the frequency of rs444904 AA,
GA, and GG genotypes associated with sorafenib-induced
hypertension.
[0040] FIG. 10 shows the effect of genotypes of rs427554 associated
with bevacizumab-induced hypertension.
[0041] FIG. 11 is a graphic showing the mechanism of action of
sorafenib and bevacizumab.sup.65.
[0042] FIG. 12 is a graphic showing the function of the SP1
transcription factor..sup.67 DNMT: DNA methyl transferase.
[0043] FIG. 13 shows the cumulative incidence of grade.gtoreq.2
hypertension for rs2350620 and rs6770663.
DETAILED DESCRIPTION
[0044] Provided herein are methods of predicting risk and/or
treating a subject. In some embodiments, the methods comprise
detecting one or more mutations in one or more nucleic acids in a
sample obtained from the subject. In some aspects, the methods
comprise detecting one or more mutations in one or more genes in a
sample obtained from the subject.
[0045] In one aspect, provided herein is a method comprising
detecting one or more mutations (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or
10 mutations) in one or more nucleic acids or genes in a sample
obtained from a subject. In some embodiments, the method further
comprises determining the risk of developing one or more
VEGF-pathway inhibitor-induced toxicities in the subject based upon
the presence or absence of one or more mutations in the one or more
nucleic acids or genes in the sample.
[0046] In another aspect, provided herein is a method of predicting
the risk of developing one or more toxicities induced by a
therapeutic agent (e.g., a VEGF-pathway inhibitor) in a subject.
The method comprises detecting one or more mutations (e.g., 1, 2,
3, 4, 5, 6, 7, 8, 9 or 10 mutations) in one or more nucleic acids
or genes in a sample obtained from the subject, and determining the
risk of developing one or more VEGF-pathway inhibitor-induced
toxicities in the subject based upon the presence or absence of the
mutation in the one or more nucleic acids or genes in the
sample.
[0047] In another aspect, provided herein is a method of treating a
subject comprising detecting one or more mutations in one or more
nucleic acids or genes in a sample obtained from a subject,
determining the risk of developing one or more VEGF-pathway
inhibitor-induced toxicities in the subject based upon the presence
or absence of one or more mutations in the one or more nucleic
acids or genes in the sample, and modulating therapy with a
VEGF-pathway inhibitor based upon the determined risk of developing
one or more VEGF-pathway inhibitor-induced toxicities in the
subject. Modulating the therapy may include, for example,
monitoring the subject for improvement or worsening of the
toxicity, administering a supportive therapy to the subject, and/or
adjusting the dose of the VEGF-pathway inhibitor. For example, in
embodiments, the present disclosure provides methods of treating a
subject comprising detecting one or more mutations in one or more
nucleic acids or genes in a sample obtained from a subject,
determining the risk of hypertension or severe hypertensive crisis
in the subject based upon the presence or absence of one or more
mutations in the one or more nucleic acids or genes in the sample,
and administering to the subject an anti-hypertensive agent prior
to or concurrently with administration of the VEGF-pathway
inhibitor.
[0048] In another aspect, provided herein is a method of treating a
subject, comprising determining the risk of developing one or more
VEGF-pathway inhibitor-induced toxicities in the subject based upon
the presence or absence of one or more (e.g., 1, 2, 3, 4, 5, 6, 7,
8, 9 or 10 or more mutations) in one or more nucleic acids or genes
in a sample obtained from a subject, and modulating therapy with a
VEGF-pathway inhibitor based upon the determined risk of developing
one or more VEGF-pathway inhibitor-induced toxicities in the
subject. In some aspects, the method of treating a subject may be
performed by one party. In other aspects, the method of treating a
subject may be performed by two or more parties. For example, the
presence or absence of one or more mutations in one or more nucleic
acids in a sample may be measured by one party and a different
party could modulate therapy with a VEGF-pathway inhibitor. For
example, one party could analyze the sample to detect one or more
mutations in nucleic acids or genes and provide information
regarding these mutations to enable a second party to determine the
risk in the subject and modulate therapy with the VEGF-pathway
inhibitor based upon the determined risk. Alternatively, one party
could analyze the sample to detect one or more mutations in nucleic
acids or genes and determine the risk of developing one or more
VEGF-pathway inhibitor-induced toxicities based upon the analysis,
and a second party (e.g. a physician) could then modulate therapy
with a VEGF-pathway inhibitor based upon the risk determination
provided by the first party.
[0049] In an aspect, provided herein is a method for treating a
subject having a disease or disorder associated with
neovascularization or angiogenesis, the method comprising
identifying the subject as having a mutation in the gene KCNAB1;
treating the subject with an anti-hypertensive agent; and treating
the subject with an angiogenesis inhibitor (e.g., a VEGF pathway
inhibitor). In embodiments, the mutation is an SNP. In embodiments,
the SNP is rs6770663. In embodiments, the base identified at
rs6770663 is a guanine. In embodiments, provided herein is a method
for treating a population of patients with a VEGF-pathway
inhibitor, the method comprising providing a first population of
patients who have a disease or disorder indicated for treatment
with a VEGF-pathway inhibitor; separating patients who have the SNP
rs6770663 into a second population of patients; and treating the
second population of patients with an anti-hypertensive agent prior
to or concurrently with administering the VEGF pathway inhibitor to
the subject.
[0050] In accordance with any of the aspects and embodiments
described herein, the subject may be a mammal. In particular
embodiments, the subject is a human. The subject may be undergoing
treatment or a candidate for treatment with a VEGF-pathway
inhibitor.
[0051] Detecting a mutation in one or more nucleic acids in the
sample may comprise detecting one or more single-nucleotide
polymorphisms (SNPs) in the one or more nucleic acids in the
sample, one or more deletions, insertions, copy number variations,
inversions, or dislocations; and/or deletion of an entire gene of
interest; and/or one or more mutations in one or more genes that
affect the expression or function of a gene of interest. In some
embodiments, the method comprises detecting a single SNP. In some
embodiments, the method comprises detecting two SNPs. In yet other
embodiments, the method comprises detecting three SNPs. In other
embodiments, the method comprises detecting four SNPs, etc. In some
embodiments, one or more SNPs is located in one or more genes
provided in Table 8 or Table 9. In embodiments, the mutations
provided herein that are associated with the risk of developing a
VEGF-pathway-inhibitor-induced toxicity are present in one or more
genes selected from the group consisting of KCNAB1 and ASPH.
[0052] KCNAB1 encodes the K.sup.+ voltage activated channel
subfamily 1 subunit .beta.1 (K.sub.v.beta.1.1-1.3) and it is highly
expressed in arteries (aorta, coronary, tibial), and endothelial
cells. Variant rs6770663 is located in a region of H3K4me1
enhancers in the aorta (see Table 14).
[0053] In embodiments, the present disclosure provides mutations
that predispose for lower expression of KCNAB1. For example, the
present disclosure provides methods for treating patients with
rs6770663 with a VEGF pathway inhibitor (e.g., bevacizumab),
wherein the method comprises modifying the VEGF pathway inhibitor
treatment by including monitoring for hypertension,
prophylactically treating to prevent hypertension, and/or reducing
the dosing level or dosing regimen for the VEGF pathway inhibitor
in view of the patient's increased risk of hypertension. Variant
rs6770663 has a frequency of about 10% in Europeans and a global
frequency of 30%.
[0054] ASPH (aspartate .beta.-hydroxylase) encodes the junction
protein which is expressed in arteries and in endothelial
cells.
[0055] In some embodiments, the SNP is selected from the SNPs
provided in Table 4, Table 5, Table 6, Table 7, Table 10, Table 11,
Table 12, Table 13, rs444904, rs427554, or any combinations
thereof. For example, one or more SNPs may be selected from the
group consisting of rs339947, rs12482855, rs13135230, rs2350620,
rs11662763, rs6770663, rs408130, rs418173, rs12482855, rs444904,
and rs427554, or any combinations thereof. In some embodiments, a
single mutation may be detected. In embodiments, more than one
mutation (e.g., 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more mutations) may
be detected. For example, multiple SNPs may be evaluated for
mutations in the subject. In embodiments, SNP rs6770663 confers
susceptibility to VEGF-pathway inhibitor-induced hypertension.
[0056] The present disclosure provides data and validation of the
mutations (e.g. SNPs) provided herein as clinically relevant
biomarkers of VEGF pathway inhibitor toxicities. For example, the
present disclosure demonstrates that mutations provided herein are
biomarkers for hypertension and/or proteinuria elicited by more
than one different type of VEGF pathway inhibitor. The skilled
person will understand that the results provided herein apply to
any angiogenesis inhibitor, e.g., any VEGF pathway inhibitor.
[0057] The methods described herein may involve determining the
risk of developing one or more VEGF-pathway inhibitor-induced
toxicities in the subject. Any suitable toxicity may be evaluated.
VEGF inhibitor-induced toxicities include, for example, fatigue,
asthenia, weight loss, pain, depression, pyrexia, chills, myalgia,
neurologic-sensory neuropathy, gastrointestinal toxicities (e.g.
anorexia, decreased appetite, dry mouth, stomatitis, mucositis,
nausea, vomiting, diarrhea, constipation, GI perforation), skin
toxicities (e.g. HFS, rash, alopecia, depigmentation, pruritus, dry
skin, wound healing complications), cardiovascular toxicities (e.g.
hypertension, CHF, cardiac ischemia, cerebrovascular ischemia,
embolism/thrombosis, bleeding, dyspnea, cough, pneumonitis,
dysphonia), myelotoxicities (e.g. anemia, hemoglobin elevation,
leukopenia, neutropenia, thrombocytopenia, lymphopenia), metabolic
abnormalities (e.g. bilirubin, ALT, AST, gamma-GT abnormalities,
INR abnormalities, PTT abnormalities, increased alkaline
phosphatase, hypoalbuminemia, lipase elevation, amylase elevation,
creatinine increase, increased uric acid, proteinuria,
hypophosphatemia, hypothyroidism, increased triglycerides,
increased cholesterol, hyperglycemia, hypoglycemia, hypercalcemia,
hypocalcemia, hyponatremia), and the like.
[0058] In particular embodiments, VEGF-pathway inhibitor-induced
toxicities are selected from proteinuria, hypertension, or both.
For example, determining the risk of developing one or more
VEGF-pathway inhibitor-induced toxicities may comprise diagnosing
the subject as having a high risk of developing proteinuria. In
particular embodiments, the subject is diagnosed as having a high
risk of developing proteinuria when the base identified at rs339947
is an adenine, the base identified at rs12482855 is an adenine, the
base identified at rs11662763 is an adenine, the base identified at
rs408130 is an adenine, the base identified at rs418173 is an
adenine, or the base identified at rs12482855 is an adenine.
[0059] As another example, determining the risk of developing one
or more VEGF-pathway inhibitor-induced toxicities may comprise
diagnosing the subject as having a high risk of developing
hypertension. In particular embodiments, the subject is diagnosed
as having a high risk of developing hypertension when the base
identified at rs13135230 is an adenine, the base identified at
rs11662763 is an adenine, the base identified at rs6770663 is a
guanine, the base identified at rs444904 is an adenine, or the base
identified at rs427554 is an adenine. In embodiments, the subject
is determined to be of high risk of developing hypertension when
the base identified at rs6770663 is a guanine.
[0060] In some embodiments, determining the risk of developing one
or more VEGF-pathway inhibitor-induced toxicities comprises
diagnosing the subject as having a low risk of developing
hypertension. For example, the subject may be diagnosed as having a
low risk of developing hypertension when the base identified at
rs2350620 is a guanine.
[0061] In some embodiments, determining the risk of developing one
or more VEGF-pathway inhibitor-induced toxicities comprises
diagnosing the subject as having a high risk of developing either
proteinuria, or hypertension, or both (e.g. composite toxicity).
For example, the subject may be diagnosed as having a high risk of
developing proteinuria or hypertension or both when the base
identified at rs11662763 is an adenine.
[0062] In some embodiments, the methods described herein further
comprise modulating therapy with a VEGF-pathway inhibitor based
upon the risk determined in the subject. For example, the method
may comprise providing the subject with a VEGF-pathway inhibitor or
increasing the therapeutic dose of the VEGF pathway inhibitor when
the subject is determined to have a low risk of developing one or
more VEGF-pathway inhibitor toxicities. For example, the method may
comprise providing the subject with a VEGF-pathway inhibitor or
increasing the therapeutic dose of the VEGF pathway inhibitor when
the subject is diagnosed as having a low risk of developing
proteinuria, hypertension, or both. In some embodiments, the method
may comprise lowering the dose of a VEGF-pathway inhibitor or
ceasing treatment with the VEGF-pathway inhibitor when the subject
is determined to have a high risk of developing one or more
VEGF-pathway inhibitor toxicities, such as a high risk of
developing proteinuria, hypertension, or both. In embodiments, the
method may comprise starting the subject who is determined to have
a high risk of developing one or more VEGF pathway inhibitor
toxicities, such as the high risk of developing proteinuria,
hypertension, or both, at a lower dose and/or lower dosing
frequency compared to the dose and/or regimen that is recommended
on the package insert for the VEGF pathway inhibitor, monitoring
the subject for the one or more toxicities, and titrating the dose
and/or dosing frequency upwards, if appropriate based on the
monitoring for the toxicity.
[0063] In some embodiments, the methods described herein further
comprise modulating therapy with or providing the subject with one
or more supportive therapies. The term "supportive therapies"
refers to a therapy other than the therapy with an anti-cancer
agent (e.g. a VEGF pathway inhibitor or other anti-cancer agent).
For example, the supportive therapy may be an anti-hypertensive
agent and/or a proteinuria medication. Suitable anti-hypertensive
agents and/or proteinuria medications include, for example,
diuretics, beta blockers, alpha and beta blockers, calcium channel
blockers, angiotensin-converting enzyme (ACE) inhibitors,
angiotensin II receptor antagonists (ARBs), adrenergic receptor
antagonists, vasodilators (e.g. direct vasodilators), renin
inhibitors, aldosterone receptor antagonists, alpha-2 adrenergic
receptor agonists, central alpha-2 agonists and other centrally
acting drugs, endothelin receptor blockers, and the like.
[0064] In embodiments, if the subject is determined to be at risk
of developing one or more VEGF-pathway inhibitor toxicities, the
methods provided herein comprise adding a supportive therapy to the
subject's treatment regimen, increasing the dose and/or dosing
frequency of a supportive therapy that is already a part of the
subject's treatment regimen, and/or adding one, two, three, or more
additional supportive therapies to the subject's treatment regimen.
In embodiments, the added one, two, three or more additional
supportive therapies may be different drugs in the same class as
one another and/or as a supportive therapy that was already a part
of the subject's treatment regimen; or the one, two, three, or more
additional supportive therapies may be drugs in a different class
as one another and/or as a supportive therapy that was already part
of the subject's treatment regimen. Classes of supportive therapies
are known in the art and exemplified herein, such as, for example,
diuretics, beta blockers, ACE inhibitors, angiotensin II receptor
antagonists, calcium channel blockers, direct renin inhibitors,
alpha-2 adrenergic receptor agonists, central alpha-2 agonists, and
vasodilators.
[0065] Exemplary diuretics may be thiazide or thiazide-type
diuretics. For example, the diuretic may be chlorthalidone,
hydrochlorothiazide, indapamide, or metolazone. Chlorthalidone or
hydrochlorothiazide may be administered, for example, at a dose of
about 12.5 to about 50 mg/day, once daily. Indapamide may be
administered, for example at a dose of about 1.25 to about 2.5
mg/day, once daily. Metolazone may be administered, for example, at
a dose of about 2.5 to about 5 mg/day, once daily. Exemplary
diuretics may also be loop diuretics, such as bumetanide,
furosemide, or torsemide. Bumetanide may be administered, for
example, twice daily at a dose of about 0.5 to about 2 mg/day.
Furosemide may be administered, for example, twice daily at a dose
of about 20 to about 80 mg/day. Torsemide may be administered, for
example, once daily at a dose of about 5 to about 10 mg/day.
Exemplary diuretics may also be potassium sparing diuretics, such
as amiloride or triamterene. Amiloride may be administered, for
example, once or twice daily at a dose of about 5 to about 10
mg/day. Triamterene may be administered, for example, once or twice
daily at a dose of about 50 to about 100 mg/day. Exemplary
diuretics may also be aldosterone antagonists, such as eplerenone
or spironolactone. Eplerenone may be administered, for example,
once or twice daily at a dose of about 50 to about 100 mg/day.
Spironolactone may be administered, for example, twice daily at a
dose of about 25 to about 100 mg/day. Exemplary diuretics may also
include thiazide/potassium-sparing combination diuretics, such as
hydrochlorothiazide/triamterene. Hydrochlorothiazide/triamterene
may be administered once daily, for example, at a dose of about 25
mg/about 37.5 mg to about 50 mg/about 75 mg.
[0066] Exemplary beta blockers may be cardioselective (e.g.,
atenolol, betaxolol, bisoprolol, metoprolol (tartate), or
metoprolol (succinate) extended release), noncardioselective (e.g.,
nadolol, propranolol, or long-acting propranolol), cardioselective
and vasodilatory (e.g., nebivolol), or intrinsic and
sympathomimetic activity beta-blockers (e.g., acebutolol,
penbutolol, and pindolol). Atenolol may be administered, for
example, once or twice daily at a dose of about 25 to about 100
mg/day. Betaxolol may be administered, for example, once daily at a
dose of about 5 to about 20 mg/day. Bisoprolol may be administered,
for example, once daily at a dose of about 2.5 mg to about 20
mg/day. Metoprolol (tartate) may be administered once or twice
daily at a dose of about 50 to about 200 mg/day. Metoprolol
(succinate) extended release may be administered, for example, once
daily at a dose of about 50 to about 200 mg/day. Nadolol may be
administered, for example, once daily at a dose of about 40 to
about 120 mg/day. Propanolol may be administered, for example,
twice daily at a dose of about 40 to about 160 mg/day. Long-acting
propranolol may be administered, for example, once daily at a dose
of about 60 to about 180 mg/day. Nebivolol may be administered, for
example, once daily at a dose of about 5 to about 40 mg/day.
Acebutolol may be administered, for example, twice daily at a dose
of about 200 to about 800 mg/day. Penbutolol may be administered,
for example, once daily at a dose of about 10 to about 40 mg/day.
Pindolol may be administered, for example, twice daily at a dose of
about 10 to about 60 mg/day. Exemplary combined alpha and beta
blockers include carvedilol, carvedilol phosphate, and labetalol.
Carvedilol may be administered, for example, twice daily at a dose
of about 12.5 to about 50 mg/day. Carvedilol phosphate may be
administered, for example, once daily at a dose of about 20 to
about 80 mg/day. Labetalol may be administered, for example, twice
daily at a dose of about 100 mg to about 400 mg/day.
[0067] Exemplary ACE inhibitors include benazepril, captopril,
enalapril, fosinopril, lisinopril, moexipril, perindopril,
quinapril, ramipril, and trandolapril. Benazepril may be
administered, for example, once or twice daily at a dose of about
10 to about 40 mg/day. Captopril may be administered, for example,
twice or three times daily at a dose of about 12.5 to about 150
mg/day. Enalapril may be administered, for example, once or twice
daily at a dose of about 5 to about 40 mg/day. Fosinopril may be
administered, for example, once daily at a dose of about 10 to
about 40 mg/day. Lisinopril may be administered, for example, once
daily at a dose of about 5 mg to about 40 mg/day. Moexipril may be
administered, for example, once or twice daily at a dose of about
7.5 mg to about 30 mg/day. Perindopril may be administered, for
example, once daily at a dose of about 2 to about 16 mg/day.
Quinapril may be administered, for example, once or twice daily at
a dose of about 10 to about 80 mg/day Ramipril may be administered,
for example, once or twice daily at a dose of about 2.5 to about 20
mg/day. Trandolapril may be administered, for example, once daily
at a dose of about 1 to about 4 mg/day.
[0068] Exemplary angiotensin II receptor antagonists include
candesartan, eprosartan, irbesartan, losartan, olmesartan,
telmisartan, valsartan, and azilsartan. Candesartan may be
administered, for example, once daily at a dose of about 8 to about
32 mg/day. Eprosartan may be administered, for example, once or
twice daily at a dose of about 400 to about 800 mg/day. Irbesartan
may be administered, for example, once daily at a dose of about 150
to about 300 mg/day. Losartan may be administered, for example,
once daily at a dose of about 25 to about 100 mg/day. Olmesartan
may be administered, for example, once daily at a dose of about 20
about 40 mg/day. Telmisartan may be administered, for example, once
daily at a dose of about 20 to about 80 mg/day. Valsartan may be
administered, for example, once or twice daily at a dose of about
80 to about 320 mg/day. Azilsartan may be administered, for
example, once daily at a dose of about 40 to about 80 mg/day.
[0069] Exemplary calcium channel blockers may be dihydropyridines
(e.g., amlodipine, felodipine, nifedipine long-acting, nisoldipine,
isradipine, and nicardipine SR) or nondihydropyridines (e.g.,
diltiazem ER, verapamil IR, verapamil SR, and verapamil-delayed
onset ER). Amlodipine may be administered, for example, once daily
at a dose of about 2.5 to about 10 mg/day. Felodipine may be
administered, for example, once daily at a dose of about 2.5 to
about 20 mg/day. Nifedipine long acting may be administered, for
example, once daily at a dose of about 30 to about 90 mg/day.
Nisoldipine may be administered, for example, once daily at a dose
of about 10 to about 40 mg/day. Isradipine may be administered, for
example, twice daily at a dose of about 5 to about 10 mg/day.
Nicardipine SR may be administered, for example, twice daily at a
dose of about 60 to about 120 mg/day. Diltiazem may be
administered, for example, once daily at a dose of about 120 to
about 360 mg/day. Verapamil IR may be administered, for example,
three times daily at a dose of about 120 to about 360 mg/day.
Verapamil SR maybe administered, for example, once or twice daily
at a dose of about 120 to about 360 mg/day. Verapamil-delayed onset
ER may be administered, for example, once daily in the evening at a
dose of about 100 to about 300 mg/day.
[0070] An exemplary direct renin inhibitor is aliskiren. Aliskiren
may be administered, for example, once daily at a dose of about 150
to about 300 mg/day. Exemplary alpha-1 blockers include doxazosin,
prazosin, and terazosin. Doxazosin may be administered, for
example, once daily at a dose of about 1 to about 16 mg/day.
Prazosin may be administered, for example, two or three times daily
at a dose of about 2 to about 20 mg/day. Terazosin may be
administered, for example, once or twice daily at a dose of about 1
to about 20 mg/day. Exemplary central alpha2-agonists and other
centrally acting drugs include, for example, clonidine oral,
clonidine patch, methyldopa, and guanfacine. Clonidine oral may be
administered, for example, twice daily at a dose of about 0.1 to
about 0.8 mg/day. Clonidine patch may be administered, for example,
once weekly at a dose of 0.1 to about 0.3 mg. Methyldopa maybe
administered, for example, twice daily at a dose of about 250 to
about 1000 mg/day. Guanfacine may be administered, for example,
once daily at a dose of about 0.5 to about 2 mg/day. Exemplary
direct vasodilators include hydralazine and minoxidil. Hydralazine
may be administered, for example, two or three times daily at a
dose of about 100 to about 200 mg/day. Minoxidil may be
administered, for example once, twice, or three times daily at a
dose of about 5 to about 100 mg/day.
[0071] In embodiments, any two or more supportive therapies may be
used in combination. The skilled person will recognize that the
decision of which agents to combine should be based on the
complementarity of mechanism of action, evidence of better
antihypertensive effect of the combination than either individual
agent, and favorable tolerability of the combination. For example,
the following combinations of supportive therapies may be used in
the methods provided herein: calcium antagonist and ACE inhibitor;
calcium antagonist and angiotensin receptor antagonist; calcium
antagonist (dihydropiridine) and beta-blocker; calcium antagonist
and thiazide diuretic; thiazide diuretic and ACE inhibitor; and
thiazide diuretic and angiotensin receptor antagonist.
[0072] In embodiments, a newly added supportive therapy and/or an
increased dose of a supportive therapy may be administered prior to
treatment with the VEGF-pathway inhibitor. For example, a subject
may be identified as having a high risk of developing one or more
VEGF-pathway inhibitor toxicities as provided herein, and may be
administered a new supportive therapy, and additional supportive
therapy, an increased dose of supportive therapy, and/or an
increased frequency of dosing of a supportive therapy, for at least
1, at least 2, at least 3, at least 4, at least 5, at least 6, at
least 7, at least 8, at least 9, at least 10, at least 11, at least
12, at least 13, at least 14, or more days before initiation of
treatment with the VEGF-pathway inhibitor. In embodiments, the
subject is monitored for evidence that the risk of developing one
or more VEGF-pathway inhibitor toxicities, or that the likely
severity of any such VEGF-pathway inhibitor toxicity, has been
reduced prior to initiating therapy with the VEGF-pathway
inhibitor. For example, in embodiments, the subject's blood
pressure is monitored and the VEGF-pathway inhibitor is withheld
until the subject has been determined to be in a safe range for
blood pressure.
[0073] In embodiments, a subject has been identified as being at
risk of developing one or more VEGF pathway inhibitor toxicities,
wherein the subject's blood pressure monitoring is increased prior
to, during, or following initiation of therapy with a VEGF pathway
inhibitor. In embodiments, increasing blood pressure monitoring may
mean increasing the intensity of monitoring. For example,
increasing blood pressure monitoring may comprise increasing the
frequency of monitoring. For subjects who were not currently
monitoring blood pressure regularly, increasing blood pressure
monitoring may mean initiating ambulatory blood pressure
monitoring, and/or monitoring blood pressure more than once daily,
once daily, once every 2, 3, 4, 5, or 6, days, or once weekly. For
subjects who were monitoring blood pressure regularly at home,
increasing blood pressure monitoring may mean initiating ambulatory
blood pressure monitoring where the subject previously only
periodically measured blood pressure; or may mean periodic blood
pressure monitoring that is performed more often, for example,
twice as often. Blood pressure monitoring may be conducted at home
by the subject, using single blood pressure measurement devices
and/or ambulatory blood pressure monitoring, and/or may be
conducted in a hospital or clinic. Ambulatory blood pressure
monitoring is blood pressure monitoring using a device that records
blood pressure automatically and periodically over a period of
time, for example, of 12 hours, 18 hours, 24 hours, 36 hours, 48
hours, or longer.
[0074] In some embodiments, therapy with a VEGF-pathway inhibitor
may be modulated and one or more supportive therapies may be
provided to the subject based upon the determined risk. For
example, the method may comprise lowering the dose of a
VEGF-pathway inhibitor and providing a supportive therapy to the
subject when the subject is determined to have a high risk of
developing one or more VEGF-pathway inhibitor-induced toxicities.
In embodiments, lowering the dose of the VEGF pathway inhibitor may
comprise starting the subject at a lower dose and/or lower dosing
frequency compared to the recommended dose on the package insert
for the VEGF pathway inhibitor, and may further comprise monitoring
the subject for the toxicity and/or providing a supportive therapy
for the toxicity, and titrating the dose and/or dosing frequency
upwards as appropriate. In embodiments, the method may comprise
lowering the dose of the VEGF-pathway inhibitor and providing an
anti-hypertensive agent or increasing the dose of an
anti-hypertensive agent provided to the subject when the subject is
determined to have a high risk of developing VEGF-pathway
inhibitor-induced hypertension. As another example, the method may
comprise lowering the dose of the VEGF-pathway inhibitor and
providing a proteinuria medication or increasing the dose of a
proteinuria medication provided to the subject when the subject is
determined to have a high risk of developing VEGF-pathway
inhibitor-induced proteinuria.
[0075] VEGF-pathway inhibitors may be any suitable agent, such as
an antibody or a small molecule. VEGF-pathway inhibitors include
agents that inhibit any part of the VEGF pathway, including
antibodies that bind to VEGF or a VEGF receptor (VEGFR), soluble
proteins that bind to or otherwise block interaction of VEGF and
VEGFR, small molecule drugs that interfere with the VEGF/VEGFR
interaction, and kinase inhibitors. Exemplary VEGF-pathway
inhibitors include, without limitation, bevacizumab,
bevacizumab-awwb, bevacizumab-bvzr, ranibizumab, aflibercept,
ziv-aflibercept, lenalidomide, lenvatinib, ramucirumab,
cabozantinib, pazopanib, sunitinib malate, regorafenib, axitinib,
tipiracil and trifluridine, ponatinib, vandetanib, sorafenib,
everolimus, thalidomide, temsirolimus, interferon alfa, interferon
alfa-2B, interferon alfa-N3, peginterferon alfa-2B, peginterferon
alfa-2A, rhEndostatin, cediranib, semaxanib, pomalidomide,
alitretinoin, imiquimod, sinecatechins, vismodegib, sonidegib,
pegaptanib sodium, dexamethasone intravitreal implant, fluocinolone
acetonide, conbercept, brolucizumab-dbll, selpercatinib,
nintedanib, apatinib, and motesanib. VEGF-pathway inhibitors
encompassed by the disclosure also include any biosimilar, generic,
salt, ester, ether, isomer, mixture of isomers, complex, prodrug,
or derivative of a VEGF-pathway inhibitor. The skilled person will
understand how to obtain prescribing information (e.g., information
from the product insert or approved label) for VEGF pathway
inhibitors; exemplary prescribing information is also provided
herein.
[0076] In embodiments, the VEGF-pathway inhibitor is bevacizumab
(AVASTIN) or bevacizumab-awwb (MVASI) or bevacizumab-bvzr
(ZIRABEV). Bevacizumab is a vascular endothelial growth factor
inhibitor indicated for the treatment of metastatic colorectal
cancer, in combination with intravenous fluorouracil based
chemotherapy for first- or second-line treatment; metastatic
colorectal cancer, in combination with fluoropyrimidine-irinotecan-
or fluoropyrimidine-oxaliplatin-based chemotherapy for second-line
treatment in patients who have progressed on a first-line
bevacizumab-containing regimen; unresectable, locally advanced,
recurrent or metastatic non-squamous non-small cell lung cancer, in
combination with carboplatin and paclitaxel for first-line
treatment; recurrent glioblastoma in adults; metastatic renal cell
carcinoma in combination with interferon alfa; persistent,
recurrent, or metastatic cervical cancer, in combination with
paclitaxel and cisplatin, or paclitaxel and topotecan; and
epithelial ovarian, fallopian tube, or primary peritoneal cancer
(i) in combination with carboplatin and paclitaxel, followed by
bevacizumab as a single agent, for stage III or IV disease
following initial surgical resection, (ii) in combination with
paclitaxel, pegylated liposomal doxorubicin, or topotecan for
platinum-resistant recurrent disease who received no more than 2
prior chemotherapy regimens, and (iii) in combination with
carboplatin and paclitaxel or carboplatin and gemcitabine, followed
by bevacizumab as a single agent, for platinum sensitive recurrent
disease. Bevacizumab is administered intravenously and is provided
in dosage forms of 100 mg/4 mL (25 mg/mL) or 400 mg/16 mL (25
mg/mL) in a single-dose vial.
[0077] For metastatic colorectal cancer, bevacizumab is
administered at a dose of 5 mg/kg every 2 weeks with bolus-IFL
(irinotecan 125 mg/m.sup.2, fluorouracil 500 mg/m.sup.2, and
leucovorin 20 mg/m.sup.2 given once weekly for 4 weeks every 6
weeks); 10 mg/kg every 2 weeks with FOLFOX4; or 5 mg/kg every 2
weeks or 7.5 mg/kg every 3 weeks with fluoropyrimidine-irinotecan-
or fluoropyrimidine-oxaliplatin-based chemotherapy after
progression on a first-line bevacizumab containing regimen. For
first-line non-squamous non-small cell lung cancer, bevacizumab is
administered at a dose of 15 mg/kg every 3 weeks with carboplatin
and paclitaxel. For recurrent glioblastoma, bevacizumab is
administered at a dose of 10 mg/kg every 2 weeks. For metastatic
renal cell carcinoma, bevacizumab is administered at a dose of 10
mg/kg every 2 weeks with interferon alfa. For persistent,
recurrent, or metastatic cervical cancer, bevacizumab is
administered at a dose of 15 mg/kg every 3 weeks with paclitaxel
and cisplatin, or paclitaxel and topotecan. For stage III or IV
epithelial ovarian, fallopian tube or primary peritoneal cancer
following initial surgical resection, bevacizumab is administered
at a dose of 15 mg/kg every 3 weeks with carboplatin and paclitaxel
for up to 6 cycles, followed by 15 mg/kg every 3 weeks as a single
agent, for a total of up to 22 cycles. For platinum-resistant
recurrent epithelial ovarian, fallopian tube or primary peritoneal
cancer, bevacizumab is administered at a dose of 10 mg/kg every 2
weeks with paclitaxel, pegylated liposomal doxorubicin, or
topotecan given every week, or 15 mg/kg every 3 weeks with
topotecan given every 3 weeks. For platinum-sensitive recurrent
epithelial ovarian, fallopian tube, or primary peritoneal cancer,
bevacizumab is administered at a dose of 15 mg/kg every 3 weeks
with carboplatin and paclitaxel for 6-8 cycles, followed by 15
mg/kg every 3 weeks as a single agent; or 15 mg/kg every 3 weeks
with carboplatin and gemcitabine for 6-10 cycles, followed by 15
mg/kg every 3 weeks as a single agent.
[0078] Arterial thromboembolic events, venous thromboembolic
events, hypertension, and proteinuria are among the adverse
reactions that can occur in patients administered bevacizumab. For
hypertension, blood pressure may be monitored and patients may be
treated for the hypertension, e.g., with an anti-hypertensive
agent; bevacizumab may be withheld if hypertension is not medically
controlled. Bevacizumab can be resumed once controlled, but should
be discontinued for hypertensive crisis or hypertensive
encephalopathy. For renal injury and proteinuria, doctors are
instructed to monitor urine protein and to discontinue bevacizumab
for nephrotic syndrome, and withhold until less than 2 grams of
protein are detectable in urine. Presently, there is no known
method for identifying patients at risk of hypertension and/or
proteinuria prior to treatment with bevacizumab.
[0079] In embodiments, the VEGF-pathway inhibitor is ranibizumab.
Ranibizumab (LUCENTIS) is a vascular endothelial growth factor
(VEGF) inhibitor, indicated for the treatment of patients with
neovascular (wet) Age-Related Macular Degeneration (AMD), macular
edema following retinal vein occlusion (RVO), diabetic macular
edema (DME), diabetic retinopathy (DR), and myopic choroidal
neovascularization (mCNV). Ranibizumab is for ophthalmic
intravitreal injection. For wet AMD, 0.5 mg (0.05 mL) is
recommended to be administered by intravitreal injection once a
month (approximately 28 days). Although not as effective, patients
may be treated with 3 monthly doses followed by less frequent
dosing, or may be treated with one dose every 3 months after 4
monthly doses, with regular assessment. For macular edema following
RVO, 0.5 mg (0.05 mL) is recommended to be administered by
intravitreal injection once a month (approximately 28 days). For
DME and DR, 0.3 mg (0.05 mL) is recommended to be administered by
intravitreal injection once a month (approximately 28 days). For
mCNV, 0.5 mg (0.05 mL) is recommended to be initially administered
by intravitreal injection once a month (approximately 28 days) for
up to three months. Patients may be retreated if needed. The dosage
forms provided for ranibizumab are single-use prefilled syringe or
glass vials containing 10 mg/mL solutions designed to provide 0.05
mL for intravitreal injections; or containing 6 mg/mL solution (0.3
mg). There is a potential risk of arterial thromboembolic events
following intravitreal use of VEGF inhibitors.
[0080] In embodiments, the VEGF-pathway inhibitor is aflibercept.
Aflibercept (EYLEA) is a vascular endothelial growth factor (VEGF)
inhibitor indicated for the treatment of patients with wet AMD,
macular edema following RVO, DME, and DR. For wet AMD, the
recommended dose is 2 mg (0.05 mL) administered by intravitreal
injection every 4 weeks (approximately every 28 days, monthly) for
the first 3 months, followed by 2 mg (0.05 mL) via intravitreal
injection once every 8 weeks (2 months). Some patients may need
every 4 week (monthly) dosing after the first 12 weeks (3 months).
Although not as effective as the recommended every 8 week dosing
regimen, patients may also be treated with one dose every 12 weeks
after one year of effective therapy. For macular edema following
RVO, the recommended dose is 2 mg (0.05 mL) administered by
intravitreal injection once every 4 weeks (approximately every 25
days, monthly). For DME and DR, the recommended dose is 2 mg (0.05
mL) administered by intravitreal injection every 4 weeks
(approximately every 28 days, monthly) for the first 5 injections
followed by 2 mg (0.05 mL) via intravitreal injection once every 8
weeks (2 months). Some patients may need every 4 week (monthly)
dosing after the first 20 weeks (5 months). Aflibercept is provided
in dosage forms for injection of 2 mg/0.05 mL solution in a
single-dose pre-filled syringe or a single-dose vial. As with
ranibizumab, there is a potential risk of arterial thromboembolic
events following intravitreal use of aflibercept.
[0081] In embodiments, the VEGF-pathway inhibitor is
ziv-aflibercept. Ziv-aflibercept (ZALTRAP) is indicated for the
treatment of patients with metastatic colorectal cancer that is
resistant to or has progressed following an oxaliplatin-containing
regimen, a vascular endothelial growth factor inhibitor, in
combination with fluorouracil, leucovorin, irinotecan (FOLFIRI).
Ziv-aflibercept is administered 4 mg/kg as an intravenous infusion
over 1 hour every 2 weeks in combination with FOLFIRI until disease
progression or unacceptable toxicity. Ziv-aflibercept is to be
administered prior to any component of the FOLFIRI regimen on the
day of treatment. Arterial thromboembolic events, hypertension, and
proteinuria are among the adverse effects that may be induced by
zif-aflibercept administration. For hypertension, doctors may
monitor blood pressure and treat hypertension; may temporarily
suspend ziv-aflibercept if hypertension is not controlled (and upon
resumption, permanently reduce to 2 mg/kg); and may discontinue it
if hypertensive crisis develops. For proteinuria, doctors may
monitor urine protein; may suspend ziv-aflibercept for proteinuria
of 2 grams per 24 hours or more (to be resumed when proteinuria is
less than 2 grams per 24 hours, and then permanently reduce to 2
mg/kg for recurrent proteinuria); and may discontinue it if
nephrotic syndrome or thrombotic microangiopathy (TMA) develops.
The provided dosage forms of ziv-aflibercept are a 100 mg/4 mL (25
mg/mL) and a 200 mg/8 mL (25 mg/mL) solution in a single-dose vial
for injection.
[0082] In embodiments, the VEGF-pathway inhibitor is lenalidomide.
Lenalidomide (REVLIMID) is a thalidomide analogue indicated for the
treatment of adult patients with multiple myeloma (MM), in
combination with dexamethasone (25 mg once daily orally on Days
1-21 of repeated 28-day cycles in combination with dexamethasone);
MM, as maintenance following autologous hematopoietic stem cell
transplantation (auto-HSCT) (initiated after therapy after adequate
hematologic recovery (ANC at least 1000/mcL and/or platelet counts
at least 75,000/mcL, recommended starting dose of 10 mg once daily
continuously (Days 1-28 of repeated 28-day cycles) until disease
progression or unacceptable toxicity, and after 3 cycles of
maintenance therapy, the dose can be increased to 15 mg once daily
if tolerated); transfusion-dependent anemia due to low- or
intermediate-1-risk myelodysplastic syndromes (MDS) associated with
a deletion 5q abnormality with or without additional cytogenetic
abnormalities (10 mg once daily); mantle cell lymphoma (MCL) whose
disease has relapsed or progressed after two prior therapies, one
of which included bortezomib (25 mg once daily orally on Days 1-21
of repeated 28-day cycles); previously treated follicular lymphoma
(FL), in combination with a rituximab product (20 mg once daily
orally on Days 1-21 of repeated 28-day cycles for up to 12 cycles
in combination with a rituximab-product); and previously treated
marginal zone lymphoma (MZL), in combination with a rituximab
product (20 mg once daily orally on Days 1-21 of repeated 28-day
cycles for up to 12 cycles in combination with a
rituximab-product). Lenalidomide is provided as 2.5 mg, 5 mg, 10
mg, 15 mg, 20 mg, and 25 mg capsules. There is significantly
increased risk of deep vein thrombosis an pulmonary embolism as
well as risk of myocardial infarction and stroke in patients
receiving REVLIMID with dexamethasone; anti-thrombotic prophylaxis
is recommended.
[0083] In embodiments, the VEGF-pathway inhibitor is lenvatinib
(LENVIMA). Lenvatinib is a kinase inhibitor that is indicated for
the treatment of patients with locally recurrent or metastatic,
progressive, radioactive iodine-refractory differentiated thyroid
cancer (DTC); combination with everolimus, for the treatment of
patients with advanced renal cell carcinoma (RCC) following one
prior antiangiogenic therapy; for the first-line treatment of
patients with unresectable hepatocellular carcinoma (HCC); and in
combination with pembrolizumab, for the treatment of patients with
advanced endometrial carcinoma that is not microsatellite
instability-high (MSI-H) or mismatch repair deficient (dMMR), who
have disease progression following prior systemic therapy and are
not candidates for curative surgery or radiation. Lenvatinib is
available as 4 mg and 10 mg capsules. Lenvatinib is taken daily at
a recommended dosage of 24 mg orally (for DTC), 18 mg orally with 5
mg everolimus (for RTC), and 20 mg orally with 200 mg i.v.
pembrolizumab (for endometrial carcinoma). For HCC, the recommended
dosage is based on body weight:12 mg orally once daily for patients
greater than or equal to 60 kg and 8 mg orally once daily for
patients less than 60 kg. Doses are modified for adverse reactions
as follows. For DTC, the first reduction is to 20 mg once daily,
the second is to 14 mg once daily, the third is to 10 mg once
daily. For RCC and endometrial carcinoma, the first reduction is to
14 mg once daily, the second is to 10 mg once daily, the third is
to 8 mg once daily. For HCC patients that weigh 60 kg or more, the
first reduction is to 8 mg once daily, the second reduction is to 4
mg once daily, and the third reduction is to 4 mg every other day;
and for HCC patients that weight less than 60 kg, the first
reduction is to 4 mg once daily, the second reduction is to 4 mg
every other day, and the third is to discontinue. Hypertension,
cardiac dysfunction, arterial thromboembolic events, and
proteinuria are adverse reactions that may occur. For hypertension,
blood pressure is monitored during treatment and lenvatinib is
withheld for grade 3 hypertension despite optimal antihypertensive
therapy. The drug can be resumed at a reduced dose when
hypertension is controlled at less than or equal to grade 2.
Lenvatinib is discontinued for grade 4 hypertension, grade 4
cardiac dysfunction, an arterial thromboembolic event of any grade,
and nephrotic syndrome.
[0084] In embodiments, the VEGF-pathway inhibitor is ramucirumab.
Ramucirumab (CYRAMZA) is a VEGFR2 antagonist indicated as a single
agent or in combination with paclitaxel, for treatment of advanced
or metastatic gastric or gastro-esophageal junction adenocarcinoma
with disease progression on or after prior fluoropyrimidine- or
platinum-containing chemotherapy; in combination with docetaxel,
for treatment of NSCLC with disease progression on or after
platinum-based chemotherapy; in combination with FOLFIRI, for the
treatment of metastatic colorectal cancer with disease progression
on or after prior therapy with bevacizumab, oxaliplatin, and a
fluoropyrimidine; and as a single agent, for the treatment of
hepatocellular carcinoma in patients who have an alpha fetoprotein
of .gtoreq.400 ng/mL and have been treated with sorafenib.
Ramucirumab is for intravenous infusion (first infusion over 60
minutes and if tolerated, all subsequent infusions may be
administered over 30 minutes) and is supplied as a mg/10 mL (10
mg/mL) or 500 mg/50 mL (10 mg/mL) solution in a single-dose vial.
Patients are premedicated with an intravenous histamine-1 receptor
antagonist (e.g., diphenhydramine hydrochloride) before each
infusion; or, for patients who have experienced a Grade 1 or 2 IRR,
premedicate with a histamine-1 receptor antagonist, dexamethasone
(or equivalent), and acetaminophen prior to each infusion. For
gastric cancer, 8 mg/kg is administered every 2 weeks as a single
agent or in combination with weekly paclitaxel. For non-small cell
lung cancer (NSCLC), 10 mg/kg is administered on Day 1 of a 21-day
cycle prior to docetaxel. For colorectal cancer, 8 mg/kg is
administered every 2 weeks prior to FOLFIRI. For hepatocellular
carcinoma, 8 mg/kg is administered every 2 weeks. ATEs,
proteinuria, and hypertension are among the adverse events that may
be induced by ramucirumab administration. For the first occurrence
of increased urine protein levels greater than or equal to 2 g per
24 hours, doctors may withhold ramucirumab until urine protein
level is less than 2 g per 24 hours and resume at a reduced dose
(reduce 8 mg dose to 6 mg, and 10 mg dose to 8 mg). Upon a
recurrence of urine protein level greater than 2 g per 24 hours
following initial dose reduction, doctors may withhold ramucirumab
until urine protein level is less than 2 g per 24 hours and resume
at a reduced dose (reduce 6 mg dose to 5 mg, and 8 mg dose to 6
mg). Ramucirumab is permanently discontinued for urine protein
levels greater than 3 g per 24 hours or nephrotic syndrome. For
hypertensive adverse events, blood pressure should be monitored and
hypertension should be treated. Ramucirumab should be withheld for
severe hypertension until it is controlled; and should be
permanently discontinued if it cannot be controlled with
antihypertensive therapy and for hypertensive crisis or
hypertensive encephalopathy
[0085] In embodiments, the VEGF-pathway inhibitor is cabozantinib.
Cabozantinib (CABOMETYX, COMETRIQ) is a kinase inhibitor. CABOMETYX
is indicated for the treatment of advanced renal cell carcinoma
(RCC) and patients with hepatocellular carcinoma (HCC) who have
been previously treated with sorafenib CABOMETRYX is provided as 20
mg, 40 mg, and 60 mg tablets and is administered once daily at a
dose of 60 mg orally. COMETRIQ.RTM. is indicated for the treatment
of patients with progressive, metastatic medullary thyroid cancer
(MTC). The recommended dose is 140 mg orally, once daily, and
COMETRIQ is supplied as a 20 mg or 80 mg capsule.
[0086] For both CABOMETRYX and COMETRIZ, doses can be reduced if
coadministered with strong CYP3A4 inhibitors (e.g., ketoconazole,
ritonavir, clarithromycin), or if adverse reactions occur. For
example, CABOMETRYX can be reduced from 60 mg daily to 40 mg daily,
or from 40 mg daily to 20 mg daily, and if 20 mg daily is not
tolerated, CABOMETRYX should be discontinued; and COMETRIZ daily
administration can be reduced by 40 mg (e.g., from 140 to 100, or
from 100 to 60). For coadministration with strong CYPA34 induces,
CABOMETRYX should be increased by 20 mg daily (for example, from 60
mg to 80 mg daily or from 40 mg to 60 mg daily) as tolerated; and
COMETRIQ should be increased by 40 mg (e.g., 140 mg to 180 mg daily
or 100 mg to 140 mg daily) as tolerated. Patients are monitored for
hypertension and proteinuria, and cabozantinib is interrupted for
hypertension that is not adequately controlled with
anti-hypertensive therapy; and is discontinued for hypertensive
crisis or severe hypertension that cannot be controlled with
anti-hypertensive therapy. Cabozantinib is discontinued for
nephrotic syndrome.
[0087] In embodiments, the VEGF-pathway inhibitor is pazopanib.
Pazopanib (VOTRIENT) is a kinase inhibitor indicated for the
treatment of patients with advanced renal cell carcinoma (RCC) or
advanced soft tissue sarcoma (STS) who have received prior
chemotherapy. 800 mg is administered once daily. For RCC, the
initial dose reduction should be 400 mg, and additional dose
decrease or increase should be in 200-mg steps based on individual
tolerability. For STS, a decrease or increase should be in 200-mg
steps based on individual tolerability. The recommended dose for
patients with moderate hepatic impairment is 200 mg orally once
daily and pazopanib is not recommended in patients with severe
hepatic impairment. Concomitant use with strong CYP3A4 inhibitors
should be avoided; if it is warranted, the pazopanib dose should be
reduced to 400 mg. VOTRIENT is provided in a dosage form of 200 mg
tablets. Cardiac dysfunction, arterial thromboembolic events,
venous thromboembolic events, hypertension including hypertensive
crisis, and proteinuria are among the adverse events for which
patients should be monitored. Blood pressure should be well
controlled before initiating pazopanib.
[0088] In embodiments, the VEGF-pathway inhibitor is sunitinib.
Sunitinib malate (SUTENT) is a kinase inhibitor indicated for
treatment of gastrointestinal stromal tumor (GIST) after disease
progression on or intolerance to imatinib mesylate, treatment of
advanced RCC, adjuvant treatment of adult patients at high risk of
recurrent ACC following nephrectomy, and treatment of progressive,
well-differentiated pancreatic neuroendocrine tumors (pNET) in
patients with unresectable locally advanced or metastatic disease.
The dosage form of sunitinib malate is 12.5 mg, 25 mg, 37.5 mg, or
50 mg capsules. For GIST and advanced RCC, the treatment regimen is
50 mg orally once daily, 4 weeks on treatment followed by 2 weeks
off. For adjuvant RCC, the treatment regimen is 50 mg orally once
daily, 4 weeks on treatment followed by 2 weeks off for nine 6-week
cycles. For pNET, the treatment regimen is 37.5 mg orally once
daily, continuously without a scheduled off-treatment period.
Strong CYP3A4 inhibitors such as ketoconazole may increase
sunitinib plasma concentrations and coadministration should be
avoided. A dose reduction for to a minimum of 37.5 mg (GIST and
RCC) or 25 mg (pNET) daily should be considered if sunitinib must
be co-administered with a strong CYP3A4 inhibitor. CYP3A4 inducers
such as rifampin may decrease sunitinib plasma concentrations and
coadministration should be avoided. A dose increase for to a
maximum of 87.5 mg (GIST and RCC) or 62.5 mg (pNET) daily should be
considered if sunitinib must be co-administered with a CYP3A4
inducer. Adverse events that may occur and should be monitored for
include cardiovascular events, hypertension, and proteinuria.
[0089] In embodiments, the VEGF-pathway inhibitor is regorafenib.
Regorafenib (STIVARGA) is a kinase inhibitor indicated for the
treatment of patients with metastatic colorectal cancer (CRC) who
have been previously treated with fluoropyrimidine-, oxaliplatin-
and irinotecan-based chemotherapy, an antiVEGF therapy, and, if RAS
wild-type, an anti-EGFR therapy; patients with locally advanced,
unresectable or metastatic GIST who have been previously treated
with imatinib mesylate and sunitinib malate; and HCC patients who
have been previously treated with sorafenib. The dosage form is 40
mg tablets. The recommended dose is 160 mg orally, once daily for
the first 21 days of each 28-day cycle. If dose modifications are
required, the dose should be reduced in 40 mg (one tablet)
increments; the lowest recommended daily dose of regorafenib is 80
mg daily. Regorafenib should be temporarily or permanently withheld
for severe or uncontrolled hypertension. For cardiac ischemia and
infarction, regorafenib should be withheld and resumed only after
resolution of acute ischemic events.
[0090] In embodiments, the VEGF-pathway inhibitor is axitinib.
Axitinib (INLYTA) is a kinase inhibitor indicated for the treatment
of advanced RCC after failure of one prior systemic therapy.
Axitinib is provided in a dosage form 1 mg and 5 mg tablets. The
starting dose is 5 mg orally twice daily. Over the course of
treatment, patients who tolerate axitinib for at least two
consecutive weeks with no adverse reactions>Grade 2 (according
to the CTCAE), are normotensive, and are not receiving
anti-hypertension medication, may have their dose increased. When a
dose increase from 5 mg twice daily is recommended, the axitinib
dose may be increased to 7 mg twice daily, and further to 10 mg
twice daily using the same criteria. Over the course of treatment,
management of some adverse drug reactions may require temporary
interruption or permanent discontinuation and/or dose reduction. If
dose reduction from 5 mg twice daily is required, the recommended
dose is 3 mg twice daily. If additional dose reduction is required,
the recommended dose is 2 mg twice daily. If coadministration with
strong CYPA4/5 inhibitors is required, the dose of axitinib should
be decreased by approximately half. Blood pressure should be
well-controlled prior to initiating axitinib therapy and patients
should be monitored for hypertension and treated as needed. For
persistent hypertension despite use of anti-hypertensive
medications, the axitinib dose should be reduced. Patients should
also be monitored for arterial and venous thromboembolic events,
cardiac failure, and proteinuria. For moderate to severe
proteinuria, the axitinib dose should be reduced or temporarily
interrupted
[0091] In embodiments, the VEGF-pathway inhibitor is LONSURF.
LONSURF is a combination of trifluridine, a nucleoside metabolic
inhibitor, and tipiracil, a thymidine phosphorylase inhibitor, and
is indicated for the treatment of adult patients with metastatic
colorectal cancer who have been previously treated with
fluoropyrimidine-, oxaliplatin- and irinotecan-based chemotherapy,
an anti-VEGF biological therapy, and if RAS wild-type, an anti-EGFR
therapy; or for the treatment of metastatic gastric or
gastroesophageal junction adenocarcinoma previously treated with at
least two prior lines of chemotherapy that included a
fluoropyrimidine, a platinum, either a taxane or irinotecan, and if
appropriate, HER2/neu-targeted therapy. The dosage form of
LONSURF.RTM. is 15 mg trifluridine/6.14 mg tipiracil or 20 mg
trifluridine/8.19 mg tipiracil. The recommended dosage is 35
mg/m.sup.2 up to a maximum of 80 mg per dose (based on the
trifluridine component) orally twice daily with food on Days 1
through 5 and Days 8 through 12 of each 28-day cycle. Doses are
rounded to the nearest 5 mg increment. Within a treatment cycle,
LONSURF is withheld for any of the following: absolute neutrophil
count (ANC) less than 500/mm.sup.3 or febrile neutropenia,
platelets less than 50,000/mm.sup.3, Grade 3 or 4 non-hematologic
adverse reaction. After recovery, LONSURF can be resumed after
reducing the dose by 5 mg/m.sup.2/dose. A maximum of 3 dose
reductions are permitted LONSURF dosage is not escalated after it
has been reduced. LONSURF is discontinued in patients who are
unable to tolerate a dose of 20 mg/m.sup.2 orally twice daily.
[0092] In embodiments, the VEGF-pathway inhibitor is ponatinib.
Ponatinib (ICLUSIG) is a kinase inhibitor indicated for treatment
of adult patients with chronic phase, accelerated phase, or blast
phase chronic myeloid leukemia (CML) or Ph+ ALL for whom no other
tyrosine kinase inhibitor (TKI) therapy is indicated; or for
treatment of adult patients with T315I-positive CML (chronic phase,
accelerated phase, or blast phase) or T315I-positive Philadelphia
chromosome positive acute lymphoblastic leukemia (Ph+ ALL). The
dosage form is 15 mg, 30 mg, and 45 mg tablets. The recommended
starting dose is 45 mg taken orally once daily with or without
food. Dose modifications may be made for neutropenia and
thrombocytopenia that are unrelated to leukemia; or for
hepatotoxicity or pancreatitis and elevation of lipase. The
recommended dose is reduced to 30 mg once daily when administering
ICLUSIG with strong CYP3A inhibitors. Arterial occlusion, venous
thromboembolism, heart failure, hypertension, and cardiac
arrhythmias are among the adverse events that can occur. Blood
pressure should be monitored.
[0093] In embodiments, the VEGF-pathway inhibitor is vandetanib.
Vandetanib (CAPRELSA) is a kinase inhibitor indicated for the
treatment of symptomatic or progressive medullary thyroid cancer in
patients with unresectable locally advanced or metastatic disease.
The dosage form is 100 mg and 300 mg tablets, and the dosing
regimen is 300 mg once daily. The dose can be reduced to 200 mg
(two 100 mg tablets) and then to 100 mg for CTCAE Grade 3 or
greater toxicities. Vandetanib should be discontinued or
interrupted in the event of ischemic cerebrovascular events,
hemorrhage, heart failure, diarrhea, hypertension, and/or
reversible posterior leukoencephalopathy syndrome.
[0094] In embodiments, the VEGF-pathway inhibitor is sorafenib.
Sorafenib (NEXAVAR) is a kinase inhibitor indicated for the
treatment of unresectable HCC, advanced RCC, and locally recurrent
or metastatic, progressive, differentiated thyroid carcinoma
refractory to radioactive iodine treatment. The dosage form is 200
mg tablets. For dosing, 400 mg is administered orally twice daily
at least 1 hour before or 2 hours after a meal. Treatment should
continue until the patient is no longer clinically benefiting from
therapy or until unacceptable toxicity occurs. When dose reduction
is necessary, the dose may be reduced to 400 mg once daily. If
additional dose reduction is required, vandetanib may be reduced to
a single 400 mg dose every other day. Dermatologic toxicities,
cardiovascular events, and hypertension should be monitored.
[0095] In embodiments, the VEGF-pathway inhibitor is everolimus.
Everolimus is an inhibitor of mammalian target of rapamycin (mTOR)
marketed as AFINITOR, AFINITOR DISPERZ, or ZORTRESS. AFFINITOR is
indicated for treatment of postmenopausal women with advanced
hormone receptor-positive, HER2-negative breast cancer in
combination with exemestane after failure of treatment with
letrozole or anastrozole; adults with progressive neuroendocrine
tumors of pancreatic origin (PNET) and adults with progressive,
well-differentiated, non-functional neuroendocrine tumors (NET) of
gastrointestinal (GI) or lung origin that are unresectable, locally
advanced or metastatic; adults with advanced RCC after failure of
treatment with sunitinib or sorafenib; and adults with renal
angiomyolipoma and tuberous sclerosis complex (TSC), not requiring
immediate surgery. AFINITOR and AFINITOR DISPERZ are indicated for
the treatment of adult and pediatric patients aged 1 year and older
with TSC who have subependymal giant cell astrocytoma (SEGA) that
requires therapeutic intervention but cannot be curatively
resected. AFINITOR DISPERZ is also indicated for the adjunctive
treatment of adult and pediatric patients aged 2 years and older
with TSC associated partial-onset seizures. Zortess is indicated
for prophlylaxis of kidney transplant rejection (in combination
with basiliximab, cyclosporine, and corticosteroids) or liver
transplant rejection (in combination with tacrolimus and
corticosteroids). The dosage form of AFINITOR is 2.5 mg, 5 mg, 7.5
mg, and 10 mg tablets; the dosage form of AFINITOR DISPERZ is 2 mg,
3 mg, and 5 mg tablets; the dosage form of ZORTRESS is 0.25 mg, 0.5
mg, and 0.75 mg. For breast cancer, NET, RCC, and TSC-associated
angiomyolipoma, the approved dosage is 10 mg orally once daily. For
TSC-associated SEGA, the approved dosage is 4.5 mg/m.sup.2 orally
once daily, with dose adjustments to attain trough concentrations
of 5-15 mg/mL. For kidney transplantation, the starting dose is
0.75 mg orally twice daily starting as soon as possible after
transplantation; for liver transplantation the starting dose is 1.0
mg twice daily starting 30 days after transplantation. Everolimus
concentrations are monitored and maintenance doses are adjusted to
achieve trough concentrations within 3-8 ng/mL target range using
LC/MS/MS assay method. Patients taking concomitant
angiotensin-converting enzyme (ACE) inhibitors may be at increased
risk of angioedema and proteinuria.
[0096] In embodiments, the VEGF-pathway inhibitor is thalidomide.
Thalidomide (THALOMID) is indicated for the treatment of patients
with newly diagnosed multiple myeloma (MM) in combination with
dexamethasone; treatment of acute treatment of the cutaneous
manifestations of moderate to severe erythema nodosum leprosum
(ENL); and as a maintenance therapy for prevention and suppression
of the cutaneous manifestations of ENL recurrence. Thalidomide is
provided in a dosage form of 50 mg, 100 mg, 150 mg, and 200 mg. For
MM, patients are administered 200 mg orally once daily, and the
recommended dose of dexamethasone is 40 mg/day on days 1-4, 9-12,
and 17-20 every 28 days. For ENL, patients are administered 100 to
300 mg/day for an episode of cutaneous ENL and up to 400 mg/day for
severe cutaneous ENL. Dosing is continued until signs and symptoms
of active reaction have subsided, usually a period of at least 2
weeks. Patients should be monitored for venous thromboembolism and
ischemic heart disease (including myocardial infarction) and
stroke.
[0097] In embodiments, the VEGF-pathway inhibitor is temsirolimus.
Temsirolimus (TORISEL) is a kinase inhibitor indicated for
treatment of advanced RCC. The dosage form is a 25 mg/mL solution
for injection. The recommended dose of TORISEL is 25 mg infused
over a 30-60 minute period once a week, until disease progression
or unacceptable toxicity. Antihistamine pre-treatment is
recommended. Temsirolimus should be held for absolute neutrophil
count (ANC)<1,000/mm{circumflex over ( )}3, platelet
count<75,000/mm{circumflex over ( )}3, or NCI CTCAE grade 3 or
greater adverse reactions. Once toxicities have resolved to grade 2
or less, it may be restarted with the dose reduced by 5 mg/week to
a dose no lower than 15 mg/week. The concomitant use of strong
CYP3A4 inhibitors should be avoided (e.g. ketoconazole,
itraconazole, clarithromycin, atazanavir, indinavir, nefazodone,
nelfinavir, ritonavir, saquinavir, telithromycin, and
voriconazole). Grapefruit juice may also increase plasma
concentrations of sirolimus (a major metabolite of temsirolimus)
and should be avoided. If patients must be co-administered a strong
CYP3A4 inhibitor, based on pharmacokinetic studies, a temsirolimus
dose reduction to 12.5 mg/week should be considered. The use of
concomitant strong CYP3A4 inducers should be avoided (e.g.
dexamethasone, phenytoin, carbamazepine, rifampin, rifabutin,
rifampacin, phenobarbital). If patients must be co-administered a
strong CYP3A4 inducer, based on pharmacokinetic studies, a
temsirolimus dose increase from 25 mg/week up to 50 mg/week should
be considered. Patients should be monitored for proteinuria and
nephrotic syndrome.
[0098] In embodiments, the VEGF-pathway inhibitor is interferon
alfa. Interferon alfa (interferon alfa-2B, interferon alfa-N3,
peginterferon alfa-2B, and peginterferon alfa-2A) is marketed as
INTRON A, PEGASYS, PEGINTRON, ALFERON N, and SYLATRON.
[0099] INTRON A is indicated for treatment with hairy cell leukemia
(2 million IU/m.sup.2 administered intramuscularly or
subcutaneously 3 times per week for up to 6 months), malignant
melanoma (20 million IU/m.sup.2 as an intravenous infusion 5
consecutive days per week, for 4 weeks, with maintenance of
treatment of 10 million IU/m.sup.2 as a subcutaneous injection
three times per week for 48 weeks), follicular lymphoma (5 million
IU subcutaneously three times per week for up to 18 months in
conjunction with anthracycline-containing chemotherapy regimen and
following completion of the chemotherapy regimen), condylomata
acuminate 1.0 million IU per lesion in a maximum of 5 lesions in a
single course; lesions are injected three times weekly on alternate
days for 3 weeks), AIDS-related Kaposi's sarcoma (30 million
IU/m.sup.2/dose administered subcutaneously or intramuscularly
three times per week until disease progression or maximal response
has been achieved after 16 weeks of treatment), chronic hepatitis C
(3 million IU three times per week subcutaneously or
intramuscularly), and chronic hepatitis B (in adults, 30 to 35
million IU per week, administered subcutaneously or
intramuscularly, either as 5 million IU daily or as 10 million IU
three times per week for 16 weeks; and in pediatrics, 3 million
IU/m.sup.2 three times per week for the first week followed by dose
escalation to 6 million IU/m.sup.2 three times per week
subcutaneously, for a total duration of 16 to 24 weeks). PEGASYS is
indicated for chronic hepatitis (180 mcg per week or 1.5
mcg/kg/week in adults; and 180 mcg/1.73 m.sup.2.times.BSA per week
or 60 mcg/m.sup.2 per week in pediatrics). Potential adverse events
include cardiovascular disorders and ischemic and hemorrhagic
cerebrovascular events.
[0100] In embodiments, the VEGF-pathway inhibitor is rhEndostatin.
rhEndostatin (ENDOSTAR) is indicated for HCC, NSCLC (squamous or
non-squamous), postoperative NSCLC, advanced NSCLC with EGFR
mutations, solid tumors in pediatric patients, and metastatic
melanoma. For HCC, dosing is 30 mg/d, from 5 days before
radiotherapy, for 7 days, 21 per cycle, with concurrent standard
radiotherapy for HCC. For squamous NSCLC, dosing is 15
mg/m{circumflex over ( )}2 for 5 days and 200 mg of pembrolizumab
at day 1 in each cycle, repeating every 3 weeks till PD or
unacceptable toxicities. Squamous NSCLC patients also receive
carboplatin (5U/AUC) or cisplatin (75 mg/m.sup.2) and
[nab]-paclitaxel (100 mg/m.sup.2) for the first 4 cycles. For
non-squamous NSCLC, dosing is 15 mg/m.sup.2 for 5 days, 200 mg of
pembrolizumab at day 1 and pemetrexed (500 mg/m.sup.2 day 1) are
given in each cycle, repeating every 3 weeks till to PD or
unacceptable toxicities. Squamous and non-squamous NSCLC also
receive carboplatin (5U/AUC) or cisplatin (75 mg/m.sup.2) and
[nab]-paclitaxel (100 mg/m.sup.2) (squamous) or pemetrexed (500
mg/m.sup.2 day 1) (non-squamous) for the first 4 cycles. For
untreated stage IIIB/IV NSCLC, dosing is continuous intravenous
infusion rh-endostatin at 7.5 mg/m.sup.2 for 14 days each cycle, 21
days as one cycle, 4 cycles in total, with docetaxel or pemetrexed.
For advanced NSCLC with EGFR mutations, dosing is 15 mg CIV days
1-9, Q3W with icotinib. For postoperative NSCLC, dosing is
rh-Endostatin 7.5 mg/m.sup.2 days 1-14; 21 d as a cycle with
pemetrexed and cis-platinum or with docetaxel and cis-platinum. For
phase III B/IV squamous lung cancer with GP, dosing is
rh-Endostatin at 7.5 mg/m.sup.2, continuous intravenous infusion
for 14 days each cycle, 21 days as one cycle, 4 cycles in total
with gemcitabine, cisplatin. For advanced NSCLC with docetaxel,
dosing is rh-endostatin at 7.5 mg/m.sup.2, IV on day 1-14 of each
21-28 day cycle with docetaxel. For metastatic melanoma, dosing is
based on body surface area as 15 mg/m.sup.2 rh-endostatin with
cisplatin and dacarbazine.
[0101] In embodiments, the VEGF-pathway inhibitor is cediranib.
Cediranib (RECENTIN) is approved for use in cancer, including
ovarian, breast, colorectal, metastatic colorectal, renal, lung,
non-small cell lung cancer, sarcoma, glioblastoma, fallopian tube,
peritoneal cancer, and triple-negative breast cancer. Dosing is as
follows. For metastatic colorectal cancer: 20 mg cediranib once a
day in combination with FOLFOX or XELOX chemotherapy. For recurrent
glioblastoma: 30 mg as monotherapy once daily; 20 mg once daily in
combination with lomustine (110 mg/m.sup.2) every 6 weeks. For
recurrent, platinum chemotherapy-sensitive disease or ovarian
cancer related to mutations in BRCA genes: 30 mg once a day with
200 mg olaparib twice a day. For recurrent ovarian, fallopian tube,
peritoneal, or triple-negative breast cancer: (1) 20 mg daily and
olaparib 100 mg twice daily (BID) (2) cediranib 20 mg daily,
olaparib 200 mg BID; (3) cediranib 30 mg daily, olaparib 200 mg
BID; (4) cediranib 30 mg daily, olaparib 400 mg BID. For advanced
non-small cell lung cancer: cisplatin 80 mg/m.sup.2 on day 1 and
gemcitabine 1250 mg/m.sup.2 on days 1 and 8 of a 3-week cycle, and
daily oral cediranib at either 30 mg or 45 mg.
[0102] In embodiments, the VEGF-pathway inhibitor is semaxanib.
Semaxanib is a tyrosine kinase inhibitor indicated for colorectal
cancer, solid tumors, brain tumors, kidney cancer, melanoma, head
and neck cancer, hematologic cancers, mesothelioma, soft tissue
sarcomas, breast cancer, AIDS-Related Kaposi's Sarcoma, multiple
myeloma, cervical cancer, prostate cancer, and ovarian cancer. For
metastatic melanoma, 145 mg/m.sup.2 semaxanib is administered
intravenously twice-weekly in combination with thalidomide,
commencing at 200 mg daily with intrapatient dose escalation as
tolerated; or 85 or 145 mg/m.sup.2 in combination with standard
irinotecan/bolus 5-fluorouracil/leucovorin (IFL) for 4 weeks on/2
weeks off. For solid tumors, semaxanib is administered at a dose of
145 mg/m.sup.2 twice weekly. For metastatic colon cancer, semaxanib
is administered at a dose of 85 or 145 mg/m.sup.2 twice weekly in
combination with fluorouracil and leucovorin (given either weekly
or daily for 5 days every 4 weeks). For Kaposi's sarcoma, semaxanib
is administered at a dose of 65-145 mg/m.sup.2 i.v. biw for six
cycles (of 29 days).
[0103] In embodiments, the VEGF-pathway inhibitor is pomalidomide.
Pomalidomide (POMALYST) is a thalidomide analogue indicated for the
treatment of adult patients with multiple myeloma (MM) who have
received at least two prior therapies including lenalidomide and a
proteasome inhibitor and have demonstrated disease progression on
or within 60 days of completion of the last therapy; in combination
with dexamethasone. POMALYST is also indicated for adult patients
with AIDS-related Kaposi sarcoma (KS) after failure of highly
active antiretroviral therapy (HAART) or in patients with KS who
are HIV negative. For MM, pomalidomide is administered at a dose of
4 mg per day orally on days 1 through 21 of repeated 28-day cycles
in combination with dexamethasone until disease progression. For
KS, pomalidomide is administered at a dose of 5 mg per day taken
orally on Days 1 through 21 of repeated 28-day cycles until disease
progression or unacceptable toxicity. Coadministration with strong
CYP1A2 Inhibitors should be avoided, but if unavoidable,
pomalidomide dosing should be reduced to 2 mg. The dosage form of
pomalidomide is 1 mg, 2 mg, 3 mg, or 4 mg capsules. Deep venous
thrombosis (DVT), pulmonary embolism (PE), myocardial infarction,
and stroke may occur in patients with multiple myeloma treated with
POMALYST.
[0104] In embodiments, the VEGF-pathway inhibitor is alitretinoin.
Alitretinoin (PANRETIN) is a gel indicated for topical treatment of
cutaneous lesions in patients with AIDS-related Kaposi's sarcoma.
Panretin gel is not indicated when systemic anti-KS therapy is
required (e.g., more than 10 new KS lesions in the prior month,
symptomatic lymphedema, symptomatic pulmonary KS, or symptomatic
visceral involvement). Panretin gel should initially be applied two
(2) times a day to cutaneous KS lesions. The application frequency
can be gradually increased to three (3) or four (4) times a day
according to individual lesion tolerance. Panretin gel is available
in tubes containing 60 grams.
[0105] In embodiments, the VEGF-pathway inhibitor is imiquimod.
Imiquimod is marketed as ALDARA and ZYCLARA. ALDARA is a 5% cream
supplied in single-use packets (24 per box), each of which contains
250 mg of the cream, equivalent to 12.5 mg of imiquimod. ZYCLARA is
provided as a 2.5% or 3.75% cream in packets or a pump. Imiquimod
is indicated for the topical treatment of clinically typical,
nonhyperkeratotic, nonhypertrophic actinic keratoses (AK) on the
face or scalp in immunocompetent adults; biopsy-confirmed, primary
superficial basal cell carcinoma (sBCC) in immunocompetent adults;
maximum tumor diameter of 2.0 cm on trunk, neck, or extremities
(excluding hands and feet), only when surgical methods are
medically less appropriate and patient follow-up can be reasonably
assured; and external genital and perianal warts/condyloma
acuminata in patients 12 years old or older.
[0106] In embodiments, the VEGF-pathway inhibitor is sinecatechins.
Sinecatechins (VEREGEN) is a 15% topical ointment indicated for the
treatment of external genital and perianal warts (Condylomata
acuminata) in immunocompetent patients 18 years and older. VEREGEN
is to be applied three times per day to all external genital and
perianal warts.
[0107] In embodiments, the VEGF-pathway inhibitor is vismodegib.
Vismodegib (ERIVEDGE) is a hedgehog pathway inhibitor indicated for
the treatment of adults with metastatic basal cell carcinoma, or
with locally advanced basal cell carcinoma that has recurred
following surgery or who are not candidates for surgery and who are
not candidates for radiation. The recommended dosage is 150 mg
orally once daily. The dosage form is 150 mg capsules.
[0108] In embodiments, the VEGF-pathway inhibitor is sonidegib.
Sonidegib (ODOMZO) is a hedgehog pathway inhibitor indicated for
the treatment of adult patients with locally advanced basal cell
carcinoma (BCC) that has recurred following surgery or radiation
therapy, or those who are not candidates for surgery or radiation
therapy. The recommended dosage is 200 mg orally once daily taken
on an empty stomach, at least 1 hour before or 2 hours after a
meal. Serum creatine kinase (CK) levels and renal function tests
are prior to initiating ODOMZO treatment. The dosage form is 200 mg
capsules.
[0109] In embodiments, the VEGF-pathway inhibitor is pegaptanib
sodium. Pegaptanib sodium (MACUGEN) is indicated for the treatment
of neovascular (wet) age-related macular degeneration. MACUGEN is
administered in a dose of 0.3 mg once every six weeks by
intravitreous injection into the eye. The dosage form is a 0.3
mg/90 .mu.L solution in a single-use syringe for intravitreal
injection.
[0110] In embodiments, the VEGF-pathway inhibitor is dexamethasone.
Dexamethasone intravitreal implant (OZURDEX) is a corticosteroid
indicated for the treatment of macular edema following branch
retinal vein occlusion (BRVO) or central retinal vein occlusion
(CRVO), the treatment of non-infectious uveitis affecting the
posterior segment of the eye, or the treatment of diabetic macular
edema. The dosage form is an intravitreal implant containing 0.7 mg
dexamethasone in the NOVADUR solid polymer drug delivery
system.
[0111] In embodiments, the VEGF-pathway inhibitor is fluocinolone
acetonide. Fluocinolone acetonide (ILUVIEN) contains a
corticosteroid and is indicated for the treatment of diabetic
macular edema (DME) in patients who have been previously treated
with a course of corticosteroids and did not have a clinically
significant rise in intraocular pressure. The dosage form is a
non-bioerodible intravitreal implant containing 0.19 mg
fluocinolone acetonide in a drug delivery system, and is intended
for intravitreal injection.
[0112] In embodiments, the VEGF-pathway inhibitor is conbercept.
Conbercept (COMPAQ SIQQ) is indicated for treatment of age-related
macular degeneration (AMD) and other macular diseases, Idiopathic
Choroidal Neovascularization, Diabetic Retinopathy, Macular Edema,
Central Retinal Vein Occlusion, Tractional Retinal Detachment,
Circumscribed Choroidal Haemangioma, uveitis, Polypoidal Choroidal
Vasculopathy, and Corneal Neovascularization. For AMD and other
retinal vascular disorders, conbercept may be administered at a
dose of 0.5 mg/eye monthly for 3 months followed by 0.5 mg/eye
every 3 months; or just 0.5 mg/eye every 3 months without the 3
month loading period; or 0.5 mg or 2.0 mg for 3 consecutive monthly
doses, after which either monthly or as-needed (PRN) therapy is
administered at the same previous dose; or 0.5 mg every 8 weeks and
1.0 mg every 12 weeks after 3 monthly injections as a loading
phase.
[0113] In embodiments, the VEGF-pathway inhibitor is brolucizumab.
Brolucizumab-dbll (BEOVU) is a human vascular endothelial growth
factor (VEGF) inhibitor indicated for the treatment of AMD. BEOVU
is administered by intravitreal injection. The recommended dose for
BEOVU is 6 mg (0.05 mL of 120 mg/mL solution) monthly
(approximately every 25-31 days) for the first three doses,
followed by one dose of 6 mg (0.05 mL) every 8-12 weeks. The dosage
form is a 6 mg/0.05 mL solution for intravitreal injection in a
single-dose vial. There is a potential risk of arterial
thromboembolic events (ATE) following intravitreal use of VEGF
inhibitors
[0114] In embodiments, the VEGF-pathway inhibitor is selpercatinib.
Selpercatinib (RETEVMO) is a kinase inhibitor indicated for the
treatment of adult patients with metastatic RET fusion-positive
NSCLC, adult and pediatric patients 12 years of age and older with
advanced or metastatic RET-mutant medullary thyroid cancer (MTC)
who require systemic therapy, and adult and pediatric patients 12
years of age and older with advanced or metastatic RET
fusion-positive thyroid cancer who require systemic therapy and who
are radioactive iodine-refractory (if radioactive iodine is
appropriate). Patients are selected for treatment with RETEVMO
based on the presence of a RET gene fusion (NSCLC or thyroid) or
specific RET gene mutation (MTC). The recommended dosage in adults
and pediatric patients 12 years of age or older is based on weight
as follows. Less than 50 kg: 120 mg orally twice daily; 50 kg or
greater: 160 mg orally twice daily. RETEVMO may be administered
orally twice daily (approximately every 12 hours) until disease
progression or unacceptable toxicity. Concomitant use of strong and
moderate CYP3A inhibitors should be avoided, but if it cannot be
avoided, the RETEVMO dose may be reduced as follows. If taking 120
mg twice daily: reduce to 80 mg twice daily with a moderate
inhibitor and 40 mg twice daily with a strong inhibitor; if taking
160 mg twice daily: reduce to 120 mg twice daily with a moderate
inhibitor and 80 mg twice daily with a strong inhibitor.
Concomitant use of a PPI, a histamine-2 (H2) receptor antagonist,
or a locally-acting antacid with RETEVMO should be avoided, but if
it cannot be avoided, RETEVMO may be administered with food and/or
2 hours before or 10 hours after an H2 receptor antagonist; or 2
hours before or 2 hours after a locally-acting antacid. Dosing may
also be reduced for severe hepatic impairment. The dosage form is
40 mg and 80 mg capsules. RETEVMO should not be initiated in
patients with uncontrolled hypertension. Blood pressure should be
monitored and RETEVMO should be withheld, reduced in dose, or
permanently halted based on severity.
[0115] In embodiments, the VEGF-pathway inhibitor is nintedanib
(OFEV). Nintedanib is a kinase inhibitor indicated for treatment of
idiopathic pulmonary fibrosis (IPF), treatment of chronic fibrosing
interstitial lung diseases (ILDs) with a progressive phenotype, and
for slowing the rate of decline in pulmonary function in patients
with systemic sclerosis-associated interstitial lung disease.
Nintedanib is administered at a dose of 150 mg twice daily, about
12 hours apart. The dosage form is 150 mg or 100 mg capsules.
Arterial thromboembolic events have been reported. Caution should
be taken when treating patients at higher cardiovascular risk
including known coronary artery disease. Treatment may be
interrupted in patients who develop signs or symptoms of acute
myocardial ischemia. For patients with mild hepatic impairment, the
dose may be modified to 100 mg twice daily approximately 12 hours
apart. In addition to symptomatic treatment, if applicable, dose
reduction or temporary interruption may be indicated for the
management of adverse reactions, until the specific adverse
reaction resolves to levels that allow continuation of therapy.
Treatment may be resumed at the full dosage (150 mg twice daily),
or at the reduced dosage (100 mg twice daily), which subsequently
may be increased to the full dosage. If a patient does not tolerate
100 mg twice daily, treatment with nintedanib may be discontinued.
Dose modifications or interruptions may be necessary for liver
enzyme elevations. Liver function tests (aspartate aminotransferase
(AST), alanine aminotransferase (ALT), and bilirubin) may be
conducted prior to initiation of treatment with nintedanib, at
regular intervals during the first three months of treatment, and
periodically thereafter or as clinically indicated. In patients who
report symptoms that may indicate liver injury, including fatigue,
anorexia, right upper abdominal discomfort, dark urine or jaundice,
liver tests may be measured promptly. In patients with AST or ALT
greater than 3 times the upper limit of normal (ULN) with signs or
symptoms of liver injury and for AST or ALT elevations greater than
5 times the upper limit of normal, treatment may be discontinued.
For AST or ALT greater than 3 times to less than 5 times the ULN
without signs of liver damage, treatment may be interrupted or
reduced to 100 mg twice daily. Once liver enzymes have returned to
baseline values, treatment may be reintroduced at a reduced dosage
(100 mg twice daily), which subsequently may be increased to the
full dosage (150 mg twice daily).
[0116] In embodiments, the VEGF-pathway inhibitor is apatinib.
Apatinib is indicated for treatment of advanced or metastatic
gastric carcinoma, metastatic breast cancer, advanced
hepatocellular carcinoma, metastatic colorectal cancer, esophageal
cancer (advanced esophageal squamous cell carcinoma), and
glioblastoma. Apatinib generally may be administered at a dose of
750 mg once daily. Other possible doses include 250, 500, 750, 850,
and 1000 mg once daily. For advanced or metastatic gastric
carcinoma, apatinib may be administered at a dose of 850 mg once
daily or 425 mg twice daily. For advanced progressed lung
adenocarcinoma patients with EGFR-TKI resistance, apatinib may be
administered at a dose of 500 mg/m.sup.2 per day for 21 consecutive
days alone or in combination with traditional chemotherapy drugs
pemetrexed (50 mg/m.sup.2, once every 21 days) and docetaxel (75
mg/m.sup.2, once every 21 days). For metastatic colorectal cancer,
apatinib may be administered at a dose of 125 mg, 250 mg, 500 mg,
850 mg once per day, alone or in combination with other agents in
either 21 or 28 day cycles. For advanced esophageal squamous cell
carcinoma, apatinib may be administered at a dose of 500 mg daily
in a 28 day cycle, which may be reduced to 250 mg.
[0117] In embodiments, the VEGF-pathway inhibitor is motesanib.
Motesanib is indicated for thyroid cancer (progressive or
symptomatic, advanced or metastatic medullary thyroid cancer;
progressive differentiated thyroid cancer), non-small cell lung
cancer (advanced nonsquamous), gastrointestinal stromal cancer,
colorectal cancer, breast cancer (HER2-negative locally recurrent
or metastatic breast cancer), persistent or recurrent ovarian
cancer, fallopian tube and primary peritoneal carcinomas, advanced
solid tumors, and low-grade neuroendocrine tumors. For advanced
nonsquamous non-small-cell lung cancer (NSCLC), motesanib may be
administered at a dose of 125 mg once daily, or 75 mg twice daily
(5 days on/2 days off), both with carboplatin (AUC, 6 mg/ml min)
and paclitaxel (200 mg/m2) for up to six 3-week cycles. For
HER2-negative locally recurrent or metastatic breast cancer:
motesanib 125 mg orally once per day with paclitaxel (90 mg/m 2 on
days 1, 8, and 15 every 3 weeks). For progressive or symptomatic,
advanced or metastatic medullary thyroid cancer, progressive
differentiated thyroid cancer, advanced solid tumors, and for
persistent or recurrent ovarian, fallopian tube, and primary
peritoneal carcinomas, motesanib may be administered at a dose of
125 mg daily. For ow-grade neuroendocrine tumors, motesanib may be
administered at a dose of 125 mg once daily in combination with
octreotide-LAR (30 mg administered on day 1 of each cycle 28-day
cycle).
[0118] VEGF-pathway inhibitors may be administered in combination
with one or more additional anti-cancer therapies. For example,
VEGF-pathway inhibitors may be administered in combination with
surgical therapy, radiation therapy, chemotherapy, immunotherapies
(e.g. checkpoint inhibitors, adoptive cell transfer, antibodies,
vaccines, cytokines, etc.), targeted therapies (e.g. small-molecule
drugs, antibodies), hormone therapy, stem-cell transplant, and the
like. The subject may be a candidate for or currently provided with
any suitable combination of therapies prior to determination of
risk of VEGF-inhibitor toxicities in the subject. Any suitable
combination of therapies (e.g. VEGF-inhibitors, other anti-cancer
therapies, supportive therapies, or any combination thereof) may be
provided to the subject following determination of risk in the
subject.
[0119] Any of the therapies described herein (e.g. VEGF-pathway
inhibitors, supportive therapies, other anti-cancer therapies) may
be provided by any suitable route. For example, the therapy may be
provided orally. Alternatively, the therapy may be provided
parenterally. Suitable doses and modes of administration may be
determined based upon various factors, including the age, sex,
weight, health of the subject, other medications being administered
to the subject, and the like, using routine techniques known in the
art.
[0120] By way of example and not of limitation, examples of the
present disclosure will now be provided.
EXPERIMENTAL EXAMPLES
Example 1
[0121] The objective of the current study was to perform a GWAS of
four randomized phase III clinical trials from the Cancer and
Leukemia Group B (CALGB, now Alliance for Clinical Trials in
Oncology, Alliance) to identify novel genes and genetic variants
that showed a consistent risk of toxicity across the different
studies.
[0122] Methods
[0123] Patients and Randomized, Phase III Clinical Trials
[0124] CALGB 80303 was conducted in advanced pancreatic cancer
patients treated with gemcitabine and either 10 mg/kg bevacizumab
or placebo. CALGB 40503 was conducted in hormone receptor-positive
advanced-stage breast cancer patients treated with letrozole and
either 15 mg/kg bevacizumab or placebo. CALGB 90401 was conducted
in metastatic castration-resistant prostate cancer patients treated
with docetaxel/prednisone with either 15 mg/kg bevacizumab or
placebo. CALGB 40502 was conducted in locally recurrent or
metastatic breast cancer patients treated with either
nab-paclitaxel, ixabepilone, or paclitaxel, all administered in
combination with 10 mg/kg bevacizumab. Patient eligibility,
characteristics, stratifications, treatments, and the methods to
detect progression of disease have been previously described.
[0125] Toxicity
[0126] Proteinuria and hypertension were recorded according to
Common Toxicity Criteria for Adverse Events (CTCAE) version 3.0
(Table 1), per protocol. The composite toxicity is defined as the
occurrence of either proteinuria or hypertension or both. For CALGB
40502, data on proteinuria and composite toxicity were not
available. Urine protein levels were measured on day 1 and every
four weeks after starting treatment in CALGB 80303; on day 1 of the
1.sup.st cycle and up to 5 days before or on the day of treatment
for subsequent cycles in CALGB 40503; and within 48 hours prior to
every treatment cycle in CALGB 90401. Blood pressure was obtained
on day 1 of each cycle in all trials, and plus on day 15 in CALGB
80303.
TABLE-US-00001 TABLE 1 Hypertension and proteinuria grades of
toxicity according to Common Toxicity Criteria of Adverse Events
(CTCAE) v3.0. Urine dipstick test result: 1+ (15-30 mg/dL), 2+
(100-300 mg/dL), 3+ (300-1000 mg/dL), and 4+ (>1000 mg/dL). WNL
within normal limits. Toxicity Grade 1 Grade 2 Grade 3 Grade 4
Grade 5 Proteinuria 1+ or 2+ to 3+ or 4+ or Nephrotic Death
0.15-1.0 >1.0-3.5 >3.5 syndrome g/24 hrs g/24 hrs g/24 hrs
Hyper- Asympto- Recurrent or Requiring Life- Death tension matic,
persistent more than threatening transient (>24 hrs) or one
conse- (<24 hrs) symptomatic quences increase by increase by
drug or (e.g., >20 mmHg >20 mmHg more hyper- (diastolic)
(diastolic) or intensive tensive or to to >150/100 therapy
crisis) >150/100 if if previously than previously WNL;
previously WNL; monotherapy intervention may be not indicated
indicated
[0127] Bevacizumab-related toxicity was defined as the occurrence
of toxicity (grade.gtoreq.2 or grade.gtoreq.3 of hypertension,
proteinuria, or either proteinuria or hypertension--composite
toxicity) after the start of treatment. Only toxicities with
attribution of "possibly related" or higher were included. The
occurrence of treatment-terminating events was used for censoring,
as they determined the exit of the patients from the trial.
Treatment-terminating events included death, disease progression,
other toxicities defined per protocol, withdrawal of consent, loss
to follow up, or unknown recorded events. The time to event was
reconstructed manually for each patient in each study, as performed
previously. The time to event was calculated as the time from the
first administration of bevacizumab to the first date of
experiencing the toxicity of interest, or other
treatment-terminating events, whichever occurred first.
[0128] Genotyping and Quality Control
[0129] DNA for genotyping was obtained from peripheral blood. The
genotyping platforms used in each study are described in Table 2,
and the number of SNPs used for analysis after quality control (QC)
are described in FIG. 1. Additional information on the quality
control procedures can be found in the individual publications of
the GWAS data.
TABLE-US-00002 TABLE 2 Patients of European ancestry treated with
bevacizumab used in the GWAS data. CALGB Cancer and Leukemia Group
B, SD standard deviation, composite toxicity is defined as the
occurrence of either proteinuria or hypertension or both. 80303
40503 90401 40502 CALGB trial n = 154 n = 105 n = 316 n = 466 Age
Mean (SD) 64.1 (10.2) 68.4 (8.3) 56.9 (11.7) 57.2 (10.7) Gender
Male 90 0 316 0 Female 64 105 0 466 Cancer type Advanced Hormone
receptor- Metastatic castration- Recurrent or pancreatic cancer
positive advanced- resistant prostate metastatic breast stage
breast cancer cancer cancer Treatment Gemcitabine 1,000 Letrozole
2.5 mg Docetaxel 75 mg/m.sup.2 Paclitaxel 90 mg/m.sup.2 or
mg/m.sup.2 on days 1, orally/day plus either in combination with
nab-paclitaxel 150 8, and 15 plus placebo or prednisone 5 mg
mg/m.sup.2 or ixabepilone either placebo or bevacizumab 15 orally
on day 1 plus 16 mg/m.sup.2 on days 1, bevacizumab 10 mg/kg every
21 days either placebo or 8, and 15 plus mg/kg on days 1
bevacizumab 15 bevacizumab 10 and 15 mg/kg every 21 days mg/kg on
days 1 and 15 Genotype platform IIlumina IIlumina Human IIlumina
IIlumina Human HumanHap550- OmniExpressExome-8 HumanHap610-Quad
OmniExpressExome-8 Quad Grade .gtoreq. 2 Grade .gtoreq. 3 Grade
.gtoreq. 2 Grade .gtoreq. 3 Grade .gtoreq. 2 Grade .gtoreq. 3 Grade
.gtoreq. 2 Grade .gtoreq. 3 Hypertension (n, %) 26 (16.9) 19 (12.3)
53 (50.5) 29 (27.6) 47 (15.0) 22 (7.0) 143 (30.7) 50 (10.7)
Proteinuria (n, %) 26 (16.9) 9 (5.8) 32 (30.5) 10 (9.5) 20 (6.4) 5
(1.6) -- Composite toxicity (n, %) 43 (27.9) 26 (16.9) 73 (69.5) 34
(32.4) 61 (19.4) 26 (8.2) --
[0130] Statistical Analysis
[0131] SNP-Based Association Testing
[0132] The association between SNPs and toxicities (grade.gtoreq.2
or grade.gtoreq.3) was tested in genetic European patients in the
bevacizumab arm. Ethnicity information was determined by estimating
the genetic ancestral origin of patients using the principal
components analysis software implemented in Eigenstrat. A
cause-specific Cox model, where the outcome is defined as the pair
of time event and the censoring indicator, was fitted to obtain the
estimate of the SNP effect (and the corresponding standard error
estimate) on toxicity in each individual study. The analyses were
powered against an additive genetic model. The inverse variance
formula was used to combine the SNP effect in each study to obtain
the estimate (.beta.) of the SNP-toxicity association and its
standard error. The heterogeneity across studies was examined by
the Cochran's test (no heterogeneity was detected). Cox analyses
for each variant, adjusting for age and gender, were performed by
adding those variables as covariates in the model. The reported
results are unadjusted, unless stated otherwise. The reported p
values are not corrected for multiple comparisons.
Quantile-quantile (Q-Q) plots were generated.
[0133] Gene-Based Association Testing
[0134] Under the same model described above, a gene-based analysis
was also performed. First, all the human protein-coding genes were
mapped to SNPs according to the location of SNPs with a margin
equaling 50 by using the R package "snplist". Next, the
cause-specific Cox model was fitted to obtain the score statistics
for SNP by toxicity association in each study. Last, the Sequence
Kernel Association Test (SKAT) was used to combine the SNP-level
test statistics. This method allowed for different directions of
the SNP effect in a gene and could accommodate also common alleles.
From the SKAT test, the weighted quadratic statistics were computed
using the MASS software, with p-values determined by the
re-sampling method. The reported results are unadjusted, unless
stated otherwise. The reported p values are not corrected for
multiple comparisons. Q-Q plots were also generated for this
analysis.
[0135] Functional Annotation of Variants
[0136] Functional annotation of SNPs and genes was performed using
the SCAN database. Variants were analyzed by the LDlink web-based
application for analyses of linkage disequilibrium (LD). UCSC
Genome Browser (http://genome.ucsc.edu/), RegulomeDB and Haploreg
v4 were used for functional inference. The Genotype-Tissue
Expression project (GTEx v7) and NephQTL were used for expression
quantitative trait loci (eQTL) analyses.
[0137] Results
[0138] A total of 1,041 cancer patients of European ancestry
treated with bevacizumab with available genotyping information were
included in the study. The characteristics of patients from each
trial, as well as the prevalence of toxicities, are shown in Table
2. Grade.gtoreq.2 hypertension (15.0%-50.5%) was more prevalent
than grade.gtoreq.2 proteinuria (5.4-30.5%). The prevalence of
either grade.gtoreq.2 proteinuria or grade.gtoreq.2 hypertension
(composite toxicity) was 19.4-69.5%. Considering only the patients
who had both toxicities, the prevalence was 1.9%-11.4%. The
prevalence of these toxicities was higher in female patients in the
breast cancer studies (CALGB 40502 and 40503) than in male patients
in the prostate cancer study (CALGB 90401). A higher prevalence was
also observed in females compared to males in the pancreatic cancer
study (CALGB 80303) (Table 3).
TABLE-US-00003 TABLE 3 Prevalence of hypertension and proteinuria
in CALGB 80303 by gender. Composite toxicity is defined as the
occurrence of either proteinuria or hypertension or both. Grade
.gtoreq.2 Grade 3 Female Male Female Male (n = 64) (n = 90) (n =
64) (n = 90) Hypertension (n, %) 14 (21.9) 12 (13.3) 9 (14.1) 10
(11.1) Proteinuria (n, %) 11 (17.2) 15 (16.7) 6 (9.4) 3 (3.3)
Composite toxicity (n, %) 20 (31.2) 23 (25.6) 14 (21.9) 12
(13.3)
[0139] Variants and Genes Associated with Bevacizumab-Induced
Proteinuria
[0140] For the SNP-based analysis of grade.gtoreq.2, the Manhattan
and Q-Q plots are shown in FIG. 2. 90 variants were identified as
associated with bevacizumab-induced proteinuria (Table 4).
TABLE-US-00004 TABLE 4 SNP's associated with Proteinuria (grade
.gtoreq. 2) effect reference MAF MAF MAF SNP CH BP allele allele
80303 40503 90401 gene feature Flanking gene Flanking gene p-value
unadjusted effect (.beta.) unadjusted p-value adjusted effect
(.beta.) adjusted rs339947 5 14071067 A C 0.12 . 0.14 NA NA DNAH5
TRIO 7.66E-08 1.27 1.58E-07 1.26 rs13293961 9 104807170 A C . .
0.08 CYLC2 missense LOC100131879 SMC2 2.39E-06 1.56 2.60E-06 1.61
rs12612153 2 44755864 C A 0.11 . 0.11 C2orf34 intron PREPL
LOC100130502 3.89E-06 1.16 6.93E-06 1.15 rs7180310 15 22890430 A C
0.06 0.05 . NA NA SNORD116-24 SNORD116-25 4.10E-06 1.54 4.19E-06
1.55 rs12482855 21 42065030 A G 0.06 0.06 0.06 NA NA RIPK4 PRDM15
6.28E-06 1.20 1.09E-05 1.20 rs408130 5 14059289 A G 0.21 . 0.28 NA
NA DNAH5 TRIO 6.33E-06 1.07 6.94E-06 1.09 rs418173 5 14058033 A G
0.21 . 0.28 NA NA DNAH5 TRIO 6.33E-06 1.07 6.94E-06 1.09 rs11716628
3 35851495 G A . 0.18 . NA NA ARPP-21 LOC100131711 6.87E-06 1.39
1.04E-05 1.39 rs7959783 12 67109382 G A 0.31 0.26 0.33 NA NA MDM1
LOC729376 7.01E-06 0.72 6.56E-06 0.73 rs627761 11 125330918 G A
0.10 . 0.09 LOC338667 intron DDX25 CDON 7.49E-06 1.19 1.34E-05 1.18
rs2688994 3 126300783 A G 0.13 0.14 0.14 SLC12A8 intron HEG1 ZNF148
8.13E-06 0.92 4.38E-06 0.98 rs10486445 7 24980507 G A 0.42 0.35
0.39 OSBPL3 intron DFNA5 CYCS 1.17E-05 0.75 1.11E-05 0.78
rs17345945 8 68674808 A G 0.09 . 0.08 CPA6 intron LOC100132812
PREX2 1.36E-05 1.15 1.30E-05 1.19 rs13276511 8 86959167 G A 0.06 .
. NA NA REXO1L7P LOC642137 1.39E-05 1.40 4.01E-05 1.37 rs17624773
12 33136580 A G 0.10 0.06 0.14 NA NA ASSP14 SYT10 1.79E-05 0.96
1.59E-05 0.97 rs1509247 4 22952896 G A 0.43 0.43 0.52 LOC643751
intron GBA3 PPARGC1A 1.83E-05 0.70 1.09E-05 0.72 rs12345440 9
102993955 G A 0.09 . 0.10 RP11-35N6.1 intron LOC392374 LOC347275
1.89E-05 1.23 1.45E-05 1.28 rs4916009 1 65144006 A G 0.08 . 0.09
JAK1 intron RAVER2 LOC100130270 2.10E-05 1.17 8.86E-06 1.24
rs2378865 14 30952224 G A . 0.42 . NA NA HEATRSA C14orf126 2.35E-05
1.11 2.10E-05 1.14 rs2064949 20 19756654 G A . 0.19 . NA NA RPL12L3
RIN2 2.38E-05 1.07 6.46E-06 1.07 rs12536799 7 133378576 C A 0.11 .
0.08 EXOC4 intron FAM10A7 LRGUK 2.82E-05 1.24 6.20E-06 1.25
rs6483735 11 20844275 A G 0.19 0.20 0.17 NELL1 intron LOC100132634
LOC100130160 2.92E-05 0.80 1.61E-05 0.83 rs12352151 9 102995858 A G
0.10 . 0.10 RP11-35N6.1 intron LOC392374 LOC347275 3.07E-05 1.20
2.60E-06 1.22 rs1431477 9 102994274 C A 0.10 . 0.10 RP11-35N6.1
intron LOC392374 LOC347275 3.07E-05 1.20 4.19E-06 1.22 rs11662763
18 5847091 A G 0.14 0.11 0.13 NA NA LOC645355 TTMA 3.11E-05 0.78
1.87E-05 0.79 rs4780054 15 27387295 A G 0.38 0.40 0.40 NA NA NDNL2
LOC100130736 3.16E-05 0.72 1.11E-05 0.70 rs17725486 7 25037388 A G
. 0.30 . NA NA OSBPL3 CYCS 3.26E-05 1.00 4.38E-06 1.03 rs2391081 7
25034923 A G . 0.30 . NA NA OSBPL3 CYCS 3.26E-05 1.00 6.18E-06 1.03
rs879965 7 46015867 G A 0.46 0.47 0.44 NA NA LOC222052 LOC730338
3.29E-05 0.71 5.05E-05 0.68 rs5927577 X 30558644 A G . 0.38 . NA NA
LOC652904 GK 3.53E-05 1.13 1.34E-05 1.12 rs12910488 15 59578470 C T
. 0.42 . NA NA RORA VPS13C 3.60E-05 -1.32 6.94E-06 -1.33 rs7616936
3 85886475 C A 0.08 . 0.12 CADM2 intron LOC440970 LOC728144
3.71E-05 1.04 3.43E-05 1.01 rs13255802 8 80730920 G A . 0.23 .
STMN2 intron LOC100128963 HEY1 3.85E-05 1.16 3.15E-05 1.15
rs11532247 12 19614829 A G 0.50 . 0.49 NA NA AEBP2 LOC400013
3.90E-05 0.91 2.09E-05 0.95 rs7614155 3 74196658 G A 0.25 . 0.27 NA
NA LOC100129282 HSP90AB5P 3.95E-05 0.90 8.86E-06 0.90 rs11196791 10
116323964 G A . 0.23 . ABLIM1 intron AFAP1L2 PPIAP19 3.97E-05 1.16
1.61E-05 1.15 rs2901044 10 116317439 A G . 0.23 . ABLIM1 intron
AFAP1L2 PPIAP19 3.97E-05 1.16 1.73E-05 1.15 rs6996073 8 18594558 C
T . 0.06 . PSD3 intron NAT2 NSAP11 4.21E-05 1.36 1.72E-04 1.39
rs972433 8 18599078 C T . 0.06 . PSD3 intron NAT2 NSAP11 4.30E-05
1.35 1.77E-04 1.38 rs2491608 1 105673803 A G 0.44 . 0.46 NA NA
LOC642337 LOC100130867 4.32E-05 0.94 3.25E-05 0.92 rs13275710 8
41514221 A G 0.17 . 0.13 GINS4 intron KRT18P37 AGPAT6 4.57E-05 1.05
1.45E-05 1.06 rs12777350 10 90351816 A G 0.06 0.07 0.06 LIPJ intron
C10orf59 LOC389992 4.69E-05 1.10 3.74E-05 1.10 rs6597976 11 1101474
A G 0.06 0.06 0.07 NA NA MUC2 LOC100132635 5.03E-05 0.99 3.87E-05
1.01 rs5904577 X 21604594 A G . 0.05 . NA NA KLHL34 SMPX 6.06E-05
1.68 2.10E-05 1.71 rs2328452 20 19713174 A G . 0.17 . LOC100130408
intron SLC24A3 RPL12L3 6.46E-05 0.98 5.10E-05 0.97 rs6112574 20
19710695 G A . 0.17 . LOC100130408 intron SLC24A3 RPL12L3 6.46E-05
0.98 5.31E-05 0.97 rs7804806 7 75433618 A G 0.32 0.29 . POR intron
SNORA14A TMEM120A 6.67E-05 0.74 7.41E-05 0.73 rs4579610 9 89230980
G A 0.25 0.26 . NA NA LOC100132348 DAPK1 6.82E-05 0.76 1.25E-04
0.74 rs546913 6 112396275 A G 0.05 . 0.05 NA NA FYN WISP3 6.84E-05
1.41 2.61E-05 1.51 rs689328 6 112393380 A G 0.05 . 0.05 NA NA FYN
WISP3 6.84E-05 1.41 2.61E-05 1.51 rs1358206 3 74198360 G A 0.30 .
0.31 NA NA LOC100129282 HSP90AB5P 7.03E-05 0.86 3.29E-05 0.87
rs2980872 8 126486102 A G 0.47 0.44 0.49 NA NA NSMCE2 TRIB1
7.10E-05 -0.70 4.93E-05 -0.70 rs2899258 22 34685304 C A 0.10 . 0.09
RBM9 intron LOC100131802 APOL3 7.11E-05 1.16 1.02E-04 1.14
rs5750200 22 34641716 C A 0.10 . 0.09 RBM9 intron NDUFA9P1
LOC100131802 7.11E-05 1.16 1.02E-04 1.14 rs339429 5 14032101 G A
0.14 0.13 0.16 NA NA DNAH5 TRIO 7.34E-05 0.85 1.20E-04 0.84
rs11794832 9 18900581 C T . 0.22 . ADAMTSL1 utr-3 LOC100129109
FAM154A 7.41E-05 1.24 3.15E-05 1.24 rs6737965 2 159744839 A G 0.08
. 0.10 TANC1 intron BTF3L4P WDSUB1 7.49E-05 1.00 1.82E-04 -0.96
rs4676847 3 72081959 C T . 0.15 . NA NA PROK2 CCDC137P 7.66E-05
1.15 4.62E-05 1.21 rs2184352 10 121762442 G A 0.10 0.07 0.07 NA NA
LOC651144 LOC729402 7.74E-05 0.89 4.98E-05 0.89 rs7552510 1
243234661 A C 0.09 0.08 0.10 EFCAB2 intron LOC100129656
LOC100128825 7.93E-05 0.93 3.63E-05 0.95 rs17262815 8 130560347 C T
. 0.14 . NA NA LOC100129525 LOC100130376 8.10E-05 1.25 5.66E-05
1.24 rs11020388 11 92880495 A C 0.18 0.17 0.17 C11orf75 intron
CCDC67 LOC729466 8.12E-05 0.75 4.98E-05 0.77 rs555397 11 125341540
A G 0.11 0.07 0.09 CDON intron LOC338667 LOC729561 8.22E-05 0.97
1.66E-04 -0.95 rs1874797 12 30027638 G A 0.14 0.15 0.16 NA NA TMTC1
IPO8 8.35E-05 0.80 2.16E-04 0.76 rs11919628 3 111812972 T G . 0.08
. NA NA LOC440973 LOC389141 8.48E-05 1.48 1.53E-04 -1.47 rs17298333
7 25010467 A C . 0.31 . NA NA OSBPL3 CYCS 8.52E-05 0.97 7.04E-05
0.99 rs1563591 4 180515297 G A 0.10 . 0.10 NA NA LOC391719
hCG_2025798 8.71E-05 1.25 7.35E-05 1.27 rs294027 11 26485638 A G
0.15 . 0.19 TMEM16C intron LOC645705 MUC15 8.77E-05 1.00 3.92E-05
1.02 rs17017895 2 36029204 A G 0.10 0.09 0.11 NA NA MRPL50P1 CRIM1
8.78E-05 0.88 1.04E-05 0.93 rs6884748 5 31527072 G A 0.06 . 0.07
RNASEN intron CDH6 C5orf22 8.82E-05 1.13 2.61E-05 1.19 rs6884823 5
31526878 A G 0.06 . 0.07 RNASEN intron CDH6 C5orf22 8.82E-05 1.13
2.61E-05 1.19 rs2757491 1 170533424 A G 0.06 . 0.06 DNM3 intron
LOC100128178 LOC100131486 8.85E-05 1.10 1.17E-04 -1.08 rs2757500 1
170545644 A G 0.06 . 0.06 DNM3 intron LOC100128178 LOC100131486
8.85E-05 1.10 1.17E-04 -1.08 rs12777191 10 95052323 G A 0.14 0.14
0.14 NA NA LOC643863 FER1L3 9.06E-05 0.77 1.10E-04 0.76 rs957615 4
23518663 T C . 0.10 . NA NA PPARGC1A LOC729175 9.22E-05 1.33
5.67E-05 1.36 rs11898024 2 58115520 C A 0.08 . 0.10 NA NA
LOC100131953 VRK2 9.24E-05 1.15 6.94E-06 1.25 rs10169411 2 42491253
A G . 0.13 . NA NA COX7A2L KCNG3 9.25E-05 1.16 1.22E-04 -1.14
rs11693549 2 42543983 T C . 0.13 . KCNG3 intron COX7A2L
LOC100129718 9.25E-05 1.16 1.22E-04 -1.14 rs222468 2 42496035 A G .
0.13 . NA NA COX7A2L KCNG3 9.25E-05 1.16 1.22E-04 -1.14 rs222471 2
42491561 G A . 0.13 . NA NA COX7A2L KCNG3 9.25E-05 1.16 1.22E-04
1.14 rs3794002 11 92892707 G A 0.18 . 0.16 C11orf75 intron CCDC67
LOC729466 9.29E-05 0.91 6.50E-05 0.95 rs11028782 11 25574425 A G
0.24 . 0.18 NA NA LOC554234 LOC645705 9.40E-05 0.86 1.26E-04 -0.85
rs2076766 13 106979661 A G 0.18 0.16 0.16 FAM155A intron
RP11-282A11.1 LIG4 9.43E-05 0.71 1.65E-04 -0.70 rs1871072 10
54571008 A G . 0.31 . NA NA MBL2 PCDH15 9.49E-05 1.21 1.42E-04
-1.07 rs6750890 2 208719259 T G . 0.10 . CRYGB near-gene-5 CRYGB
CRYGA 9.49E-05 1.08 1.93E-04 -1.20 rs6712962 2 234577772 G A 0.49
0.42 0.45 TRPM8 intron LOC100130859 SPP2 9.60E-05 -0.70 1.39E-04
-0.69 rs318422 1 82792064 A G 0.44 0.40 0.41 NA NA LPHN2 TTLL7
9.70E-05 0.64 1.21E-04 -0.63 rs17182641 14 21146287 G A 0.11 0.08
0.13 NA NA OR10G1P TRA@ 9.71E-05 0.92 1.09E-05 0.97 rs10179237 2
42369005 T C . 0.12 . EML4 intron SGK493 COX7A2L 9.81E-05 1.19
1.35E-04 -1.18 rs2053349 2 42369709 A G . 0.12 . EML4 intron SGK493
COX7A2L 9.81E-05 1.19 1.35E-04 -1.18
[0141] Fifty-nine out of 90 variants had the same direction of
effect (either reduced or increased risk) in at least two out of
the three studies (cutoff p<1.times.10.sup.-4). The top ten most
statistically significant variants of that list are shown in Table
5.
TABLE-US-00005 TABLE 5 Ten most statistically significant variants,
according to unadjusted p values, associated with grade 22
proteinuria, hypertension and composite toxicity with the same
direction of effect (either reduced or increased risk) in at least
two out of three trials for proteinuria and composite toxicity, and
three out of four trials for hypertension. Ch chromosome, NA
Intergenic SNP, MAF minor allele frequencies in CALGB 80303, 40503,
90401, and 40502 respectively, "--" SNP not present in the genotype
platform of the trial, "." data on proteinuria were not available.
Composite toxicity is defined as the occurrence of either
proteinuria or hypertension or both. Base Effect SNP Ch Gene
Feature Flanking gene Flanking gene change MAF size (.beta.)
p-value Proteinuria rs339947 5 NA NA DNAH5 TRIO C > A
0.12/_/0.14/. 1.27 7.66 .times. 10.sup.-8 rs12612153 2 C2orf34
Intron PREPL LOC100130502 A > C 0.11/_/0.11/. 1.16 3.89 .times.
10.sup.-6 rs7180310 15 NA NA SNORD116-24 SNORD116-25 C > A
0.06/0.05/_/. 1.54 4.10 .times. 10.sup.-6 rs12482855 21 NA NA RIPK4
PRDM15 G > A 0.06/0.06/0.06/. 1.20 6.28 .times. 10.sup.-6
rs408130 5 NA NA DNAH5 TRIO G > A 0.21/_/0.28/. 1.07 6.33
.times. 10.sup.-6 rs418173 5 NA NA DNAH5 TRIO G > A
0.21/_/0.28/. 1.07 6.33 .times. 10.sup.-6 rs7959783 12 NA NA MDM1
LOC729376 A > G 0.31/0.26/0.33/. 0.72 7.01 .times. 10.sup.-6
rs627761 11 LOC338667 Intron DDX25 CDON A > G 0.10/_/0.09/. 1.19
7.49 .times. 10.sup.-6 rs2688994 3 SLC12A8 Intron HEG1 ZNF148 G
> A 0.13/0.14/0.14/. 0.92 8.13 .times. 10.sup.-6 rs10486445 7
OSBPL3 Intron DFNA5 CYCS A > G 0.42/0.35/0.39/. 0.75 1.17
.times. 10.sup.-5 Hypertension rs13135230 4 NA NA CCDC149 LGI2 G
> A 0.27/0.28/0.25/0.28 0.46 1.26 .times. 10.sup.-6 rs2350620 8
ASPH Intron hCG_1988300 LOC645551 A > G 0.32/0.26/0.32/0.32
-0.49 1.44 .times. 10.sup.-6 rs6770663 3 KCNAB1 Intron LOC751837
SSR3 A > G 0.09/0.09/0.08/0.09 0.57 4.79 .times. 10.sup.-6
rs1145786 6 NA NA MAP3K7 LOC100129847 A > G 0.33/0.32/0.34/0.33
0.39 5.10 .times. 10.sup.-6 rs7130734 11 NA NA LRRC4C LOC100131020
C > A 0.35/0.30/_/0.33 0.42 1.17 .times. 10.sup.-5 rs2179218 20
PTPRT Intron LOC6431 72 PPIAL G > A 0.13/0.15/0.14/0.13 0.49
1.99 .times. 10.sup.-5 rs10519829 5 NA NA LOC644659 LOC100130551 G
> A 0.44/0.46/0.47/0.47 0.36 2.28 .times. 10.sup.-5 rs1530837 15
PLA2G4E Intron EHD4 PLA2G4D A > G 0.23/0.19/0.18/0.17 0.43 2.59
.times. 10.sup.-5 rs2000611 14 KCNK10 Intron KCNK10 SPATA 7 A >
G 0.44/0.43/0.50/0.48 -0.37 3.49 .times. 10.sup.-5 rs4611262 12
NUP37 Intron CCDC53 C12orf48 G > A 0.20/0.25/0.23/0.23 0.39 3.74
.times. 10.sup.-5 Composite toxicity rs11662763 18 NA NA LOC645355
TTMA G > A 0.14/0.11/0.13/. 0.67 9.19 .times. 10.sup.-7
rs8006648 14 NA NA LOC730121 GALC G > A 0.27/0.28/0.26/. 0.58
2.33 .times. 10.sup.-6 rs2456761 10 NA NA LOC729184 CDC2 C > A
0.35/_/0.34/. 0.72 2.80 .times. 10.sup.-6 rs1000032 2 NA NA KIAA1
715 EVX2 C > A 0.13/0.18/0.19/. 0.62 3.21 .times. 10.sup.-6
rs2687640 7 CPVL Intron KIAA0644 LOC100131724 G > A
0.06/_/0.06/. 1.03 3.55 .times. 10.sup.-6 rs9310707 3 CNTN4 Intron
LOC727810 LOC100130346 G > A 0.37/0.37/0.36/. 0.53 4.03 .times.
10.sup.-6 rs13156044 5 DNAH5 Intron LOC391738 TRIO G > A
0.15/0.11/0.11/. 0.60 8.51 .times. 10.sup.-6 rs12328055 2 NA NA
FSHR LOC130728 G > A 0.06/_/0.05/. 0.99 9.19 .times. 10.sup.-6
rs4799369 18 DTNA Intron LOC646842 MAPRE2 A > G 0.20/0.20/0.18/.
0.59 1.14 .times. 10.sup.-5 rs2757491 1 DNM3 Intron LOC100128178
LOC100131486 G > A 0.06/_/0.06/. 0.90 1.21 .times. 10.sup.-5
[0142] rs339947 (C>A, minor allele frequency, MAF 0.12-0.14) was
the most statistically significant (p=7.66.times.10-8,
.beta.=1.27), with the A allele increasing the risk of proteinuria
(FIG. 3). rs339947 is an intergenic variant located 73 kb 5' from
DNAH5 and 130 kb 5' from TRIO (FIG. 4A). rs408130 and rs418173
(G>A and MAF 0.21-0.28 for both) are among the ten most
statistically significant variants and in complete LD with each
other (R.sup.2=1.00) and in moderate LD with rs339947
(R.sup.2=0.51). rs12482855 (G>A, MAF 0.06) had the same
direction of effect in all three trials (p=6.28.times.10.sup.-6,
.beta.=1.20), with the A allele increasing the risk of proteinuria
(FIG. 3). rs12482855 is 4.7 kb 5' from RIPK4, an intergenic variant
and does not have any variant in high LD (r.sup.2>0.8) with it
(FIG. 4C).
[0143] For the SNP-based analysis of grade the Manhattan and Q-Q
plots are shown in FIG. 5. 67 variants were identified as
associated with proteinuria. Results are shown in Table 6.
TABLE-US-00006 TABLE 6 SNPs associated with proteinuria (grade
.gtoreq. 3) effect reference MAF MAF MAF effect SNP CH BP allele
allele 80303 40503 90401 gene feature Flanking gene Flanking gene
p-value (.beta.) rs2303028 5 150485987 A G 0.19 0.20 0.16 ANXA6
intron TNIP1 CCDC69 5.75E-07 1.57 rs3792775 5 150483530 A G 0.25
0.24 0.21 ANXA6 intron TNIP1 CCDC69 1.56E-06 1.49 rs17525472 15
49756960 G A 0.14 . 0.12 NA NA DMXL2 SCG3 2.05E-06 1.98 rs7579312 2
189590930 A G . 0.06 . NA NA COL3A1 COL5A2 3.65E-06 2.49 rs7761644
6 6933004 G A . 0.08 . NA NA RP11-320C15.1 LOC643936 5.28E-06 1.96
rs6772933 3 136335379 G A 0.05 0.10 0.07 EPHB1 intron LOC645218
PPP2R3A 5.31E-06 1.85 rs10188246 2 189879253 G A . 0.06 0.06 NA NA
COL5A2 KRT18P19 5.86E-06 1.68 rs12636883 3 133912212 A C 0.13 0.13
0.15 NPHP3 intron UBA5 NCRNA00119 6.57E-06 1.49 rs9502527 6 6930995
G A . 0.08 . NA NA RP11-320C15.1 LOC643936 9.56E-06 1.94 rs2070492
3 38332821 A G 0.09 0.10 0.10 SLC22A14 missense SLC22A13 XYLB
1.04E-05 1.77 rs7341475 7 103192051 A G 0.16 0.11 0.15 RELN intron
SLC26A5 ORC5L 1.07E-05 1.66 rs6434309 2 189591411 A C 0.08 0.08
0.10 NA NA COL3A1 COL5A2 1.22E-05 1.47 rs2105632 11 131842137 G A
0.14 0.14 0.13 OPCML intron HNT LOC100128095 1.36E-05 1.61
rs1590347 9 10325382 A G . 0.12 . PTPRD intron RN7SLP2 LOC646087
1.48E-05 1.90 rs17460569 3 85702141 G A 0.08 . 0.13 NA NA LOC440970
CADM2 1.55E-05 2.33 rs10061011 5 36478917 G A . 0.07 0.05 NA NA
RANBP3L SLC1A3 1.77E-05 2.57 rs7341301 6 6930714 A G 0.11 0.08 0.09
NA NA RP11-320C15.1 LOC643936 2.20E-05 1.28 rs12248682 10 131200410
A G 0.09 0.07 0.10 MGMT intron hCG_1795091 LOC100129103 2.36E-05
1.65 rs12864893 13 97867240 A C 0.06 . 0.08 FARP1 intron RNF113B
STK24 2.56E-05 1.87 rs893911 15 64715542 A G 0.19 0.14 0.18 NA NA
LCTL SMAD6 2.56E-05 1.28 rs280877 16 76215748 G A 0.19 0.14 0.16 NA
NA ADAMTS18 NUDT7 2.70E-05 1.22 rs7581769 2 105053248 A G 0.11 .
0.09 MRPS9 intron LOC100128684 LOC100133048 2.82E-05 1.62 rs2974319
8 42594234 G A 0.06 0.08 0.08 NA NA C8orf40 CHRNB3 2.88E-05 1.92
rs61737465 7 94378463 A G . 0.06 . NA NA ARF1P1 PON1 2.89E-05 1.84
rs551112 9 14433468 A C 0.05 0.09 0.07 NA NA NFIB ZDHHC21 2.92E-05
1.61 rs6781294 3 86413784 G A 0.07 0.12 0.12 NA NA CADM2 VGLL3
2.93E-05 1.48 rs1999184 1 176940266 G A 0.09 . 0.07 NA NA C1orf220
LOC646976 3.03E-05 2.29 rs9860570 3 86372146 G A 0.07 0.12 0.12 NA
NA CADM2 VGLL3 3.15E-05 1.48 rs9899787 17 62161091 G A . 0.10 .
PRKCA intron APOH CACNG5 3.34E-05 2.46 rs7875861 9 10275562 G A .
0.08 . PTPRD intron RN7SLP2 LOC646087 3.47E-05 2.87 rs10184895 2
189788608 A T . 0.06 . NA NA COL5A2 KRT18P19 3.53E-05 1.67
rs9864170 3 85693598 A G 0.13 . 0.18 NA NA LOC440970 CADM2 3.77E-05
1.68 rs280866 16 76211348 A G 0.07 0.07 0.07 NA NA ADAMTS18 NUDT7
3.87E-05 1.59 rs282999 16 76151802 G A 0.22 0.17 0.19 NA NA
ADAMTS18 NUDT7 4.13E-05 1.29 rs9912154 17 62159169 A G . 0.11 .
PRKCA intron APOH CACNG5 4.21E-05 2.44 rs4979476 9 116740531 G A
0.09 0.09 0.08 NA NA TNFSF8 TNC 4.26E-05 1.50 rs4916009 1 65144006
A G 0.08 . 0.09 JAK1 intron RAVER2 LOC100130270 4.39E-05 1.96
rs1583609 18 26882002 A G 0.10 0.10 0.11 NA NA DSC3 DSC2 4.46E-05
1.72 rs10798628 1 176918995 A G 0.10 . 0.08 NA NA C1orf220
LOC646976 4.76E-05 2.29 rs7826830 8 95723804 A G 0.17 0.13 0.14
RBM35A intron K1AA1429 DPY19L4 5.25E-05 1.36 rs8116164 20 61083073
A G 0.13 0.08 0.12 NA NA LOC100128172 BHLHB4 5.38E-05 1.49
rs12486323 3 133913494 G A . 0.16 . NPHP3 intron UBA5 NCRNA00119
5.56E-05 1.84 rs9922975 16 26847848 G A 0.13 0.11 0.12 NA NA HS3ST4
C16orf82 5.57E-05 1.27 rs661198 9 10289084 A G 0.10 0.10 0.09 PTPRD
intron RN7SLP2 LOC646087 5.61E-05 1.33 rs17717970 5 150954894 G A .
0.11 . NA NA FAT2 SPARC 5.79E-05 1.71 rs11965083 6 45935458 G A .
0.18 . NA NA RUNX2 CLIC5 5.96E-05 1.80 rs7637944 3 132912301 A C
0.15 0.14 0.13 CPNE4 intron MRPL3 LOC729674 5.98E-05 1.26
rs12533538 7 105218549 A C 0.06 0.06 0.07 ATXN7L1 intron
LOC100131028 LOC100129553 6.14E-05 1.47 rs546913 6 112396275 A G
0.05 . 0.05 NA NA FYN WISP3 6.73E-05 2.19 rs689328 6 112393380 A G
0.05 . 0.05 NA NA FYN WISP3 6.73E-05 2.19 rs1332175 9 25493034 G A
0.07 0.06 0.06 NA NA C9orf134 TUSC1 6.78E-05 1.65 rs4479482 20
59037337 A G 0.11 0.10 0.09 NA NA MTCO2L CDH4 6.98E-05 1.53
rs445775 13 32422448 A G . 0.06 0.06 NA NA PDS5B hCG_1643176
7.14E-05 1.84 rs10959051 9 10320850 G A 0.24 0.30 0.22 PTPRD intron
RN7SLP2 LOC646087 7.23E-05 1.17 rs10516313 4 17028411 A G 0.14 .
0.16 NA NA LOC729006 LOC645097 7.55E-05 1.78 rs7948079 11 96725167
A G 0.10 0.09 0.08 NA NA LOC100131233 LOC643381 7.74E-05 1.29
rs2167171 8 133556707 C A 0.08 0.09 0.07 KCNQ3 intron HHLA1 LRRC6
7.77E-05 1.39 rs2277719 18 54350509 A C 0.06 . 0.07 ALPK2 intron
NEDD4L LOC100128163 7.79E-05 1.77 rs3844600 10 49353903 A G 0.22
0.20 0.22 ARHGAP22 intron MAPK8 WDFY4 7.90E-05 1.23 rs1285295 17
75513707 A C . 0.09 . NA NA CBX4 TBC1D16 8.12E-05 1.71 rs2723129 2
23438312 G A 0.09 0.07 0.09 NA NA LOC100130841 KLHL29 8.33E-05 1.33
rs1330656 5 26084219 A C 0.17 0.17 0.13 NA NA MSNL1 LOC100132866
8.68E-05 1.50 rs10065544 5 136592476 G A 0.20 0.19 0.21 SPOCK1
intron LOC391834 KLHL3 8.78E-05 1.19 rs992803 3 86325620 A C 0.14
0.16 0.19 NA NA CADM2 VGLL3 8.83E-05 1.20 rs9825532 3 89169850 A G
. 0.27 . NA NA LOC728432 EPHA3 9.32E-05 2.36 rs2302840 18 41326985
A G 0.13 . 0.11 NA NA LOC100131669 SLC14A2 9.40E-05 1.93 rs17237607
3 126170122 A G 0.08 0.10 0.08 HEG1 utr-3 MUC13 SLC12A8 9.87E-05
1.36
[0144] Forty-nine out of 67 variants had the same direction of
effect (either reduced or increased risk) in at least two out of
the three studies (cutoff p<1.times.10.sup.-4). The top ten most
statistically significant variants of that list are shown in Table
7. rs2303028 (G>A, MAF 0.16-0.20) was the most statistically
significant (p=5.75.times.10.sup.-7, .beta.=1.57), with the A
allele increasing the risk of proteinuria. rs2303028 is an intronic
variant in ANXA6 (FIG. 6). rs3792775 (G>A and MAF 0.21-0.25) was
the next most statistically significant variant (p=1.56.times.10-6,
.beta.=1.49), also located in intron of ANXA6 and in moderate LD
with rs2303028 (R.sup.2=0.77) (FIG. 6), with the A allele
increasing the risk of proteinuria. rs12636883 (A>G, MAF
0.05-0.10) also had the same direction of effect in all three
trials (p=5.57.times.10.sup.-6, .beta.=1.49), with the A allele
increasing the risk of proteinuria. rs12636883 is an intronic
variant in NPHP3 (FIG. 6).
TABLE-US-00007 TABLE 7 Ten most statistically significant variants,
according to unadjusted p values grade .gtoreq. 3, associated with
proteinuria, hypertension and composite toxicity with the same
direction of effect (either reduced or increased risk) in at least
two out of three trials for proteinuria and composite toxicity, and
three out of four trials for hypertension. Ch chromosome, NA
Intergenic SNP, MAF minor allele frequencies in CALGB 80303, 40503,
90401, and 40502 respectively, "_" SNP not present in the genotype
platform of the trial, "." data on proteinuria were not available.
Composite toxicity is defined as the occurrence of either
proteinuria or hypertension or both. Base Effect SNP Ch Gene
Feature Flanking gene Flanking gene change MAF size (.beta.)
p-value Proteinuria rs2303028 5 ANXA6 Intron TNIP1 CCDC69 G > A
0.19/0.20/0.16/. 1.57 5.75 .times. 10.sup.-7 rs3792775 5 ANXA6
Intron TNIP1 CCDC69 G > A 0.25/0.24/0.21/. 1.49 1.56 .times.
10.sup.-6 rs17525472 15 NA NA DMXL2 SCG3 A > G 0.14/_/0.12/.
1.98 2.05 .times. 10.sup.-6 rs6772933 3 EPHB1 Intron LOC645218
PPP2R3A A > G 0.05/0.10/0.07/. 1.85 5.31 .times. 10.sup.-6
rs10188246 2 NA NA COL5A2 KRT18P19 A > G _/0.06/0.06/. 1.68 5.86
.times. 10.sup.-6 rs12636883 3 NPHP3 Intron UBA5 NCRNA00119 C >
A 0.13/0.13/0.15/. 1.49 5.57 .times. 10.sup.-6 rs2070492 3 SLC22A14
Missense SLC22A13 XYLB G > A 0.09/0.10/0.10/. 1.77 1.04 .times.
10.sup.-5 rs7341475 7 RELN Intron SLC26A5 ORC5L G > A
0.16/0.11/0.15/. 1.66 1.07 .times. 10.sup.-5 rs6434309 2 NA NA
COL3A1 COL5A2 C > A 0.08/0.08/0.10/. 1.47 1.22 .times. 10.sup.-5
rs2105632 11 OPCML Intron HNT LOC100128095 A > G
0.14/0.14/0.13/. 1.61 1.36 .times. 10.sup.-5 Hypertension rs4782946
16 ATP2C2 Intron WFDC1 KIAA1609 G > A 0.37/0.38/0.37/0.43 0.66
3.09 .times. 10.sup.-7 rs17439529 14 AKAP6 Intron MTCO1P2 NPAS3 G
> A 0.36/0.40/0.38/0.40 -0.72 2.08 .times. 10.sup.-6 rs1530837
15 PLA2G4E Intron EHD4 PLA2G4D A > G 0.23/0.19/0.18/0.17 0.66
4.87 .times. 10.sup.-6 rs11863271 16 ATP2C2 Intron WFDC1 KIAA1609 G
> A 0.20/0.17/0.19/0.22 0.63 5.23 .times. 10.sup.-6 rs1171065 13
DCLK1 Intron NBEA SOHLH2 A > C 0.19/0.26/0.19/0.21 0.62 5.73
.times. 10.sup.-6 rs670362 18 NA NA VAPA APCDD1 G > A
0.18/0.14/0.11/0.12 0.67 6.10 .times. 10.sup.-6 rs2665917 8 NIBP
Intron C8orf17 LOC100131910 G > A 0.44/0.48/0.47/0.47 0.63 7.13
.times. 10.sup.-6 rs10967306 9 VLDLR Intron FL135024 KCNV2 G > A
0.07/0.07/0.09/0.08 0.87 8.16 .times. 10.sup.-6 rs1320881 8 NA NA
LOC100132107 ADAM28 G > A 0.24/0.18/0.21/0.24 0.61 9.86 .times.
10.sup.-6 rs4691370 4 NA NA hCG_1814936 PDGFC A > G
0.06/0.09/_/0.07 0.82 1.00 .times. 10.sup.-5 Composite toxicity
rs10867852 9 NA NA LOC442427 RASEF G > A 0.08/0.07/0.06/. 1.16
1.46 .times. 10.sup.-6 rs7717673 5 SLC25A48 Intron LOC153328 IL9 G
> A 0.11/0.12/0.12/. 0.94 3.93 .times. 10.sup.-6 rs2454331 8 NA
NA LOC100129100 RIPK2 A > G 0.43/0.40/0.43/. -0.77 1.43 .times.
10.sup.-6 rs873224 8 NA NA FL143860 LOC100131146 A > G
0.11/0.10/0.08/. 0.86 1.48 .times. 10.sup.-6 rs966439 14 NA NA
LOC283584 LOC283585 A > G 0.21/0.17/0.16/. 0.70 1.52 .times.
10.sup.-6 rs7849777 9 COL5A1 Intron RXRA LOC100130622 G > A
0.09/0.05/0.06/. 1.31 1.56 .times. 10.sup.-6 rs10869538 9 PIP5K1B
Intron LOC100131240 PRKACG A > G 0.15/0.16/0.15/. 0.74 1.74
.times. 10.sup.-6 rs11664759 18 NA NA LOC400655 FBX015 G > A
0.11/0.15/0.15/. 0.83 2.21 .times. 10.sup.-6 rs1978259 14 NA NA
LOC283584 LOC283585 C > A 0.20/_/0.16/. 0.81 2.63 .times.
10.sup.-6 rs17109031 12 NA NA SMUG1 LOC100132010 G > A
0.13/0.08/0.10/. 0.85 2.93 .times. 10.sup.-6
[0145] For the gene-based analysis of grade the Q-Q plot is shown
in FIG. 7. Identified genes associated with proteinuria,
hypertension, and composite toxicity are shown in Table 8.
TABLE-US-00008 TABLE 8 Genes associated with proteinuria,
hypertension, or composite toxicity (grade .gtoreq. 2) Proteinuria
Hypertension Composite toxicity p-value p-value p-value p-value
p-value p-value Gene unadjusted adjusted Gene unadjusted adjusted
Gene unadjusted adjusted C1D 2.00E-08 2.00E-08 UNC50 2.30E-05
3.20E-05 SLC25A24 4.00E-06 3.00E-06 IL17F 1.80E-07 5.90E-07 KATNB1
2.50E-05 7.30E-05 SMS 5.00E-06 5.00E-06 MCM3 5.10E-07 1.15E-06
MGAT4A 4.60E-05 6.10E-05 CEP295 1.00E-05 7.00E-06 SMPX 1.20E-05
8.91E-06 FBXO9 5.10E-05 3.60E-05 YWHAE 1.60E-05 1.30E-05 KLHL34
1.26E-05 1.50E-05 STRIP1 9.80E-05 1.05E-04 PTPN3 4.00E-05 7.10E-05
EAPP 2.70E-05 2.70E-05 CCDC54 1.01E-04 7.70E-05 KLHL35 4.50E-05
3.50E-05 CNKSR2 3.50E-05 2.70E-05 COA5 1.06E-04 1.46E-04 H6PD
5.10E-05 4.00E-05 LIPJ 4.80E-05 7.10E-05 KIFC3 1.18E-04 2.76E-04
MBTPS2 7.50E-05 7.10E-05 ITGB6 5.00E-05 5.50E-05 ICK 1.21E-04
7.70E-05 CRK 1.37E-04 1.51E-04 XCR1 5.70E-05 1.86E-04 AHCYL1
1.45E-04 1.75E-04 SLC17A6 1.50E-04 1.44E-04 RFPL4AL1 1.03E-04
1.42E-04 CAPZA2 1.63E-04 1.36E-04 ALDH4A1 2.13E-04 2.42E-04 PDE3A
1.48E-04 7.86E-04 A4GALT 2.96E-04 1.93E-04 HSD3B2 2.43E-04 2.37E-04
SNX6 1.81E-04 1.11E-04 LUZP4 3.10E-04 2.59E-04 ZNF217 2.74E-04
3.05E-04 PWWP2A 1.82E-04 3.60E-04 CFAP69 3.80E-04 3.21E-04 STAT4
3.44E-04 1.97E-04 NDFIP2 2.01E-04 6.17E-04 STK10 4.30E-04 4.79E-04
TAS1R2 3.46E-04 3.42E-04 VCP 2.09E-04 2.13E-03 TMPRSS12 5.03E-04
4.01E-04 HDAC11 3.55E-04 4.02E-04 CRYBB2 2.34E-04 9.40E-05 AQP12A
5.12E-04 5.00E-04 AZI2 4.00E-04 4.26E-04 RFPL4A 2.38E-04 2.24E-04
CYSLTR2 5.38E-04 3.81E-04 CMC1 4.26E-04 4.35E-04 CRYBB3 2.47E-04
9.00E-05 DTD1 6.85E-04 5.41E-04 FAM155B 4.36E-04 2.96E-04 ALDH6A1
2.87E-04 3.69E-04 BRD1 6.94E-04 9.23E-04 TGM3 6.14E-04 4.83E-04
CTRB2 3.03E-04 5.53E-04 CSRP2 7.46E-04 7.00E-04 MC3R 6.37E-04
1.07E-03 FANCG 3.12E-04 3.94E-03 FUK 7.74E-04 6.71E-04 IL17F
6.75E-04 5.61E-04 PIGO 3.21E-04 4.29E-03 ST3GAL2 8.16E-04 5.12E-04
HSD3B1 6.93E-04 6.49E-04 KIAA1671 3.29E-04 1.14E-04 CDK14 8.68E-04
8.26E-04 RGPD6 7.04E-04 6.84E-04 DDB2 3.33E-04 1.75E-04 SEPT2
9.21E-04 1.14E-03 RPS3 9.49E-04 1.01E-03 ACP2 3.38E-04 1.99E-04
SF3B3 9.23E-04 6.91E-04 MALL 1.09E-03 7.92E-04 MSANTD1 3.61E-04
4.62E-04 RDH14 9.27E-04 9.37E-04 SPAG4 1.10E-03 1.32E-03 TGFA
3.78E-04 4.88E-04 CCDC58 1.03E-03 7.33E-04 MYH11 1.16E-03 1.47E-03
CTRB1 3.81E-04 6.26E-04 COLGALT2 1.05E-03 8.33E-04 RBL1 1.16E-03
1.43E-03 C9orf131 3.85E-04 1.73E-03 ZDHHC22 1.05E-03 7.83E-04 MRPL9
1.22E-03 1.30E-03 SPRY4 4.63E-04 1.02E-03 NT5C1B 1.10E-03 1.02E-03
SKAP1 1.24E-03 1.58E-03 DIRC2 5.26E-04 2.13E-04 CSTA 1.14E-03
9.29E-04 IFFO2 1.25E-03 1.21E-03 PTGR2 5.43E-04 8.58E-04 IL33
1.16E-03 1.06E-03 C1QTNF7 1.26E-03 7.18E-04 GPX5 6.26E-04 3.13E-04
RYR2 1.20E-03 1.97E-03 GDPD5 1.32E-03 1.11E-03 DNAJB5 6.38E-04
4.62E-04 ACKR3 1.27E-03 8.26E-04 PIK3C2B 1.32E-03 1.03E-03 RGS12
6.72E-04 1.02E-03 EPB41L4B 1.28E-03 1.68E-03 RASGRF1 1.34E-03
1.07E-03 URB2 8.40E-04 4.09E-04 CTSK 1.35E-03 2.17E-03 CCDC172
1.54E-03 1.46E-03 MLH1 8.86E-04 1.38E-03 MFSD2A 1.39E-03 1.48E-03
TMEM182 1.59E-03 1.08E-03 RAN 1.02E-03 1.91E-04 S100P 1.44E-03
1.28E-03 GLRA3 1.76E-03 1.72E-03 FZD6 1.02E-03 1.07E-03 COG4
1.45E-03 1.49E-03 HOMER1 1.88E-03 1.98E-03 TTC1 1.03E-03 9.29E-04
CASR 1.46E-03 1.02E-03 NEFM 1.90E-03 1.60E-03 GNG7 1.04E-03
5.33E-04 CNBD2 1.48E-03 1.19E-03 TET1 2.01E-03 2.22E-03 TAF5L
1.08E-03 5.84E-04 PDE4DIP 1.48E-03 9.00E-04 SLC25A16 2.02E-03
2.01E-03 ZBTB3 1.14E-03 1.75E-04 TIAL1 1.60E-03 1.47E-03 MCM3
2.03E-03 1.87E-03 PITPNM2 1.15E-03 1.39E-03 UBE4B 1.62E-03 1.22E-03
PLCL1 2.03E-03 2.18E-03 CALCR 1.16E-03 1.82E-03 ARNT 1.75E-03
2.47E-03 GABRA3 2.10E-03 2.09E-03 POLR2G 1.18E-03 2.76E-04 ARHGAP42
1.81E-03 1.61E-03 MPP3 2.10E-03 1.93E-03 SLC25A24 1.21E-03 1.21E-03
LRRC3B 1.83E-03 1.42E-03 NPTX2 2.10E-03 2.27E-03 RWDD2B 1.22E-03
6.29E-04 NYAP2 1.86E-03 1.84E-03 NFS1 2.11E-03 2.48E-03 CCT8
1.24E-03 7.50E-04 SSX5 1.89E-03 2.53E-03 RBM12 2.15E-03 2.09E-03
STOML2 1.32E-03 1.85E-02 PAQR4 1.93E-03 2.15E-03 SEMA5B 2.26E-03
2.36E-03 KRTAP12-4 1.35E-03 1.60E-03 KREMEN2 2.02E-03 2.20E-03
GPATCH2 2.28E-03 1.33E-03 STX2 1.35E-03 2.65E-04 SNX11 2.06E-03
3.48E-03 CPNE1 2.29E-03 2.39E-03 PRB3 1.40E-03 2.34E-03 FLYWCH1
2.07E-03 2.31E-03 PEX11G 2.32E-03 1.93E-03 FER1L6 1.41E-03 2.01E-03
PKMYT1 2.10E-03 2.48E-03 XYLB 2.40E-03 2.87E-03 PRB4 1.45E-03
7.21E-02 PACSIN2 2.28E-03 1.79E-03 ADAM12 2.43E-03 1.92E-03 MPP3
1.48E-03 1.08E-03 GP1BA 2.32E-03 1.98E-03 SCYL2 2.43E-03 2.67E-03
OR4N5 1.54E-03 1.82E-03 KIF1A 2.38E-03 1.39E-03 YY2 2.52E-03
2.09E-03 PLEKHB1 1.61E-03 1.06E-03 NBPF9 2.45E-03 1.79E-03 TMEM165
2.56E-03 2.11E-03 RBM7 1.62E-03 1.51E-03 SKAP1 2.50E-03 3.75E-03
RHAG 2.58E-03 2.42E-03 KRTAP12-3 1.63E-03 2.14E-03 STEAP2 2.50E-03
2.45E-03 ANAPC5 2.61E-03 2.70E-03 FAM214B 1.64E-03 1.83E-02 RBM42
2.52E-03 3.81E-03 CHRNG 2.66E-03 2.17E-03 TMEM223 1.74E-03 5.45E-04
TMEM115 2.69E-03 2.31E-03 BIVM 2.73E-03 3.12E-03 PHOSPHO2 1.79E-03
2.85E-03 CIPC 2.70E-03 2.17E-03 CAM KK2 2.78E-03 2.43E-03 NXF1
1.88E-03 5.13E-04 ARFGAP3 2.80E-03 2.01E-03 LMTK3 2.83E-03 2.37E-03
TMEM179B 1.90E-03 5.93E-04 C10orf142 2.83E-03 2.07E-03 C1D 2.92E-03
2.62E-03 OR4M1 1.94E-03 3.15E-03 TTLL5 2.91E-03 1.63E-03 DLL3
2.92E-03 2.65E-03 TAF6L 1.99E-03 5.44E-04 PRDM2 2.93E-03 3.37E-03
ERCC5 2.94E-03 3.90E-03 SCYL2 2.02E-03 1.99E-03 ZC2HC1B 3.04E-03
3.48E-03 RBM39 2.97E-03 3.34E-03 GRHL2 2.04E-03 1.01E-02 LTV1
3.10E-03 3.23E-03 TNKS 2.98E-03 3.51E-03 TTC9C 2.04E-03 3.82E-04
CCNI 3.29E-03 3.61E-03 ZNF835 3.07E-03 2.27E-03 DLG5 2.13E-03
1.62E-03 IL23R 3.30E-03 3.29E-03 EIF4E2 3.10E-03 1.94E-03 OR4Q3
2.19E-03 3.31E-03 MRFAP1L1 3.33E-03 3.55E-03 PRPF38A 3.16E-03
2.94E-03 PPP1R16A 2.26E-03 3.27E-03 CLDN9 3.38E-03 4.11E-03 TLK1
3.17E-03 3.19E-03 GCNT2 2.29E-03 1.51E-02 ZBED4 3.45E-03 3.96E-03
TMC1 3.24E-03 2.78E-03 GPT 2.29E-03 3.28E-03 ENO3 3.52E-03 2.97E-03
TRAPPC4 3.28E-03 3.96E-03 MFSD3 2.29E-03 3.23E-03 ZNF774 3.55E-03
3.04E-03 PPP1R15B 3.31E-03 2.80E-03 LRRC24 2.32E-03 3.41E-03 SEL1L
3.59E-03 3.43E-03 CCDC84 3.35E-03 3.88E-03 FOXH1 2.33E-03 3.27E-03
NDNF 3.64E-03 2.61E-03 RPS25 3.35E-03 3.69E-03 C11orf71 2.39E-03
1.97E-03 AP2B1 3.76E-03 3.88E-03 KCTD12 3.43E-03 3.24E-03 SLC40A1
2.40E-03 3.24E-03 COX6B1 3.83E-03 4.82E-03 TCOF1 3.45E-03 2.60E-03
RFC3 2.42E-03 3.46E-03 CLDN6 3.97E-03 3.87E-03 SLC37A4 3.49E-03
4.14E-03 RECQL4 2.45E-03 3.25E-03 ETV2 3.97E-03 5.02E-03 TIMM50
3.63E-03 3.14E-03 NCOA3 2.46E-03 1.42E-03 PFN1 3.98E-03 3.33E-03
TIGD1 3.76E-03 2.34E-03 STX5 2.47E-03 6.63E-04 DGKE 4.11E-03
4.43E-03 TRIM28 3.84E-03 3.09E-03 WDR37 2.47E-03 1.75E-03 SLC25A11
4.23E-03 3.71E-03 PDZRN3 3.91E-03 3.97E-03 LGALS2 2.51E-03 9.13E-04
ZNF485 4.23E-03 3.78E-03 KATNB1 3.92E-03 3.13E-03 CYHR1 2.53E-03
3.66E-03 TSPAN33 4.41E-03 3.42E-03 RIIAD1 3.99E-03 4.39E-03 DSG1
2.54E-03 3.00E-03 FBXW11 4.52E-03 6.35E-03 CHMP2A 4.02E-03 2.98E-03
KIFC2 2.54E-03 3.64E-03 IL2 4.52E-03 5.88E-03 MZF1 4.04E-03
3.34E-03 BBS5 2.55E-03 5.94E-03 TBX5 4.55E-03 3.19E-03 UBE2M
4.04E-03 3.17E-03 TONSL 2.56E-03 3.72E-03 C17orf100 4.57E-03
6.94E-03 FBXO47 4.27E-03 4.89E-03 LRRC14 2.58E-03 3.01E-03 XAGE2
4.60E-03 5.24E-03 PGLS 4.49E-03 5.44E-03 REXO2 2.62E-03 3.09E-03
HNMT 4.68E-03 4.21E-03 RALY 4.49E-03 4.18E-03 CCDC173 2.74E-03
2.83E-03 ASPH 4.69E-03 5.83E-03 ZBTB45 4.51E-03 3.64E-03 CYLC1
2.75E-03 2.05E-03 RNF167 4.73E-03 3.72E-03 CTNNB1 4.60E-03 4.57E-03
PCBP2 2.75E-03 5.19E-03 DAB2IP 4.84E-03 4.68E-03 NAMPT 4.73E-03
2.83E-03 SOST 2.79E-03 1.74E-03 KIF1B 4.86E-03 4.48E-03 STAT1
4.77E-03 3.79E-03 DLGAP1 2.82E-03 6.77E-03 CENPL 4.88E-03 2.88E-03
CRISP3 4.81E-03 4.96E-03 SMIM18 2.83E-03 6.26E-04 NUP155 4.88E-03
2.56E-03 PLEKHA6 4.89E-03 4.08E-03 SNRPA 2.84E-03 2.93E-03 ATP10A
4.97E-03 1.06E-02 SLC22A14 4.93E-03 5.34E-03 KLHL41 2.88E-03
6.49E-03 FOXG1 5.02E-03 4.55E-03 CGB8 5.05E-03 4.18E-03 RNF19A
2.89E-03 2.69E-03 CRHR2 5.16E-03 5.36E-03 ZNF446 5.08E-03 3.84E-03
EFNA5 2.90E-03 3.64E-03 ZNF707 5.17E-03 4.53E-03 UBC 5.18E-03
3.48E-03 RC3H1 2.94E-03 2.07E-03 HOMER1 5.18E-03 4.44E-03 PTAR1
5.20E-03 2.76E-03 SP1 2.94E-03 1.57E-03 PIM2 5.18E-03 5.38E-03
NPHP1 5.24E-03 5.06E-03 FASTKD1 2.95E-03 6.60E-03 GPAT2 5.32E-03
4.94E-03 TEX13B 5.24E-03 5.56E-03 NUMBL 3.02E-03 2.90E-03 AQP12B
5.38E-03 5.56E-03 IGF1R 5.25E-03 4.61E-03 ZNF256 3.05E-03 2.69E-03
TNFRSF12A 5.48E-03 6.02E-03 LHB 5.31E-03 3.58E-03 ITPKC 3.12E-03
3.79E-03 CPNE6 5.50E-03 1.24E-02 CD74 5.36E-03 3.92E-03 ACCSL
3.15E-03 7.81E-02 HS6ST1 5.61E-03 1.29E-02 DNAJB5 5.38E-03 6.12E-03
VWA5B1 3.15E-03 3.67E-03 HERC5 5.66E-03 5.20E-03 CITED1 5.39E-03
3.93E-03 DUSP3 3.18E-03 1.79E-03 GPR139 5.69E-03 7.03E-03 KLHL26
5.39E-03 4.53E-03 SERPINC1 3.25E-03 2.56E-03 FLYWCH2 5.73E-03
6.61E-03 C9orf135 5.42E-03 4.63E-03 RNLS 3.26E-03 3.51E-03 TXNDC2
5.76E-03 5.92E-03 ROMO1 5.51E-03 5.81E-03 C19orf54 3.30E-03
3.12E-03 HCFC1R1 5.77E-03 6.77E-03 ZCCHC11 5.55E-03 4.16E-03 ZNF429
3.36E-03 2.88E-03 ZXDA 5.84E-03 7.91E-03 DIRC2 5.59E-03 4.89E-03
C2orf88 3.45E-03 4.75E-03 THOC6 5.85E-03 6.99E-03 DIRAS2 5.62E-03
5.21E-03 KRT25 3.45E-03 3.73E-03 GSTA2 5.94E-03 6.16E-03 AKAP1
5.63E-03 5.12E-03 SHMT1 3.60E-03 2.50E-05 CETP 5.95E-03 5.20E-03
KCNJ14 5.63E-03 5.16E-03 HERC6 3.71E-03 2.85E-03 RIMBP2 5.95E-03
4.68E-03 TXNL1 5.86E-03 3.61E-03 KRTAP10-10 3.74E-03 5.55E-03
C1QTNF7 6.15E-03 5.50E-03 ELOVL2 5.91E-03 8.74E-03 MIA 3.74E-03
4.27E-03 ZNF592 6.21E-03 1.16E-02 ZDHHC7 5.94E-03 3.65E-03 SMCR8
3.81E-03 2.06E-03 GIPC2 6.22E-03 5.12E-03 DUSP3 6.01E-03 6.00E-03
RAB6A 3.82E-03 1.96E-03 ARHGAP15 6.34E-03 5.07E-03 SOST 6.04E-03
6.47E-03 TAS2R42 3.82E-03 5.90E-03 PLAGL1 6.43E-03 6.22E-03 MPZ
6.06E-03 6.28E-03 RBPMS 3.84E-03 1.33E-03 ZNF787 6.44E-03 7.05E-03
COPG2 6.08E-03 5.69E-03 EVPLL 3.88E-03 3.10E-05 ZNF835 6.45E-03
8.13E-03 ETAA1 6.09E-03 7.90E-03 ST6GALNAC3 3.93E-03 1.03E-02
NAPEPLD 6.46E-03 1.10E-02 NF2 6.11E-03 6.26E-03 RAB4B 4.00E-03
4.65E-03 FAM83H 6.49E-03 5.92E-03 SLC27A5 6.13E-03 5.15E-03
KRTAP10-11 4.06E-03 4.98E-03 CNTF 6.52E-03 7.36E-03 GRWD1 6.23E-03
5.43E-03 OVOL2 4.06E-03 6.26E-03 MAPK15 6.55E-03 5.72E-03 COLGALT1
6.28E-03 7.51E-03 SLC25A33 4.10E-03 2.97E-03 SMO 6.55E-03 6.00E-03
CTSH 6.32E-03 4.97E-03 WDR1 4.24E-03 5.07E-03 CCDC166 6.68E-03
5.83E-03 CELF3 6.34E-03 5.66E-03 RPUSD2 4.26E-03 7.35E-04 GOLGA78
6.69E-03 7.37E-03 FAM129C 6.38E-03 7.67E-03 BOD1L1 4.39E-03
4.92E-03 GATAD1 6.73E-03 8.39E-03 DRC7 6.40E-03 5.35E-03 ID12
4.56E-03 3.28E-03 C3orf38 6.75E-03 6.86E-03 MAP9 6.56E-03 2.67E-03
WDR74 4.59E-03 1.58E-03 ATP182 6.79E-03 6.32E-03 VCX2 6.56E-03
5.70E-03 EGLN2 4.66E-03 5.51E-03 MED12 6.83E-03 2.72E-02 YTHDF2
6.60E-03 6.20E-03 IDI1 4.68E-03 4.16E-03 UR82 6.83E-03 8.02E-03
OR4M1 6.68E-03 1.16E-02 MEDI 4.73E-03 1.80E-03 PCED18 6.88E-03
9.27E-03 MACROD2 6.70E-03 4.69E-03 MAGEA1 4.82E-03 7.16E-03 MOAP1
6.89E-03 7.75E-03 MAPK15 6.71E-03 5.51E-03 KLHL35 4.83E-03 5.01E-03
NLGN3 6.90E-03 2.77E-02 UGGT1 6.72E-03 1.89E-02 MSTN 4.93E-03
3.60E-03 HAUS5 6.91E-03 8.60E-03 CGB5 6.74E-03 4.91E-03 CLIC4
4.96E-03 9.75E-03 OTOP1 6.97E-03 7.63E-03 PIM3 6.81E-03 6.29E-03
SLC3A2 4.96E-03 1.95E-03 TMEM251 7.05E-03 7.71E-03 GUCD1 6.87E-03
7.38E-03 CYP781 5.25E-03 6.55E-03 DARS2 7.08E-03 4.44E-03 KANSL1
6.95E-03 7.57E-03 PTGIS 5.40E-03 6.26E-03 WASF3 7.08E-03 1.10E-02
OR4Q3 6.97E-03 1.12E-02 VPS28 5.43E-03 6.67E-03 RGPD6 7.13E-03
7.15E-03 FAM83H 6.99E-03 5.87E-03 ZNF138 5.47E-03 6.10E-03 MAPK8IP3
7.19E-03 8.33E-03 RNF103 7.08E-03 5.69E-03 RPS10 5.53E-03 4.86E-03
UACA 7.23E-03 9.30E-03 UBXN11 7.16E-03 6.68E-03 SLC30A1 5.61E-03
4.78E-03 GRIPAP1 7.25E-03 7.16E-03 CREB3L3 7.19E-03 9.51E-03
CDC42EP1 5.69E-03 4.23E-03 MEF2D 7.33E-03 6.78E-03 LIPJ 7.30E-03
8.04E-03 HSPA13 5.83E-03 7.30E-03 CRTAC1 7.40E-03 9.06E-03 EFHD1
7.34E-03 5.26E-03 SMIM10L1 5.90E-03 4.24E-03 OR5M1 7.59E-03
5.59E-03 SATL1 7.34E-03 5.24E-03 BANP 6.22E-03 8.91E-03 ZFP91
7.61E-03 5.47E-03 IZUMO2 7.43E-03 7.49E-03 CDK2AP1 6.28E-03
7.38E-03 TUBGCP3 7.62E-03 9.74E-03 CGB1 7.49E-03 5.21E-03 IRF5
6.31E-03 7.71E-03 CERS5 7.70E-03 9.45E-03 LARP1B 7.49E-03 6.48E-03
NXPH3 6.32E-03 8.94E-03 GSTP1 7.74E-03 8.33E-03 CGB2 7.56E-03
5.27E-03 SULT1C2 6.40E-03 6.67E-03 HEY1 7.93E-03 1.00E-02 KLF14
7.65E-03 5.81E-03 BIRC7 6.45E-03 1.08E-02 BLOC1S4 8.04E-03 7.91E-03
CYTH2 7.67E-03 7.05E-03 KPNA3 6.51E-03 1.72E-03 CLIC6 8.06E-03
7.77E-03 MAP3K7 7.68E-03 8.11E-03 FGFR1OP 6.57E-03 1.86E-03 RGL4
8.22E-03 1.89E-02 TTLL10 7.71E-03 6.72E-03 PASD1 6.58E-03 7.01E-03
WFIKKN2 8.30E-03 6.80E-03 ZNF707 7.71E-03 6.07E-03 ABCB10 6.64E-03
5.38E-03 HSD3B1 8.45E-03 9.51E-03 PPP2R1A 7.73E-03 5.78E-03 NKAIN4
6.65E-03 1.10E-02 SPAG4 8.49E-03 7.10E-03 HSPA13 7.77E-03 8.48E-03
DSG4 6.81E-03 9.69E-03 11-Sep 8.62E-03 9.72E-03 NBPF4 7.77E-03
7.72E-03 NKX3-2 6.82E-03 4.65E-03 SST 8.64E-03 1.15E-02 PAIP2
7.86E-03 8.55E-03 AMHR2 6.86E-03 4.81E-03 UPK1A 8.86E-03 8.32E-03
SCAND1 7.91E-03 8.12E-03 PRR13 6.90E-03 5.07E-03 ADAMTS20 8.93E-03
8.28E-03 DHRS7 7.99E-03 7.25E-03 OGT 6.93E-03 7.99E-03 CXCL3
8.94E-03 9.32E-03 NCL 8.02E-03 7.61E-03 MR0H9 6.95E-03 9.50E-03
C17orf67 8.98E-03 1.07E-02 KRT25 8.05E-03 8.57E-03 A1CF 7.00E-03
6.01E-03 WDR87 8.99E-03 9.91E-03 GPR63 8.08E-03 8.11E-03 MAPT
7.12E-03 7.20E-03 TOB1 9.37E-03 5.88E-03 ALPK2 8.21E-03 7.95E-03
MFHAS1 7.12E-03 1.86E-02 BCAR1 9.47E-03 7.97E-03 CABP5 8.23E-03
9.68E-03 TAF1 7.13E-03 8.69E-03 CPNE4 9.48E-03 1.34E-02 HES7
8.23E-03 9.19E-03 ATG101 7.28E-03 6.35E-03 MGARP 9.55E-03 1.06E-02
DEFB112 8.24E-03 9.00E-03 TOP3A 7.37E-03 4.99E-03 TERT 9.55E-03
6.65E-03 PCGF6 8.26E-03 7.65E-03 EFHB 7.44E-03 6.63E-03 FMOD
9.67E-03 5.49E-03 ORC1 8.32E-03 7.96E-03 NR1H3 7.46E-03 5.63E-03
LYPD3 9.68E-03 9.51E-03 CD300LG 8.52E-03 8.06E-03 PET117 7.52E-03
7.36E-03 SUCLA2 9.71E-03 8.49E-03 NEFL 8.60E-03 7.96E-03 PPIG
7.57E-03 1.95E-02 TNMD 9.72E-03 9.27E-03 HNRNPD 8.61E-03 8.20E-03
DAZAP2 7.66E-03 4.69E-03 NREP 9.86E-03 8.78E-03 STAG2 8.64E-03
7.66E-03 PPP1R14D 7.78E-03 3.53E-03 FBXO3 9.91E-03 6.76E-03 FBRS
8.82E-03 8.84E-03 ZFYVE19 7.85E-03 3.07E-03 STON1 9.97E-03 9.49E-03
CC2D2A 8.88E-03 7.08E-03 SNTG1 7.89E-03 8.43E-03 HTRA3 9.99E-03
1.03E-02 CCDC166 8.94E-03 7.44E-03 PRPS1 7.94E-03 8.51E-03 CFAP69
8.98E-03 8.17E-03 SLC36A4 7.95E-03 5.05E-03 TFB1M 9.12E-03 1.16E-02
SMAGP 8.02E-03 4.61E-03 C14orf177 9.17E-03 8.13E-03 CD300LG
8.10E-03 7.00E-03 IQCA1 9.17E-03 8.03E-03 CTXN2 8.11E-03 1.02E-02
MROH8 9.20E-03 8.00E-03 ZSWIM6 8.17E-03 1.52E-03 AUTS2 9.21E-03
7.21E-03 KRTAP10-12 8.24E-03 1.05E-02 SMG1 9.26E-03 1.06E-02 PRRG3
8.26E-03 7.78E-03 NSUN3 9.32E-03 9.80E-03 DEPDC4 8.30E-03 6.83E-03
SSBP3 9.38E-03 1.02E-02
CTHRC1 8.34E-03 1.36E-02 ING3 9.47E-03 1.18E-02 C19orf18 8.39E-03
7.28E-03 SND1 9.50E-03 7.05E-03 KRTAP12-1 8.42E-03 1.04E-02 KPNA3
9.51E-03 5.29E-03 SOCS4 8.44E-03 5.01E-03 NCALD 9.55E-03 1.10E-02
PLSCR5 8.48E-03 1.18E-02 TERT 9.55E-03 7.97E-03 AVP 8.58E-03
5.39E-03 KLF3 9.56E-03 1.09E-02 NR2E1 8.69E-03 2.43E-02 UBN2
9.74E-03 9.79E-03 C4orf36 8.79E-03 7.50E-03 ZFP37 9.76E-03 6.02E-03
GNGT1 8.83E-03 1.04E-01 GPI 9.80E-03 1.03E-02 MANSC1 8.83E-03
1.10E-02 ODF1 9.84E-03 8.11E-03 YTHDF1 8.91E-03 1.08E-02 HIST2H2BF
9.98E-03 9.42E-03 MUCS5AC 9.02E-03 2.03E-02 GTPBP4 9.10E-03
6.79E-03 SEMA5B 9.11E-03 6.34E-03 ZNF410 9.13E-03 1.16E-02 MADD
9.28E-03 6.45E-03 ETNPPL 9.30E-03 5.88E-03 ATP1A1 9.31E-03 2.53E-02
FREM3 9.35E-03 6.61E-03 SLC22A2 9.40E-03 1.04E-02 SLC25A26 9.41E-03
2.16E-02 KRTAP12-2 9.42E-03 1.21E-02 FBN1 9.43E-03 1.05E-02 OXT
9.44E-03 6.54E-03 TRAF5 9.48E-03 3.38E-03 GDPD5 9.52E-03 1.07E-02
BIN2 9.58E-03 5.65E-03 C9orf47 9.64E-03 6.01E-03 PTCHD4 9.71E-03
1.31E-02 SNCAIP 9.79E-03 3.00E-02
[0146] The ten most statistically significant genes are shown in
Table 9. CID (p=2.00.times.10.sup.-8) was the most significant,
followed by IL17F (p=1.80.times.10.sup.-7).
TABLE-US-00009 TABLE 9 Ten most statistically significant genes,
according to unadjusted p values, associated with proteinuria,
hypertension, and composite toxicity from the gene-based
association analysis grade .gtoreq.2. Composite toxicity is defined
as the occurrence of either proteinuria or hypertension or both.
Proteinuria Hypertension Composite toxicity Gene p-value Gene
p-value Gene p-value C1D 2.00 .times. 10.sup.-8 UNC50 2.30 .times.
10.sup.-5 SLC25A24 4.00 .times. 10.sup.-6 IL17F 1.80 .times.
10.sup.-7 KATNB1 2.50 .times. 10.sup.-5 SMS 5.00 .times. 10.sup.-6
MCM3 5.10 .times. 10.sup.-7 MGAT4A 4.60 .times. 10.sup.-5 CEP295
1.00 .times. 10.sup.-5 SMPX 1.20 .times. 10.sup.-5 FBXO9 5.10
.times. 10.sup.-5 YWHAE 1.60 .times. 10.sup.-5 KLHL34 1.26 .times.
10.sup.-5 STRIP1 9.80 .times. 10.sup.-5 PTPN3 4.00 .times.
10.sup.-5 EAPP 2.70 .times. 10.sup.-5 CCDC54 1.01 .times. 10.sup.-4
KLHL35 4.50 .times. 10.sup.-5 CNKSR2 3.50 .times. 10.sup.-5 COA5
1.06 .times. 10.sup.-4 H6PD 5.10 .times. 10.sup.-5 LIPJ 4.80
.times. 48.sup.-5 KIFC3 1.18 .times. 10.sup.-4 MBTPS2 7.50 .times.
10.sup.-5 ITGB6 5.00 .times. 10.sup.-5 ICK 1.21 .times. 10.sup.-4
CRK 1.37 .times. 10.sup.-4 XCR1 5.70 .times. 10.sup.-5 AHCYL1 1.45
.times. 10.sup.-4 SLC17A6 1.50 .times. 10.sup.-4
[0147] Variants and Genes Associated with Bevacizumab-Induced
Hypertension
[0148] For the SNP-based analysis of grade hypertension, the
Manhattan and Q-Q plots are shown in FIG. 2. 104 variants
associated with hypertension were identified (Table 10).
TABLE-US-00010 TABLE 10 SNPs associated with hypertension (grade
.gtoreq. 2). effect reference MAF MAF MAF MAF p-value effect
(.beta.) effect SNP CH BP allele allele 80303 40503 90401 40502
gene feature Flanking gene Flanking gene unadjusted unadjusted
p-value adjusted (.beta.) adjusted rs3793027 6 70727823 G A 0.09 .
. . COL19A1 intron LMBRD1 COL9A1 1.21E-06 1.87 4.12E-06 2.00
rs13135230 4 24605796 A G 0.27 0.28 0.25 0.28 NA NA CCDC149 LGI2
1.26E-06 0.46 1.36E-06 0.47 rs2350620 8 62660161 G A 0.32 0.26 0.32
0.32 ASPH intron hCG_1988300 LOC645551 1.44E-06 -0.49 1.23E-06
-0.50 rs7204266 1 98760046 G A 0.28 . 0.28 . GRIN2A intron
LOC653737 LOC727844 3.61E-06 0.76 2.58E-06 0.79 rs6770663 3
157514872 G A 0.09 0.09 0.08 0.09 KCNAB1 intron LOC751837 SSR3
4.79E-06 0.57 4.16E-06 0.58 rs1145786 6 91678597 G A 0.33 0.32 0.34
0.33 NA NA MAP3K7 LOC100129847 5.10E-06 0.39 7.18E-06 0.39
rs7038808 9 91931116 A G 0.13 . 0.15 . NA NA IL6RL1 OR7E31P
5.20E-06 0.91 9.36E-06 0.90 rs11036390 11 41387322 C A . 0.27 .
0.31 NA NA LRRC4C LOC100131020 5.23E-06 0.46 5.57E-06 0.47
rs10905087 10 7082276 A G . 0.25 . 0.23 NA NA LOC439949 SFMBT2
6.01E-06 -0.64 5.30E-06 -0.65 rs12316952 12 46238282 G A 0.06 .
0.08 . NA NA LOC100127978 RPAP3 6.17E-06 1.14 8.30E-06 1.14
rs17097718 14 98252288 T C . 0.06 . . C14orf177 missense
LOC100132612 RPL3P4 8.56E-06 1.48 8.45E-03 -0.54 rs757354 12
46233818 C A 0.06 . 0.08 . NA NA LOC100127978 RPAP3 1.11E-05 1.11
1.42E-05 1.11 rs7553399 1 3406309 C A . 0.25 . . MEGF6 missense
ARHGEF16 TPRG1L 1.14E-05 1.06 1.34E-05 1.06 rs7130734 11 41385931 A
C 0.35 0.30 . 0.33 NA NA LRRC4C LOC100131020 1.17E-05 0.42 8.77E-06
0.43 rs13176984 5 151653739 C T . 0.11 . 0.18 NA NA GLRA1 NMUR2
1.20E-05 0.55 6.10E-06 0.57 rs11714367 3 176714180 A G 0.14 . 0.17
. NAALADL2 intron LOC647212 LOC100128870 1.40E-05 0.83 1.49E-05
0.82 rs2179218 20 40502874 A G 0.13 0.15 0.14 0.13 PTPRT intron
LOC643172 PPIAL 1.99E-05 0.49 3.00E-05 0.48 rs16986558 20 40207824
A G 0.06 . 0.06 . PTPRT intron LOC643172 PPIAL 2.18E-05 0.93
1.02E-05 0.99 rs10519829 5 125045325 A G 0.44 0.46 0.47 0.47 NA NA
LOC644659 LOC100130551 2.28E-05 0.36 1.84E-05 0.37 rs1530837 15
40069082 G A 0.23 0.19 0.18 0.17 PLA2G4E intron EHD4 PLA2G4D
2.59E-05 0.43 2.28E-05 0.44 rs4697273 4 21844894 A G . 0.28 . 0.20
NA NA KCNIP4 GPR125 2.60E-05 0.50 3.76E-05 0.49 rs2949929 17
62943076 T C . 0.27 . 0.25 PITPNC1 intron LOC729822 NOL11 2.98E-05
0.48 3.75E-05 0.48 rs1564470 8 136290117 A C 0.30 . 0.32 . NA NA
ZFAT LOC286094 3.10E-05 0.74 2.70E-05 0.75 rs7201930 16 9866156 G A
0.29 . 0.33 . GRIN2A intron LOC653737 LOC727844 3.15E-05 0.72
2.35E-05 0.74 rs2125944 4 42421675 A G 0.08 . 0.10 . NA NA ATP8A1
GRXCR1 3.19E-05 0.86 5.09E-05 0.84 rs10828545 10 18669609 A G .
0.34 . 0.37 CACNB2 intron SLC39Al2 NSUN6 3.21E-05 -0.47 1.79E-05
-0.49 rs4688081 3 119398144 G A . 0.41 . 0.40 NA NA LOC728873
IGSF11 3.38E-05 -0.44 4.05E-05 -0.44 rs9921541 16 9899263 A C 0.23
. 0.24 . GRIN2A intron LOC653737 LOC727844 3.38E-05 0.71 3.17E-05
0.72 rs4899947 14 0.88769467 C T . 0.36 . 0.32 KCNK10 intron KCNK10
SPATA7 3.48E-05 0.44 1.75E-05 0.45 rs2000611 14 87837079 G A 0.44
0.43 0.50 0.48 KCNK10 intron KCNK10 SPATA7 3.49E-05 -0.37 2.25E-05
-0.38 rs11732343 4 89722914 A G 0.08 . . . NA NA LOC100129137 HERC3
3.62E-05 1.70 2.22E-05 1.78 rs4611262 12 101026889 A G 0.20 0.25
0.23 0.23 NUP37 intron CCDC53 C12orf48 3.74E-05 0.39 1.59E-05 0.40
rs9512328 13 26149803 G A 0.06 0.09 0.09 0.08 WASF3 intron
LOC646527 GPR12 3.84E-05 0.54 8.30E-05 0.52 rs996784 3 164707301 T
G . 0.23 . 0.27 NA NA LOC647107 LOC730129 3.86E-05 0.45 5.91E-05
0.44 rs13161952 5 125046494 G A . 0.30 . 0.21 NA NA LOC644659
LOC100130551 3.96E-05 0.45 2.11E-05 0.46 rs1517527 2 206252547 A G
0.41 . 0.42 . NA NA PARD3B NRP2 4.11E-05 0.69 7.39E-05 0.68
rs760122 21 40701616 A G 0.23 . 0.26 . DSCAM intron PCP4 BACE2
4.15E-05 0.69 7.05E-05 0.69 rs11713383 3 63523900 A G 0.38 . 0.35 .
SYNPR intron LOC100129031 S100A1L 4.17E-05 0.71 7.36E-05 0.71
rs9933832 16 9856135 A G 0.29 . 0.32 . GRIN2A intron LOC653737
LOC727844 4.19E-05 0.70 3.09E-05 0.73 rs1350117 4 34666752 G A 0.40
0.33 0.38 0.39 NA NA LOC727819 LOC100132690 4.32E-05 -0.39 3.35E-05
-0.40 rs2220706 9 104673784 G A 0.05 . 0.06 0.07 NA NA LOC100131879
CYLC2 4.40E-05 0.65 6.89E-05 0.64 rs17648695 11 100363635 C T .
0.14 . 0.11 LOC100129602 intron FLJ32810 TMEM133 4.41E-05 0.54
3.70E-05 0.55 rs17654410 11 100369356 T C . 0.14 . 0.11 TMEM133
utr-3 LOC100129602 PGR 4.41E-05 0.54 3.70E-05 0.55 rs2456761 10
62200548 A C 0.35 . 0.34 . NA NA LOC729184 CDC2 4.57E-05 0.74
5.35E-05 0.74 rs7738087 6 939790 G A 0.42 0.40 0.37 0.37 NA NA
EXOC2 FOXQ1 4.67E-05 0.36 6.59E-05 0.36 rs17787479 8 140579876 A C
0.21 0.26 0.20 0.20 NA NA COL22A1 KCNK9 4.68E-05 0.40 5.88E-05 0.40
rs7618831 3 63531349 A G 0.38 . 0.36 . SYNPR intron LOC100129031
S100A1L 4.69E-05 0.71 8.08E-05 0.70 rs873766 2 106042957 C T . 0.12
. 0.10 NA NA LOC100132455 C2orf40 4.71E-05 0.57 5.40E-05 0.57
rs2886725 5 37770836 A G . 0.14 . . NA NA WDR70 GDNF 4.80E-05 1.02
6.25E-05 1.07 rs10087981 8 23282409 A C . 0.32 . 0.28 LOXL2 intron
R3HCC1 ENTPD4 4.84E-05 -0.49 6.10E-05 -0.49 rs6302 6 87782302 T C .
0.10 . 0.08 HTR1E reference LOC643971 CGA 4.85E-05 0.63 8.23E-05
0.61 rs365277 13 61808609 G A 0.47 0.46 0.41 0.45 NA NA
LOC100133193 LOC647259 4.93E-05 -0.37 6.04E-05 -0.37 rs3858416 11
100230559 T C . 0.06 . 0.05 FLJ32810 intron LOC100128386
LOC100129602 4.95E-05 0.66 3.14E-05 0.68 rs7821773 8 9748866 G A
0.08 0.05 0.08 . NA NA TNKS MSRA 4.97E-05 0.78 2.07E-03 0.46
rs10842185 12 23625382 G A 0.10 0.13 0.10 0.10 SOX5 intron
LOC100131418 LOC100129937 4.97E-05 0.50 2.92E-05 0.52 rs6445360 3
63523420 A G 0.38 . 0.36 . SYNPR intron LOC100129031 S100A1L
5.26E-05 0.71 9.10E-05 0.70 rs2825322 21 19343047 G A 0.27 0.34
0.27 0.26 NA NA PPIAL3 SLC6A6P 5.51E-05 -0.43 5.98E-05 -0.43
rs805772 20 5619460 T G . 0.13 . 0.12 NA NA RPS-1022P6.2 C20orf196
5.58E-05 0.57 5.50E-05 0.58 rs1352981 9 104625739 G A 0.08 . 0.08 .
NA NA LOC100131879 CYLC2 5.74E-05 0.85 6.63E-05 0.85 rs12170867 22
30292076 A G . 0.09 . 0.11 SFI1 intron LOC100128535 PISD 5.76E-05
0.57 8.56E-05 0.56 rs2278495 18 52838811 A G 0.25 . 0.24 . WDR7
intron LOC100130858 FAM44C 6.11E-05 0.72 8.93E-05 0.71 rs2729007 3
2132357 A G 0.21 0.26 0.22 0.22 CNTN4 intron LOC727810 LOC100130346
6.14E-05 0.40 8.80E-05 0.39 rs2991492 13 78625387 A G . 0.48 . 0.48
NA NA LOC390415 LOC100128339 6.15E-05 -0.43 9.05E-05 -0.42
rs2267796 16 9884214 C A 0.24 . 0.24 . GRIN2A intron LOC653737
LOC727844 6.60E-05 0.69 5.78E-05 0.70 rs2232030 4 24614069 G A 0.15
0.18 0.13 0.15 LGI2 utr-3 CCDC149 SEPSECS 6.67E-05 0.46 7.23E-05
0.47 rs7659172 4 24609653 A G . 0.18 . 0.15 NA NA CCDC149 LGI2
6.83E-05 0.53 9.37E-05 0.53 rs1171566 1 154766593 C T . 0.28 . 0.32
IQGAP3 reference MEF2D TTC24 6.84E-05 0.41 7.42E-05 0.41 rs1370215
18 52839937 G A 0.25 . 0.24 . WDR7 intron LOC100130858 FAM44C
6.99E-05 0.72 1.02E-04 0.70 rs540509 7 17071448 G A . 0.19 . 0.23
NA NA LOC100131425 LOC100131512 7.03E-05 0.45 4.91E-05 0.46
rs1288934 1 224894661 G A 0.24 0.27 0.24 0.26 ITPKB intron C1orf95
PSEN2 7.05E-05 -0.43 7.60E-05 -0.43 rs3745539 19 56219853 A G 0.08
. 0.06 . KLK11 missense KLK10 KLK12 7.08E-05 0.93 7.94E-05 0.92
rs2860529 4 105672170 G A 0.22 0.20 0.23 0.23 NA NA LOC728847
LOC391679 7.11E-05 0.37 8.67E-05 0.37 rs2172102 5 125024395 G A .
0.28 . 0.19 NA NA LOC644659 LOC100130551 7.12E-05 0.44 5.08E-05
0.45 rs1219508 10 123451644 A G 0.22 0.24 0.23 0.23 NA NA LOC729426
ATE1 7.14E-05 -0.46 1.42E-04 0.44 rs4580675 4 80827274 A G 0.43
0.47 0.44 0.47 NA NA 0 R7E94 P GDEP 7.15E-05 -0.36 8.47E-05 -0.36
rs12480201 20 59812166 A G 0.14 . 0.15 . CDH4 intron LOC100131417
TAF4 7.18E-05 0.85 4.39E-05 0.88 rs1268663 14 64335834 A G 0.20
0.22 0.20 0.21 SPTB intron LOC100129913 CH URC1 7.34E-05 0.41
5.26E-05 0.42 rs4775610 15 61119110 A G . 0.31 . 0.28 NA NA TLN2
TPM1 7.37E-05 0.42 7.35E-05 0.42 rs11133274 4 53994137 A G 0.21
0.20 0.21 0.20 FIP1L1 intron LOC100130982 LNX1 7.50E-05 0.38
2.46E-05 0.41 rs4813886 20 912652 G A 0.11 0.12 0.12 0.12 RSPO4
intron ANGPT4 PSMF1 7.61E-05 0.46 5.87E-05 0.47 rs4743599 9
104651778 G A 0.08 . 0.08 . NA NA LOC100131879 CYLC2 7.73E-05 0.84
9.03E-05 0.84 rs2713289 4 134759843 A G 0.48 0.49 0.49 0.47 NA NA
PCDH10 PABPC4L 7.89E-05 0.34 8.57E-05 0.34 rs1884114 20 914504 T G
. 0.08 . 0.08 RSPO4 intron ANGPT4 PSMF1 7.90E-05 0.62 5.11E-05 0.64
rs338248 1 58703893 C A 0.29 0.24 0.27 0.29 NA NA DAB1 OMA1
7.90E-05 0.37 8.49E-05 0.37 rs3767867 1 210624222 G A 0.35 . 0.38 .
TMEM206 intron PPP2R5A NENF 7.91E-05 -0.81 1.00E-04 -0.80 rs9530488
13 75370156 A G 0.36 . 0.42 . NA NA FLJ35379 LOC100132423 8.04E-05
0.68 1.49E-04 -0.66 rs11251166 10 2357939 C A . . . 0.28 NA NA
LOC728209 LOC727878 8.22E-05 0.50 7.30E-05 0.51 rs1452232 12
83750362 C A 0.37 . 0.37 . NA NA LOC100128335 SLC6A15 8.38E-05 0.69
1.03E-04 0.69 rs7667510 4 41913903 G A . 0.15 . 0.15 NA NA BEND4
SHISA3 8.39E-05 0.49 9.27E-05 0.49 rs2687640 7 29138781 A G 0.06 .
0.06 0.05 CPVL intron KIAA0644 LOC100131724 8.45E-05 0.66 9.57E-05
0.66 rs711272 6 91667454 A G 0.28 0.27 0.30 0.27 NA NA MAP3K7
LOC100129847 8.72E-05 0.35 8.10E-05 0.36 rs16924767 12 22260834 G A
0.13 . 0.16 . ST8SIA1 intron CMAS KIAA0528 8.98E-05 0.89 9.26E-05
0.90 rs12757197 1 233657182 A G 0.07 . 0.10 . TBCE intron GGPS1
B3GALNT2 9.19E-05 0.83 4.07E-05 0.91 rs11164023 1 84861990 G A 0.20
0.17 0.19 0.22 NA NA CTBS C1orf180 9.25E-05 0.40 5.75E-05 0.41
rs4948291 10 59770095 T C . 0.33 . 0.36 UBE2D1 intron CISD1 TFAM
9.30E-05 0.40 7.00E-05 0.41 rs17156773 10 1740763 A G . 0.07 . 0.09
ADARB2 intron C10orf109 LOC100129465 9.42E-05 0.63 8.49E-05 0.64
rs2288502 5 156582630 A G 0.07 0.07 0.06 0.06 ITK intron FAM71B
CYFIP2 9.45E-05 0.61 1.04E-04 -0.61 rs1362972 12 94599424 A C 0.12
. 0.18 . NTN4 intron LOC100132594 SNRPF 9.47E-05 0.79 1.73E-04
-0.78 rs1480802 8 136293393 C A 0.37 . 0.38 . NA NA ZFAT LOC286094
9.54E-05 0.71 6.70E-05 0.73 rs6681946 1 17358138 G A 0.20 . 0.21 .
NA NA PADI2 LOC400743 9.59E-05 0.73 1.18E-04 0.72 rs4735993 8
1141126 G A . 0.27 . 0.26 NA NA LOC401442 DLGAP2 9.70E-05 0.42
4.38E-05 0.45 rs2515034 8 119565108 G A 0.06 . . . SAMD12 intron
EXT1 LOC441377 9.86E-05 1.68 7.67E-05 1.77 rs4691370 4 157809201 G
A 0.06 0.09 . 0.07 NA NA hCG_1814936 PDGFC 9.91E-05 0.59 1.02E-04
0.60 rs2077923 16 9788282 G A 0.29 . 0.32 . GRIN2A intron LOC653737
LOC727844 9.95E-05 0.68 8.64E-05 0.69
[0149] Thirty-four out of the 104 variants had the same direction
of effect in at least three out of the four studies (cutoff
p<1.times.10.sup.-4). The top ten most statistically significant
variants of that list in shown in Table 5. rs13135230 (G>A, MAF
0.25-0.28) was the most statistically significant
(p=1.26.times.10.sup.-6, .beta.=0.46), with the A allele increasing
the risk of hypertension (FIG. 3). rs13135230 is 3.8 kb 3' from
LGI2 (FIG. 4B). rs2350620 (A>G, MAF 0.26-0.32) is the next most
statistically significant (p=1.44.times.10.sup.-6, .beta.=0.49)
with the G allele decreasing the risk of hypertension (FIG. 13).
rs2350620 is located in the intron 14 of ASPH (FIG. 4B). rs6770663
(A>G, MAF 0.08-0.09) is the next most statistically significant
(p=4.79.times.10.sup.-6, .beta.=0.57) with the G allele increasing
the risk of hypertension (FIG. 13). rs6770663 is located in the
intron 1 of KCNAB1 (FIG. 4C) Among these ten variants, the only two
with p-value<0.05 in three out of the four studies were
rs2350620 and rs6770663 (Table 5). FIG. 13 shows the cumulative
incidence of grade.gtoreq.2 hypertension for rs2350620 and
rs6770663. For the SNP-based analysis of grade the Manhattan and
Q-Q plots are shown in FIG. 5. 106 variants were identified as
associated with hypertension (Table 11).
[0150] Forty-seven out of 106 variants had the same direction of
effect (either reduced or increased risk) in at least three out of
the four studies (cutoff p<1.times.10.sup.-4). The top ten most
statistically significant variants of that list are shown in Table
7. rs4782946 (G>A, MAF 0.37-0.43) was the most statistically
significant (p=3.09.times.10.sup.-7, .beta.=0.66) with the A allele
increasing the risk of hypertension. rs4782946 is an intronic
variant in ATP2C2 (FIG. 6). rs17439529 (G>A, MAF 0.36-0.40) was
the next most statistically significant (p=2.08.times.10-6,
.beta.=-0.72) with the A allele decreasing the risk of
hypertension. rs17439529 is located in the intron of AKAP6 (FIG.
6).
TABLE-US-00011 TABLE 11 SNPs associated with hypertension (grade
.gtoreq.3) refer- effect ence MAF MAF MAF MAF Flanking Flanking
effect SNP CH BP allele allele 80303 40503 90401 40502 gene feature
gene gene p-value (.beta.) rs- 16 82979663 A G 0.37 0.38 0.37 0.43
ATP2C2 intron WFDC1 KIAA1609 3.09E-07 0.66 4782946 rs- 11 100230559
A G . 0.06 . 0.05 FLJ32810 intron LOC- LOC- 7.29E-07 1.06 3858416
100128386 100129602 rs- 3 120338347 C A . . 0.06 . IGSF11 intron
LOC728873 C3orf30 1.27E-06 1.70 6807110 rs- 14 32253709 A G 0.36
0.40 0.38 0.40 AKAP6 intron MTCO1P2 NPAS3 2.08E-06 -0.72 17439529
rs- 14 77017051 G A . 0.06 . 0.09 THSD3 intron AHSA1 SPTLC2
3.47E-06 1.04 10129969 rs- 16 78434745 G A 0.06 . 0.05 . NA NA
LOC440389 LOC729847 4.68E-06 1.44 9933396 rs- 15 40069082 G A 0.23
0.19 0.18 0.17 PLA2G4E intron EHD4 PLA2G4D 4.87E-06 0.66 1530837
rs- 16 82980316 A G 0.20 0.17 0.19 0.22 ATP2C2 intron WFDC1
KIAA1609 5.23E-06 0.63 11863271 rs- 13 35359822 C A 0.19 0.26 0.19
0.21 DCLK1 intron NBEA SOHLH2 5.73E-06 0.62 1171065 rs- 14 77018319
G A . 0.07 . 0.09 THSD3 intron AHSA1 SPTLC2 5.92E-06 1.01 8010861
rs- 18 10056414 A G 0.18 0.14 0.11 0.12 NA NA VAPA APCDD1 6.10E-06
0.67 670362 rs- 2 182712983 G A 0.07 . 0.06 . NA NA PPP1R1C PDE1A
7.08E-06 1.60 17649232 rs- 8 141032458 A G 0.44 0.48 0.47 0.47 NIBP
intron C8orf17 LOC- 7.13E-06 0.63 2665917 100131910 rs- 14 77209741
A C . 0.18 . 0.18 ALKBH1 utr-3 SPTLC2 RPL21P10 7.63E-06 0.78
1048147 rs- 14 77207812 A G . 0.18 . 0.18 ALKBH1 near- SPTLC2
ALKBH1 7.63E-06 0.78 11624101 gene-3 rs- 14 77250973 G A . 0.18 .
0.18 C14orf156 intron ALKBH1 SNW1 7.63E-06 0.78 176955 rs- 9
2630805 A G 0.07 0.07 0.09 0.08 VLDLR intron FLJ35024 KCNV2
8.16E-06 0.87 10967306 rs- 10 115923895 A G 0.13 . 0.10 . C10orf118
utr-5 ADRB1 TDRD1 9.41E-06 1.17 17091403 rs- 13 95897355 G A 0.06 .
0.07 . HS6ST3 intron UGCGL2 HSP90AB6P 9.44E-06 1.35 732121 rs- 14
77270338 C A . 0.18 . 0.18 SNW1 intron C14orf156 C14orf178 9.68E-06
0.77 12887282 rs- 8 23934297 A G 0.24 0.18 0.21 0.24 NA NA LOC-
ADAM28 9.86E-06 0.61 1320881 100132107 rs- 4 124693385 G A . 0.16 .
0.17 NA NA SPRY1 LOC644624 1.00E-05 0.77 10011590 rs- 4 157809201 G
A 0.06 0.09 . 0.07 NA NA hCG_1814936 PDGFC 1.00E-05 0.82 4691370
rs- 14 77330548 A G . 0.18 . 0.18 NA NA C14orf178 ADCK1 1.06E-05
0.77 1008988 rs- 15 68821216 C A . 0.13 . 0.09 UACA intron TLE3
LOC729611 1.08E-05 0.93 11852645 rs- 14 77317035 A G . 0.18 . 0.18
NA NA C14orf178 ADCK1 1.09E-05 0.77 4632066 rs- 5 58097612 A G 0.19
0.18 0.17 0.16 RAB3C intron GAPT PDE4D 1.12E-05 0.64 10073306 rs-
18 10052583 G A . 0.10 . 0.10 NA NA VAPA APCDD1 1.26E-05 0.84
8088993 rs- 2 178188309 A G 0.09 0.10 0.08 0.08 TTC30A utr-3 TTC30B
PDE11A 1.31E-05 0.83 3821004 rs- 10 30375128 G A . 0.40 . .
KIAA1462 intron SVIL LOC729663 1.33E-05 1.27 2505083 rs- 7 36284221
A G 0.07 0.13 0.09 0.07 EEPD1 intron LOC- KIAA0895 1.37E-05 0.75
196584 100131181 rs- 9 84353502 A G 0.08 0.07 0.06 0.06 NA NA
LOC442427 RASEF 1.54E-05 1.01 10867852 rs- 11 130222650 G A . 0.45
. 0.49 NA NA C11orf44 SNX19 1.54E-05 0.72 1944142 rs- 6 1657305 C A
. 0.20 . 0.15 GMDS intron FLJ46552 LOC- 1.68E-05 0.78 7765461
100128372 rs- 3 5538371 A G 0.12 0.15 0.09 0.12 NA NA MRPS35P1
MRPS36P1 1.72E-05 0.70 17749328 rs- 5 58106740 A C 0.14 0.17 0.14
0.13 RAB3C intron GAPT PDE4D 1.76E-05 0.67 10051270 rs- 16 88183752
A G 0.45 0.47 0.50 0.48 CPNE7 intron RPL13 DPEP1 1.86E-05 0.58
464349 rs- 22 48127214 G A . 0.20 . 0.19 NA NA LOC643653 FLJ44385
2.04E-05 0.75 2858536 rs- 6 116992250 C A 0.19 0.16 0.19 0.19 NA NA
FAM26D RWDD1 2.09E-05 0.64 17078062 rs- 20 17569201 A G 0.08 . 0.08
. RRBP1 intron DSTN BANF2 2.10E-05 1.30 7267054 rs- 15 99119567 G A
. . 0.41 . NA NA ASB7 LOC440313 2.27E-05 1.42 7174784 rs- 5
156582630 A G 0.07 0.07 0.06 0.06 ITK intron FAM71B CYFIP2 2.47E-05
0.89 2288502 rs- 7 17071448 G A . 0.19 . 0.23 NA NA LOC- LOC-
2.64E-05 0.73 540509 100131425 100131512 rs- 18 57190720 A G 0.08
0.12 0.09 0.09 NA NA hCG_1659830 LOC- 2.66E-05 0.77 8084568
100129867 rs- 2 165199471 G A . 0.26 . 0.29 NA NA GRB14 COBLL1
2.77E-05 0.70 4425091 rs- 3 2330167 A G . 0.30 0.33 0.34 CNTN4
intron LOC727810 LOC- 2.99E-05 -0.75 11129096 100130346 rs- 2
29947713 C A 0.11 0.15 0.17 0.21 ALK intron CLIP4 YPEL5 3.06E-05
0.60 7574859 rs- 2 226443471 G A . 0.09 . 0.11 NA NA KIAA1486
LOC646736 3.13E-05 0.88 35969878 rs- 3 182528567 G A . 0.45 . 0.42
NA NA DNAJC19 SOX2OT 3.21E-05 0.68 2879464 rs- 2 46019476 G A 0.13
0.12 0.14 0.12 PRKCE intron SRBD1 EPAS1 3.50E-05 0.70 10206343 rs-
15 27520966 G A 0.32 0.34 0.34 0.35 NA NA NDNL2 LOC- 3.54E-05 0.55
511092 100130736 rs- 15 68781337 A G . 0.13 . 0.09 UACA intron TLE3
LOC729611 3.68E-05 0.89 6494889 rs- 22 27789732 G A 0.22 0.22 0.24
. NA NA C22orf31 KREMEN1 3.71E-05 0.73 760628 rs- 14 77217446 A G .
0.19 . 0.20 ALKBH1 intron SPTLC2 RPL21P10 3.76E-05 0.69 2267760 rs-
8 141012685 G A 0.45 0.48 0.47 0.48 NIBP intron KCNK9 LOC- 3.78E-05
0.58 2233230 100131910 rs- 11 104627661 A G . 0.49 . 0.46 NA NA
OR2AL1P GRIA4 3.85E-05 -0.72 4320922 rs- 2 174261681 C A 0.13 0.11
0.14 0.11 NA NA LOC- LOC644056 4.04E-05 0.73 752280 100129456 rs-
17 11806187 A G 0.20 0.18 0.19 0.18 DNAH9 missense FLJ45455 ZNF18
4.11E-05 0.59 1990236 rs- 3 23458540 A G 0.40 0.40 0.43 0.45 UBE2E2
intron LOC- UBE2E1 4.17E-05 0.53 13062101 100130785 rs- 1 54625582
C A . 0.44 . . SSBP3 intron C1orf191 LOC645436 4.18E-05 -1.19
11206344 rs- 7 1106944 A C 0.19 . . 0.21 C7orf50 intron GPER
ZFAND2A 4.18E-05 0.75 6463224 rs- 15 68789686 G A . 0.13 . 0.09
UACA intron TLE3 LOC729611 4.32E-05 0.88 16954699 rs- 15 68792114 C
A . 0.13 . 0.09 UACA intron TLE3 LOC729611 4.32E-05 0.88 2059322
rs- 10 76203313 A G 0.07 . 0.08 . NA NA LOC645646 MYST4 4.36E-05
1.10 7075347 rs- 9 130559781 G A 0.45 . 0.46 . ZER1 intron ZDHHC12
TBC1D13 4.39E-05 -1.09 10988111 rs- 16 85631051 C A 0.30 0.33 0.32
0.34 NA NA LOC729979 LOC730018 4.39E-05 0.52 1364075 rs- 15
49594756 A C . 0.14 . 0.15 DMXL2 intron GLDN SCG3 4.48E-05 0.76
11855184 rs- 8 68660493 G A . . . 0.11 CPA6 intron LOC- PREX2
4.50E-05 1.02 16933415 100132812 rs- 11 104720707 A G . 0.15 . 0.16
NA NA OR2AL1P GRIA4 4.52E-05 0.79 1449047 rs- 15 31357207 G A 0.11
0.08 0.06 0.08 NA NA FMN1 RYR3 4.64E-05 0.81 1514035 rs- 13
92633700 A C . 0.20 . 0.20 NA NA GPC5 GPC6 4.88E-05 0.71 9584088
rs- 14 48194882 A G 0.34 0.44 0.44 0.41 NA NA RPL18P1 ATP5GP2
4.92E-05 0.54 2585348 rs- 6 90700670 G A 0.23 0.22 0.25 0.22 BACH2
intron GJA10 LOC- 5.03E-05 0.56 17708487 100129711 rs- 15 21400911
G A . 0.11 . 0.13 NA NA MKRN3 MAGEL2 5.15E-05 0.83 7173605 rs- 19
5031647 A G 0.09 . 0.08 . JMJD2B intron UHRF1 LOC- 5.26E-05 1.12
11673509 100128439 rs- 15 68795974 A G . 0.12 . 0.09 UACA intron
TLE3 LOC729611 5.32E-05 0.87 1078097 rs- 5 58117438 A G 0.17 0.20
0.18 0.17 RAB3C intron GAPT PDE4D 5.54E-05 0.61 406992 rs- 13
102681443 G A . 0.10 . 0.10 NA NA SLC10A2 LOC728183 6.04E-05 0.79
6650294 rs- 17 11825241 A G 0.20 0.18 0.19 0.18 ZNF18 intron DNAH9
MAP2K4 6.18E-05 0.58 10852800 rs- 11 335595 A G 0.35 0.37 0.29 0.31
NA NA IFITM3 B4GALNT4 6.23E-05 -0.62 6598035 rs- 5 13323090 A G .
0.17 0.17 0.14 NA NA CTNND2 LOC391738 6.28E-05 0.66 6554770 rs- 15
68818494 A G . 0.13 . 0.09 UACA intron TLE3 LOC729611 6.30E-05 0.88
1011236 rs- 17 11809087 G A 0.21 0.18 0.19 0.19 DNAH9 intron
FLJ45455 ZNF18 6.34E-05 0.56 12449769 rs- 3 182516536 G A 0.44 0.46
0.42 0.43 NA NA DNAJC19 SOX2OT 6.36E-05 0.53 6778227 rs- 2
178196274 A G 0.07 0.08 . 0.06 PDE11A utr-3 TTC30A LOC- 6.59E-05
0.87 2293473 100131480 rs- 11 112699658 C A 0.15 0.12 0.12 0.11
TTC12 intron NCAM1 ANKK1 6.62E-05 0.62 723079 rs- 9 111119949 A G
0.39 0.37 0.35 0.36 EPB41L4B intron C9orf4 PTPN3 6.69E-05 -0.60
966697 rs- 11 129067604 G A . 0.16 . 0.16 NA NA BARX2 LOC729717
6.74E-05 0.74 11221807 rs- 2 205209582 A C 0.09 . 0.08 . PARD3B
intron LOC- NRP2 6.78E-05 1.12 1978368 100132669 rs- 5 113989891 A
C 0.10 0.09 0.06 0.09 NA NA KCNN2 TRIM36 6.84E-05 0.76 17365340 rs-
15 68823323 C A . 0.13 0.10 0.09 UACA intron TLE3 LOC729611
6.91E-05 0.83 16954789 rs- 18 10055917 G A 0.21 0.15 0.15 0.15 NA
NA VAPA APCDD1 6.99E-05 0.57 1292299 rs- 19 9175135 C A 0.14 0.16
0.18 0.15 NA NA OR7E16P OR7E25P 7.00E-05 0.59 10415904 rs- 16
72370567 A C 0.32 . 0.30 . NA NA C16orf47 LOC441506 7.03E-05
0.89
2386717 rs- 13 103355842 G A 0.12 0.11 0.11 0.13 NA NA LOC728183
DAOA 7.27E-05 0.69 7328957 rs- 1 182693445 G A 0.08 . 0.07 0.07
C1orf21 intron TSEN15 LOC- 7.57E-05 0.93 13374607 100129573 rs- 12
22260834 G A 0.13 . 0.16 . ST8SIA1 intron CMAS KIAA0528 7.58E-05
1.17 16924767 rs- 5 89989605 A G 0.06 . 0.08 . GPR98 synony- LYSMD3
LOC729040 7.77E-05 1.12 17543819 mous rs- 13 103339702 G A 0.10
0.11 0.09 0.11 NA NA LOC728183 DAOA 7.85E-05 0.67 17344132 rs- 13
72567440 A G . 0.06 . 0.06 NA NA KLF5 FABP5L1 8.96E-05 0.90 2503697
rs- 5 90031559 G A 0.06 . 0.08 . GPR98 intron LYSMD3 LOC729040
9.33E-05 1.11 17622455 rs- 5 135239365 A G 0.11 0.12 0.12 0.11 NA
NA LOC153328 IL9 9.37E-05 0.68 7717673 rs- 18 63045205 A G . 0.10 .
0.08 NA NA CDH19 DSEL 9.42E-05 0.83 4519437 rs- 11 84849951 A G
0.07 . . 0.07 NA NA DLG2 TMEM126B 9.49E-05 0.94 1213236 rs- 2
36780787 G A 0.13 0.11 0.14 0.14 VIT intron FEZ2 STRN 9.93E-05
0.6266 17019472 rs- 16 75154359 G A 0.40 . 0.41 . NA NA CNTNAP4
LOC- 9.93E-05 -1.0612 4506930 100128497
[0151] For the gene-based analysis of grade.gtoreq.2, the Q-Q plot
is shown in FIG. 7. Table 9 shows the ten most statistically
significant genes. UNC50 was the most statistically significant
gene (p=2.30.times.10.sup.-5).
[0152] Variants and Genes Associated with Bevacizumab-Induced
Proteinuria and Hypertension (Composite Toxicity)
[0153] For the SNP-based analysis of grade.gtoreq.2, the Manhattan
and Q-Q plots are shown in FIG. 2. 100 variants associated with
composite toxicity were identified (Table 12).
TABLE-US-00012 TABLE 12 SNPs associated with composite toxicity
(grade .gtoreq.2) reference MAF MAF MAF SNP CH BP effect allele
allele 80303 40503 90401 gene feature Flanking gene Flanking gene
p-value unadjusted effect (.beta.) unadjusted p-value adjusted
effect (.beta.) adjusted rs17084411 6 122692679 A G . 0.11 . NA NA
LOC644502 HSF2 4.24E-08 1.52 4.74E-08 1.55 rs1927869 6 122627419 T
C . 0.11 . NA NA LOC644502 HSF2 4.24E-08 1.52 4.74E-08 1.55
rs17084371 6 122612111 G A . 0.11 . NA NA LOC644502 HSF2 7.24E-08
1.47 8.05E-08 1.49 rs11036390 11 41387322 C A . 0.27 . NA NA LRRC4C
LOC100131020 2.15E-07 1.02 2.37E-07 1.02 rs11662763 18 5847091 A G
0.14 0.11 0.13 NA NA LOC645355 TTMA 9.19E-07 0.67 9.48E-05 0.61
rs2937754 5 17308803 G A . 0.19 . BASP1 intron FLJ34047 LOC646012
1.52E-06 0.95 1.52E-06 0.97 rs8006648 14 87359052 A G 0.27 0.28
0.26 NA NA LOC730121 GALC 2.33E-06 0.58 2.87E-05 0.55 rs2456761 10
62200548 A C 0.35 . 0.34 NA NA LOC729184 CDC2 2.80E-06 0.72
4.57E-05 0.69 rs1000032 2 176643771 A C 0.13 0.18 0.19 NA NA
KIAA1715 EVX2 3.21E-06 0.62 9.26E-06 0.63 rs2203208 12 57257435 G A
. 0.20 . NA NA LOC100127973 LRIG3 3.54E-06 0.96 3.05E-06 1.00
rs2687640 7 29138781 A G 0.06 . 0.06 CPVL intron KIAA0644
LOC100131724 3.55E-06 1.03 1.09E-06 1.13 rs9310707 3 2307104 A G
0.37 0.37 0.36 CNTN4 intron LOC727810 LOC100130346 4.03E-06 0.53
1.33E-05 0.52 rs7197696 16 6110274 G A . 0.14 . A2BP1 intron
LOC100129334 LOC440337 5.95E-06 1.15 6.41E-06 1.16 rs9991738 4
182341049 C T . 0.49 . NA NA hCG_2025798 LOC132386 7.26E-06 0.84
5.79E-06 0.86 rs12597709 16 6102147 G A . 0.13 . A2BP1 intron
LOC100129334 LOC440337 7.29E-06 1.14 7.36E-06 1.14 rs13156044 5
13920851 A G 0.15 0.11 0.11 DNAH5 intron LOC391738 TRIO 8.51E-06
0.60 7.40E-05 0.59 rs12328055 2 49824743 A G 0.06 . 0.05 NA NA FSHR
LOC130728 9.19E-06 0.99 2.27E-03 0.76 rs4799369 18 30594128 G A
0.20 0.20 0.18 DTNA intron LOC646842 MAPRE2 1.14E-05 0.59 1.63E-03
0.44 rs11610946 12 3985117 G A . 0.14 . NA NA PARP11 LOC399988
1.19E-05 0.96 1.21E-05 0.96 rs750585 5 168644898 G A . 0.13 . SLIT3
intron LOC728095 CCDC99 1.24E-05 1.03 1.30E-05 1.04 rs2757491 1
170533424 A G 0.06 . 0.06 DNM3 intron LOC100128178 LOC100131486
1.25E-05 0.90 1.39E-02 -0.68 rs2757500 1 170545644 A G 0.06 . 0.06
DNM3 intron LOC100128178 LOC100131486 1.25E-05 0.90 1.39E-02 0.28
rs17752325 4 65927951 A G 0.11 . 0.13 EPHA5 intron LOC644682
LOC642828 1.38E-05 0.77 1.05E-05 0.82 rs7204266 16 9876004 G A 0.28
. 0.28 GRIN2A intron LOC653737 LOC727844 1.44E-05 0.60 6.84E-06
0.69 rs12754186 1 19638913 T G . 0.11 . CAPZB intron LOC100130193
C1orf151 1.65E-05 0.98 1.14E-05 0.99 rs7202526 16 6808380 A G 0.30
0.30 0.29 A2BP1 intron LOC100131413 LOC100131080 1.67E-05 0.51
2.35E-05 0.52 rs1001952 11 41421246 C T . 0.26 . NA NA LRRC4C
LOC100131020 1.74E-05 0.87 1.74E-05 0.87 rs11154658 6 132422252 G T
. 0.13 . LOC100131774 intron CTGF MOXD1 1.75E-05 0.98 1.51E-05 0.99
rs7553399 1 3406309 C A . 0.25 . MEGF6 missense ARHGEF16 TPRG1L
1.81E-05 0.95 1.46E-05 0.91 rs1358206 3 74198360 G A 0.30 . 0.31 NA
NA LOC100129282 HSP90AB5P 1.81E-05 0.62 3.89E-03 0.45 rs17867545 4
118873138 T C . 0.10 . NA NA NT5C3P1 NDST3 1.84E-05 1.20 1.57E-05
1.23 rs16945809 17 1241236 G A 0.08 0.08 0.06 YWHAE intron TUSC5
LOC727845 2.00E-05 0.80 2.16E-06 0.94 rs7234672 18 5875157 A G 0.15
. 0.14 NA NA LOC645355 TTMA 2.06E-05 0.72 1.03E-03 0.64 rs13062101
3 23458540 A G 0.40 0.40 0.43 UBE2E2 intron LOC100130785 UBE2E1
2.34E-05 0.45 4.35E-05 0.46 rs10820743 9 106711480 G A 0.29 0.28
0.27 ABCA1 intron NIPSNAP3B SLC44A1 2.42E-05 0.48 8.05E-05 0.47
rs7201930 16 9866156 G A 0.29 . 0.33 GRIN2A intron LOC653737
LOC727844 2.90E-05 0.60 4.51E-05 0.65 rs12706180 7 117784949 A G
0.34 . . NA NA ANKRD7 LOC648442 3.03E-05 0.91 8.37E-04 0.97
rs9933832 16 9856135 A G 0.29 . 0.32 GRIN2A intron LOC653737
LOC727844 3.24E-05 0.59 5.18E-05 0.64 rs6706281 2 190160993 C A .
0.26 . NA NA SLC40A1 ASNSD1 3.27E-05 0.91 2.54E-05 0.94 rs1437883 2
190167713 C T . 0.25 . NA NA SLC40A1 ASNSD1 3.35E-05 0.90 2.81E-05
0.93 rs4407684 6 85500368 A G 0.47 . 0.53 TBX18 near- LOC442233
TBX18 3.48E-05 0.59 1.40E-03 0.49 gene- 3 rs4149265 9 106712319 A G
0.29 0.28 0.27 ABCA1 intron NIPSNAP3B SLC44A1 3.57E-05 0.47
1.20E-04 0.46 rs17202944 8 13848320 G T . 0.33 . NA NA C8orf48 SGCZ
3.70E-05 -0.82 2.53E-05 -0.85 rs4738274 8 56645881 A C 0.29 . 0.27
NA NA XKR4 TMEM68 3.72E-05 0.60 3.16E-03 0.49 rs277311 5 154473983
A G 0.14 0.14 0.14 NA NA LOC100131520 LOC100130088 3.88E-05 0.62
3.47E-04 0.60 rs2866223 4 101744971 G A 0.19 0.18 0.21 NA NA EMCN
LOC728771 3.96E-05 0.56 2.40E-03 0.43 rs7614155 3 74196658 G A 0.25
. 0.27 NA NA LOC100129282 HSP90AB5P 4.05E-05 0.61 8.67E-03 0.42
rs6966727 7 130025354 G A 0.06 . . NA NA TSGA13 KLF14 4.07E-05 1.31
1.26E-01 0.78 rs6982610 8 14557840 C A . 0.36 . SGCZ intron
LOC100131565 TUSC3 4.39E-05 0.77 3.36E-05 0.78 rs924945 18 67586419
A G 0.34 0.41 0.34 NA NA LOC100132647 CBLN2 4.48E-05 0.46 3.54E-05
0.49 rs17021160 2 37717573 T G . 0.07 . NA NA QPCT CDC42EP3
4.52E-05 1.29 4.99E-05 1.30 rs9921541 16 9899263 A C 0.23 . 0.24
GRIN2A intron LOC653737 LOC727844 4.52E-05 0.59 5.20E-05 0.64
rs2250378 12 73914832 C T . 0.23 . LOC100130268 near- KCNC2
LOC100130268 4.63E-05 0.88 4.85E-05 0.89 gene- 5 rs351572 8
16065839 G A 0.40 0.49 0.44 MSR1 intron hCG_1794003 LOC646440
4.81E-05 -0.46 1.43E-04 -0.45 rs11642239 16 9904081 G A 0.25 0.28
0.25 GRIN2A intron LOC653737 LOC727844 4.83E-05 0.48 1.14E-04 0.49
rs1480802 8 136293393 C A 0.37 . 0.38 NA NA ZFAT LOC286094 4.97E-05
0.63 2.50E-05 0.70 rs2886725 5 37806593 A G . 0.14 . NA NA WDR70
GDNF 4.99E-05 0.97 4.89E-05 1.02 rs1524145 2 35975892 T G . 0.43 .
NA NA MRPL50P1 CRIM1 5.01E-05 0.84 5.05E-05 0.84 rs12525751 6
109444416 A G 0.24 0.19 0.22 SESN1 intron ARMC2 C6orf182 5.04E-05
0.51 1.31E-03 0.43 rs2077923 16 9788282 G A 0.29 . 0.32 GRIN2A
intron LOC653737 LOC727844 5.21E-05 0.59 1.20E-04 0.61 rs7853963 9
82908731 A G 0.15 . 0.14 NA NA LOC100128222 TLE1 5.21E-05 0.72
5.12E-03 0.56 rs1410171 6 85459030 A G 0.47 . 0.53 NA NA LOC442233
TBX18 5.23E-05 0.57 2.18E-03 0.47 rs1904982 1 105061407 T C . 0.50
. NA NA LOC642337 LOC100130867 5.24E-05 -0.75 3.54E-05 -0.80
rs12706181 7 117789716 A G 0.34 . . NA NA ANKRD7 LOC648442 5.28E-05
0.88 1.09E-03 0.95 rs1345697 5 147922431 G A 0.48 0.49 0.51 HTR4
intron FBXO38 ADRB2 5.49E-05 -0.46 6.06E-04 -0.41 rs11255686 10
8496013 C A . 0.46 . NA NA LOC389935 KRT8P16 5.56E-05 0.80 5.51E-05
0.81 rs1814343 11 129070462 A G 0.23 0.23 0.26 NA NA BARX2
LOC729717 5.86E-05 0.50 1.32E-03 0.42 rs7724465 5 4723864 A G .
0.06 . NA NA IRX1 LOC340094 5.92E-05 1.11 4.19E-05 1.15 rs13258175
8 13873685 A G . 0.45 . NA NA C8orf48 SGCZ 5.97E-05 0.72 3.14E-05
0.77 rs7821773 8 9748866 G A 0.08 0.05 0.08 NA NA TNKS MSRA
5.98E-05 0.71 1.75E-05 0.80 rs1564470 8 136290117 A C 0.30 . 0.32
NA NA ZFAT LOC286094 6.02E-05 0.62 5.09E-06 0.75 rs6763279 3
74195448 G A 0.25 0.29 0.27 NA NA LOC100129282 HSP90AB5P 6.28E-05
0.46 5.01E-03 0.34 rs2243628 10 7553828 A G 0.37 . 0.34 NA NA
LOC728777 ITIH5 6.39E-05 0.53 1.87E-03 0.46 rs10792038 11 56079983
G A 0.34 . 0.38 NA NA OR5M11 OR5M10 6.59E-05 0.61 1.81E-05 0.72
rs13024296 2 224298740 A G 0.17 . 0.20 NA NA LOC646696 AP1S3
6.83E-05 -0.97 4.35E-03 -0.71 rs7968026 12 83754187 A G 0.31 . 0.30
NA NA LOC100128335 SLC6A15 6.89E-05 0.57 3.63E-05 0.64 rs41958 7
117760681 A G 0.35 . . NA NA ANKRD7 LOC648442 7.07E-05 0.87
1.26E-03 0.94 rs2543540 17 7572396 A G . 0.40 . DNAH2 intron EFNB3
RPL29P2 7.09E-05 -0.77 7.26E-05 -0.77 rs17615862 14 43931394 T C .
0.25 . NA NA YWHAZP1 LOC729165 7.21E-05 0.86 7.33E-05 0.86 rs693996
11 56046568 A G 0.34 . 0.38 NA NA OR5M6P OR5M5P 7.58E-05 0.60
2.16E-05 0.71 rs1123110 2 190152444 C T . 0.34 . SLC40A1 intron
WDR75 ASNSD1 7.70E-05 0.72 7.56E-05 0.72 rs7754913 6 132423548 C A
0.11 0.13 0.13 LOC100131774 intron CTGF MOXD1 8.10E-05 0.58
1.07E-04 0.60 rs9863361 3 177769362 G A . . 0.03 NA NA LOC730168
TBL1XR1 8.36E-05 1.63 9.80E-05 1.62 rs2940774 4 22958441 A G 0.17 .
0.25 LOC643751 intron GBA3 PPARGC1A 8.60E-05 0.62 9.16E-04 0.58
rs1219769 1 108340149 A G 0.32 . 0.32 NA NA VAV3 SLC25A24 8.65E-05
0.62 6.64E-03 0.47 rs2977983 8 71233342 A G 0.06 . . NCOA2 intron
H2AFZP2 BTF3L2 8.76E-05 1.31 2.62E-03 1.36 rs4831257 8 13878742 A G
. 0.40 . NA NA C8orf48 SGCZ 8.93E-05 -0.72 6.57E-05 -0.74 rs8049793
16 7401978 C A 0.19 0.17 0.17 A2BP1 intron LOC100131413
LOC100131080 9.07E-05 -0.68 6.74E-04 -0.62 rs7725683 5 68255470 G A
. 0.23 . NA NA PIK3R1 LOC100130639 9.11E-05 0.82 9.54E-05 0.82
rs2206593 1 184909052 A G 0.08 . . PTGS2 utr-3 LOC100131939 PLA2G4A
9.14E-05 1.30 3.03E-04 1.49 rs7038808 9 91931116 A G 0.13 . 0.15 NA
NA IL6RL1 OR7E31P 9.17E-05 0.68 4.55E-06 0.85 rs8098087 18 67662582
A G 0.23 0.28 0.22 NA NA LOC100132647 CBLN2 9.23E-05 0.47 1.62E-04
0.49 rs17252114 3 41187757 A G 0.45 0.50 0.52 NA NA RPS27P4
MRPS31P1 9.33E-05 -0.43 6.44E-04 -0.40 rs9805752 13 113894531 A G .
. 0.16 RASA3 intron FAM70B CDC16 9.44E-05 0.86 4.96E-05 0.90
rs12272563 11 32465808 A G . 0.20 . NA NA WIT1 EIF3M 9.46E-05 0.85
8.00E-05 0.86 rs222151 21 26692482 A G 0.25 0.23 0.22 NA NA APP
CYYR1 9.49E-05 -0.57 9.10E-06 -0.73 rs873930 10 7569980 G A 0.46
0.47 0.43 NA NA LOC728777 ITIH5 9.58E-05 0.40 4.49E-04 0.39
rs10502634 18 30570172 G A 0.11 0.09 0.10 DTNA intron LOC646842
MAPRE2 9.58E-05 0.67 1.56E-03 0.57 rs1349498 2 173300852 A G 0.17
0.22 0.19 NA NA LOC100129169 RAPGEF4 9.73E-05 0.50 1.51E-03 0.45
rs2704783 2 146216429 C T . 0.28 . NA NA LOC730124 LOC727713
9.84E-05 0.87 1.00E-04 0.87
[0154] Fifty-seven out of the 100 variants had the same direction
of effect in at least two out of the three trials (cutoff
p<1.times.10.sup.-4). The top ten most statistically significant
variants of that list in shown in Table 5. rs11662763 (G>A, MAF
0.11-0.14) was the most statistically significant
(p=9.19.times.10.sup.-7, (3=0.67), with the A allele increasing the
risk of composite toxicity (FIG. 3). rs11662763 is 33 kb 3' from
TTMA (FIG. 4A).
[0155] For the SNP-based analysis of grade the Manhattan and Q-Q
plots are shown in FIG. 5. 88 variants were identified as
associated with composite toxicity (Table 13). Fifty-three out of
88 variants had the same direction of effect (either reduced or
increased risk) in at least three out of the four studies (cutoff
p<1.times.10.sup.-4). The top ten most statistically significant
variants of that list are shown in Table 7. rs10867852 (G>A, MAF
0.06-0.08) was the most statistically significant
(p=1.46.times.10.sup.-6, .beta.=1.16), with the A allele increasing
the risk of composite toxicity. rs10867852 is an intergenic variant
located 430 kb 3' from RASEF (FIG. 6). rs7717673 (G>A, MAF
0.11-0.12) was the next most statistically significant
(p=3.93.times.10.sup.-6, .beta.=0.94) with the A allele increasing
the risk of composite toxicity. rs7717673 is located in the intron
of SLC25A48 (FIG. 6).
TABLE-US-00013 TABLE 13 SNPs associated with composite toxicity
(grade .gtoreq.3) refer- Effect ence MAF MAF MAF Flanking Flanking
effect SNP CH BP allele allele 80303 40503 90401 gene feature gene
gene p-value (.beta.) rs6807110 3 120338347 C A . . 0.06 IGSF11
intron LOC728873 C3orf30 1.29E-06 1.61 rs10867852 9 84353502 A G
0.08 0.07 0.06 NA NA LOC442427 RASEF 1.46E-06 1.16 rs1022306 11
83629022 A C . 0.13 . DLG2 intron LOC- LOC- 2.11E-06 1.32 100130985
100130066 rs6954042 7 109951683 G A . 0.06 . NA NA LOC646620 IMMP2L
2.45E-06 1.76 rs7717673 5 135239365 A G 0.11 0.12 0.12 SLC25A48
intron LOC153328 IL9 3.93E-06 0.94 rs2478835 10 30357955 T C . 0.40
. KIAA1462 synony- SVIL LOC729663 8.85E-06 1.22 mous rs4842232 9
137279808 A G . 0.10 . NA NA LOC401557 C9orf62 9.83E-06 1.55
rs4320922 11 104627661 A G . 0.49 . NA NA OR2AL1P GRIA4 1.27E-05
-1.24 rs6033941 20 14243645 C A . 0.29 . MACROD2 intron SCYE1P
FLRT3 1.40E-05 1.05 rs2454331 8 89957664 G A 0.43 0.40 0.43 NA NA
LOC- RIPK2 1.43E-05 -0.77 100129100 rs873224 8 142600146 G A 0.11
0.10 0.08 NA NA FLJ43860 LOC- 1.48E-05 0.86 100131146 rs10873360 14
25663831 T G . 0.11 . NA NA LOC401767 NOVA1 1.49E-05 1.38 rs966439
14 86235074 G A 0.21 0.17 0.16 NA NA LOC283584 LOC283585 1.52E-05
0.70 rs7849777 9 136812622 A G 0.09 0.05 0.06 COL5A1 intron RXRA
LOC- 1.56E-05 1.31 100130622 rs10869538 9 70729551 G A 0.15 0.16
0.15 PIP5K1B intron LOC- PRKACG 1.74E-05 0.74 100131240 rs11664759
18 69223208 A G 0.11 0.15 0.15 NA NA LOC400655 FBXO15 2.21E-05 0.83
rs1978259 14 86265207 A C 0.20 . 0.16 NA NA LOC283584 LOC283585
2.63E-05 0.81 rs7174784 15 99119567 G A . . 0.41 NA NA ASB7
LOC440313 2.74E-05 1.25 rs17096208 14 73625022 A G 0.08 . 0.07
LIN52 intron ALDH6A1 VSX2 2.87E-05 1.05 rs4646864 14 73596456 A G
0.08 . 0.07 ALDH6A1 near- ENTPD5 ALDH6A1 2.87E-05 1.05 gene-3
rs17109031 12 52884634 A G 0.13 0.08 0.10 NA NA SMUG1 LOC- 2.93E-05
0.85 100132010 rs4696433 4 154307393 A G 0.12 0.10 0.12 NA NA FHDC1
TRIM2 3.01E-05 0.90 rs6739406 2 35467180 A G 0.11 0.13 0.09 NA NA
LOC- MRPL50P1 3.11E-05 0.84 100130842 rs10988111 9 130559781 G A
0.45 . 0.46 ZER1 intron ZDHHC12 TBC1D13 3.21E-05 -0.97 rs491451 6
12836804 A G 0.16 0.11 0.14 PHACTR1 intron RPL15P3 LOC- 3.45E-05
0.80 100130357 rs16930838 8 65151961 C T . 0.11 . NA NA IFITM8P
LOC- 3.50E-05 1.31 100130155 rs2505083 10 30375128 C T . 0.40 .
KIAA1462 intron SVIL LOC729663 3.55E-05 1.11 rs10129969 14 77017051
G A . 0.06 . THSD3 intron AHSA1 SPTLC2 3.73E-05 1.54 rs1452243 12
83695187 A C 0.38 0.34 0.39 NA NA LOC- SLC6A15 3.73E-05 0.68
100128335 rs11254929 10 7072177 G A 0.16 . 0.17 NA NA LOC439949
SFMBT2 3.91E-05 0.94 rs710392 5 87060900 T C . 0.17 . NA NA CCNH
TMEM161B 4.02E-05 1.20 rs1932065 1 70857226 G A . 0.23 . NA NA
LOC391048 PTGER3 4.03E-05 1.02 rs12157031 0 NA T C . 0.08 . NA NA
RPS6KA3 CNKSR2 4.33E-05 1.52 rs7080002 10 109119252 G A . 0.06 . NA
NA SORCS1 LOC- 4.38E-05 1.64 100128304 rs3739998 4 118873138 G C .
0.40 . NA NA NT5C3P1 NDST3 4.38E-05 1.06 rs17867545 14 61622536 T C
. 0.10 . SYT16 intron MOCS3P LOC- 4.57E-05 1.43 100128793 rs2154110
6 2465335 G T . 0.25 . NA NA LOC- C6orf195 4.68E-05 1.17 100128372
rs7764946 6 6613180 T C . 0.07 . NA NA LY86 RP11- 5.05E-05 1.55
320C15.1 rs9405313 8 33984189 A C 0.11 0.13 0.12 NA NA CYCSP3
LOC137107 5.07E-05 0.80 rs4493901 6 22511446 T C . 0.11 . NA NA PRL
HDGFL1 5.10E-05 1.18 rs2655439 6 14056368 A G 0.15 0.14 0.13 RNF182
intron CCDC90A MRPL35P1 5.42E-05 0.75 rs1192057 14 88559840 A G .
0.10 . NA NA TTC8 LOC390501 5.55E-05 1.34 rs11628605 4 56789252 A G
. 0.32 . KIAA1211 intron CEP135 MRPL22P1 5.56E-05 1.11 rs17751450 9
25541627 A G 0.36 . 0.38 NA NA C9orf134 TUSC1 5.66E-05 0.75
rs7028018 20 40742146 G A 0.29 0.38 . PTPRT intron LOC643172 PPIAL
5.76E-05 0.73 rs2206428 12 72205105 A G 0.25 . 0.30 NA NA TRHDE
LOC- 5.90E-05 0.81 100128674 rs12368298 10 76203313 G A 0.19 . . NA
NA LOC645646 MYST4 6.03E-05 1.31 rs7075347 7 36284221 A G 0.07 .
0.08 EEPD1 intron LOC- KIAA0895 6.06E-05 1.01 100131181 rs196584 9
117317136 A G 0.07 0.13 0.09 NA NA 43800 C9orf27 6.13E-05 0.76
rs9408872 20 14192971 A C . 0.22 . MACROD2 intron SCYE1P FLRT3
6.39E-05 1.06 rs1998238 11 104663936 A G . 0.29 . NA NA OR2AL1P
GRIA4 6.42E-05 0.99 rs10895805 5 39716478 A G . 0.41 . NA NA LOC-
LOC285634 6.42E-05 -1.28 100129040 rs10473145 1 25124011 T G . 0.15
. RUNX3 intron CLIC4 LOC391020 6.68E-05 1.07 rs742230 9 70717983 C
T . 0.43 . PIP5K1B intron LOC- PRKACG 6.69E-05 -1.20 100131240
rs1414954 1 156145769 A G 0.13 . 0.11 NA NA LOC649203 hCG_1994895
6.72E-05 0.85 rs4450009 12 74414178 G A 0.16 0.13 0.13 NA NA LOC-
LOC- 6.72E-05 0.72 100130336 100131830 rs4831949 13 80958452 G A .
0.08 . NA NA LOC- PTMAP5 6.80E-05 1.48 100129023 rs9545728 20
40760195 A G 0.19 . . PTPRT intron LOC643172 PPIAL 6.85E-05 1.38
rs6072833 9 116819754 A G 0.25 . 0.30 NA NA TNFSF8 TNC 6.87E-05
0.80 rs1107373 5 92355984 A G 0.06 0.08 0.09 NA NA CCT7P2 LOC391811
7.14E-05 0.83 rs12054859 10 30346810 G A 0.07 . . KIAA1462 utr-3
SVIL LOC729663 7.28E-05 1.87 rs2478839 13 66879378 T C . 0.42 . NA
NA LOC400141 LOC390411 7.37E-05 1.03 rs13378216 6 143400706 G T .
0.06 . NA NA HIVEP2 AIG1 7.41E-05 1.39 rs12664681 18 55864775 C A
0.06 0.06 0.08 NA NA LOC728115 LOC400652 7.65E-05 0.93 rs17066548
13 95897355 A C 0.05 . 0.05 HS6ST3 intron UGCGL2 HSP90AB6P 7.74E-05
1.34 rs732121 20 40763167 G A 0.06 . 0.07 PTPRT intron LOC643172
PPIAL 7.93E-05 1.12 rs3092743 1 29428986 A G 0.17 . 0.20 MECR
intron SFRS4 PTPRU 8.19E-05 0.79 rs2819606 2 174388565 T C . 0.10 .
NA NA LOC- LOC644056 8.19E-05 1.37 100129456 rs16862115 5 168644898
A G 0.20 0.21 0.24 SLIT3 intron LOC728095 CCDC99 8.61E-05 0.60
rs750585 6 134606559 G A . 0.13 . NA NA SGK1 LOC442261 8.66E-05
1.06 rs9493871 16 78430806 A C 0.09 0.07 0.08 NA NA LOC440389
LOC729847 8.66E-05 0.96 rs11644568 6 1773164 A C 0.06 . 0.05 GMDS
intron FLJ46552 LOC- 8.83E-05 1.18 100128372 rs9328072 2 50099333 G
A 0.28 0.26 0.31 NRXN1 intron LOC130728 LOC730100 9.04E-05 0.63
rs7568888 4 109997382 A G . . 0.15 COL25A1 intron LOC- ZCCHC23
9.10E-05 1.17 100129714 rs1377208 8 58380598 C A 0.18 . . NA NA
C8orf71 LOC- 9.11E-05 1.19 100130588 rs1878628 11 104715682 G A . .
0.07 NA NA OR2AL1P GRIA4 9.11E-05 1.35 rs4603276 11 104778916 G A .
0.41 . NA NA OR2AL1P GRIA4 9.13E-05 -1.22 rs7930393 8 24652844 C T
. 0.41 . NA NA ADAM7 NEFM 9.13E-05 -1.22 rs10091523 9 116740531 G A
0.34 . 0.36 NA NA TNFSF8 TNC 9.31E-05 0.82 rs4979476 13 35359822 G
A 0.09 0.09 0.08 DCLK1 intron NBEA SOHLH2 9.33E-05 0.73 rs1171065 9
92388224 C A 0.19 0.26 0.19 NA NA LOC340515 DIRAS2 9.34E-05 0.63
rs16906689 5 37808537 A G . 0.09 . NA NA WDR70 GDNF 9.45E-05 1.43
rs10472291 7 3583940 A C . 0.37 . SDK1 intron LOC- LOC730351
9.53E-05 1.04 100129603 rs9654994 17 67535422 G A 0.14 0.15 0.15 NA
NA hCG_1644301 FLJ37644 9.64E-05 0.76 rs12451606 1 61132767 G A . .
0.03 NA NA C1orf87 NFIA 9.67E-05 1.83 rs1002005 8 24655238 G A 0.06
0.08 0.07 NA NA ADAM7 NEFM 9.75E-05 0.83 rs4543550 10 93349774 G A
0.34 . 0.36 NA NA HECTD2 PPP1R3C 9.92E-05 0.82 rs7903829 3 2307104
A C 0.06 0.07 0.07 CNTN4 intron LOC727810 LOC- 9.97E-05 0.90
100130346
[0156] For the gene-based analysis of grade.gtoreq.2, the Q-Q plot
is shown in FIG. 7. Table 9 shows the ten most statistically
significant genes. SLC25A24 was the most significant
(p=4.00.times.10.sup.-6).
Discussion
[0157] It is believed that this is the largest GWAS of
bevacizumab-induced proteinuria and hypertension. The present study
included 1,041 cancer patients, with different tumor types, from
four randomized phase III clinical trials conducted at the
Alliance. The relatively large sample size, the randomized design,
and the standardized collection of the phenotypic and genotypic
data are positive features that increase the value of these
findings. The analysis of genetic associations that were consistent
across different studies led to the identification of novel SNPs
and genes associated with these toxicities.
[0158] This study has selected DNAH5, TRIO, RIPK4 and IL17F as
genes involved bevacizumab-induced proteinuria. DNAH5 and TRIO are
the closest genes from rs339947, the most statistically significant
SNP associated with proteinuria (p=7.66.times.10.sup.-8). DNAH5
encodes a dynein protein (part of a microtubule-associated motor
protein complex) that is important for the normal function of
ciliated cells in many tissues, including kidney tubule. Mutations
in DNAH5 cause a genetic disorder associated with polycystic kidney
diseases. TRIO encodes a GDP to GTP exchange factor promoting the
reorganization of the actin cytoskeleton, thereby playing a role in
cell migration and growth. TRIO is highly expressed in podocytes
and regulates the attachment of podocytes to glomerular basement
membrane. TRIO also induces Rac 1 activity, which contributes to
podocyte injury and proteinuria. DNAH5, or TRIO, or both could be
involved in the mechanism of bevacizumab-induced proteinuria.
Interestingly, our functional bioinformatic analysis that rs429023,
in moderate LD with rs339947, is an eQTL increasing TRIO expression
in the glomerulus (Table 14), potentially pointing towards TRIO as
the putative gene of proteinuria.
TABLE-US-00014 TABLE 14 Bioinformatic analysis of rs13135230,
rs2350620, and rs6770663 associated with hypertension, rs339947,
rs12482855 and rs408130 associated with proteinuria, rs11662763
associated with composite toxicity, and SNPs in complete LD
(R.sup.2 = 1.0) according to LDlink. Data from Genome Browser,
Regulome DB and/or HaploReg v4 Regulome Transcription DNaseI DB
factor sensitivity Chromatin Histone SNPs eQTL Region Score
ChIP-seq binding motifs region state markers Hypertension
rs13135230 -- 3.8 kb 3' No data -- -- -- -- from LGI2 rs2350620 --
4 FOXA1 -- -- -- rs35026059 -- 2c CTCF CTCF -- -- rs28695823 --
ASPH 5 SMARCC1 -- Yes Enhancers H3K4me1, intron 14 (fetal heart)
(HUVEC, H3K4me3, aorta and H3K27ac, fetal heart) H3K9ac (HUVEC and
heart tissue group) rs6770663 -- KCNAB1 6 -- -- -- -- H3K4me1
intron 1 (HUVEC and aorta) Proteinuria rs339947 -- 73 kb 5' 4 USF1
-- -- Repressed -- from DNAH5 polycomb 130 kb 5' (HUVEC) from TRIO
rs408130 -- No data -- -- -- -- -- rs418173 -- 60 kb 5' 5 -- -- --
-- -- from DNAH5 rs429023 TRIO in glomerulus 140 kb 5' 5 EBF1 -- --
-- -- (NES = 2.1, p = 0.039) from TRIO rs12482855 -- 4.7 kb No data
-- -- -- -- H3K4me1 from RIPK4 5' (fetal kidney) Composite toxicity
rs11662763 EPB41L3 in glomerulus 33 kb 3' No data -- -- -- -- --
(NES = 22.8, p = 0.0055) from TTMA
[0159] For Table 14, SNPs in bold are the selected SNPs from our
study and the SNPs not in bold are SNPs in LD with them. Expression
quantitative trait loci (eQTL) information was retrieved from the
GTEx v7 and NephQTL. The RegulomeDB score represents the evidence
that a variant has a regulatory function (1-strong evidence, 6-weak
evidence). Data from Genome Browser, RegulomeDB and/or HaploReg v4
includes computational and experimental data from ENCODE and
Roadmap Epigenomics Consortium. Only ChIP-seq and transcription
binding motifs from experimental data are reported. Only DNaseI
sensitivity region, chromatin state and histone markers for
relevant cell lines (HUVEC or heart tissue group) are reported.
Composite toxicity is defined as the occurrence of either
proteinuria or hypertension or both. NES: normalized effect
size.
[0160] In addition to TRIO, RIPK4 is also another putative new gene
for proteinuria. RIPK4 (selected by rs12482855, 4.7 kb 5') encodes
a protein kinase that interacts with PKC.delta., which is directly
involved in renal damage by inducing apoptosis in podocytes and
also in tubular cells. Finally, IL17F codes for interleukin-17F
(IL-17F) and was selected by the gene based analysis. Using
induced-nephrotoxic nephritis mouse model, IL-17F-deficient mice
showed less severe nephritis, with lower albuminuria and better
renal function, compared with wild-type mice. IL17F was the second
most significant gene in our gene-based analysis after C1D, the
biology of which cannot be reconciled with kidney damage by
bevacizumab. Two less common variants (rs1413920 and rs763780, that
did not pass the QC MAF<0.05 in SNP-based analysis) are driven
the effect of IL17F in gene-based analysis. The G allele of
rs1413920 (A>G, p=1.80.times.10-7, ( =2.24, MAF 0.01-0.03) and
of rs763780 (A>G, p=1.14.times.10-4, ( =1.41, MAF 0.05)
decreased the risk of proteinuria. rs1413920 is intergenic located
1.3 kb 3' from MCM3 and 20 kb from IL17F (FIG. 8), with strong
transcription in HUVEC. rs763780 is a non-synonymous variant that
alters the histidine to arginine at amino acid 161 (H161R). The A
allele (161H) has been associated with an anti-angiogenic effect by
inhibition the angiogenesis in human endothelial cells. Inversely,
patients who present the G allele (161R) could have an enhanced
angiogenesis in these cells and be more prone to bevacizumab
effect. The G allele was already associated with a better overall
survival in CALGB 80303.
[0161] This study also proposes ASPH (selected by rs2350620,
intronic, and by the gene-based 30 analysis) as novel candidate of
bevacizumab-induced hypertension. ASPH encodes the junction protein
that forms a quaternary complex with triadin, calsequestrin and the
ryanodine receptor (RyR), involved in the release of Ca.sup.2+ from
endoplasmic/sarcoplasmic reticulum. rs2350620 reduced the risk of
bevacizumab-induced hypertension and has variants in complete LD
that are located in regions of DNaseI sensitivity, chromatin state
enhancers and enriched for histone modifications in HUVEC and cells
from heart tissue group. The G allele of rs2350620 is likely to
bind FOXA1 protein (in T-47D), which acts as a transcriptional
activator. Therefore, rs2350620 might increase ASPH expression,
which might contribute to confer a reduced risk of hypertension.
Moreover, one of the variants in LD (rs35026059, .fwdarw.T) has 2c
Regulome DB score (Table 14), due to strong evidence of binding of
the T allele to CTCF motif, but not in relevant cell lines. CTCF
can acts as a transcriptional activator or repressor and
insulator.
[0162] Because genetic variants might have pleiotropic effects and
hypertension and proteinuria share a common pathophysiology, we
have also investigated the occurrence of the composite toxicity.
rs11662763 had the same direction of effect in three trials,
increasing the risk of either proteinuria or hypertension or both.
rs1166276 is 33 kb from TTMA, also known as TMEM200C. rs11662763
was shown to be an eQTL for EPB41L3 in the glomerulus, increasing
its expression (Table 14). EPB41L3 was also identified as a novel
locus for kidney function, after an intronic SNP (rs9962915) was
associated with lower glomerular filtration rate in a GWAS
meta-analysis of more than 100,000 subjects. Furthermore, SLC25A24
was also selected by the gene-based analysis of the composite
toxicity. SLC25A24 encodes a carrier protein that transports ATP-Mg
exchanging it for phosphate.
[0163] The three most significant variants associated with
composite toxicity (rs17084411, rs1927869 and rs17084371) had a
p-value of 4.24-7.24.times.10.sup.-8 but only in CALGB 40503.
[0164] In conclusion, as a result of this study, DNAH5, TRIO,
RIPK4, IL17F, ASPH, TTMA, EPB41L3 and SLC25A24, as well as all the
top significant SNPs and genes associated with grade.gtoreq.3
toxicities are proposed as new genes involved in
bevacizumab-induced proteinuria and hypertension. Despite many
years of use of bevacizumab, proteinuria and hypertension still
represent an obstacle to full delivery of effective therapy, and
pose a threat for patients and their quality of life. Because these
toxicities are also shared by many other anti-angiogenesis drugs,
the availability of these results in the public domain will
incentivize the application of these findings to other drugs with a
similar mechanism of action.
Example 2
[0165] Sorafenib is an orally administered multikinase inhibitor
that targets multiple tyrosine kinases involved in angiogenesis,
apoptosis, and tumor cell proliferation, including the vascular
endothelial growth factor receptor 2 (VEGFR2). It is approved by
the U.S. Food and Drug Administration (FDA) for the treatment of
several tumors, including metastatic renal cell carcinoma (mRCC),
advanced hepatocellular carcinoma and differentiated thyroid
cancer. The clear-cell histology of RCC is characterized by
overexpression of VEGF, which interacts with VEGFR2 to stimulate
tumor angiogenesis. In addition to sorafenib, sunitinib, pazopanib,
axitinib, lenvatinib and cabozantinib are also approved for mRCC,
sharing the same mechanisms of VEGF-pathway inhibition.
[0166] Hypertension is one of the most frequent toxicities induced
by sorafenib. A meta-analysis showed a prevalence of
sorafenib-induced all-grade and grade.gtoreq.3 hypertension of
19.1% and 4.3%, respectively. Patients with mRCC experience higher
rates of hypertension when compared to other tumor types
(all-grade: 24.9% vs 15.7%, high-grade: 8.6% versus 1.8%). Similar
to sorafenib, other VEGF-pathway inhibitors can also induce
hypertension, including bevacizumab, sunitinib and pazopanib.
[0167] The objective of this study was to identify and validate
genetic biomarkers that are predictive of VEGF-pathway
inhibitor-induced hypertension using a two-step,
discovery-validation approach. Sorafenib-treated patients from the
phase 3 Treatment Approaches in Renal Cancer Global Evaluation
Trial (TARGET) were used as the discovery set, while a genome-wide
association study (GWAS) of bevacizumab-treated patients from four
Cancer and Leukemia Group B (CALGB, now Alliance for Clinical
Trials in Oncology, Alliance) studies was used as a validation
set.
[0168] TARGET was a double-blind, randomized, placebo-controlled
phase III trial of patients with mRCC treated with 400 mg sorafenib
orally twice daily or placebo. Hypertension was recorded according
to CTCAE version 3.0. This analysis was conducted in patients who
received at least one cycle (28 days) of sorafenib treatment. DNA
was obtained from the peripheral blood of 140 patients treated with
sorafenib. A total of 1,536 SNPs in 56 candidate genes were
genotyped using the Illumina GoldenGate assay. Genes were selected
based upon biological function, including genes involved in
VEGF-pathway signaling, genes from additional signaling pathways
targeted by sorafenib, genes associated with perycite survival,
sorafenib disposition and toxicity, and genes associated with RCC
prognosis/pathogenesis or general cancer prognosis. SNPs were
excluded if the genotype call rate was <97.5% and were selected
based upon a MAF>0.05 in Europeans from the 1,000 Genomes
Project, and other criteria.
[0169] A flowchart showing the quality control for the study is
provided as FIG. 9A. After quality control, a total of 973 of the
1,536 initial SNPs were used in this study. Tests for association
between SNPs and grade.gtoreq.2 hypertension were performed in the
sorafenib arm by calculating the odds ratio (OR) from a logistic
regression analysis, where grade.gtoreq.2 hypertension was the
binary outcome and SNPs were the independent variables, under an
additive model. Age and gender were used as covariates. A
p-value.ltoreq.0.01 was used as a feature selection to identify
SNPs for replication in the validation set.
[0170] For the validation cohort, the association between SNPs and
hypertension was tested in genetic European patients treated with
bevacizumab. A GWAS of four randomized phase III clinical trials
from the CALGB/Alliance (CALGB 80303, 40503, 90401, and 40502) was
used as the validation set. The details of the individual studies
are described in Table 15. Patient eligibility, characteristics,
stratifications and treatments can be found in the individual
publications for all four trials. Blood pressure was measured on
day 1 of each cycle in all four trials (and on day 15 in CALGB
80303), and hypertension was recorded according to CTCAE version
3.0. Bevacizumab-induced hypertension was defined as the occurrence
of grade.gtoreq.2 hypertension after the start of treatment. DNA
was obtained from peripheral blood. The genotyping platforms used
in each study are described in Table 15. A cause-specific Cox
model, where the outcome was defined as the pair of time event and
the censoring indicator (defined as the time from the first
administration of bevacizumab to the first incidence of the
toxicity of interest, or other treatment-terminating events,
whichever occurred first, under a competing risk model), was fitted
to obtain the estimate of the SNP effect on hypertension in each
individual study. The analyses were powered against an additive
genetic model. The inverse variance formula was used to combine the
SNP effect in each study to obtain the estimate (.beta.) of the
SNP-hypertension association. Age and sex were added as covariates
in the model. The exponential function of .beta. was used to
calculate OR.
[0171] The SNPs from the TARGET study (discovery set) associated
with grade.gtoreq.2 hypertension (p-value.ltoreq.0.01) were tested
in the CALGB GWAS (validation set). If the variant was not
genotyped in the validation set, a SNP in high linkage
disequilibrium (LD, R.sup.2>0.8, Europeans in the 1,000 Genomes
Project) according to LDlink, was selected for testing. In the
validation set, SNPs with a p-value.ltoreq.0.01 for association and
the same direction of effect (increased or reduced risk) were
considered as validated.
[0172] Functional annotation of SNPs was performed using the SCAN
database. LDlink was used for analyses of LD. RegulomeDB and
SNPnexus were used for functional inference. The Genotype-Tissue
Expression project (GTEx v7) was used for expression quantitative
trait loci (eQTL) analysis. atSNP was also used to quantify impact
of SNPs on transcription factor binding.
[0173] A total of 140 mRCC patients treated with sorafenib in
TARGET were included in this study. The characteristics of the
patients, and the prevalence of grade.gtoreq.2 hypertension are
shown in Table 15. Variants rs444904 (G>A, MAF 0.14) and
rs1346563 (C>T, MAF 0.30) were both selected for testing in the
validation set based on p<0.01 (Table 16). Both variants were
associated with an increased risk of grade.gtoreq.2 hypertension
(OR=3.88, 95%, CI 1.54-9.81, p=0.0057 and OR=3.50, 95%, CI
1.48-8.24, p=0.0064, respectively) (Table 16).
TABLE-US-00015 TABLE 15 Patient characteristics and trials.
Discovery set Validation set (n = 1,041) (n = 140) CALGB 80303
CALGB 40503 CALGB 90401 CALGB 40502 Trial TARGET n = 154 n = 105 n
= 316 n = 466 Hypertension (n, %) Grade .gtoreq.2 12 (8.6) 26
(16.9) 53 (50.5) 47 (15.0) 143 (30.7) Grade 3 5 (3.6) 19 (12.3) 29
(27.6) 22 (7.0) 50 (10.7) Age-Mean (SD) 59.6 (9.8) 64.1 (10.2) 68.4
(8.3) 56.9 (11.7) 57.2 (10.7) Gender Male 105 90 0 105 0 Female 35
64 316 0 466 Cancer type Advanced and Advanced Hormone Metastatic
Recurrent or metastatic renal pancreatic cancer receptor-positive
castration-resistant metastatic breast cell carcinoma
advanced-stage prostate cancer cancer breast cancer Treatment
Sorafenib 400 mg Gemcitabine 1,000 Letrozole 2.5 mg Docetaxel 75
mg/m.sup.2 Paclitaxel 90 mg/m.sup.2 orally twice daily mg/m.sup.2
on days 1, orally/day plus in combination with or nab-paclitaxel
administered in 6- 8, and 15 plus either placebo or prednisone 5 mg
150 mg/m.sup.2 or week cycles for either placebo or bevacizumab 15
orally on day 1 plus ixabepilone 16 the first 24 weeks bevacizumab
10 mg/kg every 21 either placebo or mg/m.sup.2 on days 1, 8, and in
8-week mg/kg on days 1 days bevacizumab 15 and 15 plus cycles
thereafter and 15 mg/kg every 21 days bevacizumab 10 mg/kg on days
1 and 15 Genotyping Illumina Illumina Illumina Human Illumina
Illumina Human platform GoldenGate HumanHap550- OmniExpressExome-8
HumanHap610- OmniExpressExome-8 Quad Quad
TABLE-US-00016 TABLE 16 SNPs associated with sorafenib-induced
hypertension in the TARGET study. The SNPs in bold are the ones
tested in the validation (p .ltoreq. 0.01). Results are shown for
associations with p-value < 0.05, adjusted for age and gender.
Chr: chromosome, NA: Intergenic SNP, MAF: minor allele frequency,
OR: odds ratio, SNP: single nucleotide polymorphism. 3' Flanking
Base p- SNP Chr Gene Feature 5' Flanking gene gene change MAF OR
(95% CI) value rs444904 17 PIK3R5 Intron PIK3R6 LOC100129978 G >
A 0.14 3.88 (1.54-9.81) 0.0057 rs1346563 16 ADAMTS18 Intron VN2R10P
NUDT7 C > T 0.30 3.50 (1.48-8.24) 0.0064 rs2330951 7 EGFR Intron
LOC643168 LOC100133256 A > C 0.23 4.23 (1.78-10.05) 0.0118
rs11125039 2 PRKCE Intron SRBD1 EPAS1 A > G 0.24 3.51
(1.49-8.25) 0.0122 rs56367980 7 EGFR Intron LOC643168 LOC100133256
G > A 0.12 3.33 (1.27-8.76) 0.0188 rs16917099 10 NA NA RTKN2
ZNF365 T > C 0.13 3.58 (1.37-9.35) 0.0207 rs2740761 7 EGFR
Intron LOC643168 LOC100130121 C > T 0.18 3.46 (1.39-8.59) 0.0222
rs3754565 2 PRKCE Intron SRBD1 EPAS1 G > T 0.11 4.07
(1.48-11.19) 0.0222 rs3754566 2 PRKCE Intron SRBD1 EPAS1 G > A
0.11 4.07 (1.48-11.19) 0.0222 rs4596024 2 PRKCE Intron SRBD1 EPAS1
A > G 0.11 4.07 (1.48-11.19) 0.0222 rs251312 5 NA NA NLN ERBB2IP
C > T 0.48 3.26 (1.31-8.14) 0.0223 rs12366035 11 VEGFB reference
DNAJC4 FKBP2 C > T 0.34 3.09 (1.31-7.24) 0.0227 rs35539903 4 KDR
Intron LOC100132311 LOC100128865 A > G 0.15 3.44 (1.33-8.90)
0.0254 rs35597368 4 PDGFRA Missense LOC442108 KIT T > C 0.10
3.69 (1.32-10.29) 0.0256 rs3797102 5 FLT4 Intron SCGB3A1 OR2AI1P T
> C 0.42 2.78 (1.17-6.59) 0.0262 rs3804158 4 NUDT6/ FGF2 Intron/
UTR-3 BBS12 SPATA5 A > G 0.43 0.30 (0.11-0.84) 0.0272 rs45492196
1 PIK3C2B Reference PPP1R15B LOC100130573 G > A 0.05 3.68
(1.07-12.60) 0.0279 rs7187665 16 WWOX Intron LOC100131126 LOC645947
T > C 0.45 0.34 (0.13-0.89) 0.0298 rs11980616 7 GNAIl Intron
LOC100128030 GNAT3 A > G 0.13 3.24 (1.24-8.50) 0.0322 rs659441 3
NA NA UMPS ITGB5 G > C 0.40 0.28 (0.11-0.73) 0.0327 rs315498 17
NA NA LOC100130112 C17orf79 T > C 0.33 0.24 (0.07-0.84) 0.0335
rs41348645 4 FGF2/ NUDT6 UTR-3/ Intron BBS12 SPATA5 G > A 0.41
0.31 (0.11-0.87) 0.0350 rs3950680 11 PIK3C2A Intron RPS13 LOC732199
G > A 0.36 2.61 (1.12-6.06) 0.0385 rs6743202 2 TGFA Intron
LOC100128042 ADD2 A > T 0.32 0.27 (0.08-0.93) 0.0421 rs11644322
16 WWOX Intron LOC645947 LOC729251 C > T 0.21 2.66 (1.10-6.42)
0.0431 rs446086 2 TGFA Intron LOC100128042 ADD2 C > A 0.23 0.19
(0.04-0.84) 0.0431 rs3804452 6 MAPK14 utr-3 SLC26A8 MAPK13 C > T
0.11 2.86 (1.04-7.84) 0.0439 rs2293348 7 EGFR Intron LOC100133256
LOC100130121 G > A 0.36 0.32 (0.11-0.96) 0.0466 rs16947173 16
WWOX Intron LOC100131126 LOC645947 A > G 0.20 0.12 (0.02-0.93)
0.0480 rs11644207 16 WWOX Intron LOC100131126 LOC645947 T > G
0.24 0.22 (0.05-0.64) 0.0484 rs8193040 6 NA NA IL17A LOC730141 T
> G 0.48 0.39 (0.16-0.97) 0.0499
[0174] A total of 1,041 patients treated with bevacizumab in the
CALGB trials were included in this study. Because neither rs444904
nor rs1346563 were genotyped on the GWAS platforms, rs427554
(G>A, MAF 0.10-0.11 in complete LD R.sup.2=1.0 with rs444904)
and rs4888628 (A>G, MAF 0.26-0.29, LD R.sup.2=0.96 with
rs1346563) were used as proxies. Variant rs427554 was associated
with an increased risk of hypertension (p=0.008, 13=0.33, OR=1.39,
CI 1.09-1.78) (FIG. 10). This result is consistent with the
discovery set, where the frequencies of patients without
hypertension with the AA and GA genotypes are 2.3% and 20.3%,
respectively, versus 25.0% and 16.7% in patients with hypertension
(FIG. 9B).
[0175] Table 17 provides bioinformatic analyses for both rs444904
and rs427554. There is evidence in GTex that rs444904 and rs427554
are both eQTLs for PIK3R5 in whole blood, with the A allele of both
variants associated with decreased gene expression. DNase 1
hypersensitivity peaks indicate that both rs444904 and rs427554 are
located in areas of open chromatin, thus permitting selective
binding of transcription factors, while ChIP-seq revealed that the
two SNPs are potential loci for binding with putative transcription
factors. RegulomeDB, utilizing data from the ENCODE-motif database,
indicates that rs427554 is located in the binding motif for the SP1
transcription factor. Additional data from the JASPAR database
(using atSNP) predicts preferential binding of SP1 to the G allele
of rs444904 rather than the A allele (p=0.01 for the G allele, and
p=0.30 for the A allele). The majority of non-coding variation
scores provided by SNPnexus shows a higher evidence of regulatory
function of rs427554 compared to rs444904 (Table 17).
TABLE-US-00017 TABLE 17 Bioinformatic analysis of rs444904 and
rs427554. The RegulomeDB score represents the evidence that a SNP
has a regulatory function (1-strong evidence, 6-weak evidence).
SNPnexus non-coding variation scoring predicts functional impact of
non-coding SNPs using 8 non-coding SNP scoring algorithms. Higher
scores in CADD (range 0-99), FitCons (range 0-1), Eigen (range
0-1), FATHMM (range 0-1), GWAVA (3 scores, range 0-1), funSeq2
(range 0-5) ReMM (range 0-1) mean that the SNP is most likely to be
functional/deleterious, while a lower score in DeepSEA (range 0-1)
means that the SNP is most likely to be functional/deleterious.
eQTL: expression quantitative trait loci, NES: normalized effect
size RegulomeDB/ ENCODE SNP DNase I SNPnexus non-coding variation
rankings (Regulome eQTL Sensitivity CA- Fit- EIG- FAT- GWA- Deep-
Fun- Re- DB score) (GTEx) ChIP-seq region Motif DD Cons EN HMM VA
SEA Seq2 MM rs444904 Whole blood POLR2A, RELA, EP300, Yes -- 0.775
0.102 0.176 0.110 0.38/ 0.035 1.560 0.019 (4) (p = TCF12, EBF1,
IKZF2, IKZF1, 0.48/ 2.7 .times. 10.sup.-12, TAF1, MEF2C, TBL1XR1,
0.44 NES = -0.16) FOXM1, ZNF687, TARDBP, NFATC1, MTA3, ZEB1, MTA2,
YY1, CBFB, RUNX3, GATAD2B, CHD2, ELF1, BCLAF1, ETS1, ARNT, EGR1,
IRF4, PBX3, TCF7, NFIC, BHLHE40, POU2F2, CREM, BCL3, MEF2A, ETV6.
rs427554 Whole blood POLR2A, GATA1, SPI1, Yes SP1 2.641 0.102 0.614
0.141 0.45/ 0.118 1.560 0.122 (2c) (p = IKZF1, IKZF2, ZBTB40, 0.53/
9.4 .times. 10.sup.-13, TCF7, MLLT1, EP300, ELF1, 0.41 NES = -0.17)
LEF1, PAX5, BCLAF1, DPF2, TRIM22, RELB, ARNT, MXI1, FOXM1, NR2F1,
SMARCA5, ZMYM3, SP1, MEF2A, RBM25, TARDBP, NBN, TAF1, BHLHE40,
BCL3, RUNX3, KLF5, BATF, ETV6, NFATC3, ZFHX2, ZBTB33, ETS1, IRF4,
NKRF, VEZF1, ZBED1, SKIL, ZNF207, CREM, ETV1, CBFB, HDGF, TBX21,
ARID3A, BCL11A, POU2F2, EGR1, COMMD3- BMI1, BMI1, ATF2, REST, RFX1,
MAZ, EBF1, ZNF143, EED.
[0176] The results of the study identified a common intronic SNP
(rs444904) located in PIK3R5 that increased the risk of
grade.gtoreq.2 hypertension in patients treated with the
VEGF-pathway inhibitors sorafenib and bevacizumab.
[0177] Bioinformatic analyses of rs444904 and rs427554 in PIK3R5
showed that both SNPs are located in a region that binds numerous
transcription factors, indicating a potential regulatory role for
each SNP in gene expression (Table 17). rs427554 is located within
a binding motif for SP1, and rs444904 may alter an SP1 binding
motif as described above. Considering that both SNPs are in
complete LD with each other, it is plausible to suggest that the G
allele of both variants may increase binding of the SP1
transcription factor to DNA.
[0178] In embodiments, the data provided herein proposes a novel
mechanism through which rs444904 and rs427554 regulate the
expression of PIK3R5 and mediate hypertension induced by sorafenib,
bevacizumab, or other VEGF pathway inhibitors. The G allele of both
SNPs allows the binding of SP1, which, by inhibiting the action of
DNMT, activates PIK3R5 transcription (FIG. 12). Conversely, the A
allele decreases the binding of the SP1, which allows DNA
methylation by DNMT, downregulating PIK3R5 transcription, (FIGS. 11
and 12).
[0179] The validation of rs444904 in an external dataset utilizing
a different VEGF-pathway inhibitor (such as bevacizumab) provides
additional evidence of clinical applicability of biomarkers of
hypertension induced by different anti-angiogenic drugs. Taken
together, the study provides evidence for rs444904 in PIK3R5 as a
biomarker of hypertension induced by sorafenib, bevacizumab, and
other VEGF pathway inhibitors. Common genetic variants in PIK3R5,
rs444904 and rs427554 in complete LD with each other
(R.sup.2=1.00), increased the risk of sorafenib and
bevacizumab-induced hypertension in two independent datasets, and
may be used as predictor biomarkers of hypertension induced by the
whole class of VEGF-pathway inhibitors
Example 3
[0180] Two SNPs associated with grade.gtoreq.2 hypertension in
Example 1 above, rs2350620 and rs6770663, were evaluated for
replication in European ancestry patients from ECOG-ACRIN E5103. A
summary of the cohort evaluated is provided as Table 18.
TABLE-US-00018 TABLE 18 GWAS patients of European ancestry treated
with bevacizumab from ECOG- ACRIN E5103. ECOG Eastern Cooperative
Oncology Group, ACRIN American College of Radiology Imaging
Network, SBP systolic blood pressure, SD standard deviation.
Validation set ECOG-5103 SBP .gtoreq. 160 mm Hg Grade .gtoreq.3 n =
582 n = 564 Hypertension* (n, %) 195 (33.5) 177 (37.8) Age-Mean
(SD) 55.3 55.1 Gender Male 0 0 Female 582 564 Cancer type Breast
cancer Treatment Doxorubicin (60 mg/m.sup.2) and cyclophosphamide
(600 mg/m.sup.2) for four cycles, followed by 12 weeks (4 cycles)
of weekly paclitaxel. Concurrently to chemotherapy, patients
received either placebo (arm A) or bevacizumab 10-15 mg/kg (arms B
and C). Patients in arm C continued bevacizuma monotherapy (15
mg/kg every 3 weeks) for an additional 10 cycles. Genotype platform
Illumina Human Omni1-Quad and Illumina Human OmniExpress
[0181] Variants rs2350620 and rs6770663 were selected because they
were among the top ten SNPs that also had a concordant effect in
three out of four studies (p-value<0.05 for each study) (Table
5). FIG. 13 shows the cumulative incidence of grade.gtoreq.2
hypertension for rs2350620 and rs6770663. Table 19 shows the
results of the SNPs tested for replication. The G allele of
rs6770663 (A>G, MAF 0.08-0.09) was associated with a higher risk
of SBP>160 mm Hg (odds ratio, OR=1.76, p-value=0.005) in
ECOG-ACRIN E5103 (Table 20), similar to the increased risk of
grade.gtoreq.2 hypertension in our study (.beta.=0.57,
p-value=4.79.times.10.sup.-6) (Table 5).
TABLE-US-00019 TABLE 19 Top two SNPs ranked by unadjusted p-value
with a concordant effect in three out of four studies for grade
.gtoreq.2 hypertension in the CALGB trials tested for replication
in the ECOG-ACRIN E5103 GWAS. ECOG Eastern Cooperative Oncology
Group, ACRIN American College of Radiology Imaging Network, MAF
minor allele frequency, SBP systolic blood pressure, OR odds ratio.
The row in bold is the one SNP that replicated in ECOG-ACRIN E5103.
MAF ECOG- Risk ACRIN OR p-value SNP allele E5103 (SBP .gtoreq. 160
mm Hg) (SBP .gtoreq. 160 mm Hg) Grade .gtoreq.2 rs2350620 T 0.33
1.14 0.235 rs6770663 G 0.10 1.76 0.005
TABLE-US-00020 TABLE 20 Frequency of rs6770663 AA, GA, and GG
genotypes associated with bevacizumab-induced hypertension in
ECOG-ACRIN E5103. ECOG Eastern Cooperative Oncology Group, ACRIN
American College of Radiology Imaging Network, SBP systolic blood
pressure. rs6770663 AA GA GG SBP .gtoreq. 160 147 (75.4%) 45
(23.1%) 3 (1.5%) (cases, n = 195) No hypertension 327 (84.5%) 59
(15.2%) 1 (0.3%) (controls, n = 387)
[0182] Table 21 shows published studies that reported associations
between 37 SNPs and bevacizumab-induced hypertension with
p-value<0.05. Out of 37 SNPs, 26 of them had either the same SNP
or a proxy for it. Three out of the 26 SNPs were associated with
composite toxicity (but with neither hypertension nor proteinuria)
with the same direction of the effect (either reduced or increased
risk) in the herein provided study (Table 22).
TABLE-US-00021 TABLE 21 SNPs previously associated with
bevacizumab-induced hypertension in the literature. VEGF vascular
endothelial growth factor, NO nitric oxide, CTCAE Common Toxicity
Criteria for Adverse Events, FOLFIRI 5-fluorouracil (5-FU) +
irinotecan, FOLFOX 5-FU + oxaliplatin, XELOX capecitabine +
oxaliplatin, SBP systolic blood pressure. Not on platform means
that either the reported SNP or SNPs in high LD (R.sup.2 > 0.8)
were not on the genotype platforms in our study. Number of SNP
bevacizumab selection Genes Hypertension Concomitant treated
Clinical trial Reference method associated phenotype treatment
patients discovery set Li et al. Sequencing HSP90AB1 Grade
.gtoreq.3 FOLFIRI or 61 Discovery: (2018) of PRKCA (CTCAE FOLFOX6
CALGB 174 CACNA1C v3.0) 80405 candidate HSP90AB1 Validation: genes
CCL2 CALGB (VEGF PDE3B 40502, signaling, NOSIP CALGB endothelial
FLT4 90401, and cell biology, ECOG-5103 NO signaling or essential
hypertension genes) Frey et al. 103 SNPs in GRK4 Grade .gtoreq.1
Cisplatin and 114 6 clinical (2017) 11 genes KLKB1 (CTCAE taxotere/
trials at (VEGF and VEGF v3.0) doxorubicin, and Memorial essential
WNK1 cyclophosphamide/ Sloan- hypertension paclitaxel and Kettering
associated cisplatin/ erlotinib/ Cancer genes) letrozole/ S-1 and
Center oxaliplatin Berger et al. 12 SNPs in FIP200 Grade .gtoreq.2
FOLFIRI 219 TRIBE (2017) 8 ATG13 (CTCAE autophagy- v3.0) related
genes Gampenrieder 10 SNPs in VEGFA Grade .gtoreq.3 Capecitabine or
163 Retrospective et al. (2017) VEGFA, taxane selection of FLT1,
patients from STK39, hospital EDN1, and records UMOD Sibertin- 10
SNPs in VEGFA Grade .gtoreq.1 5-FU based 89 Retrospective Blanc et
al. VEGFA, (CTCAE chemotherapy (the selection of (2015) FLT1, KDR,
v3.0) majority FOLFIRI) patients from and HIF1A hospital records
Lambrechts et 236 SNPs in EGLN3 Grade .gtoreq.1 XELOX or 807
NO16966, al. (2014) 14 genes KDR (CTCAE FOLFOX4/ AViTA, (VEGF and
EPAS1 v3.0) gemcitabine and AVAiL, essential FLT1 erlotinib/
cisplatin AVOREN, hypertension FLT4 and gemcitabine/ AVADO,
associated EGF interferon .alpha.-2a/ AVAGAST genes). WNK1
docetaxel/ capecitabine and cisplatin Morita et al. 5 SNPs in VEGFA
Grade .gtoreq.2 FOLFIRI or 60 Retrospective (2013) VEGFA (CTCAE
FOLFOX6 or selection of v4.0) 5-FU or patients from XELOX hospital
records Etienne- 5 SNPs in VEGFA Grade .gtoreq.1 Paclitaxel or 137
ATHENA Grimaldi et VEGFA (CTCAE docetaxel or al. (2011) v3.0)
navelbine Schneider et 7 SNPs in VEGFA Grade .gtoreq.3 Paclitaxel
180 ECOG-2100 al. (2008) VEGF and (CTCAE KDR v2.0)
TABLE-US-00022 TABLE 22 Previously reported variants associated
with bevacizumab-induced hypertension. The associations with a
p-value <0.05 and same direction of effect for grade .gtoreq.2
composite toxicity in our study are shown. Proxy rs9900205 was
genotyped only in CALGB 90401, and proxy rs833070 was genotyped
only in CALGB 40503. SNP Base (literature) Region change Risk
(literature) Risk (our study) rs59189065 PRKCA G > A Increased
grade .gtoreq.3 Proxy rs9900205 (R.sup.2 = 0.82) intronic
hypertension in CALGB Increased grade .gtoreq.2 composite 80405
toxicity in CALGB 90401 (.beta. = 0.49, p = 0.02) rs9381299 3 kb 5'
from T > C Increased grade .gtoreq.3 Increased grade .gtoreq.2
composite HSP90AB1 hypertension in CALGB toxicity in CALGB 80303,
40503, and 10 kb 3' 80405 (discovery set), and 90401 (.beta. =
0.39, p = 0.02) from of and in CALGB 40502 SLC29A1 and ECOG 5103
(validation sets), but not in CALGB 90401 rs833061 5' of VEGFA C
.gtoreq. T Decreased grade .gtoreq.2 (7) Proxy rs833070 (R.sup.2 =
0.98) and grade .gtoreq.3 (6) Decreased grade .gtoreq.2 composite
hypertension toxicity in CALGB 40503 (.beta. = 0.44, p = 0.03)
[0183] Taken together, the studies provided herein were the largest
genome-wide analysis of bevacizumab-induced hypertension and
proteinuria, which included 1,041 cancer patients from four
randomized phase III clinical trials. The large sample size,
randomized design, and standardized collection of the phenotypic
and genotypic data facilitated the testing of genetic associations
of drug response in patients. The use of genomic data from
different studies allowed the evaluation of concordance of the
effect, increasing the validity of these associations. For the
first time, a variant in KCNAB1 for bevacizumab-induced
hypertension was identified from an independent, external dataset
provided and provided evidence of clinical actionability.
Accordingly, the results of the study provide a critical
identification of SNPs and gene variants that can be used to
provide improved and safer methods for treating patients with
bevacizumab or other VEGF pathway inhibitor drugs. For example,
patients indicated for or being treated with an inhibitor of the
VEGF pathway (e.g., bevacizumab) can be assessed for the presence
of rs6770663, and treatment modified accordingly (e.g.,
pre-treatment with anti-hypertensive supportive therapy and/or dose
modification and/or delivery of an alternative to the VEGF pathway
inhibitor).
[0184] Importantly, the study established replication of the effect
of rs6770663 (A>G), intronic in KCNAB1, as a variant for the
risk of hypertension. Similar to the CALGB studies where it
increased the risk of grade.gtoreq.2 hypertension, rs6770663 was
also associated with a higher risk of SBP.gtoreq.160 mm Hg in
ECOG-ACRIN E5103 (Table 14, FIG. 13).
[0185] In addition to KCNAB1, the studies provided herein
identified other new candidate genes associated with VEGF pathway
inhibitor-induced toxicity. This selection was based upon the
strength and probability of the associations, the biological
plausibility of gene, and the bioinformatic prediction of the SNP
effect on the gene function or expression. Under this set of
evaluations, ASPH was also identified as a new gene for VEGF
pathway inhibitor-induced hypertension, based upon the signal of
intronic rs2350620 (FIG. 13). Variant rs2350620 (A>G) reduced
the risk of bevacizumab-induced hypertension and has SNPs in
complete LD located in regulatory regions in HUVEC, aorta and the
heart (Table 14). Also, rs2350620 is in complete LD with a deletion
in ASPH (rs35026059, T>-), and CTCF can act as an insulator of
the expression of ASPH because of binding in the presence the T
allele (Table 14).
[0186] Despite many years of use of bevacizumab, hypertension and
proteinuria still represent an obstacle to full delivery of
effective therapy and pose a threat for patients and their quality
of life. The studies provided herein identified rs6770663 in KCNAB1
as a novel marker of bevacizumab-induced hypertension that can be
used to guide decisions on the risk assessment of patients treated
with any VEGF pathway inhibitor. Other novel candidate genes are
ASPH for hypertension, and TRIO and DNAH5 for proteinuria. Because
these toxicities are also shared by many other antiangiogenesis
drugs, the availability of these results in the public domain will
expedite their translation into clinical application for other
drugs with a similar mechanism of action.
[0187] In summary, the results of the studies provided herein
showed that variant rs6770663 in KCNAB1 was associated with an
increased the risk of hypertension (p=4.79.times.10.sup.-6). This
was validated in ECOG-ACRIN E5103 (p=0.005). Variant rs2350620 in
APSH was associated with a decreased risk of hypertension
(p=1.44.times.10.sup.-6) and rs339947 (between DNAH5 and TRIO) was
associated with an increased risk of proteinuria
(p=7.66.times.10.sup.-8). Three variants previously associated with
bevacizumab-induced hypertension were associated with composite
toxicity (but not hypertension) with the same direction of effect
in our study. To the knowledge of the inventors, this was the
largest GWAS of bevacizumab-treated patients from randomized
trials. The study has identified new genes involved in
bevacizumab-induced hypertension and proteinuria. Genetic variation
in KCNAB1 can be regarded to as a new validated biomarker to
predict the risk of bevacizumab-induced hypertension.
[0188] All literature and similar materials cited in this
application, including but not limited to, patents, patent
applications, articles, books, treatises, and internet web pages
are expressly incorporated by reference in their entirety for any
purpose. Unless defined otherwise, all technical and scientific
terms used herein have the same meaning as is commonly understood
by one of ordinary skill in the art to which the various
embodiments described herein belongs. When definitions of terms in
incorporated references appear to differ from the definitions
provided in the present teachings, the definition provided in the
present teachings shall control.
[0189] Various modifications and variations of the described
compositions, methods, and uses of the technology will be apparent
to those skilled in the art without departing from the scope and
spirit of the technology as described. Although the technology has
been described in connection with specific exemplary embodiments,
it should be understood that the disclosure as claimed should not
be unduly limited to such specific embodiments. Indeed, various
modifications of the described modes for carrying out the
disclosure that are obvious to those skilled in pharmacology,
biochemistry, medical science, or related fields are intended to be
within the scope of the following claims.
REFERENCES
[0190] 1. F Ferrara N, Adamis A P. Ten years of anti-vascular
endothelial growth factor therapy. Nat Rev Drug Discov 2016, 15,
385-403. [0191] 2. Ellis L M, Kirkpatrick P. Bevacizumab. Nat Rev
Drug Discov 2005, 3, 995-996. [0192] 3. Zhu X, Wu S, Dahut W L,
Parikh C R. Risks of Proteinuria and Hypertension With Bevacizumab,
an Antibody Against Vascular Endothelial Growth Factor: Systematic
Review and Meta-Analysis. Am J Kidney Dis 2007, 49, 186-19. [0193]
4. Izzedine H, Ederhy S, Goldwasser F, Soria J C, Milano G, Cohen A
et al. Management of hypertension in angiogenesis inhibitor-treated
patients. Ann Oncol 2009, 20, 807-815. [0194] 5. Hurwitz H,
Fehrenbacher L, Novotny W, Cartwright T, Hainsworth J, Heim W et
al. Bevacizumab plus Irinotecan, Fluorouracil, and Leucovorin for
Metastatic Colorectal Cancer. N Engl J Med 2004, 350, 2335-2342.
[0195] 6. Syrigos K N, Karapanagiotou E, Boura P, Manegold C,
Harrington K. Bevacizumab-induced hypertension: pathogenesis and
management. Biodrugs 2011, 25, 159-169. [0196] 7. Schneider B P,
Wang M, Radovich M, Sledge G W, Badve S, Thor A et al. Association
of vascular endothelial growth factor and vascular endothelial
growth factor receptor-2 genetic polymorphisms with outcome in a
trial of paclitaxel compared with paclitaxel plus bevacizumab in
advanced breast cancer: ECOG 2100. J Chn Oncol 2008, 28, 4672-4678.
[0197] 8. Jain L, Sissung T M, Danesi R, Kohn E C, Dahut W L,
Kummar S et al. Hypertension and hand-foot skin reactions related
to VEGFR2 genotype and improved clinical outcome following
bevacizumab and sorafenib. J Exp. Chn Cancer Res 2010, 29, 95.
[0198] 9. Morita S, Uehara K, Nakayama G, Shibata T, Oguri T,
Inada-Inoue M et al. Association between bevacizumab-related
hypertension and vascular endothelial growth factor (VEGF) gene
polymorphisms in Japanese patients with metastatic colorectal
cancer. Cancer Chemother Pharmacol 2013, 71, 405-411. [0199] 10.
Lambrechts D, Moisse M, Delmar P, Miles D W, Leighl N, Escudier B
et al. Genetic markers of bevacizumab-induced hypertension.
Angiogenesis 2014, 17, 685-694. [0200] 11. Sibertin-Blanc C,
Mancini J, Fabre A, Lagarde A, Del Grande J, Levy N et al. Vascular
Endothelial Growth Factor A c. 237C T polymorphism is associated
with bevacizumab efficacy and related hypertension in metastatic
colorectal cancer. Dig Liver Dis 2015, 47, 331-337. [0201] 12.
Gampenrieder S P, Hufnagl C, Brechelmancher S, Huemer F, Hackl H,
Rinnerthaler G et al. Endothelin-1 genetic polymorphism as
predictive marker for bevacizumab in metastatic breast cancer.
Pharmacogenomics J 2017, 17, 344-350. [0202] 13. Etienne-Grimaldi M
C, Formento P, Degeorges A, Pierga J Y, Delva R, Pivot X et al.
Prospective analysis of the impact of VEGF-A gene polymorphisms on
the pharmacodynamics of bevacizumab-based therapy in metastatic
breast cancer patients. Br J Clin Pharmacol 2011, 71, 921-928.
[0203] 14. Frey M K, Dao F, Olvera N, Konner J A, Dickler M N,
Levine D A et al. Genetic predisposition to bevacizumab-induced
hypertension. Gynecol Oncol 2017, 147, 621-625. [0204] 15.
Schneider B P, Li L, Shen F, Miller K D, Radovich M, O'Neill A et
al. Genetic variant predicts bevacizumab-induced hypertension in
ECOG-5103 and ECOG-2100. Br J Cancer 2014, 111, 1241-1248. [0205]
16. Li M, Kroetz D L. Bevacizumab-induced hypertension: Clinical
presentation and molecular understanding. Pharmacol Ther 2018, 182,
152-160. [0206] 17. Kindler H L, Niedzwiecki D, Hollis D,
Sutherland S, Schrag D, Hurwitz H B et al. Gemcitabine plus
bevacizumab compared with gemcitabine plus placebo in patients with
advanced pancreatic cancer: Phase III trial of the Cancer and
Leukemia Group B (CALGB 80303). J Clin Oncol 2010, 28, 3617-3622.
[0207] 18. Dickler M N, Barry W T, Cirrincione C T, Ellis M J,
Moynahan M E, Innocenti F et al. Phase III trial evaluating
letrozole as first-line endocrine therapy with or without
bevacizumab for the treatment of postmenopausal women with hormone
receptor-positive advanced-stage breast cancer: CALGB 40503
(Alliance). J Clin Oncol 2016, 34, 2602-2609. [0208] 19. Kelly W K,
Halabi S, Carducci M, George D, Mahoney J F Stadler W M et al.
Randomized, double-blind, placebo-controlled phase III trial
comparing docetaxel and prednisone with or without bevacizumab in
men with metastatic castration-resistant prostate cancer: CALGB
90401. J Chn Oncol 2012, 30, 1534-1540 [0209] 20. Rugo H S, Barry W
T, Moreno-Aspitia A, Lyss A P, Cirrincione C, Leung E et al.
Randomized phase III trial of paclitaxel once per week compared
with nanoparticle albumin-bound nab-paclitaxel once per week or
ixabepilone with bevacizumab as first line chemotherapy for locally
recurrent or metastatic breast cancer: CALGB 40502/NCCTG N063H
(Alliance). J O M Oncol 2015, 33, 2361-2369. [0210] 21. Innocenti
F, Jiang C, Sibley A B, Denning S, Etheridge A S, Watson D et al.
An initial genetic analysis of gemcitabine-induced high-grade
neutropenia in pancreatic cancer patients in CALGB 80303
(Alliance). Pharmacogenet Genomics 2019, 29, 123-131. [0211] 22.
Innocenti F, Owzar K, Cox N L, Evans P, Kubo M, Zembutsu H et al. A
genome-wide association study of overall survival in pancreatic
cancer patients treated with gemcitabine in CALGB 80303. O M Cancer
Res 2012, 18, 577-584. [0212] 23. Baldwin R M, Owzar K, Zembutsu H,
Chhibber A, Kubo M, Jiang C et al. A genome-wide association study
identifies novel loci for paclitaxel-induced sensory peripheral
neuropathy in CALGB 40101. O M Cancer Res 2012, 18, 5099-5109.
[0213] 24. Rashkin S R, Chua K C, Ho C, Mulkey F, Jiang C,
Mushiroda T et al. A Pharmacogenetic Prediction Model of
Progression-Free Survival in Breast Cancer using Genome-Wide
Genotyping Data from CALGB 40502 (Alliance). Clin Pharmacol Ther
2019, 105, 738-745. [0214] 25. Price A L, Patterson N J, Plenge R
M, Weinblatt M E, Shadick N A, Reich D. Principal components
analysis corrects for stratification in genome-wide association
studies. Nat Genet 2006, 38, 904-909. [0215] 26. European
Bioinformatics Institute,
ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/locusgroups/protein-c-
odinggene.txt. Accessed on May 7 (2018). [0216] 27. Carlson M,
Maintainer B P. TxDb.Hsapiens.UCSC.hg18.knownGene: Annotation
package for TxDb object(s). R package version 3.2.2. (2015). [0217]
28. Carlson M, Maintainer B P. TxDb.Hsapiens.UCSC.hg19.knownGene:
Annotation package for TxDb object(s). R package version 3.2.2.
(2015). [0218] 29. Yi C, Sibley A, Owzar K. snplist: Tools to
Create Gene Sets. R package version 0.18.1. (2017). [0219] 30. Wu M
C, Lee S, Cai T, Li Y, Boehnke M, Lin X. Rare-variant association
testing for sequencing data with the sequence kernel association
test. Am J Hum Genet 2011, 89, 8293. [0220] 31. Tang Z Z, Lin D Y.
MASS: Meta-analysis of score statistics for sequencing studies.
Bioinformatics 2013, 29, 1803-1805. [0221] 32. Zhang W, Gamazon E
R, Zhang X, Konkashbaev A, Liu C, Szilagyi K L et al. SCAN
database: Facilitating integrative analyses of cytosine
modification and expression QTL. Database 2015, 27, bav025. [0222]
33. Machiela M J, Chanock S J. LDlink: A web-based application for
exploring population-specific haplotype structure and linking
correlated alleles of possible functional variants. Bioinformatics
2015, 31, 3555-3557. [0223] 34. James Kent W, Sugnet C W, Furey T
S, Roskin K M, Pringle T H, Zahler A M et al. The human genome
browser at UCSC. Genome Res 2002, 12, 996-1006. [0224] 35. Boyle A
P, Hong E L, Hariharan M, Cheng Y, Schaub M A, Kasowski M et al.
Annotation of functional variation in personal genomes using
RegulomeDB. Genome Res 2012, 22, 1790-1797. [0225] 36. Ward L D,
Kellis M. HaploReg: A resource for exploring chromatin states,
conservation, and regulatory motif alterations within sets of
genetically linked variants. Nucleic Acids Res 2012, 40, D930-D934.
[0226] 37. GTEx Consortium. The Genotype-Tissue Expression (GTEx)
pilot analysis: Multitissue gene regulation in humans. Science
2015, 8, 648-660. [0227] 38. Gillies C E, Putler R, Menon R, Otto
E, Yasutake Kl, Nair V et al. An eQTL Landscape of Kidney Tissue in
Human Nephrotic Syndrome. Am J Hum Genet 2018, 103, 232-244. [0228]
39. Leigh M W, Pittman J E, Carson J L, Ferkol T W, Dell S D, Davis
S D et al. Clinical and genetic aspects of primary ciliary
dyskinesia/kartagener syndrome. Genet Med 2009, 11, 473-87. [0229]
40. Maier M, Baldwin C, Aoudjit L, Takano T. The role of trio, a
rho guanine nucleotide exchange factor, in glomerular podocytes.
Int J Mol Sci 2018, 19, E479. [0230] 41. Robins R, Baldwin C,
Aoudjit L, Cote J F, Gupta I R, Takano T. Racl activation in
podocytes induces the spectrum of nephrotic syndrome. Kidney Int
2017, 92, 349-364. [0231] 42. Yu H, Suleiman H, Kim A H, Miner J H,
Dani A, Shaw A S et al. Racl Activation in Podocytes Induces Rapid
Foot Process Effacement and Proteinuria. Mol Cell Biol 2013, 33,
4755-4764. [0232] 43. Li X, Pabla N, Wei Q, Dong G, Messing R O,
Wang C Y et al. PKC-6 Promotes Renal Tubular Cell Apoptosis
Associated with Proteinuria. J Am Soc Nephrol 2010, 21, 1115-1124.
[0233] 44. Riedel J H, Paust H J, Krohn S, Turner J E, Kluger M A,
Steinmetz O M et al. IL-17F Promotes Tissue Injury in Autoimmune
Kidney Diseases. J Am Soc Nephrol 2016, 27, 3666-3677. [0234] 45.
Starnes T, Robertson M J, Sledge G, Kelich S, Nakshatri H,
Broxmeyer H E et al. Cutting Edge: IL-17F, a Novel Cytokine
Selectively Expressed in Activated T Cells and Monocytes, Regulates
Angiogenesis and Endothelial Cell Cytokine Production. J Immunol
2001, 167, 4137-4140. [0235] 46. Oyadomari S, Araki E, Mori M.
Endoplasmic reticulum stress-mediated apoptosis in pancreatic
.beta.-cells. Apoptosis 2002, 7, 335-345. [0236] 47. Bucci M,
Gratton J P, Rudic R D, Acevedo L, Roviezzo F, Cirino G et al. In
vivo delivery of the caveolin-1 scaffolding domain inhibits nitric
oxide synthesis and reduces inflammation. Nat Med 2000, 6,
1362-1367. [0237] 48. 49. Yang Y A, Zhao J C, Fong K W, Kim J, Li
S, Song C et al. FOXA1 potentiates lineage-specific enhancer
activation through modulating TET1 expression and function. Nucleic
Acids Res 2016, 44, 8153-8164. [0238] 49. Holwerda S J, de Laat W.
CTCF: The protein, the binding partners, the binding sites and
their chromatin loops. Philos Trans R Soc Lond B Biol Sci 2013,
368, 20120369. [0239] 50. Gorski M, Most P J V, Teumer A, Chu A Y,
Li M, Mijatovic V et al. Corrigendum: 1000 Genomes-based
meta-analysis identifies 10 novel loci for kidney function. Sci
Rep. 2017, 7, 46835. [0240] 51. De Francesco E M, Maggiolini M,
Tanowitz H B, Sotgia F, Lisanti M P. Targeting hypoxic cancer stem
cells (CSCs) with Doxycycline: Implications for optimizing
anti-angiogenic therapy. Oncotarget 2017, 8, 56126-56142. [0241]
52. Calbet J A L. Chronic hypoxia increases blood pressure and
noradrenaline spillover in healthy humans. J Physiol 2003, 551,
379-386. [0242] 53. Gueler F, Shushakova N, Mengel M, Hueper K,
Chen R, Liu X et al. A novel therapy to attenuate acute kidney
injury and ischemic allograft damage after allogenic kidney
transplantation in mice. PLoS One 2015, 10, e0115709. [0243] 54.
Chen R, Liliental J E, Kowalski P E, Lu Q, Cohen S N. Regulation of
transcription of hypoxia-inducible factor-la (HIF-1 a) by heat
shock factors HSF2 and HSF4. Oncogene 2011, 30, 2570-2580. [0244]
55. Huang C Y, Pal P Y, Kuo C H, Ho T J, Lin J Y, Lin D Y et al.
p53-mediated miR-18 repression activates HSF2 for IGF-IIR-dependent
myocyte hypertrophy in hypertension induced heart failure. Cell
Death Dis 2017, 8, e2990. [0245] 56. Berger M D, Lenz H J. The
safety of monoclonal antibodies for treatment of colorectal cancer.
Expert Opin Drug Saf 2016, 15, 799-808. [0246] 57. An M M, Zou Z,
Shen H, Liu P, Chen M L, Cao Y B et al. Incidence and risk of
significantly raised blood pressure in cancer patients treated with
bevacizumab: An updated meta-analysis. Eur J Clin Pharmacol 2010,
66, 813-821. [0247] 58. Schneider B P, Li L, Radovich M, Shen F,
Miller K D, Flockhart D A et al. Genome-Wide Association Studies
for Taxane-Induced Peripheral Neuropathy in ECOG-5103 and
ECOG-1199. Clin Cancer Res 2015, 21, 5082-5091. [0248] 59. Han J Y,
Shin E S, Lee Y S, Ghang H Y, Kim S Y, Hwang J A et al. A
genome-wide association study for irinotecan-related severe
toxicities in patients with advanced non-small-cell lung cancer.
Pharmacogenomics J 2013, 13, 417-422. [0249] 60. Tesa ova P, Tesa
V. Proteinuria and hypertension in patients treated with inhibitors
of the VEGF signalling pathway--incidence, mechanisms and
management. Folia Biol (Praha) 2013, 59, 15-25. [0250] 61. D J et
al. Genetic Variants of VEGFA and FLT4 Are Determinants of Survival
in Renal Cell Carcinoma Patients Treated with Sorafenib. Cancer Res
2019, 79, 231-41. [0251] 62. GTEx Consortium. The Genotype-Tissue
Expression (GTEx) pilot analysis: Multitissue gene regulation in
humans. Science 2015, 8, 648-60. [0252] 63. Machiela M J et al.
LDlink: A web-based application for exploring population-specific
haplotype structure and linking correlated alleles of possible
functional variants. Bioinformatics 2015, 31, 3555-7. [0253] 64.
Angiogenisis Inhibitor.
https://www.wikiwand.com/en/Angiogenesis_inhibitor. Accessed on
Aug. 7 (2019). [0254] 65. James Kent W et al. The human genome
browser at UCSC. Genome Res 2002, 12, 996-1006. [0255] 66. Blattler
A et al. Cross-talk between site-specific transcription factors and
DNA methylation states. J Biol Chem 2013 288, 34287-94. [0256] 67.
Mir O, Coriat R, Cabanes L et al. An Observational Study of
Bevacizumab-Induced Hypertension as a Clinical Biomarker of
Antitumor Activity. Oncologist 2011; 16: 1325-1332. [0257] 68.
Hertz D L, Owzar K, Lessans S et al. Pharmacogenetic discovery in
CALGB (alliance) 90401 and mechanistic validation of a VAC14
polymorphism that increases risk of docetaxel-induced neuropathy.
Clin Cancer Res 2016; 22: 4890-4900. [0258] 69. Thul P J, Akesson
L, Wiking M et al. A subcellular map of the human proteome. Science
2017; 356: pii:eaa13321. [0259] 70. Gonzalez C, Baez-Nieto D,
Valencia I et al. K+ channels: Function-structural overview. Compr
Physiol 2012; 2: 2087-2149. [0260] 71. Tipparaju S M, Liu S Q,
Barski O A et al. NADPH binding to .beta.-subunit regulates
inactivation of voltage-gated K+ channels. Biochem Biophys Res
Commun 2007; 359: 267-276. [0261] 72. Sobey C G. Potassium channel
function in vascular disease. Arterioscler Thromb Vasc Biol 2001;
21: 28-38. [0262] 73. Martens J R, Gelband C H. Alterations in rat
interlobar artery membrane potential and K+ channels in genetic and
nongenetic hypertension. Circ Res 1996; 79: 295-301. [0263] 74.
Banerjee B, Peiris D N, Koo S H et al. Genomic imbalances in key
ion channel genes and telomere shortening in sudden cardiac death
victims. Cytogenet Genome Res 2009; 122: 350-355. [0264] 75. Tur J,
Chapalamadugu K C, Padawer T et al. Deletion of Kv.beta.1.1 subunit
leads to electrical and haemodynamic changes causing cardiac
hypertrophy in female murine hearts. Exp Physiol 2016; 101:
494-508.
[0265] 76. Kulakovskiy I V, Vorontsov I E, Yevshin I S et al.
HOCOMOCO: Towards a complete collection of transcription factor
binding models for human and mouse via large-scale ChIP-Seq
analysis. Nucleic Acids Res 2018; 46: D252-D259. [0266] 77. Niu Z,
Li A, Zhang S X et al. Serum response factor micromanaging
cardiogenesis. Curr Opin Cell Biol 2007; 19: 618-627. [0267] 78.
Rouillard A D, Gundersen G W, Fernandez N F et al. The harmonizome:
a collection of processed datasets gathered to serve and mine
knowledge about genes and proteins. Database (Oxford) 2016; pii:
baw100. [0268] 79. Sherry S T, Ward M H, Kholodov M et al. dbSNP:
the NCBI database of genetic variation. Nucleic Acids Res 2001; 29:
308-311. [0269] 80. Reddish F N, Miller C L, Gorkhali R et al.
Calcium dynamics mediated by the endoplasmic/sarcoplasmic reticulum
and related diseases. Int J Mol Sci 2017; pii: E1024. [0270] 81.
West A G, Gaszner M, Felsenfeld G. Insulators: Many functions, many
mechanisms. Genes Dev 2002; 16: 271-288. [0271] 82. Brahmer J R,
Dahlberg S E, Gray R J et al. Sex differences in outcome with
bevacizumab therapy: Analysis of patients with advanced-stage
non-small cell lung cancer treated with or without bevacizumab in
combination with paclitaxel and carboplatin in the eastern
cooperative oncology group trial 459. J Thorac Oncol 2011; 6:
1031-08. [0272] 83. Li M, Mulkey F, Jiang C et al. Identification
of a genomic region between SLC29A1 and HsP90AB1 associated with
risk of bevacizumab-induced hypertension: CALGB 80405 (Alliance).
Clin Cancer Res 2018; 24: 4734-4744 [0273] 84. Wilhelm S M, Carter
C, Tang L Y, et al. BAY 43-9006 exhibits broad spectrum oral
antitumor activity and targets the RAF/MEK/ERK pathway and receptor
tyrosine kinases involved in tumor progression and angiogenesis.
Cancer Res 2004; 64:7099-109.
https://doi.org/10.1158/0008-5472.CAN-04-1443. [0274] 85. Nexavar
(Sorafenib).
<https://www.accessdata.fda.gov/drugsatfda_docs/label/2018/021923s0201-
b1.pdf>. Accessed 16 May 2020. [0275] 86. Costa U, Drabkin H A.
Renal Cell Carcinoma: New Developments in Molecular Biology and
Potential for Targeted Therapies. Oncologist 2007; 12:1404-15.
https://doi.org/10.1634/theoncologist.12-12-1404. [0276] 87. Li Y,
Li S, Zhu Y, et al. Incidence and risk of sorafenib-induced
hypertension: A systematic review and meta-analysis. J Clin
Hypertens 2014; 16:177-85. https://doi.org/10.1111/jch.12273.
[0277] 88. Qi W X, Lin F, Sun Y J, et al. Incidence and risk of
hypertension with pazopanib in patients with cancer: A
meta-analysis. Cancer Chemother Pharmacol 2013; 71:431-9.
https://doi.org/10.1007/s00280-012-2025-5. [0278] 89. Zhu X,
Stergiopoulos K, Wu S. Risk of hypertension and renal dysfunction
with an angiogenesis inhibitor sunitinib: Systematic review and
meta-analysis. Acta Oncol (Madr) 2009; 8:9-17.
https://doi.org/10.1080/02841860802314720. [0279] 90. Maitland M L,
Kasza K E, Karrison T, et al. Ambulatory monitoring detects
sorafenib-induced blood pressure elevations on the first day of
treatment. Clin Cancer Res 2009; 15:6250-7.
https://doi.org/10.1158/1078-0432.CCR-09-0058. [0280] 91. Karar J,
Maity A. PI3K/AKT/mTOR Pathway in Angiogenesis. Front Mol Neurosci
2011; 4:51. https://doi.org/10.3389/fnmol.2011.00051. [0281] 92.
Horowitz J R, Rivard A, Van Der Zee R, et al. Vascular endothelial
growth factor/vascular permeability factor produces nitric
oxide-dependent hypotension: Evidence for a maintenance role in
quiescent adult endothelium. Arterioscler Thromb Vasc Biol 1997;
17:2793-800. https://doi.org/10.1161/01.ATV.17.11.2793. [0282] 93.
Rini B I. Quantifying hypertension in patients with cancer treated
with sorafenib. Lancet Oncol 2008; 9:86-7.
https://doi.org/10.1016/S1470-2045(08)70009-3. [0283] 94. Qin C,
Cao Q, Li P, et al. The influence of genetic variants of sorafenib
on clinical outcomes and toxic effects in patients with advanced
renal cell carcinoma. Sci Rep 2016; 6:20089.
https://doi.org/10.1038/srep20089. [0284] 95. Robinson E S, Khankin
E V, Karumanchi S A, et al. Hypertension induced by vascular
endothelial growth factor signaling pathway inhibition: Mechanisms
and potential use as a biomarker. Semin Nephrol 2010; 30:591-601.
https://doi.org/10.1016/j.semnephrol.2010.09.007. [0285] 96.
Escudier B, Eisen T, Stadler W M, et al. Sorafenib in advanced
clear-cell renal-cell carcinoma. N Engl J Med 2007; 356:125-34.
https://doi.org/10.1056/NEJMoa060655. [0286] 97. Crona D J, Skol A
D, Leppanen V M, et al. Genetic variants of VEGFA and FLT4 are
determinants of survival in renal cell carcinoma patients treated
with sorafenib. Cancer Res 2019; 79:231-41.
https://doi.org/10.1158/0008-5472.CAN-18-1089. [0287] 98.
Quintanilha J C F, Wang J, Sibley A B et al. Bevacizumab-induced
hypertension and proteinuria: A genome-wide analysis of more than
1,000 patients. Submitted to J Natl Cancer Inst. [0288] 99. Baldwin
R M, Owzar K, Zembutsu H, et al. A genome-wide association study
identifies novel loci for paclitaxel-induced sensory peripheral
neuropathy in CALGB 40101. Clin Cancer Res 2012; 18:5099-109.
https://doi.org/10.1158/1078-0432.CCR-12-1590. [0289] 100. Dayem
Ullah A Z, Oscanoa J, Wang J, et al. SNPnexus: Assessing the
functional relevance of genetic variation to facilitate the promise
of precision medicine. Nucleic Acids Res 2018; 46:W109-W113.
https://doi.org/10.1093/nar/gky399. [0290] 101. Ardlie K G, DeLuca
D S, Segre A V., Sullivan T J, Young T R, Gelfand E T, et al. The
Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene
regulation in humans. Science 2015; 8:648-60.
https://doi.org/10.1126/science.1262110. [0291] 102. Zuo C, Shin S,
Kele S. AtSNP: Transcription factor binding affinity testing for
regulatory SNP detection. Bioinformatics 2015; 31:3353-5.
https://doi.org/10.1093/bioinformatics/btv328. [0292] 103. Zhong H,
Chiles K, Feldser D, et al. Modulation of hypoxia-inducible factor
1.alpha. expression by the epidermal growth
factor/phosphatidylinositol 3-kinase/PTEN/AKT/FRAP pathway in human
prostate cancer cells: Implications for tumor angiogenesis and
therapeutics. Cancer Res 2000; 60:1541-1545. [0293] 104. Forsythe J
A, Jiang B H, Iyer N V, et al. Activation of vascular endothelial
growth factor gene transcription by hypoxia-inducible factor 1. Mol
Cell Biol 1996; 16:4604-4613.
https://doi.org/10.1128/mcb.16.9.4604. [0294] 105. Shymanets A,
Prajwal, Bucher K, et al. P87 and p101 subunits are distinct
regulators determining class I B phosphoinositide 3-kinase (PI3K)
specificity. J Biol Chem 2013; 288:31059-68.
https://doi.org/10.1074/jbc.M113.508234. [0295] 106. Serban D, Leng
J, Cheresh D. H-ras regulates angiogenesis and vascular
permeability by activation of distinct downstream effectors. Circ
Res 2008; 102:1350-8.
https://doi.org/10.1161/CIRCRESAHA.107.169664.
* * * * *
References