U.S. patent application number 10/457639 was filed with the patent office on 2004-12-09 for detection of high grade dysplasia in cervical cells.
Invention is credited to King, Walter, Morrison, Larry E., Seelig, Steven A., Sokolova, Irina A..
Application Number | 20040248107 10/457639 |
Document ID | / |
Family ID | 33490368 |
Filed Date | 2004-12-09 |
United States Patent
Application |
20040248107 |
Kind Code |
A1 |
Sokolova, Irina A. ; et
al. |
December 9, 2004 |
Detection of high grade dysplasia in cervical cells
Abstract
Methods of using probes and probe sets for the detection of high
grade dysplasia and carcinoma in cervical cells are described.
Methods of the invention include hybridizing one or more
chromosomal probes to a biological sample obtained from a subject
and detecting the hybridization pattern of the chromosomal probes
to the sample to determine whether the subject has high grade
dysplasia or carcinoma. Methods of the invention also include
preliminary screening the cells for a marker associated with a risk
for cancer.
Inventors: |
Sokolova, Irina A.; (Villa
Park, IL) ; King, Walter; (Wheaton, IL) ;
Morrison, Larry E.; (Glenn Ellyn, IL) ; Seelig,
Steven A.; (Elmhurst, IL) |
Correspondence
Address: |
VYSIS, INC
LAW DEPARTMENT
3100 WOODCREEK DRIVE
DOWNERS GROVE
IL
60515
|
Family ID: |
33490368 |
Appl. No.: |
10/457639 |
Filed: |
June 9, 2003 |
Current U.S.
Class: |
435/6.14 |
Current CPC
Class: |
C12Q 2600/112 20130101;
C12Q 1/6886 20130101 |
Class at
Publication: |
435/006 |
International
Class: |
C12Q 001/68 |
Claims
What is claimed is:
1. A method for screening for high grade dysplasia in a subject,
the method comprising: (a) obtaining a biological sample from the
subject; (b) contacting a set of one or more chromosomal probes
able to selectively detect high grade dysplasia in the biological
sample under conditions sufficient to enable hybridization of the
probes to chromosomes in the sample if any; and (c) detecting the
hybridization pattern of the chromosomal probes to the biological
sample to determine whether the subject has high grade
dysplasia.
2. The method of claim 1, wherein the biological sample comprises a
biopsy.
3. The method of claim 1, wherein the biological sample comprises a
cervical smear or cervical scrape sample.
4. The method of claim 1, wherein the chromosomal probes are
fluorescently labeled.
5. The method of claim 1, wherein the set of one or more
chromosomal probes is characterized by a vector value of less then
about 60.
6. The method of claim 1, wherein the set of one or more
chromosomal probes is characterized by a vector value of less than
about 40.
7. The method of claim 1, wherein the set of one or more
chromosomal probes is characterized by a vector value of less than
about 30.
8. The method of claim 1, wherein the set of one or more
chromosomal probes comprises a probe selected from the group of
probes for the specific loci 3q26 and 8q24.
9. The method of claim 1, wherein the set of one or more
chromosomal probes comprises probes for the specific loci 3q26 and
8q24.
10. The method of claim 1, wherein the set of one or more
chromosomal probes comprises probes for the specific loci 8q24,
3q26, Xp22 and CEP 15.
11. The method of claim 1, wherein the set of one or more
chromosomal probes comprises probes for the specific loci 8q24,
20q13, Xp22 and CEP 15.
12. The method of claim 1, wherein the set of one or more
chromosomal probes comprises probes for the specific loci 3p21, 3
p14, 3q26 and CEP 3.
13. The method of claim 1 wherein cells from the biological sample
are prescreened for a marker associated with risk for cancer.
14. The method of claim 1 wherein cells from the biological sample
are prescreened for infection by HPV.
15. The method of claim 14 wherein the sample is screened for
infection by one or more of the high risk HPV types 16, 18, 31, 33,
35, 42, 52, 55 and 58.
16. The method of claim 1 wherein cells from the biological sample
are prescreened for the presence of a cell cycle protein or a cell
proliferation marker.
17. The method of claim 16 wherein the cell cycle protein is p16 or
Cyclin E.
18. The method of claim 16 wherein the cell proliferation marker is
the protein Ki67 or the protein PCNA.
Description
BACKGROUND OF THE INVENTION
[0001] Cervical cancer remains one of the most common cancer types
affecting women worldwide. The biological pathway to cervical
carcinoma begins with normal intraepithelial cells, and develops
through low and then high grade dysplasia before malignancy
obtains. Cytologists mark the passage to malignancy as progression
from normal epithelial cells to atypical squamous cells of
undetermined significance (ASCUS) to Low Grade squamous
intraepithelial lesions (LSIL) and then high grade squamous
intraepithelial lesions (HSIL) before carcinoma in situ and finally
malignancy result. Histologists mark the progression from normal
cells to various grades of cervical intraepithelial neoplasia (CIN
I, II and III), then to carcinoma in situ and finally malignancy.
CIN I is considered low grade dysplasia comparable to LSIL. CIN II
and III are considered high grade dysplasia comparable to HSIL.
[0002] The current standard of care includes regular cytologic
testing with a Papanicolau (Pap) smear to identify abnormalities as
indicating dysplasia or carcinoma in patient cells. When high grade
dysplasia is detected and confirmed by histological examination,
the transformation zone of the patient's cervix is removed
immediately by loop excision or cone biopsy. More radical
procedures are required when carcinoma is detected. At the same
time, however, the progression from normal to malignancy is not
strict and the presence of low grade dysplasia does not necessarily
indicate that the patient will progress to high grade dysplasia or
malignancy. Significantly, the negative predictive value of
cytologic methods (e.g., Pap smears) for detecting high grade
dysplasia is poor. Thus, low grade dysplasia may be misdiagnosed as
high grade, thereby subjecting the patient to unwarranted treatment
and high grade dysplasia may be misdiagnosed as low grade
dysplasia, thereby delaying appropriate treatment. Accordingly,
there is a need for a diagnostic method that will accurately
distinguish between low and high grade dysplasia.
[0003] Patient specimens typically comprise many thousands of cells
for evaluation. Diagnosis based on evaluation of individual cells
can be enormously time consuming and tedious for technicians to
perform due to the large number of cells that are required for
evaluation. Thus, there is a need for a means to simplify a cell
evaluation method.
[0004] Others have noted that genetic abnormalities (e.g., changes
in chromosome regions or changes in ploidy levels) accompany the
progression from normal cells to cervical malignancy. See, e.g.,
U.S. Pat. No. 5,919,624 to Ried, et al. Ried et al. noted that
chromosomal abnormalities can be used to classify the progression
of dysplastic cervical cells in late stages, e.g., from noninvasive
cervical to invasive cervical carcinoma. Still others have
demonstrated that cervical cancer is associated with infection by
certain human papilloma viruses (HPV) types, particularly HPV types
16, 18, 31, 33, 35 and 42. See, e.g., Lazo, Brit. J. Cancer, (1999)
80(12), 2008-2018. Additionally, many cell cycle proteins such as
p16 and Cyclin E and cell proliferation markers such as the
proteins Ki67 and PCNA are also known to be highly active in
neoplastic cells. Thus, cells containing abnormal amounts of these
markers have been suggested as good candidates for cells that may
progress to malignancy. However, Applicants are not aware that
anyone has demonstrated that any chromosomal abnormality with or
without the presence of another marker can be used to distinguish
low from high grade dysplasia or has combined such a diagnostic
method with the known association of HPV and cervical cancer.
SUMMARY OF THE INVENTION
[0005] The invention is based on the discovery that certain
chromosomal abnormalities can be used to selectively detect high
grade cervical intraepithelial neoplasia (CIN II and CIN III) and
malignant carcinoma in cervical biopsy and Pap smear specimens
without detecting low grade cervical intraepithelial neoplasia. The
method can detect high grade cervical intraepithelial neoplasia
(CIN II and CIN III) and malignant carcinoma at high sensitivity
and specificity levels, i.e. about 95% each. The invention is based
on the use of in situ hybridization technology where labeled
nucleic acid probes are allowed to hybridize to cervical samples.
Preferably, fluorescent in situ hybridization (FISH) is used and
the nucleic acid probes are DNA probes that are fluorescently
labeled. The hybridization results are then correlated with a
clinical diagnosis of high grade cervical intraepithelial neoplasia
(CIN II and CIN III) and malignant carcinoma.
[0006] The method of the invention utilizes a set of one or more
probes demonstrating a vector value for discriminating between CIN
I and CIN II of about 60 or less, wherein the vector value is
calculated by
Vector=[(100-specificity).sup.2+(100-sensitivity).sup.2].sup.1/2.
Preferred probes for use in the method are probes to the genetic
loci 3q26, 8q24, 20q13, Xp22 and 3p21, and probes that enumerate
chromosomes 3 and 15. Multiple probe sets comprising two, three or
more probes can be used in the method of the invention. Preferred
multiprobe sets comprise probes to the genetic loci 8q24 and 3q26;
3q26, 8q24, Xp22, and chromosome 15; 8q24, 20q13, Xp22 and
chromosome 15; and the genetic loci 3p21, 3 p14, 3q26 and
chromosome 3. Probes useful in the invention can be incorporated
into kits packaged, for example, with other reagents useful in
carrying out the methods of the invention. Such kits can comprise
one or more probes useful with the invention.
[0007] Probes can be selected using the steps of: (a) providing a
first plurality of chromosomal probes (by plurality is meant one or
more probes); (b) determining the ability of each of the first
plurality of probes to distinguish high (CIN II, CIN III and
carcinoma) from low (CIN I) grade dysplasia in a cervical specimen;
and (c) selecting the probe or probes within the first plurality of
probes that distinguish high from low grade dysplasia to yield a
second plurality of probes, wherein the second plurality of probes
identifies the high grade dysplasia specimens as compared to low
grade specimens at a vector value of less than about 60. Preferred
probes can be selected by additionally: (d) determining the ability
of a combination of probes selected from the second plurality of
probes to distinguish the high grade from low grade specimens; and
(e) selecting a combination of probes that identifies the high
grade specimen as compared to the low grade specimen with a vector
value of less than about 40. More preferred embodiments can be
selected based on lower vector values (e.g., a vector value of less
than about 30).
[0008] The biological sample used with the invention can contain a
cervical biopsy specimen or a cervical smear such as a Pap smear or
a ThinPrep.RTM. sample prepared by the method of Cytyc Corp.,
Boxborough, Mass. The probes used with the invention comprise
detectably labeled nucleic acid-based probes, such as
deoxyribonucleic acid (DNA) probes or protein nucleic acid (PNA)
probes, which are designed/selected to hybridize to the specific
designed chromosomal target. Fluorescent labels such as are used in
fluorescent in situ hybridization are preferred but other
detectable labels commonly used in hybridization techniques, e.g.,
enzymatic, chromogenic and isotopic labels, can also be used.
[0009] In another aspect of the invention, the detection of the
genetic abnormalities is facilitated by adoption of a preliminary
cell screening technique whereby cervical cells are screened first
for the presence of a suitable associated marker, for example, such
as the presence of infection by HPV, e.g., high risk HPV, or
abnormal amounts of cell cycle proteins such as p16 and Cyclin E or
cell proliferation markers such as Ki67 and PCNA. Such screening
can be used to identify more suspicious cells for closer
examination and may allow the time required for specimen evaluation
to be reduced by as much as 5-10 fold. After the suspicious cells
are identified, these suspicious cells are then examined for the
presence of chromosomal abnormalities. The presence of chromosomal
abnormalities identified by use of the probes of the invention in
cells also showing markers of potential malignancy, such as HPV
infection, identifies higher grade CIN or malignancy. Such initial
screening techniques are amenable to automation, enabling greater
simplicity and speed in specimen evaluation.
DETAILED DESCRIPTION OF THE INVENTION
[0010] The invention includes (i) methods of using probes and (ii)
probe sets for the detection of high grade dysplasia and carcinoma
in cervical cells. The methods and probe sets allow for the early
detection of high grade dysplasia in biological samples, such as a
cervical biopsies and smears.
[0011] Chromosomal Probes
[0012] Suitable probes for use in the in situ hybridization methods
utilized with the invention fall into two broad groups: chromosome
enumeration probes, i.e., probes that hybridize to a chromosomal
region, usually a repeat sequence region, and indicate the presence
or absence of an entire chromosome, and locus specific probes,
i.e., probes that hybridize to a specific locus on a chromosome and
detect the presence or absence of a specific locus. Chromosome arm
probes, i.e., probes that hybridize to a chromosomal region and
indicate the presence or absence of an arm of a specific
chromosome, may also be useful. Chromosomal probes and combinations
thereof are chosen for sensitivity and/or specificity when used in
methods of the invention. Probe sets can comprise any number of
probes, e.g., 1, 2, 3, 4 or more probes. The number of probes
useful with the invention is limited only by the user's ability to
detect the probes on an individual basis.
[0013] As is well known in the art, a chromosome enumeration probe
can hybridize to a repetitive sequence, located either near or
removed from a centromere, or can hybridize to a unique sequence
located at any position on a chromosome. For example, a chromosome
enumeration probe can hybridize with repetitive DNA associated with
the centromere of a chromosome. Centromeres of primate chromosomes
contain a complex family of long tandem repeats of DNA comprised of
a monomer repeat length of about 171 base pairs, that are referred
to as alpha-satellite DNA. Non-limiting examples of chromosome
enumeration probes include probes to chromosomes 1, 6, 7, 8, 9, 10,
11, 12, 15, 16, 17, 18 and X. Examples of several specific
chromosome enumeration probes are described in Example 1.
[0014] A locus specific probe hybridizes to a specific,
non-repetitive locus on a chromosome. Non-limiting examples of
locus specific probes include probes to the following loci: 3q26,
8q24, 20q13, Xp22 and 3p21. Some of these loci comprise genes,
e.g., oncogenes and tumor suppressor genes that are altered in some
forms of cervical cancer. Thus, probes that target these genes,
either exons, introns, or regulatory chromosomal sequences of the
genes, can be used in the detection methods described herein.
Examples of target genes include: TERC (3q26); MYC (8q24); STK6
(20q13.2-13.3) and MLH (3p21-p23). Additional examples are
identified in Example 1.
[0015] Probes that hybridize with centromeric DNA and specific
chromosomal loci are available commercially from Vysis, Inc.
(Downers Grove, Ill.) and Molecular Probes, Inc. (Eugene, Oreg.).
Alternatively, probes can be made non-commercially using well known
techniques. Sources of DNA for use in constructing DNA probes
include genomic DNA, cloned DNA sequences such as bacterial
artificial chromosomes (BAC), somatic cell hybrids that contain one
or a part of a human chromosome along with the normal chromosome
complement of the host, and chromosomes purified by flow cytometry
or microdissection. The region of interest can be isolated through
cloning or by site-specific amplification via the polymerase chain
reaction (PCR). See, for example, Nath, et al., Biotechnic
Histochem, 1998, 73 (1): 6-22; Wheeless, et al., Cytometry, 1994,
17:319-327; and U.S. Pat. No. 5,491,224. Synthesized oligomeric DNA
or PNA probes can also be used.
[0016] The size of the chromosomal region detected by the probes
used in the invention can vary, for example, from the alpha
satellite 171 base pair probe sequence noted above to a large
segment of 150,000 bases. For locus-specific probes, that are
directly labeled, it is preferred to use probes of at least 100,000
bases in complexity, and to use unlabeled blocking nucleic acid, as
disclosed in U.S. Pat. No. 5,756,696, herein incorporated by
reference, to avoid non-specific binding of the probe. It is also
possible to use unlabeled, synthesized oligomeric nucleic acid or
protein nucleic acid as the blocking nucleic acid. For targeting a
particular gene locus, it is preferred that the probes span the
entire genomic coding locus of the gene.
[0017] Chromosomal probes can contain any detection moiety that
facilitates the detection of the probe when hybridized to a
chromosome. Effective detection moieties include both direct and
indirect labels as described below.
[0018] Chromosomal probes can be directly labeled with a detectable
label. Examples of detectable labels include fluorophores, i.e.,
organic molecules that fluoresce after absorbing light, and
radioactive isotopes, e.g., .sup.32P, and .sup.3H. Fluorophores can
be directly labeled following covalent attachment to a nucleotide
by incorporating the labeled nucleotide into the probe with
standard techniques such as nick translation, random priming, and
PCR labeling. Alternatively, deoxycytidine nucleotides within the
probe can be transaminated with a linker. The fluoropore can then
be covalently attached to the transaminated deoxycytidine
nucleotides. See, e.g., U.S. Pat. No. 5,491,224 to Bittner, et al.,
which is incorporated herein by reference. Useful probe labeling
techniques are described in Molecular Cytogenetics: Protocols and
Applications, Y.-S. Fan, Ed., Chap. 2, "Labeling Fluorescence In
Situ Hybridization Probes for Genomic Targets", L. Morrison et.
al., p. 21-40, Humana Press, .COPYRGT. 2002 (hereafter cited as
"Morrison 2002"), incorporated herein by reference.
[0019] Examples of fluorophores that can be used in the methods
described herein are: 7-amino-4-methylcoumarin-3-acetic acid
(AMCA), Texas Red.TM. (Molecular Probes, Inc., Eugene, Oreg.);
5-(and-6)-carboxy-X-rhodamine, lissamine rhodamine B,
5-(and-6)-carboxyfluorescein; fluorescein-5-isothiocyanate (FITC);
7-diethylaminocoumarin-3-carboxylic acid,
tetramethylrhodamine-5-(and-6)-isothiocyanate;
5-(and-6)-carboxytetramethylrhodamine;
7-hydroxycoumarin-3-carboxylic acid; 6-[fluorescein
5-(and-6)-carboxamido]hexanoic acid;
N-(4,4-difluoro-5,7-dimethyl-4-bora-3a, 4a
diaza-3-indacenepropionic acid; cosin-5-isothiocyanate;
erythrosine-5-isothiocyanate; 5-(and-6)-carboxyrhodamine 6G; and
Cascade.TM. blue aectylazide (Molecular Probes, Inc., Eugene,
Oreg.).
[0020] When multiple probes are used, flourophores of different
colors can be chosen such that each chromosomal probe in the set
can be distinctly visualized. Preferably the probe panel of the
invention will comprise four separate probes, each labeled with a
separate fluorophore. Use of four probes is preferred because
Applicants believe this provides the best balance between clinical
sensitivity (sensitivity can increase with added probes) and
imaging/detection complexity (complexity can increase with added
probes). It is also within the scope of the invention to use
multiple panels sequentially on the same sample: in this
embodiment, after the first panel is hybridized, the results are
imaged digitally, the sample is destained and then is hybridized
with a second panel.
[0021] Probes can be viewed with a fluorescence microscope and an
appropriate filter for each fluorophore, or by using dual or triple
band-pass filter sets to observe multiple fluorophores. See, e.g.,
U.S. Pat. No. 5,776,688 to Bittner, et al., which is incorporated
herein by reference. Any suitable microscopic imaging method can be
used to visualize the hybridized probes, including automated
digital imaging systems, such as those available from MetaSystems
or Applied Imaging. Alternatively, techniques such as flow
cytometry can be used to examine the hybridization pattern of the
chromosomal probes.
[0022] Probes can also be labeled indirectly, e.g., with biotin or
digoxygenin by means well known in the art. However, secondary
detection molecules or further processing are then required to
visualize the labeled probes. For example, a probe labeled with
biotin can be detected by avidin conjugated to a detectable marker,
e.g., a fluorophore. Additionally, avidin can be conjugated to an
enzymatic marker such as alkaline phosphatase or horseradish
peroxidase. Such enzymatic markers can be detected in standard
calorimetric reactions using a substrate for the enzyme. Substrates
for alkaline phosphatase include
5-bromo-4-chloro-3-indolylphosphate and nitro blue tetrazolium.
Diaminobenzoate can be used as a substrate for horseradish
peroxidase.
[0023] The probes and probe sets useful with the methods of the
invention can be packaged with other reagents into kits to be used
in carrying out the methods of the invention. Useful kits can
comprise one or more probes from the group of probes to the genetic
loci 3q26, 8q24, 20q13, Xp22 and 3p21, and probes that enumerate
chromosomes 3 and 15.
Determining the Presence of High Grade Dysplasia
[0024] Pre-Selection of Cells
[0025] Cell samples can be evaluated preliminarily by a variety of
methods and using a variety of criteria. The probes and methods
described herein are not limited to usage with a particular
screening methodology. One example is the "scanning method" wherein
the observer scans hundreds to thousands of cells for cytologic
abnormalities, e.g., as viewed with a DAPI filter. The number of
cells assessed will depend on the cellularity of the specimen,
which varies from patient to patient. Cytologic abnormalities
commonly but not invariably associated with dysplastic and
neoplastic cells include nuclear enlargement, nuclear irregularity,
and abnormal DAPI staining (frequently mottled and lighter in
color). In the scanning step, the observer preferably focuses the
evaluation of the cells for chromosomal abnormalities (as
demonstrated by FISH) to those cells that also exhibit cytological
abnormalities. In addition, a proportion of the cells that do not
have obvious cytologic abnormalities can be evaluated since
chromosomal abnormalities also occur in the absence of cytologic
abnormalities. This scanning method is described in further detail
in U.S. Pat. No. 6,174,681 to Halling, et al., which is
incorporated herein by reference.
[0026] More preferably, the observer can scan the cells for a
marker associated with cancer. For example, the cells can be
scanned for the presence of an associated marker such as the
presence of HPV or high risk HPV (e.g., one or more of HPV types
16, 18, 31, 33, 35 or 42). Additionally, cells with abnormal
amounts of the cell cycle proteins p16 and Cyclin E or the
proliferation markers Ki67 and PCNA are likely to be suspicious and
good candidates for closer examination. Cells can be scanned for
the presence of these markers using well know methods. Cell
scanning is generally amenable to automation. Automated scanning
permits increased efficiency by permitting assays to be performed
more rapidly and eliminating much of the tedium present in manual
scanning.
[0027] Preparation of Samples
[0028] The presence or absence of high grade dysplasia and
carcinoma can be determined by identifying chromosomal aberration
in the cells. This can be accomplished by in situ hybridization. In
general, in situ hybridization includes the steps of fixing a
biological sample, hybridizing a chromosomal probe to target DNA
contained within the fixed sample, washing to remove
non-specifically bound probe, and detecting the hybridized probe.
The in situ hybridization can also be carried out with the specimen
cells in liquid suspension, followed by detection by flow
cytometry.
[0029] Abnormal cells are characterized by abnormal numbers of
chromosomes within the cells and/or structural alterations within
the cells' chromosomes. Structural alterations can include gains or
losses (e.g., hemizygous or homozygous loss) of a specific
chromosomal region, such as a locus or centromeric region as
indicated in Example 1. Positive test indicators can be developed
accordingly. For example, a cell having one or more chromosomal
gains, i.e., three or more copies of any given chromosome, can be
considered to test positive in the methods described herein. Cells
exhibiting monosomy or nullisomy may also be considered test
positive under certain circumstances.
[0030] A biological sample is a sample that contains cells or
cellular material, e.g., cells or material derived from the uterine
cervix of the uterus. Examples of cervical specimens include
cervical biopsies, smears, scrapes and the like. Typically, cells
are harvested from a biological sample and prepared using
techniques well known in the art. Numerous methods are available
for collecting cervical cells for evaluation. For example, cells
from the ectocervix and endocervix/transformation zone are
collected using well-known devices such as endocervical brushes (or
"brooms") or wooden and plastic spatulas. Conventional smears are
prepared by spreading cells evenly and thinly onto a glass slide.
The slide is then fixed rapidly by immersion into 95% ethanol or
spraying with a commercial fixative according to manufacturer
instructions.
[0031] For the ThinPrep.RTM. collection method (Cytyc Corp.,
Boxborough, Mass.), cells are transferred from the cervix into the
fixative PreservCyt.RTM.. This allows cells to be preserved until
ready for further processing. Cells are then gently dispersed,
randomized and collected onto a TransCyt.RTM. membrane filter by
drawing the sample across the filter with a vacuum until an optimal
number of cells is deposited into the filter. The cells can be
further processed as desirable. In another method, the cells
collected into PreservCytg or other fixative solution can be
further washed by centrifuging, removing the supernatant and
resuspending in Carnoys solution (3:1 Methanol:Acetic acid),
repeating (e.g., three times) as desired. Cells are then
transferred to a glass slide by dropping a small aliquot of cell
suspension directly onto the slide. Slides are typically dried
overnight.
[0032] Detection of Chromosomal Abnormalities
[0033] Gain or loss of chromosomes or chromosomal regions within a
cell is assessed by examining the hybridization pattern of the
chromosomal probe or set of chromosomal probes (e.g., the number of
signals for each probe) in the cell, and recording the number of
signals. Test samples can comprise any number of cells that is
sufficient for a clinical diagnosis, and typically contain at least
about 100 cells. In a typical assay, the hybridization pattern is
assessed in about 25-5,000 cells. Test samples are typically
considered "test positive" when found to contain a plurality of
chromosomal abnormalities, e.g., cells present gains or losses of
one or more chromosomes, loci or chromosomal arms as described
herein. Criteria for "test positive" can include testing positive
with one, two, three, four or more probes. Testing positive with
one probe is a typical test criterion; testing positive with two
probes is more preferred, and with four is most preferred. In
addition, when multiple probes are used test positive can include
detection of abnormal hybridization patterns with a subset of
probes, e.g., a combination of gains or losses of a subset of the
probes, e.g., two or three probes of a full set of four probes.
Hybridization patterns can be assessed in sequence for subsets of
probes. For example, the pattern of an initial subset of probes
(e.g., probes to the 3q26 and 8q24 loci) can be assessed and, if a
positive result is indicated from the subset of probes the test can
be taken as positive overall. However, if the initial result is not
positive, the pattern for an additional subset of probes (e.g.,
probes to the Xp22 locus and chromosome 15) can be assessed to
complete the test. If the combined result for all probes indicates
a positive test result, the test can be taken as positive
overall.
[0034] The number of cells identified with chromosomal
abnormalities and used to classify a particular sample as positive,
in general will vary with the number of cells in the sample. As low
as one cell may be sufficient to classify a sample as positive. It
is preferred to identify at least 30 cells as positive, more
preferred to identify at least 10 cells, and most preferred to
identify at least 5 cells as positive. The number of cells used for
a positive classification is also known as the cut-off value, which
is discussed further below.
[0035] Screening and Monitoring Patients for High Grade Dysplasia
and Cervical Carcinoma
[0036] The methods described herein can be used to screen women for
high grade dysplasia as a predecessor to cervical carcinoma. For
example, women at risk for cervical cancer, e.g., women with
abnormal PAP smear, women who are infected with a HPV, e.g., high
risk HPV, or women that show abnormal amounts of cell cycle
proteins such as p16 and Cyclin E or cell proliferation proteins
such as Ki67 and PCNA can be regularly screened with the goal of
early detection of progression to high grade dysplasia. For
example, general probes and methods to detect infection by HPV in a
sample can be used, such as, for example, a whole genomic HPV
probe. Type specific probes can also be developed to detect
infection by specific HPV types such as one or more of the high
risk HPV types HPV 16, 18, 31, 33, 35, 42, 52, 55 and 58.
Alternatively, antibodies are know and can be adapted to detect the
presence of specific proteins such as the p16 and Ki67 proteins in
a sample. In this embodiment, the sample is first assayed with the
HPV probe or the antibody probe to identify particular cells. The
labeled cells are then assessed as to the chromosomal status using
a probe panel of the invention. The HPV or antibody step can be
performed simultaneously or sequentially with the chromosomal probe
panel.
[0037] The screening test can be incorporated into the routine care
of women, e.g., as an adjunct to evaluation of routine Pap smears.
The methods described here can also be used to adjust treatment
strategies for women. As a more reliable test than the conventional
tests, e.g., Pap tests, patients can be directed more reliably to
the invasive remediation (removal of the transformation zone of the
patient's cervix) as necessary. Patients testing negative for high
grade dysplasia by the test methodology can be spared this invasive
procedure more reliably.
[0038] Probe Selection Methods
[0039] The selection of individual probes and probe sets for use
with the invention can be performed using the principles described
in the examples. Each probe selected for a probe set should have
the ability on its own to discriminate between high and low grade
dysplastic cells. Probes with high discrimination ability are
preferred. The discrimination analysis described herein comprises
calculating the sensitivity and specificity of each probe
individually for identifying high and low grade dysplasia. Various
cutoff values of cell percentages for targets gained and lost are
employed. The primary metric for combined sensitivity and
specificity will be a quantity called `vector`, which is defined as
the magnitude of the vector drawn between the points on a
sensitivity versus specificity plot representing the ideal
(sensitivity=specificity=100) and the measured sensitivity and
specificity of the particular probe or probe set, as measured in a
cohort of abnormal and normal samples. As described in Example 2,
the vector value ranges from 0 for the ideal case to 141.4 for the
worst case. Statistical analyses can also be used to compare means
and standard deviations between high and low grade dysplastic cells
as described in U.S. patent application Ser. No. 10/081,393 by
Morrison, et al. filed Feb. 20, 2002, which is incorporated herein
by reference.
[0040] For multiple probes sets, each probe should be selected to
complement the other probes in the set. That is, each probe should
identify additional high grade dysplasia markers that the other
probe(s) fail to identify. One method for identifying the best
complementing set of probes is to take the probe with the lowest
vector value, remove the group of tumor specimens it identified
from the full set of tumor specimens, and then determine the probe
with lowest vector value on the remaining tumor specimens. This
process can be continued as necessary to obtain a complete probe
set. The approach described here of generating all possible probe
combinations, and calculating the sensitivity and specificity of
each, predicts the performance of all possible probe sets and
allows selection of the minimal probe set with the highest
performance characteristics. Also, a variety of combinations with
similarly high performance characteristics is obtained. Considering
the possible errors due to the finite number of specimens tested,
several of the high ranking probe combinations can be compared
based on other practical characteristics such as relevance to
disease prognosis or difficulty in making the probe.
[0041] However, regardless of the measured ability to complement
other probes, each probe must preferably identify a statistically
different percentage of test positive cells between the high and
low grade adjacent specimen sets. If this condition is not met,
then a probe might be selected erroneously based on apparent
complementation. Moreover, data from combinations of fewer probes
is more reliable than data from combinations of more probes, e.g.,
data from combinations of two probes is more reliable than data
from combinations of three probes. This results from the reduced
ability to make correlations between greater numbers of probes with
the finite number of specimens tested.
[0042] The dependence of probe and probe combination performance as
a function of cutoff value must also be considered. "Cutoff value"
can refer to the number or percentage of cells in a population that
must have gains or losses for the sample to be considered positive.
Therefore, a sample can be considered positive or negative
depending upon whether the number (or percentage) of cells in the
specimen is above the cutoff value or equal to or less than the
cutoff value, respectively. In general, the combined specificity
and sensitivity of probes is better at low cutoff values. However,
when the high grade dysplasia cells are distributed within a matrix
containing many normal and low grade cells, such as from a cervical
smear, probes performing best at high cutoffs are more likely to be
detected. This is because good performance at high cutoffs
indicates a higher prevalence of cells containing the abnormality.
Examples of cutoff values that can be used in the determinations
include about 5, 25, 50, 100 and 250 cells or 5%, 10%, 15%, 20%,
25%, 30%, 35%, 40%, 50% and 60% of cells in the sample
population.
[0043] Measurement of gain of a target chromosome or chromosome
region is preferred over measurement of a target chromosome or
chromosome region loss, because overlapping targets or poor/failed
hybridization to some cells can falsely suggest loss.
Locus-specific or chromosomal arm probes designed to detect
deletions are also generally smaller than locus-specific or
chromosomal arm probes designed to detect gains since the deletion
probes must not extend beyond the minimally deleted region. If too
much of the "deletion probe" extends beyond the deleted sequence,
enough signal may be produced in the assay to be falsely counted.
Since "deletion probes" are usually kept small their signals are
not as intense as signals for targets typically gained. This in
turn makes it more likely that real signals from targets being
monitored for deletion may be miscounted. Likewise, repetitive
sequence probes, like some chromosome enumeration probes used here
are preferable to single locus probes because they usually provide
brighter signals and hybridize faster than locus specific probes.
On the other hand, repetitive sequence probes are more sensitive to
polymorphisms than locus specific probes.
[0044] A probe or combination of probes used with the present
invention preferably provides an improvement over conventional
methods such as cytology. Useful probes or probe combinations of
the invention identify at least about 70% and preferably above
about 85% of samples with high grade dysplasia and carcinoma
(sensitivity). Similarly, useful probes or probe combinations
identify as negative by test at least about 80% and preferably
above about 95% of negative samples (specificity).
[0045] The invention is further described in the following
examples, which are not intended to limit the scope of the
invention described in the claims.
EXAMPLES
[0046] 1. Initial Probe Selection. Thirty-five chromosomal regions,
identified in Table 1 below, known to show some level of
amplification or deletion in cervical cancer or dysplasia were
selected for evaluation. The colors in Table 1 refer to the
fluorescent label used for each of these probes.
1TABLE 1 Probes and Gene Target Locations Used for Probe Selection.
Set Gold Red Green Aqua Orange 1 1q41 CEP 15 1p31 TGFb2 Sat. III
D1S500 2 2q33-q34 2q24 2p24* CEP 6 HER-4 TBR1 MYCN Alpha sat. 3
3p14 3p21-p23 3q26 CEP 7 FHIT MLH TERC Alpha sat. 4 4p15.3 4p16.3*
CEP 12 DDX15 Wolf-Hirsch Alpha sat. 5 5p13 5p15.2 CEP X DAB2
D5S2064 Alpha sat. 6 6q16.3-q21 CEP 16 6p21.2 D6S268 Sat. II PIM1
11 11q13* 11p15.5 11q23* CEP 10 CCND1 HRAS MLL Alpha sat. CEP CEP
11 CEP 8 CEP 1 CEP 17 Alpha sat. Alpha sat. Sat. II/III Alpha sat.
X Xq12* CEP 18 Xp22.3* Androgen receptor Alpha sat. STS Mixed set
8q24* 20q13.2-q13.3 7p12* CEP 9 MYC STK6 EGFR Alpha sat.
[0047] Thirteen of these regions were detected using chromosome
enumeration probes (CEP.RTM. probes in Table 1)) targeting
repetitive centromeric sequences. Twelve of the CEP.RTM. probes
used are commercially available from Vysis, Inc. (Downers Grove,
Ill., www.vysis.com). The other twenty-two regions were detected
with locus specific probes targeting unique sequences within
amplified or deleted chromosomal regions.
[0048] Seven of these locus specific probes used are commercially
available, labeled with SpectrumOrange.TM. label, from Vysis, Inc.
(marked with an asterisk in Table 1.) The commercial STS probe was
used. For the other six probes, the same starting DNA material as
used to make the commercially available probes was used. Instead of
the SpectrumOrange label, the starting DNA was transaminated and
then chemically labeled using 5-(and-6)-carboxyrhodamine 6G,
succinimidyl ester (Molecular Probes) for the c-myc and CCND1
probes, and fluorescin succinimidyl ester for the other four. The
transamination and labeling process used is described in Bittner et
al., U.S. Pat. No. 5,491,224, incorporated herein by reference.
[0049] The CEP 11 probe labeled in gold was produced using the
starting DNA material of the commercially available CEP 11 probe
from Vysis, Inc., and using the same procedure as for the c-myc
probe.
[0050] The remaining 14 probes were produced from BAC clones
sourced as shown in Table 2.
2TABLE 2 Experimental probe details. Probe BAC clone Size of the
Probe location Probe name Identification human insert Source
2q33-q34 HER-4 RP11 384-k20 156 kb Research Genetics 3p14 FHIT
CTB-1-012 138 kb Genome Systems 4p15.3 DDX15 RP11 192p23 171 kb
Research Genetics 2q24 TBR1 RP11 334e15 184 kb Research Genetics
3p21-p23 MLH1 RP11 491d6 102 kb Research Genetics 11p15.5 HRAS GS1
137c7 138 kb Genome Systems 20q13.2-q13.3 STK6 GS1 32i19 145 kb
Genome Systems 1q41 TGFB2 RP11 224o19 177 kb Research Genetics 1p31
D1S500 RP11574n2 164 kb Research Genetics 6p21.2 PIM1 RP3 355m6 134
kb Research Genetics 5p13 DAB2 CTD-2006d4 127 kb Research Genetics
3q26 TERC: 4 clones: 490 kb All clones Clone 300H RP11 3k16 total
from Clone 300I RP11 362k14 contig size Research Clone 300K RP11
641d5 made up of Genetics Clone 300L RP11 816j6 four individual
clones 200 kb 125 kb 128 kb 48 kb 6q16.3-q21 D6S268 RP1-67a8 155 kb
Research Genetics 11q23 MLL 415 024 120 kb Genome Systems 5p.15.2
D5S2064 RP1-144E22 125.5 kb Research Genetics
[0051] The HER-4, FHIT, DDX15 and DAB2 probes were also produced
using the same method as the c-myc probe. The remaining unique
sequence probes were all produced using the nick translation method
described in Morrison 2002, Id. at p. 27-30, and the labeled
nucleotides Spectrum Orange dUTP, SpectrumRed dUTP or Spectrum
Green dUTP (all Vysis, Inc.).
[0052] The labeled probes were then separated into sets of three or
four probes each for evaluation as indicated in Table 1. The probe
sets were made up of the individual probes, COT 1 DNA (Invitrogen),
human placental DNA (Signa), and LSI/WCP Hybridization Buffer
(Vysis, Inc.). 10 .mu.l of each of the probe sets were hybridized
to ten samples each of cervical biopsy samples. The probe sets each
typically contained about 0.5 .mu.g COTI DNA and 2 .mu.g human
placental DNA. The probe set hybridization mixes also contained 50
nanograms of SpectrumAqua labeled human placental DNA to provide a
background staining of the nuclei in the sample, as described in
U.S. Pat. No. 5,789,161, Morrison et al., incorporated herein by
reference. CIN I, CIN II-Ill and invasive cervical squamous
carcinoma (CA) samples were obtained from the Cooperative Human
Tissue Network (CHTN) supported by the National Cancer Institute.
The samples were prepared for hybridization and hybridized with the
probe sets as follows. Paraffin embedded tissue sections were
placed in xylene solution for 5 min. This procedure was repeated 3
times. Slides were then washed in 100% ethanol twice for 1 min each
wash. Slides were then soaked for 15 min in 45%/0.3% peroxide
solution, rinsed in water and incubated for 10 min in Pretreatment
solution. After rinsing, slides were incubated with a proteinase,
e.g., proteinase K or pepsin, for 5-30 min to digest excess
proteins and make the DNA more accessible. The slides were then
dehydrated in ethanol series, air dried and hybridized with DNA
probes usually overnight at 37.degree. C. After hybridization,
unspecific probes were washed out in post-hybridization wash
solutions such as for example, wash for 2 minutes in
73.+-.1.degree. C. 2.times.SSC/0.3% NP40. Slides were then washed
in a second wash solution such as 2.times.SSC/0.1% NP40. A DAPI DNA
stain was then applied to the slides to facilitate sample
evaluation.
[0053] The procedure permitted all probes to hybridize to the
samples. The majority of probes showed good signal intensity
relative to background. The epithelial layers of the biopsy samples
were evaluated under a fluorescence microscope to identify any
cells that showed amplification (more than two signals) or deletion
(less than two signals) of the DNA target. Gains were recorded for
each sample that showed amplification in five or more cells for a
particular probe; losses were recorded for each sample that showed
a deletion in five or more cells. Samples showing neither gains nor
losses were considered disomic.
[0054] The sensitivity, i.e., the percentage of samples showing the
condition tested, of each probe for CIN I, CIN II-III and invasive
carcinoma was determined for gains, losses and disomies. Losses
were found to occur very infrequently in CIN II-III samples and so
were not generally useful as markers for CIN II-III and invasive
carcinoma. Probes were further assessed for their ability to show
maximum frequency of gains for CIN II-III and minimum frequency of
gains for CIN I. The results are presented in Table 3. Probes for
the targets 8q24, 20q13, 3p21, 3q26, 1p31, Xp22 and CEP 15 were
considered the most informative and were selected for further
evaluation. The 3p 14 probe showed significant loss in the CIN
II-III and invasive carcinoma samples. The ratio of the relative
gain of 3q26 to 3 p14 was also evaluated as a measure of the
relative gain of the q arm of chromosome 3 to its p arm.
3TABLE 3 Sensitivity of Probes for Detecting Gains, Losses and
Disomies in Cervical Specimens. Gain Loss Disomy Probe CIN I CIN
II-III CA CIN I CIN II-III CA CIN I CIN II-III CA 8q24 0 80 100 0 0
0 100 20 0 Xp22 0 70 75 19 0 5 81 30 20 CEP 15 0 70 90 0 0 0 100 30
10 20q13 10 80 90 0 0 0 90 20 10 1p31 10 70 80 0 0 0 90 30 20 3p21
13 85 55 6 0 18 81 15 27 CEP 10 15 70 100 10 0 0 75 30 0 3q26 25 80
100 5 0 0 70 20 0 5p13 30 80 100 5 0 0 65 20 0 CEP 8 30 78 100 5 0
0 65 22 0 5p15 40 80 100 5 0 0 55 20 0 CEP X 50 75 100 5 0 0 45 25
0 2p24 20 67 90 0 0 0 80 33 10 Xq12 14 60 95 14 0 5 74 40 0 Gain
Loss Disomy Gain Loss Disomy Gain CEP 7 25 60 90 5 0 10 70 40 0 CEP
18 12 60 90 0 0 0 88 40 10 CEP 16 20 60 100 0 0 0 80 40 0 7p12 10
60 90 0 0 10 90 40 0 3p14 10 60 9 10 20 82 80 20 9 1q41 10 60 90 0
0 10 90 40 0 11q13 25 60 85 0 0 0 75 40 15 CEP 12 10 55 100 5 0 0
85 45 0 CEP 6 10 50 100 10 0 0 80 50 0 4p16 30 50 80 0 0 0 70 50 20
4p15 20 50 70 0 0 0 80 50 30 2q33 12 50 50 12 12 15 76 38 35 11p15
15 50 90 0 0 0 85 50 10 CEP 11 20 45 100 5 0 0 75 55 0 CEP 9 0 44
100 5 0 0 95 56 0 CEP 17 10 40 100 5 0 0 85 60 0 6q16-21 10 40 73 0
10 0 90 50 27 CEP 1 13 33 100 6 0 0 81 57 0 2q23 20 30 80 0 10 0 80
60 20 11q23 45 30 80 0 0 0 55 70 20 6p21 0 10 77 5 10 0 95 80
23
[0055] 2. Discriminate Analysis of In Situ Hybridization Data and
Selection of Probe Sets. Additional paraffin embedded biopsy
samples classed as normal (WNL), CIN I, CIN II, CIN III and
Squamous cell carcinoma (CA) were obtained from the University of
Texas Southwestern Medical Center, Dallas, Tex. (Dr. Raheela
Ashfaq). The samples were prepared and hybridized to two sets of
probes (CEP 15, 8q24, Xp22 and 20q13; and CEP 3, 3q26, 3q14 and
3p21) as before. Six of the probes used--8q24, Xp22, CEP 15, 20q13,
3p21 and 3q26--were taken from the preferred probes identified in
Example 1. Two others --CEP 3 and 3p14--were compared with probes
to 3p21 and 3q26 to better assess the relationship of chromosome 3
in the progression to cervical cancer.
[0056] The ability of individual probes and certain probe
combinations to discriminate between high and low grade dysplasia
in cervical cells was evaluated by determining the number of
specimens correctly identified by each probe or probe set. A cutoff
number of five cells with gains or losses was used to evaluate
samples. A sample was called positive or negative for high grade
dysplasia or carcinoma depending upon whether the number of cells
in the sample was above the cutoff value or equal to or less than
the cutoff value, respectively. The accuracies of identifying the
positive samples (sensitivity) and negative samples (specificity)
were then used to select the best probes and probe combinations.
Table 3a lists the specificity and sensitivity of gain and loss for
certain probe targets.
4TABLE 3a Sensitivity and specificity measurements relative to
sample grades. Sensitivity Specificity Specificity Specificity
Sensitivity Sensitivity Sensitivity CIN II + CIN Probe WNL CIN I
WNL + CIN I CIN II CIN III CA III + CA CEP15 100.00 89.47 94.74
48.15 60.00 57.89 55.35 8q24 95.24 73.68 84.46 96.30 95.00 100.00
97.10 Xp22 100.00 89.47 94.74 59.26 70.00 94.74 74.67 20q13 100.00
78.95 89.48 66.67 70.00 100 78.89 CEP3 100.00 84.21 92.11 55.56
70.00 68.42 64.66 3q26 100.00 73.68 86.84 77.78 90.00 100.00 89.26
3p14 100.00 78.95 89.47 33.33 60.00 15.79 36.37 3p21 100.00 84.21
92.11 37.04 65.00 21.05 41.03 Gain 3q26 100.00 100.00 100.00 7.41
15.00 78.95 33.79 & Loss 3p14 Ratio 3q26/ 100.00 89.47 94.74
29.63 70.00 84.21 61.28 CEP3 > 1 Ratio 3q26/ 95.24 84.21 89.73
66.67 80.00 94.74 80.47 3p14 > 1 Loss: 95.24 100 97.62 29.63
15.00 89.47 44.70 3p14 < 1
[0057] The ability to discriminate between cellular types depends
on the overall specificity and sensitivity. Good discrimination
requires good specificity and sensitivity. Table 3b presents
results for a combined measure of specificity and sensitivity
designated "vector". Vector is calculated as
Vector=[(100-specificity).sup.2+(100-sensitivity).sup.2].sup.1/2
[0058] Specificity and sensitivity are defined as percentages and
range from 100% (perfect) to 0% for no specificity (or sensitivity)
at all. Hence, vector values range from 0 for perfect specificity
and sensitivity to 141 for zero specificity and sensitivity.
[0059] Table 3b is sorted by increasing vector value for each
sample category. Individual probes showing a high ability to
discriminate (low vector value) include 3q26, 8q24 and CEP 3. Other
probes showing a useful ability to discriminate high grade
dysplasia and carcinoma from low grade dysplasia are 20q13, Xp22,
CEP 15 and 3p21. Vectors determined for probe ratios such as
3q26/CEP (determined to be >1) and 3q26/3p14 (determined to be
>1) can also be useful. Other methods for evaluating and
selecting probes using discriminate and combinatorial analytical
techniques are described in U.S. Ser. No. 10/081,393 by Morrison,
et al., filed Feb. 20, 2002, which is incorporated herein by
reference.
5TABLE 3b Vector value for sample grades. CIN I WNL + CIN I (WNL +
CIN I) vs Probe/Vector vs CIN II vs CIN II (CIN II + CIN III) 3q26
27.00 17.75 13.50 8q24 28.07 16.76 16.87 CEP3 35.55 33.82 25.69
20q13 41.11 36.34 33.49 Xp22 43.73 42.66 35.88 CEP 15 51.22 50.31
46.76 3p21 54.59 53.63 39.59 Ratio 3q26/CEP 3 > 1 54.59 53.63
31.36 Ratio 3q26/3p14 > 1 54.59 53.63 31.36 3p14 62.53 60.64
47.47 Gain 3q26&Loss 3p14 93.30 93.30 88.30 Loss: 3p14 < 1
93.30 93.30 88.30
[0060] Based on results from discriminate analysis and probe
complementarity as described above, preferred probes for use in
distinguishing high from low grade dysplasia in cervical samples
include probes to the loci 3q26 and 8q24 and the CEP 3. Sets of
probes comprising the probes 3q26 and 8q24; 3q26, 8q24, Xp22, and
CEP 15; 8q24, 20q13, Xp22 and CEP 15; and 3p21, 3p14, 3q26 and CEP
3 are particularly preferred.
[0061] Other Embodiments
[0062] While the invention had been described in conjunction with
the foregoing detailed description, it is to be understood that the
foregoing description is intended to illustrate and not limit the
scope of the invention. Other aspects, advantages and modification
of the invention are within the scope of the claims set forth
below.
* * * * *
References