U.S. patent application number 11/685105 was filed with the patent office on 2007-07-19 for methods of analyzing chromosomal translocations using fluorescence in situ hybridization (fish).
This patent application is currently assigned to Cancer Genetics, Inc.. Invention is credited to Raju S. Chaganti, Nallasivam Palanisamy.
Application Number | 20070166749 11/685105 |
Document ID | / |
Family ID | 27404027 |
Filed Date | 2007-07-19 |
United States Patent
Application |
20070166749 |
Kind Code |
A1 |
Palanisamy; Nallasivam ; et
al. |
July 19, 2007 |
METHODS OF ANALYZING CHROMOSOMAL TRANSLOCATIONS USING FLUORESCENCE
IN SITU HYBRIDIZATION (FISH)
Abstract
Probes and methods of using the probes to detect chromosomal
rearrangements and/or deletions are provided. The methods utilize
probes that are free of repeat sequences to provide greater
selectivity and sensitivity; methods for producing such probes are
also disclosed. The probe sets utilized in the detection methods
are designed to hybridize to chromosomes at regions outside known
breakpoints, instead of spanning the breakpoint as with
conventional FISH methods, and, in some instances, are further
designed to bind to regions located outside the genes involved in
the rearrangement. Methods utilizing probe sets with two and four
colors are also described, as are automated methods for analyzing
rearrangements.
Inventors: |
Palanisamy; Nallasivam;
(North Andover, MA) ; Chaganti; Raju S.; (New
York, NY) |
Correspondence
Address: |
TOWNSEND AND TOWNSEND AND CREW, LLP
TWO EMBARCADERO CENTER
EIGHTH FLOOR
SAN FRANCISCO
CA
94111-3834
US
|
Assignee: |
Cancer Genetics, Inc.
Cambridge
MA
|
Family ID: |
27404027 |
Appl. No.: |
11/685105 |
Filed: |
March 12, 2007 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10146658 |
May 14, 2002 |
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11685105 |
Mar 12, 2007 |
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60357195 |
Feb 13, 2002 |
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60337653 |
Nov 8, 2001 |
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60291121 |
May 14, 2001 |
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Current U.S.
Class: |
435/6.14 ;
702/20 |
Current CPC
Class: |
C12Q 2539/105 20130101;
C12Q 1/6841 20130101; C12Q 1/6811 20130101; C12Q 1/6841 20130101;
C12Q 1/6886 20130101 |
Class at
Publication: |
435/006 ;
702/020 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; G06F 19/00 20060101 G06F019/00 |
Goverment Interests
STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED
RESEARCH AND DEVELOPMENT
[0002] One or more, but not all, of the inventions herein were made
with support from Grant Nos. IR43CA84838-01, R44CA84838-02, and
IR43CA89970-01 awarded by the National Cancer Institute of the
National Institutes of Health. Therefore, the government may have
certain rights in some of the inventions herein.
Claims
1. A method for determining the presence or absence of a reciprocal
chromosomal translocation involving a first gene, which includes
potential breakpoints for the translocation, and a second gene,
which includes potential breakpoints for the translocation, the
first and second genes being located on first and second
chromosomes, respectively, the method comprising: (a) contacting,
under hybridization conditions, a chromosomal preparation with a
set of probes comprising first and second nucleic acid probes;
wherein said chromosomal preparation comprises the first and second
chromosomes; wherein the first probe bears a first label and is
hybridizable to an untranslocated form of the first chromosome at a
region located outside the first gene and no further than 1 Mb from
the outermost known centromeric breakpoint associated with the
translocation; wherein the second probe bears a second label
different from the first label and is hybridizable to an
untranslocated form of the second chromosome at a region located
outside the second gene and no further than 1 Mb from the outermost
known telomeric breakpoint associated with the translocation;
wherein (i) if the first and second chromosomes have undergone the
reciprocal chromosomal translocation, the first and second probes
hybridize to a derivative chromosome formed via the translocation,
such that both the first and second labels appear on the derivative
chromosome; whereas (ii) if the first and second chromosomes have
not undergone the reciprocal chromosomal translocation, the first
and second probes hybridize to their respective chromosomes, such
that only the first label appears on the first chromosome and only
the second label appears on the second chromosome; (b) detecting a
pattern of hybridization for the first and second probes; (c)
determining from the pattern whether the first and second probes
appear on the derivative chromosome or appear separately on the
first and second chromosomes, respectively, thereby determining the
presence or absence of the reciprocal chromosomal
translocation.
2. The method of claim 1, wherein the regions of chromosomal DNA
bound by the first and second probes are 100-300 kb in length.
3. The method of claim 1, wherein the regions of chromosomal DNA
bound by the first and second probes are 10-1000 kb in length.
4. The method of claim 1, wherein the region that the first probe
hybridizes to is at least 400 kb and no further than 1 Mb from the
outermost known centromeric breakpoint associated with the
translocation and the region that the second probe hybridizes to is
at least 400 kb and no further than 1 Mb from the outermost known
telomeric breakpoint associated with the translocation, such that
if the first and second chromosomes have undergone the
translocation, the first and second probes as hybridized to the
derivative chromosome are separated by at least 0.8 Mb.
5. The method of claim 1, wherein the reciprocal chromosomal
translocation is selected from the group consisting of:
t(11;14)(q13; q32) (BCL1; IGH); t(14;18)(q32; q21) (IGH;BCL2);
t(8;14)(q24; q32) (MYC;IGH); and t(9;22)(q34; q11) (BCR;ABL).
6. The method of claim 5, wherein the reciprocal chromosomal
translocation is t(11;14)(q13; q32) (BCL1; IGH).
7. The method of claim 5, wherein the reciprocal chromosomal
translocation is t(14;18)(q32; q21) (IGH;BCL2).
8. The method of claim 5, wherein the reciprocal chromosomal
translocation is t(8;14)(q24; q32) (MYC;IGH).
9. The method of claim 5, wherein the reciprocal chromosomal
translocation is t(9;22)(q34; q11) (BCR;ABL).
Description
CROSS-REFERENCES TO RELATED APPLICATIONS
[0001] This application is a divisional of U.S. patent application
Ser. No. 10/146,658, filed on May 14, 2002, which claims priority
to U.S. Provisional Application Nos. 60/291,121, filed May 14,
2001; 60/337,653, filed Nov. 8, 2001; and 60/357,195, filed Feb.
13, 2002. Each of these applications is incorporated herein by
reference in its entirety for all purposes.
BACKGROUND
[0003] Chromosomal rearrangements can take a variety of forms
including exchanges of portions of one chromosome with another
chromosome (translocations), deletion of sections of chromosomes,
insertions of new material into the chromosome, and duplications or
deletions of entire chromosomes. In the majority of cases, a direct
causal link between a particular chromosomal rearrangement and a
particular disease state has been found. This concomitant
occurrence of disease with a chromosomal rearrangement can
frequently be shown to result from alterations made in particular
genes directly implicated in promoting the disease.
[0004] The use of chromosome rearrangements as diagnostic and
follow-up markers is based on several considerations. First,
rearrangements are common in hematological malignancies and solid
tumors and, as just indicated, the genes that are altered by the
rearrangements are directly implicated in the development of
malignancy. Second, rearrangements remain as clonal markers of the
tumor cells throughout the progression of the disease. Third,
rearrangements can be detected by cytogenetic or molecular methods.
Examples of rearrangements that are currently useful in diagnostic,
prognostic and follow-up evaluation of hematologic and solid tumor
neoplasms are listed in Table 1 and Table 2 infra.
[0005] Chromosome Translocations in Lymphomas. A number of
chromosomal translocations have been identified as being correlated
with certain lymphomas, including Non-Hodgkin's lymphoma (NHL). The
incidence of NHL has increased at an alarming rate in recent years.
It is now the fifth most common cancer in the U.S., and worldwide
incidence is also increasing rapidly (Weisenburger 1994; Parker et
al., 1996). Several translocations that correlate with various
lymphoma subsets involve the IGH gene located on chromosome 14, at
band q32 (14q32). Specific examples of such translocations include
the t(8;14)(q24; q32) associated with Burkitt's Lymphoma (BL), the
t(11;14)(q13; q32) in Mantle Cell Lymphoma (MCL), and t(14;18)(q32;
q21) associated with follicular B-cell lymphoma (FL).
[0006] The t(8;14)(q24; q32) translocation was the first recurring
chromosomal translocation shown to be associated with lymphomas
(Zech et al., 1976). Further studies established this translocation
as the hallmark of Burkitt's lymphoma (BL) because 100% of the
cases show this translocation; in addition, it also has been
reported in about 15% of other high grade B-cell lymphomas. (Offit
et al., 1991; 1992; Gaidano et al., 1993).
[0007] MCL originates from the mantle zone B-cells. It is seen in
5-10% of NHL in adults (Weisenburger, 1992; Raffeld, et al., 1991;
Banks, et al., 1992). The t(11;14)(q13; q32) is a consistent
cytogenetic abnormality in 70% to 90% of MCL's (Tsujimoto et al.,
1984; Williams et al., 1991; Coignet et al., 1996). The
t(14;18)(q32; q21) translocation characterizes approximately 60% of
B-cell NHL. It is seen in 85% of the FL and 25% of diffuse
aggressive large cell lymphomas (DLCL).
[0008] The physiologic consequence of each of these translocations
is deregulation of expression of a gene located at the breakpoint
of the chromosome band rearranging with 14q32. This deregulation is
brought about by replacement of the gene's regulatory signals by
those of the IGH gene, which are consistently expressed in B cells.
Thus, MYC, BCL-1, and BCL-2 are the target deregulated genes in BL,
MCL, and FL, respectively, associated translocations (Chaganti, et
al., 2000). In addition to these common or well-known
translocations, more than a dozen other less frequent, but equally
important, translocations have been identified (Chaganti, et al.,
2000). Because breakpoints of the translocations occur in
circumscribed regions of chromosomal DNA, their detection can be of
value in diagnosis and post therapy follow-up of these
neoplasms.
[0009] Methods for the Detection of Chromosomal Rearrangements.
Several approaches to detecting chromosomal rearrangements have
been developed. These include karyotype band analysis, Southern
blot analysis, and analysis by quantitative polymerase chain
reaction (PCR) or reverse-transcription PCR (RT-PCR). Of these
various methods, karyotype analysis by conventional banding is the
most accurate method currently in use.
[0010] Karyotyping involves culturing tumor cells from bone marrow
aspirate, lymph node, or other tissue biopsies. The methodology
involves accumulating metaphase cells by treatment with colcemid
and fixation on glass slides according to established preparative
procedures. Slides containing adequate numbers of cells in
metaphase-prometaphase stage are "banded" by a number of
techniques, G-banding being the most widely utilized, and observed
under a microscope. The dark and pale bands along the length of the
chromosome are consistent and reproducible (banding pattern).
Consequently, they serve as landmarks that are the basis for
chromosome identification, as well as assignment of breakpoints at
the sites of rearrangement. It is precise as long as dividing cells
are available. The drawbacks of this method include that it
requires dividing cells, which is labor intensive and time
consuming, and the method does not detect small deletions important
in evaluating both the disease and potential treatments. The
current rate of successful cytogenetic analysis of newly diagnosed
cases ranges from 60% to 80% for hematological malignancies and
<40% for solid tumors. This percentage falls dramatically in
post-treatment bone marrow/blood samples, making cytogenetics a
less useful tool for patient follow-up. Fifty percent of follow-up
specimens do not yield results due to the extreme hypocellularity
of marrow samples and poor proliferation in vitro.
[0011] Southern Blot analysis involves isolating DNA from a tumor
sample and subjecting it to endonuclease digestion and
fractionation on agarose gels using electrophoresis. The
size-separated DNA fragments are then transferred to a nylon
membrane and probed by hybridization with DNA sequences adjacent to
the breakpoint. A novel rearranged band, in addition to the germ
line band derived from the normal allele, indicate the presence of
the translocation. This method requires the use of probes in the
vicinity of the suspected breakpoints to detect rearrangements.
Moreover, detection of rearrangements depends on clustering of the
breakpoints in one of the rearranging chromosomes within a small
region, which can be detected by one or few restriction enzyme
digests. Detection of translocations, which have multiple
breakpoints, requires multiple probes and multiple enzyme digests
of DNA, which is cost inefficient. As a consequence, Southern
blotting is not readily applicable for detecting all breakpoints in
a number of disease-associated translocations [e.g.,
t(8;14)(q24q32), t(11;14)(q13q32) and t(14;18)(q32q21)]. Finally,
Southern blotting does not possess the sensitivity required to
detect translocations in heterogenous samples, as the method
requires a sample comprised of at least,5-10% tumor cells carrying
the chromosomal rearrangement.
[0012] The polymerase chain reaction (PCR) relies on amplification
of a PCR product from the translocation junction using primers
containing sequences near the vicinity of the breakpoint derived
from both chromosomes involved in the translocation. PCR
amplification will occur only from tumor cells, whereas an
amplification product will not be generated from the DNA of normal
cells in which the primer templates remain on separate chromosomes.
Genomic PCR will successfully amplify only if the breakpoints in
the two chromosomes involved in the translocation in different
tumors are distributed within a distance of 1 to 2 KB, which is the
limit of conventional PCR amplification.
[0013] Reverse transcription PCR (RT-PCR) is used to identify
fusion RNA and can also be employed in cases with widely scattered
breakpoints. As with conventional PCR, successful amplification
depends on consistent breakpoints within the same intronic regions
of the two genes. In the RT-PCR method, the primers are selected
from the sequences of the exons near the breakpoints from each of
the two genes involved in the translocation. Although both DNA and
RT-PCR methods are sensitive enough to amplify DNA, they are
difficult to quantify and do not provide information on disease in
terms of proportion of cells in a given biopsy, which is the
desired measure. In addition, necrotic cells or free DNA can lead
to biologically questionable positive results.
[0014] Both versions of the PCR analysis are difficult to
quantitate and prone to false positive results from amplification
of DNA sequences in dead tumor cells or in free DNA from lysed
cells still present in the specimen. Moreover, PCR techniques are
not readily applicable to detecting many disease-associated
translocations because of the dispersed nature of the breakpoints
found in these arrangements, with the dispersement of breakpoints
necessitating multiple PCR reactions. These methods also have a
limited utility because they are not applicable to many
rearrangements involving deletions that are frequently associated
with poor prognosis, such as those associated with the BCR/ABL
regions on der (9) (Sinclair et al., 1999) and on der(22)
(Palanisamy, unpublished data) which occur in cases of CML.
[0015] Fluorescence in situ Hybridization (FISH) is another tool
for detecting chromosomal rearrangements. The term "in situ
hybridization" generally refers to hybridization of a nucleic acid
probe to a nucleic acid target that is part of a cytological or
histological preparation. Typically, FISH methods involve the
following steps: (a) fixing the tissue or other biological material
under investigation to a support (e.g., glass slide or wall of a
micro titer well), (b) treatment of the tissue or material to
increase accessibility of probe DNA to target DNA, (c) contacting
the tissue or material containing the target DNA with probes to
form specific hybridization complexes, (d) post hybridization
washes of the complexes to selectively remove probes that are not
specifically hybridized to the target, and (e) detection of probes
that have formed hybridization complexes with target DNA molecules.
An advantage of FISH is that one can analyze individual cells,
which eliminates the need to utilize cycling cells. Such methods
are described in a number of sources, including: Gall and Pardue,
(1981) Methods of Enzymology 21:470-480; Henderson, (1982)
International Review of Cytology, 76:1-46; and Angerer, et al.,
(1985) in Genetic Engineering: Principles and Methods (Setlow and
Hollaender, Eds.) vol. 7, pp. 43-65, Plenum Press, New York.
[0016] One of the problems with interphase FISH analysis is signal
artifacts. These arise from two sources. One is non-specific
binding of labeled DNA to protein in intact fixed nuclei. This can
be partly overcome by treating the nuclei with proteolytic enzymes
such as proteinase K or trypsin. Recent advances in imaging
technology enables one to capture images using a CCD (Charge
Coupled Device) camera and processing of images using
image-processing software to reduce the background fluorescence
arising from non-specific hybridization. Another problem is
non-specific cross hybridization of repeat sequences in the probe
with those in the genome. A Cot-1 DNA suppression step can be
included in the hybridization protocols to ameliorate this problem.
Because nucleic acids in the Cot-I fraction are characterized by
containing highly repetitive sequences (e.g., Alu sequences,
.alpha.-satellite, .beta.-satellite sequences), these nucleic acids
bind to repeat sequences in the genome, thereby blocking binding of
probes to such sequences (see, e.g., Benjamin Lewin, (1994) Genes
V, Oxford University Press). The limitation of such approaches,
however, is that such steps fail to bind all repeat sequences and
fail to anneal to all the copies of any given sequence.
[0017] Application of Detection Methods to Translocations
Associated with Lymphomas. The heterogeneous nature of NHL makes
accurate disease diagnosis and follow-up particularly challenging.
Cytological and histological methods were previously the diagnostic
methods of choice. Recent advances in developing immunophenotypic
markers as well as molecular methods discussed supra, such as PCR,
have revealed the highly heterogeneous nature of lymphoma. It is
well established that each lymphoma type is characterized by a
specific immunophenotype marker as well as nonrandom chromosomal
abnormalities.
[0018] NHLs are treated by a variety of chemotherapeutic regimens
and/or autologous bone marrow transplantation, which require
regular follow-up and monitoring for recurrence or cancer in bone
marrow and blood. The gold standard currently in use for this
purpose is karyotype analysis by G-banding. As indicated supra,
although this method is precise, it is labor intensive; in
addition, 50% of follow-up specimens do not yield results, due to
extreme hypocellularity of marrow samples and poor in vitro
proliferation. Due to the dispersed nature of the breakpoints in
many translocations [e.g., t(8;14)(q24; q32), t(11;14)(q13; q32)
and t(14;18)(q32; q21)] over a large genomic region and the
requirement of multiple probes and multiple PCR reactions, Southern
blotting and PCR methods are not readily applicable for detecting
all breakpoints. Furthermore, Southern blotting and PCR methods are
prone to sensitivity and specificity problems because, as noted
above, Southern blotting requires the presence of at least 5-10%
tumor cells in the sample to detect a rearrangement, and PCR is
prone to generate false positive results due to amplification of
DNA from dead tumor cells or lysed cells that may be present in the
sample.
[0019] FACS analysis can be used to detect specific combinations of
cell surface proteins that may characterize the original blast
(i.e., the immature stage of cellular development before appearance
of the defining characteristics of the cell) population. Using FACS
analysis, abnormal populations can be detected in as few as 0.1%
(10-3) of cells. PCR has emerged as the most promising approach to
date for the detection of minimum residual disease (MRD; This is
the lowest percentage of tumor cells, within a large population of
normal cells, at which the clinical condition of the patient can be
said to be in remission. Thus, this is a symptom free disease
condition, despite the presence of a low percentage of tumor
cells), although other methods such as pathologic examination,
FACS, PCR and cytogenetics are also utilized to estimate MRD. While
PCR offers the advantage of very high sensitivity, with a detection
limit of approximately 10.sup.-5, the problems noted above
concerning lack of quantitation and generation of spurious results
during the amplification process means that the technique is not
particularly attractive for estimating MRD.
[0020] Hence, all currently available rearrangement detection
methods have various shortcomings. Consequently, new methods are
needed to successfully monitor the presence of tumor cells to
enable evaluation of treatment options and prediction of
recurrence.
SUMMARY
[0021] A variety of methods and probes are provided herein for use
in the detection of chromosomal rearrangements, including methods
utilizing fluorescent in situ hybridization (FISH) methods. By
utilizing various techniques that are disclosed herein either
singularly or in combination, the methods and probes enhance the
sensitivity and the specificity of rearrangement detection relative
to other conventional approaches.
[0022] Certain methods involve the preparation of probes that are
free of repeat sequences and which are selected to hybridize to
regions that flank potential breakpoints involved in the
translocation of interest. Such methods typically involve a series
of steps which include: (a) preparing a first collection of
fragments that hybridize to regions flanking potential break points
of a first chromosome involved in the chromosomal translocation;
(b) preparing a second collection of fragments that hybridize to
regions flanking potential break points of a second chromosome
involved in the chromosomal translocation; (c) forming a first
population of clones, each clone containing a fragment from the
first collection linked to a vector; (d) forming a second
population of clones, each clone containing a fragment from the
second collection linked to a vector; (e) hybridizing fragments
from the first population of clones with a sequence to allow
elimination of clones containing fragments hybridizing to the
repeat sequence; (f) hybridizing fragments from the second
population of clones with a sequence to allow elimination of clones
containing fragments hybridizing to the repeat sequence; (g)
preparing probes from the clones in the first population whose
vectors are linked to fragments that do not hybridize to the repeat
sequence; and (h) preparing probes from the clones in the second
population whose vectors are linked to fragments that do not
hybridize to the repeat sequence.
[0023] Probes obtained according to the foregoing approach exhibit
increased selectivity because the probes are repeat free and thus
selectively hybridize with sequences of regions involved in actual
translocations rather than simply a region containing a repeat
region. The probes are typically labeled to facilitate detection.
Such probes can be utilized to detect translocations in both
interphase and metaphase cells. The probes can also be utilized to
detect chromosomal rearrangements in diverse sample types,
including but not limited to, chromosomal preparations from lymph
node cells, bone marrow cells, blood cells and various tumor cells,
including solid tumor cells. Probes can be specifically generated
to essentially any rearrangement according to this method,
including those rearrangements listed in Table 1 and Table 2
infra.
[0024] Certain methods of detecting translocations which are
provided herein utilize a signal segregating approach. In such an
approach, the probes used to detect the translocation are selected
to hybridize to regions flanking all the known breakpoint regions
associated with a translocation. Thus, in sharp contrast to
conventional methods, these probes do no span the breakpoints
involved in a translocation.
[0025] One such method involves providing a first and second set of
differentially labeled nucleic acid probes, each set comprising a
proximal probe and a distal probe, the first set of probes
hybridizing to the first chromosome and bearing a first label, the
second set of probes hybridizing to the second chromosome and
bearing a second label. The first and second set of probes is then
contacted with a chromosomal preparation. If the translocation has
occurred between a first and second chromosome within the
preparation, a proximal probe and a distal probe from different
probe sets hybridize to each of the derivative chromosomes formed
by the translocation, such that first and second label appear on
each of the derivative chromosomes. If, however, the translocation
has not occurred between a first and second chromosome in the
preparation, the probes of the first probe set bind to the first
chromosome and the probes of the second probe set bind to the
second chromosome, such that only one label appears on the first
and second chromosome of the preparation. At least one chromosome
in the preparation that is hybridized to labeled probe is detected,
wherein the presence of the first and second label on the at least
one chromosome is an indication that the translocation has
occurred, and the presence of only the first or the second label on
the at least one chromosome is an indication that the translocation
has not occurred.
[0026] Another method generally involves providing first and second
sets of nucleic acid probes labeled with first and second labels
where these sets of probes will hybridize to a first and a second
chromosome respectively, the first and second chromosomes being
susceptible to undergoing a reciprocal translocation with each
other. The first and second probe sets each comprise at least one
proximal and at least one distal probe, where at least one proximal
probe hybridizes to a segment of chromosomal DNA that lies entirely
on the centromeric side of all known break points associated with
the translocation, and at least one distal probe hybridizing to a
segment of chromosomal DNA that lies entirely on the telomeric side
of all known break points associated with the translocation. The
two sets of probes are then contacted to a chromosomal preparation,
which may contain untranslocated forms of the first and second
chromosomes, and/or one or more translocated forms of the first and
second chromosomes. By detecting a pattern of hybridization where
the first and second sets of probes have bound to the chromosomal
preparation, the presence of a translocated and untranslocated
forms of the first and second chromosomes in the chromosomal
preparation can be determined.
[0027] In some methods the known break points in the first
chromosome occur in a first gene and the known breakpoints in the
second chromosome occur within a second gene, and the first and
second probe sets hybridize to segments outside the first and
second genes. Thus, certain methods involve, providing a first and
a second nucleic acid probe that are differentially labeled, the
first probe hybridizing to the first chromosome at a region located
outside a first gene that includes all known breakpoints for the
translocation and bearing a first label, the second probe
hybridizing to the second chromosome at a region located outside a
second gene that includes all known breakpoints for the
translocation and bearing a second label. The first and second
probes are then contacted with a chromosomal preparation. If the
preparation contains a derivative chromosome formed via the
translocation, the first and second probes hybridize to the
derivative chromosome, such that both the first and second label
appear on the derivative chromosome. If the preparation contains
the first and second chromosome, the first and second probes
hybridize to their respective chromosomes such that only the first
label appears on the first chromosome and only the second label
appears on the second chromosome. At least one chromosome in the
preparation that is hybridized to the first or second probe is
detected, wherein the presence of two labels on the at least one
chromosome indicates that the translocation has occurred, and the
presence of a single label on the at least one chromosome indicates
that the translocation has not occurred.
[0028] The first and second probe sets can hybridize from around 10
kb to around 100 kb away from all known breakpoints associated with
the translocation. In some methods the first and second probe sets
contain a plurality of proximal probes and a plurality of distal
probes hybridizing to a plurality of chromosomal segments of which
the outermost segments are from about 50 kb to about 200 kb apart
in the chromosomal DNA. In some of the methods, the first and
second probe sets hybridize about 10 kb to about 100 kb away from
all known breakpoints associated with the translocation. In some of
the methods the first and second probe sets each comprises a
plurality of probes hybridizing to a plurality of chromosomal
segments of which the outermost segments are at least 200 kb apart
in the chromosomal DNA.
[0029] In certain methods, the first and second probe sets were
prepared from a first collection of fragments flanking all of the
known breakpoints of the first chromosome and a second collection
of fragments flanking all of the known breakpoints of the second
chromosome, respectively. A first population of clones is then
formed, each clone containing a fragment from the first collection
linked to a vector, and a second population of clones is formed
where each clone contains a fragment from the second collection
linked to a vector. Fragments from the first and second populations
of clones are then hybridized with a repeat sequence to allow
elimination of clones containing fragments hybridizing to the
repeat sequence. Probes are then prepared from the clones in the
first and second populations whose vectors are linked to fragments
that do not hybridize to the repeat sequence. These two probe
populations are then differentially labeled with a first and a
second label, respectfully. When probes constructed in the above
manner are contacted to a chromosomal preparation, translocated
chromosomes are determined from a pattern of hybridization
comprising a colocalization of spots of first and second label. A
second translocated chromosome can be identified by observing a
second co-localization of spots of first and second label.
[0030] If the cell is in metaphase, which of the translocated
chromosomes is a derivative of the first chromosome comprising a
centromeric region from the first chromosome and a telomeric region
from the second chromosome and which of the translocated
chromosomes is a derivative of the second chromosome comprising a
centromeric region from the second chromosome and a telomeric
region from the first chromosome can be determined. If the pattern
of hybridization shows a spot of first label free of second label
the spot corresponds to an untranslocated form of the first
chromosome. If the cell is in metaphase and the pattern of
hybridization shows a spot of first label free of second label, and
a comparison of this first label spot to the analogous first label
spot on a homologous chromosome indicates that one spot of first
label is less intense than another spot of first label, the less
intense spot corresponds to a deletion in the region of the
chromosome containing the hybridization site for the first label.
If the cell from which the chromosomes are obtained is diploid and
in metaphase and the pattern of hybridization comprises fewer than
four spots of the first or second label, then the absent spot of
label corresponds to a deletion of the region of chromosome
recognized by the absent spot. If the cell from which the
chromosomes are obtained is in metaphase, and the pattern of
hybridization shows a spot of first label or second label on a
third chromosome different from the first and second chromosomes,
then the spot on the third chromosome corresponds to a
nonreciprocal translocation between the third chromosome and either
the first or second chromosome.
[0031] In still other methods first, second, third and fourth sets
of nucleic acid probes labeled with first, second, third and fourth
labels are prepared such that the first and second sets hybridize
to a first chromosome and the third and fourth sets hybridize to a
second chromosome. In such methods, the first and second
chromosomes are susceptible to undergoing a reciprocal
translocation with each other. The first and second probe sets
respectively contain at least one proximal and at least one distal
probe, the proximal probe hybridizing to a segment of DNA occurring
entirely on the centromeric side of all known break points on the
first chromosome associated with the translocation and the distal
probe hybridizing to a segment of DNA occurring entirely on the
telomeric side of all known break points on the first chromosome
associated with the translocation. Similarly, the third and fourth
probe sets respectively contain at least one proximal and at least
one distal probe, the proximal probe hybridizing to a segment of
DNA occurring entirely on the centromeric side of all known
breakpoints of the second chromosome associated with the
translocation, and the distal probe hybridizing to a segment of
chromosomal DNA occurring entirely on the telomeric side of all
known breakpoints of associated with the translocation.
[0032] Probes having the foregoing characteristics are contacted,
under hybridizing conditions, to a chromosomal preparation, which
may contain untranslocated forms of the first and second
chromosomes, and/or one or more translocated forms of the first and
second chromosomes, and/or translocated forms of the first or
second chromosome with a third chromosome. The first, second, third
and fourth sets of probes are bound to the chromosomal preparation.
By detecting the pattern of hybridization produced, the presence of
untranslocated forms of the first and second chromosomes,
chromosomes resulting from translocations between the first and
second chromosomes, chromosomes resulting from translocation
between the first or second chromosome and a third chromosome,
and/or deletions of any of these forms can be determined. In some
of the methods, all the known break points in the first chromosome
occur in a first gene and all the known breakpoints in the second
chromosome occur within a second gene, and the first, second, third
and fourth probe sets hybridize to segments outside the first and
second genes. In some of the methods the first, second, third and
fourth probe sets hybridize about 10 kb to about 100 kb away from
all known breakpoints associated with the translocation. In some of
the methods the first, second, third and fourth probe sets each
comprises a plurality of probes hybridizing to a plurality of
chromosomal segments of which the outermost segments are at least
200 kb apart in the chromosomal DNA.
[0033] In still other methods, the first and second probe sets are
prepared from first and second collections of fragments proximal
and distal to the known breakpoints of the first chromosome and
third and fourth probe sets are prepared from third and fourth
collections of fragments proximal and distal to the known
breakpoints the second chromosome. First, second, third and fourth
populations of clones are produced, each clone respectively
containing a fragment from the first, second, third or fourth
collection of fragments linked to a vector. Each of these clonal
populations is hybridized with a repeat sequence to allow
elimination of clones containing fragments hybridizing to the
repeat sequence. First, second, third, and fourth sets of probes
are then prepared from the respective clonal populations whose
vectors are linked to fragments that do not hybridize to the repeat
sequence.
[0034] Using probes constructed in the manner described above,
chromosomal rearrangements can be detected from the hybridization
patterns produced when the probes are hybridized to chromosomal
preparations. If the pattern of hybridization shows a
colocalization of spots of the first and fourth labels, then a
translocated form of the first and second chromosomes comprising a
centromeric region of the first chromosome and a telomeric region
of the second chromosome is present in the preparation. If the
pattern of hybridization shows a colocalization of spots of the
second and third label, then a translocated form of the first and
second chromosomes comprising a centromeric region of the second
chromosome and a telomeric region of the first chromosome is
present in the preparation. If the pattern of hybridization shows a
colocalization of spots of first and second label, then an
untranslocated form of the first chromosome is present in the
preparation. If the pattern of hybridization shows a colocalization
of spots of the third and fourth labels, then an untranslocated
form of the second chromosome is present in the preparation. If the
cell from which the chromosomal preparation is obtained is diploid
and the pattern of hybridization shows fewer than two spots of any
one of the first, second, third and fourth labels, then a deleted
form of the first or second chromosomes is present in the
preparation. If the pattern of hybridization shows two spots of any
one of the first, second, third and fourth labels, and comparison
of the intensity of the spots of like label shows that the
intensity of one of the spots is less than the intensity of the
other, then a deletion of the region corresponding to the spot of
lesser intensity is present in the preparation. If the pattern of
hybridization comprises a colocalization of spots of first and
second label, a spot of first label free of second, third and
fourth label and a spot of second label free of first, third and
fourth label, then a nonreciprocal translocation resulting in
transfer of a segment from the first chromosome to a third
chromosome is present in the preparation.
[0035] The probe constructs of the present invention do not span
translocation breakpoints, which maximizes probe hybridization to
derivative chromosomes thereby maximizing the signal intensity of
the associated fluorescent label. The probe constructs are also
free of repeat sequences, which lowers the background presented in
the methods described. The maximal signal intensity and lower
background facilitates the use of automated image analysis in
scoring translocation events by these methods. In some of these
automated methods determining the chromosome translocation involves
scanning an image of the hybridization pattern to detect presence
and location of spots of the first label and the second label,
followed by determining whether a distance between spots of first
and second labels falls within a predetermined distance as an
indication of presence of a translocated form of the first and
second chromosomes. When it is determined that the distance between
second spots of first and second labels falls within the
predetermined distance, then a second translocated form of the
first and second chromosomes is present. In such instances, the
cell is classified as cancerous if and only if both first and
second translocated forms of the first and second chromosomes are
present.
[0036] Other methods involve detecting nuclei prior to chromosomal
analysis. This is accomplished by staining the nucleus to allow its
detection by an imaging device in the scanning step. In some
methods this stain is DAPI stain. Defining the boundaries of nuclei
by staining allows for a plurality of nuclei to be screened.
Screening of the stained nuclei allows for the detection of
clustered and damaged nuclei which can be ignored in the analysis.
Single, undamaged, stained nuclei define a boundary within which
detection of chromosomal rearrangements can be carried out.
Nuclear-defined boundaries also allow multiple chromosomal
preparations to be scored from a single slide thereby facilitating
automated analysis.
[0037] In some methods the scanning step produces a plurality of
images in different focal planes of the chromosomal preparation.
Such a plurality of images can be merged to produce a 3D image of
the labeled chromosomes, or alternatively, can be merged to produce
a composite image of the labeled chromosomes each of which may only
be in focus in a single focal plane. In other methods, the images
are filtered so that the signal from only one type of fluorescent
label can be detected at a time. In such methods the spatial
pattern produced by each label is recorded. After the spatial
pattern of all labels has been determined, the presence of
chromosomal rearrangements can be scored by comparing the proximity
of each label to other labels.
[0038] Methods for detecting deletions in chromosomes involved in a
translocation are also provided. Certain of these methods involve
providing a nucleic acid probe that bears a label and hybridizes to
a first chromosome susceptible to undergoing a translocation with a
second chromosome. The probe hybridizes to a segment of the first
chromosome that lies entirely in a region that flanks the known
break points associated with the translocation. The nucleic acid
probe is contacted with a chromosomal preparation prepared from a
diploid cell, which preparation may contain a chromosome resulting
from deletion of at least part of the segment of the first
chromosome to which the probe hybridizes. The signal intensity from
the label on different chromosomes is then compared, a difference
in signal intensity indicating presence of a deletion. Such methods
can be utilized in combination with various other chromosomal
detection methods, including the signal splitting and signal
segregating methods (both S-FISH and D-FISH methods) disclosed
herein.
[0039] Probe sets for use in conducting the foregoing methods are
also provided. Certain probe sets for detecting a translocation
between first and second chromosomes include a first and second set
of nucleic acid probes labeled with first and second labels,
respectively, the first probe set comprising at least one proximal
probe and the second probe set comprising at least one distal
probe. The at least one proximal probe has a sequence such that the
proximal probe hybridizes to a segment of chromosomal DNA on the
first chromosome that lies entirely on the centromeric side of all
known break points associated with the translocation. Similarly,
the at least one distal probe has a sequence such that it
hybridizes to a segment of chromosomal DNA on the first chromosome
that lies entirely on the telomeric side of all known break points
associated with the translocation.
[0040] Other probes sets also include a third and fourth probe set
labeled with third and fourth labels, respectively, the third probe
set comprising at least one proximal probe and the fourth probe set
comprising at least one distal probe. The at least one proximal
probe of the third probe set has a sequence that can hybridize to a
segment of chromosomal DNA on the second chromosome that lies
entirely on the centromeric side of all known break points
associated with the translocation. The at least one distal probe of
the fourth probe set has a sequence that can hybridize to a segment
of chromosomal DNA on the second chromosome that lies entirely on
the telomeric side of all known break points associated with the
translocation. In certain probe sets, the first and second labels
are the same and the third and fourth labels are the same, but the
first and second labels differ from the third and fourth labels. In
other probe sets, the first, second, third and fourth label are
each distinguishable from one another.
BRIEF DESCRIPTION OF THE DRAWINGS
[0041] FIGS. 1A and 1B are schematic illustrations that show the
differences between the "Split Signal Approach" and the
"Segregating Signal Approach" in detecting chromosomal
translocations.
[0042] FIGS. 2A-2D depict a two color segregating fluorescent in
situ hybridization (S-FISH) approach for detecting the t(9;22)(q34;
q11) translocation. FIG. 2A depicts the normal chromosomal
arrangement for chromosome 22 and chromosome 9. The interphase
field is also depicted for this arrangement with an open pattern
representing the signal for the BCR gene and a single hatched
pattern representing the signal for the ABL gene. Cells carrying
the t(9;22)(q34; q11) translocation display co-localization of the
open and single hatched signals as depicted in the interphase field
of FIG. 2B. FIG. 2B also schematically depicts the chromosomal
arrangement after translocation of the chromosomal regions distal
to the breakpoint regions of the respective chromosomes. FIG. 2C
depicts a variant translocation involving chromosomes 22, 9 and 1,
together with the resulting interphase pattern. Finally, FIG. 2D
represents a deletion of BCR region on der(9).
[0043] FIGS. 3A-3D depict the four color fluorescence in situ
hyridization (F-FISH) segregated signal approach for detecting the
t(9;22)(q34; q11) translocation, with the rearrangements being
analogous to those described in FIGS. 2A-2D, respectively. FIGS.
3A-3D illustrate that the probe to the centromeric side of the most
centromeric breakpoint will always remain on the chromosome and the
probe to the telomeric side of the most telomeric breakpoint will
always segregate to the rearranged chromosome. In these figures,
the single hatched probe label is always associated with chromosome
9 and the open label is always associated with chromosome 22. This
aspect of the method allows for the detection of specific
derivative chromosomes, and to precisely define the rearrangements
undergone by the derivative chromosomes.
[0044] FIG. 4 is a diagrammatic representation of expected signal
patterns using the F-FISH assay in normal, standard translocation,
deletion and variant translocations commonly encountered in CML and
cataloged in Table 2. The letter designations for each field
correspond to those found in Table 2. Chromosomal probe
designations for FIG. 4 are: Chromosome 9, proximal probe--single
hatched pattern; distal probe--open pattern. Chromosome 22,
proximal probe--stippled pattern; distal probe--double hatched
pattern.
[0045] FIGS. 5A-5D depict the segregating signal approach for
detecting the t(11;14)(q13; q32) translocation by S-FISH and F-FISH
methods. FIG. 5A is a schematic representation of the genomic
organization of the BCL1 and the IGH genes. Vertical bars indicate
approximate positions of the breakpoint regions. The CCND1 gene and
the different coding regions of the IGH genes are shown as open
boxes. Horizontal bars indicate approximate positions of the
probes. Probes labeled 1 and 2 (represented by open bars) bind to
chromosome 11 and bear a label emitting a green signal. Probes 3
and 4 (represented by single hatched bars) bind to chromosome 14
and bear a label emitting a red signal. FIG. 5B is schematic
representation of the expected constellation of signals by two
color S-FISH in normal and tumor interphase nuclei. Probes 3 and 4
together generate a red signal, whereas probes 1 and 2 together
generate a green signal on the corresponding normal chromosomes.
The close proximity of each probe results in only a single signal
on interphase cells. The t(11;14)(q13; q32) positive nuclei,
however, display two fusing or co-localizing green and red signals,
identifying the der(14) and der(11) chromosomes. These signals
arise because labeled probes are segregated between the rearranging
chromosomes. FIG. 5C is schematic representation of the expected
constellation of signals by four color F-FISH in normal and tumor
interphase nuclei(probe 1--stippled; probe 2--open; probe 3--double
hatched; and probe 4--single hatched). Each probe generates a
unique signal. This approach allows for the detection and
identification of specific derivative chromosomes even in
interphase preparations. The alteration in signal pattern observed
for the tumor preparation arises because labeled probes are
segregated between the rearranging chromosomes. FIG. 5D is a
schematic illustration showing the way in which the probes
hybridize to the normal and derivative chromosomes in the two color
S-FISH approach.
[0046] FIGS. 6A-6C illustrate a specific set of probes in a
segregating signal approach that can be utilized to detect the
t(14;1 8)(q32; q21) translocation according to either two color
S-FISH or F-FISH methods. FIG. 6A is a schematic representation of
the genomic organization of BCL2 and IGH genes. Vertical lines
indicate approximate positions of the breakpoint regions. The three
BCL2 exons and the different coding segments of the IGH gene are
shown as open boxes. Bars beneath the gene indicate the approximate
positions of the probes. FIG. 6B is schematic representation of the
expected pattern of signals by two color D-FISH in normal and tumor
interphase nuclei. Probes 1 and 2 (represented by open bars)
together generate a green signal, while probes 3 and 4 (represented
by single hatched bars) together generate a red signal on the
corresponding normal chromosomes. These probes are close enough on
the chromosome to prevent generation of distinct individual
signals. The t(14;1 8)(q32; q21) positive nuclei, however, display
two fusion or co-localizing green and red signals identifying the
der(14) and der(18) chromosomes, due to the fact that signals are
segregated to the rearranging chromosomes. FIG. 6C is schematic
representation of the expected pattern of signals by four color
F-FISH in normal and tumor interphase nuclei. Each probe generates
a unique signal (probe 1--stippled; probe 2--open; probe 3--double
hatched; and probe 4--single hatched). This approach allows for the
detection and identification of specific derivative chromosomes
even in interphase preparations. The alteration in signal pattern
observed for the tumor preparation arises because labeled probes
are segregated between the rearranging chromosomes.
[0047] FIGS. 7A-7C show examples of a specific sets of probes that
can be utilized in a signal segregating approach to detect the
t(8;14)(q24; q32) translocation. FIG. 7A is a schematic
representation of genomic organization of the MYC and IGH genes.
Vertical bars indicate approximate positions of the breakpoint
regions in the MYC and IGH gene regions. The three MYC exons and
the different coding segments of the IGH gene are shown as open
boxes. Horizontal bars indicate the location of the probes. FIG. 7B
is schematic representation of the expected constellation of
signals by two color FISH in normal and tumor interphase nuclei.
Probes 1 and 2 (open bars) together generate a green signal on
chromosome 8, while probes 3 and 4 (single hatched bars)
collectively generate a red signal on chromosome 14 on normal
chromosomes. The probes on the normal chromosomes are sufficiently
close to one another not to result in distinct individual signals.
The t(8;14)(q24; q32) positive nuclei, however, display two fusing
or co-localizing green and red signals identifying the der(8) and
der(14) chromosome due to the fact that signals are segregated to
the rearranging chromosomes. FIG. 7C is schematic representation of
the expected pattern of signals by four color F-FISH in normal and
tumor interphase nuclei. Each probe generates a unique signal
(probe 1--stippled; probe 2--open; probe 3--double hatched; and
probe 4--single hatched). This approach allows for the detection
and identification of specific derivative chromosomes even in
interphase preparations. The alteration in signal pattern observed
for the tumor preparation arises because labeled probes are
segregated between the rearranging chromosomes.
[0048] FIG. 8 is a flow chart summarizing certain steps in a
process for removing repeat sequences from clonal libraries. The
remaining clones can be utilized in the preparation of the desired
probes. Because the resulting probes have been freed of many repeat
sequences, cross-hybridization problems are reduced or completely
eliminated.
[0049] FIGS. 9A and 9B are schematic representations of
hybridization of probes and the probe binding region of the
chromosome. FIG. 9A depicts multiple probe binding, the redundancy
in binding capacity contained in a single probe, and the absence of
repeat sequences in the probe DNA. FIG. 9B depicts the deletion
encroaching into a probe binding region. This type of deletion
adversely affects probe hybridization and reduces the signal
intensity of the fluorescent label associated with the probe.
[0050] FIGS. 10A-10C depict the split signal approach for detecting
the t(9;22)(q34; q11) translocation. FIG. 10A is a schematic
representation of the genomic organization of the BCR and ABL
genes. The coding regions of the gene are represented as open
boxes. The approximate positions of the regions used to develop
commercial probes for this translocation (based on VYSIS product
catalog) are also shown as solid bars labeled green and red to
represent the signal produced by the probe in the exemplary FISH
assay. Vertical bars indicate the approximate position of the
breakpoint regions. FIG. 10B is a schematic representation of
signal localization by two color FISH in normal and tumor
interphase nuclei, with a red signal (double hatched bar) for the
ABL gene and a green signal (single hatched bar) for the BCR gene.
Cells carrying the t(9;22)(q34; q11) translocation display
co-localization of green and red signals identifying the der(22)
chromosome. A third small red signal identifies the der(9)
chromosome. Note that in this signal split approach the probes
overlap the breakpoint region, resulting in only one of the derived
chromosomes being identified by a fusion signal. FIG. 10C is a
schematic illustration showing the way in which the probes
hybridize to the normal and derivative chromosomes.
[0051] FIGS. 11A-11E illustrate aspects of automated detection of
the t(14;18)(q32; q21) translocation associated with follicular
lymphoma. FIG. 11A is a schematic representation of the genomic
organization of BCL2 and IGH genes. Vertical lines indicate
approximate positions of the breakpoint regions. The three BCL2
exons and the different coding segments of the IGH gene are shown
as open boxes. Open and single hatched bars indicate the
approximate positions of the probes. FIGS. 11B-11C are images from
the MetaCyte scanning and capturing process. FIG. 11B shows a DAPI
counterstained nucleus. FIG. 11C is an image of a nucleus painted
with two color S-FISH probes taken through an FITC filter. FIG. 11D
is an image of a nucleus painted with two color S-FISH probes taken
through a Rhodamine filter. FIG. 11E is an integrated image
displaying both FITC and Rhodamine signals.
[0052] FIGS. 12A and 12B illustrate additional aspects of automated
detection of chromosomal rearrangements. FIG. 12A is a schematic
diagram showing the components of Metasystems image scanning
platform. FIG. 12B is a flow diagram outlining the steps in the
method of the Automated Bio-Imaging System.
[0053] FIGS. 13A-13C depict the use of a probe located in a region
flanking the breakpoints involved in a translocation to detect
delections. In the examples illustrated in these figures, the
deletion detection probe is utilized in combination with probes
utilized in a signal segregating approach. FIG. 13A shows the
regions to which the deletion detection probe and the signal
segregating probes hybridize and the hybridization pattern that is
observed prior to a translocation. FIG. 13B shows the arrangement
of the probes and the corresponding hybridization pattern following
a translocation in which there is no deletion. FIG. 13C shows the
arrangement of the probes and the corresponding hybridization
pattern following a translocation which is accompanied by a
deletion.
DESCRIPTION
I. Definitions
[0054] The practice of conventional techniques in molecular
biology, biochemistry, chromatin structure and analysis,
computational chemistry, cell culture, recombinant DNA,
bioinformatics, genomics and related fields are well-known to those
of skill in the art and are discussed, for example, in the
following literature references: Sambrook et al. MOLECULAR CLONING:
A LABORATORY MANUAL, third edition, Cold Spring Harbor Laboratory
Press, 2001; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR
BIOLOGY, John Wiley & Sons, New York, 1987 and periodic
updates; the series METHODS IN ENZYMOLOGY, Academic Press, San
Diego; Wolffe, CHROMATIN STRUCTURE AND FUNCTION, Third edition,
Academic Press, San Diego, 1998; METHODS IN ENZYMOLOGY, Vol. 304,
"Chromatin" (P. M. Wassarman and A. P. Wolffe, eds.), Academic
Press, San Diego, 1999; and METHODS IN MOLECULAR BIOLOGY, Vol. 119,
"Chromatin Protocols" (P. B. Becker, ed.) Humana Press, Totowa,
1999, each of which is incorporated by reference in its
entirety.
[0055] The terms "nucleic acid," "polynucleotide," and
"oligonucleotide" are used interchangeably and refer to a
deoxyribonucleotide or ribonucleotide polymer in either single- or
double-stranded form. For the purposes of the present disclosure,
these terms are not to be construed as limiting with respect to the
length of a polymer. The terms can encompass known analogues of
natural nucleotides, as well as nucleotides that are modified in
the base, sugar and/or phosphate moieties. In general, an analogue
of a particular nucleotide has the same base-pairing specificity
(e.g., an analogue of A will base pair with T).
[0056] The terms additionally encompass nucleic acids containing
known nucleotide analogs or modified backbone residues or linkages,
which are synthetic, naturally occurring, and non-naturally
occurring, which have similar binding properties as the reference
nucleic acid. Examples of such analogs include, without limitation,
phosphorothioates, phosphoramidates, methyl phosphonates,
chiral-methyl phosphonates, 2-O-methyl ribonucleotides, and
peptide-nucleic acids (PNAs).
[0057] A "translocation" refers to the attachment of a fragment of
one chromosome to a non-homologous chromsome (the rearrangement of
fragments within the same chromsome are referred to as
"inversions").
[0058] A "reciprocal translocation," involves the mutual exchange
of fragments between two broken chromosomes, one part of one
chromsome uniting with the part of another chromosome.
[0059] A "balanced translocation" is a translocation in which there
is no loss of genetic material during the translocation but all
genetic material is preserved during the exchange.
[0060] A "variant" or "abnormal" translocation refers to the
involvement of a third chromosome in a secondary rearrangement that
follows a first reciprocal translocation.
[0061] A "chromosome" is a chromatin complex comprising all or a
portion of the genome of a cell. The genome of a cell is often
characterized by its karyotype, which is the collection of all the
chromosomes that comprise the genome of the cell. The genome of a
cell can comprise one or more chromosomes. The term "reciprocal
chromosome" refers to one of the chromosomes engaged in a
reciprocal exchange with another chromosome involving breakage and
transfer of its parts. "Derivative chromosome" is the term used to
refer generally to an abnormal chromosome formed as a consequence
of a translocation, deletion or other chromosomal rearrangement or
combination of chromosomal rearrangements. Such chromosomes are
sometimes referred to simply as "der" chromosomes. "Interphase"
refers to a stage in cell division in which chromosomes are
elongated and entwined with one another. In contrast, "metaphase"
refers to any stage of cell division in which the chromosomes are
condensed or contracted and are distinguishable from one
another.
[0062] A "telomere" refers to the region of a chromosome located at
the distal end of the chromosome.
[0063] The term "centromere" refers to the heterochromatic region
of a eukaryotic chromosome that is the chromosomal site of
attachment of the kinetochore. The centromere divides just before
the replicated chromosomes separate, and acts to hold the paired
chromatids together.
[0064] A "breakpoint" refers to the point or region of a chromosome
at which the chromosome is cleaved during a translocation. A
"breakpoint junction" refers to the region of the chromosome at
which the different parts of chromosomes involved in a
translocation join.
[0065] A "probe" is a nucleic acid capable of binding to a
complementary target nucleic acid through one or more types of
chemical bonds, usually through complementary base pairing, usually
through hydrogen bond formation, resulting in a duplex structure.
As described further herein the probe binds to a complementary
target site in a chromosome. In translocations, the target site to
which the probe binds is usually located in a segment flanking all
the breakpoints. Each translocation represents specific target
sites. Generally, the probe is labeled with one or more detectable
labels to permit the facile detection of the probe following
hybridization on its complementary target.
[0066] A "segment" or a "subsequence" when used in reference to a
nucleic acid refers to a sequence of nucleotides that comprise a
part of a longer sequence of nucleotides.
[0067] The term "diploid" refers to a chromosomal state where there
are at least two homologues of each chromosome present, and also
refers to chromosomal states where there are more than two
homologues of one or more chromosomes present. In the context of
FISH assays, the term "diploid" refers to a chromosomal state where
there is at least one pair of homologous chromosomes, including
derivative chromosomes, which are recognized by the probes used in
the assay.
[0068] A "gene" refers to a region of genomic DNA that encodes a
gene product. A gene product can be the direct transcriptional
product of a gene (e.g., mRNA, tRNA, rRNA, antisense RNA, ribozyme,
structural RNA or any other type of RNA) or a protein produced by
translation of mRNA. Gene products also include RNAs, which are
modified, by processes such as capping, polyadenylation,
methylation, and editing, and proteins modified by, for example,
methylation, acetylation, phosphorylation, ubiquitination,
ADP-ribosylation, myristilation, and glycosylation.
[0069] A "detectable label" or simply "label" refers to any of a
variety of different labels known in the art that can be detected
by chemical, electrochemical, instrumental, or physical means, for
example. Fluorescent labels are often utilized to label the probes.
In some instances, other suitable labels include, but are not
limited to, radioisotopes, chromophores, electron dense particles,
magnetic particles, spin labels and molecules that emit
chemiluminescence, enzymes, enzyme substrates, members of binding
pairs (e.g., avidin/streptavidin and antigen/antibody).
[0070] A "pseudo-color" or "pseudo-label" is a representation of a
detectable label, and can be any one of a variety of different
representations known in the art that can be displayed or stored by
physical, chemical or electronic means. Pseudo-colors are often
graphical elements in a pictorial representation, such as the
colors displayed on a computer monitor as representations of the
fluorescent labels detected in a FISH assay. Other examples of
pseudo colors include graphical representations found on computer
printouts, digital representations stored on a magnetic disk,
pictorial representations formed through optical devices, color
transformations and three-dimensional representations rendered by
computational analysis. It is readily apparent from this definition
that any detectable label can be represented through transformation
by any pseudo-color. Such transformations allow diverse detectable
labels to be represented in a common display or storage format,
thereby easing interpretation and archiving of data.
[0071] "Co-localization" or "co-localizing spots" refers to
detectable labels that are much closer to each other than to other
detectable labels in a field of analysis. Co-localizing spots may
be discrete spots, or may show some overlap forming a "Venn
diagram-type" pattern, depending on the resolution of the detection
device employed. A common characteristic of true co-localizing
spots is that they originate from probes hybridized to the same
chromosome.
[0072] "Fusion signal" or "fusion spot" refers to a composite
signal produced when two different signals overlap to a degree such
that they appear as a single signal. The composite signal often
possesses different characteristics from either of its component
signals.
[0073] A "difference" in signal intensity generally means that
there is a detectable change in signal intensity that is above the
detection limit of the instrument used to measure signal intensity.
In some instances the difference reflects a difference in average
values obtained for signal intensity. A difference is typically
considered to be "statistically significant" if the probability of
the observed difference occurring by chance (the p-value) is less
than some predetermined level. Thus, a "statistically significant
difference" can refer to a p-value that is <0.05, preferably
<0.01 and most preferably <0.001.
II. Overview
[0074] Methods for enhancing the specificity and sensitivity of
fluorescent in situ hybridization (FISH) assays in the detection of
chromosomal rearrangements are disclosed herein. Specific methods,
probes and kits for assaying selected translocations correlated
with tumors are also provided. In particular, methods and probes
for conducting FISH assays for the t(8;14)(q24; q32), the
t(11;14)(q13; q32), the t(9;22)(q34; q11) and the t(14;18)(q32;
q21) translocations are provided. The methods described herein are
not limited to the examples provided but are generally applicable
to other rearrangements (e.g., reciprocal translocations) that are
associated with leukemia, lymphomas, or solid tumors, for
instance.
[0075] Some of the FISH assay methods provided herein utilize
probes that bind to chromosomal DNA at regions that flank the
breakpoints. This contrasts with traditional FISH methods in which
the probe(s) is (are) designed to span the breakpoint junction(s)
of the chromosomes involved in a translocation. Such traditional
approaches often result in a split signal in which labeled probe
for each chromosome is "split" between the derivative chromosome(s)
(i.e., a labeled probe that initially is hybridized to a single
chromosome is split such that a portion of the labeled probe binds
to each of the derivative chromosomes). As noted supra, splitting
of the signal in this way reduces signal intensity and
sensitivity.
[0076] By utilizing probes that hybridize to proximal or distal
regions that flank the breakpoint(s) for the rearrangement of
interest, the current methods generate a segregating signal rather
than a split signal which greatly aids analysis. At least one of
these probes is selected to bind at a region centromeric to all the
known breakpoints. Such a probe is referred to herein as a
"proximal breakpoint region probe" [(PBP), centromeric probe, or
simply a proximal probe] and anneals to a region located between
the breakpoint closest to the centromere and the centromere itself.
Such probes do not segregate in a translocation involving the
breakpoint(s) of interest. At least one other probe is selected to
hybridize to the same chromosome as the PBP, but anneals to a
region telomeric to the known breakpoints associated with the
translocation of interest. Such a probe is referred to herein as a
"distal breakpoint region probe" [(DBP), telomeric probe, or simply
distal probe] and hybridizes to a chromosomal region located
between the known breakpoint nearest the telomere and the telomere
itself. In a translocation event, such probes always segregate to
the reciprocal chromosome. Some of the methods provided herein
utilize multiple probes chosen such that a centromeric and
telomeric probe each hybridize to at least two of the chromosomes
involved in a chromosomal rearrangement.
[0077] Certain methods referred to herein as S-FISH methods utilize
two sets of probes, each set including at least one distal and at
least one proximal probe, with each of the probe sets binding to
different chromosomes that are susceptible to undergoing a
rearrangement. In the S-FISH method, the probes in each set bear
the same label, but probes in different sets bear different labels.
Other methods referred to herein as F-FISH methods utilize the same
two sets of probes, but each probe is differentially labeled, such
that even probes within a set bear different labels. As described
in greater detail below, F-FISH probe sets can be useful in
unambiguously determining the type of rearrangement.
[0078] Still other methods extend the segregating signal concept
further and utilize probes which not only flank the breakpoint(s)
involved in the translocation of interest, but also that hybridize
to proximal or distal regions located outside the genes involved in
the translocation of interest. Such methods further differ from
conventional FISH approaches in which the probes anneal to regions
located within the genes involved in the translocation under
investigation. These methods can be conducted in both the S-FISH
and F-FISH formats.
[0079] Certain of the methods provided address a problem common to
conventional FISH assays, namely the non-specific cross
hybridization of repeat sequences in the probe with those in the
genome. Such non-specific hybridization generates ambiguities in
the analysis of FISH results, in particular the formation of false
positive signals indicating the presence of a translocation when in
fact a translocation has not occurred. Some of the probe design
methods disclosed herein alleviate this problem. Such methods
generally involve identifying sequences that flank the
breakpoint(s) for a reciprocal translocation under investigation.
Genomic clones carrying these sequences are then obtained, often by
PCR screening of commercially available libraries using
region-specific primers, and then cleaved with one or more
restriction enzymes. The resulting fragments are then subcloned and
the resulting subclones probed with radioactively labeled repeat
DNA to determine if the subclone contains complementary repeat
sequence segments. Clones without repeat sequences are then
relegated to form a longer repeat free clone. Conventional methods
for addressing the cross-hybridization problem do not involve such
a cloning and subcloning approach and often involve pre-annealing
of labeled probes with unlabeled human Cot-1 DNA; the present
methods provided herein, however, are not so limited.
[0080] Some methods described herein use FISH techniques in
combination with an automated scanning platform to provide a rapid,
quantitative means for detecting tumor cells in patients undergoing
treatment and follow-up. Automated detection and counting of FISH
signals in a large number of interphase nuclei is demanding both
from a physics and an optical standpoint; the signals are small,
contrast is often inconsistent, and 3-D analysis is required due to
the thickness of the nuclei. These problems are overcome by the
methods described herein, by the use of probes from the regions
flanking all the breakpoints which significantly reduces the high
rate of false positive cells commonly encountered using the former
FISH methods. Thus, the use of probes developed using the methods
described herein facilitate analysis using automated image
scanning.
[0081] In summary, the FISH methods described herein can overcome
the limitations of cytogenetic and molecular genetic methods and is
well-suited for detecting tumor cells, even in low frequencies,
because: (1) the methods are rapid and easy to perform, (2)
dividing cells are not necessary, (3) a large number of cells can
be scored rapidly in a single assay, and (4) hybridization can be
performed in tissues preserved in virtually any form, including
paraffin embedding. In addition, careful selection of probe
reagents on either side of the breakpoint region can eliminate the
technical limitations of the previously discussed molecular
methods.
III. FISH Detection Schemes
[0082] A. General
[0083] The FISH methods provided herein find general applicability
in detecting and analyzing chromosomal rearrangements. The methods
can be utilized to develop sensitive and selective probes to detect
essentially any combination of rearrangements once the chromosomal
sequences involved with, and flanking, the breakpoints are known.
Exemplary rearrangements that occur in hematopoietic and solid
cancers that can be assayed using the methods described herein
include, but are not limited to, those listed in Tables 1 and Table
2 (see section III.C.8). TABLE-US-00001 TABLE 1 Chromosomal
translocations that serve as diagnostic and follow-up markers in
cancer (Heim & Mitelman, 1995). Translocation Genes involved
Disease Leukemia t(9; 22)(q32; q11) ABL; BCR CML t(9; 22)(q34; q11)
ABL; BCR CML t(3; 21)(q26; q22) EVI1; MDS1 CML blast crisis, AML
t(6; 9)(p23; q34) DEK; CAN MDS, M2 basophilia t(6; 11)(q27; q23)
AF6; MLL M4, M5 t(8; 21)(q22; q22) ETO; AML1 MDS, M2 with Auer rods
t(9; 11)(p21; q23) AF9; MLL M5 t(11; 17)(q23; p13) PLZF; RARA M3
t(11; 19)(q23; p13) MLL; ENL M4, M5 t(15; 17)(q22; q12.21) PML;
RARA M3 t(16; 21)(p11; q23) FUS; ERG No specific FAB type t(10;
14)(q24; q11) HOX 11; TCRD T cell ALL t(11; 14)(p13-15; q11)
RBTN1&2; TCRD T cell ALL t(11; 19)(q23; p13) MLL; ENL ALL
(LTG19, MLLT1) Lymphoma t(14; 18)(q32; q21) BCL2; IGH Follicular
lymphoma t(11; 14)(q13; q32) BCL1; IGH B-CLL t(8; 14)(q24; q32)
IGH; MYC Burkitt's lymphoma t(2; 8)(p12; q24) IGK; MYC Burkitt's
lymphoma t(8; 22)(q24; q11) IGL; MYC Burkitt's lymphoma t(9;
14)(p13; q32) PAX5; IGH Plasmacytoid lymphoma t(3; 14)(q27; q32)
BCL6; IGH Large cell lymphoma t(14; 15)(q32; q11-13) IGH; BCL8
Large cell lymphoma Solid tumor t(1; 13)(p36; q14) PAX7; FKHR
Rhabdomyosarcoma t(2; 13)(q35; q14) PAX3; FKHR Rhabdomyosarcoma
t(11; 22)(p13; q12) WT1/EWS Ewing sarcoma t(21; 22)(q24; q12)
ERG/EWS Ewing sarcoma t(X; 18)(p11; p11) SSX/SYT Synovial
sarcoma
[0084] Currently, diagnosis and post-treatment follow-up of these
particular cancers and other cancers associated with chromosomal
rearrangements are typically performed by either karyotype
analysis, Southern blotting, polymerase chain reaction (PCR) or
fluorescence in situ hybridization (FISH). As noted supra, each of
these methods has limitations of specificity and/or sensitivity,
thus creating the need for another precise, reliable and easy
method to detect tumor cells, especially in post-treatment set
up.
[0085] B. FISH Utilizing Split Signal Approach
[0086] One approach for conducting a FISH assay utilizes what is
referred to herein as a split signal approach. FIG. 1A illustrates
the use of this method for detecting a translocation event. The
method generally utilizes two differentially labeled probes (e.g.,
probes bearing a green or a red fluorophore) that each hybridize to
a segment of a gene (e.g., gene A or gene B in FIG. 1A) on one of
the chromosomes that is involved in a translocation (e.g.,
chromosome 1 or 2 in FIG. 1A). In this approach, the segment to
which the probes bind spans the breakpoint (in FIG. 1A, the binding
segments are represented by the dashed and cross-hatched bars).
Once a rearrangement occurs to form derivative chromosome(s), the
labeled probes can potentially bind to the derivative chromosomes
since each rearranged chromosome typically includes a part of the
segment complementary to each probe. Thus, while prior to the
translocation each probe hybridized to a single chromosome, after
the translocation any given labeled probe becomes "split" between
the two derivative chromosomes. Consequently, a derivative
chromosome can be detected by the formation of a fusion signal,
i.e., a combined signal resulting from different signals for the
different labels borne by the probes. Whether one or two fusion
signals are generated depends upon the location at which the probes
hybridize in relation to the breakpoints. If a probe spans the
breakpoint a significant distance on either side of the breakpoint
(e.g., probe 1 in FIG. 1A), then the probe can likely bind to both
derivative chromosomes. If, however, a probe only extends a short
distance across a breakpoint (e.g., probe 2 in FIG. 1A), the probe
may only be able to bind to one of the derivative chromosomes.
[0087] This approach is illustrated more specifically in FIGS. 10A
and 10B, which is based on the BCR/ABL fusion in the t(9;22)(q34;
q11) translocation in chronic myelogenous leukemia (CML), for which
commercial probes are available (VYSIS). The only commercially
available probe for leukemia translocations, i.e., t(9;22)(q34;
q11) in CML, were developed based on the split signal principle.
FIG. 10A provides a schematic illustration of the genomic
arrangement of the BCR and ABL genes. The coding regions of the
gene are represented as open boxes. Also shown, as single hatched
bars (e.g., green) and double hatched bars (e.g., red), are
approximate positions of the regions used in the development of
commercial probes for this translocation by VYSIS (based on VYSIS
product catalog). The vertical bars indicate the approximate
position of the breakpoint regions. FIG. 10B is schematic
representation of the localization of the labeled probes by two
color FISH in normal and tumor interphase nuclei; FIG. 10C
illustrates how the probes hybridize to the chromosomes both before
and after the translocation. Cells carrying the t(9;22)(q32; q11)
translocation display co-localization of the two signals (green and
red), thus identifying the der(22) chromosome. A third small red
signal identifies the der(9) chromosome. In this split signal
approach, only one fusion signal identifies only one of the derived
chromosomes.
[0088] There are three major disadvantages with this method. The
first relates to sensitivity. False positive signals may be
generated in normal cells by random co-apposition of normal
chromosomal signals. This is especially critical in probe systems
that detect fusion signals from only one of the two derived
chromosomes. The second disadvantage is that it is difficult to
generate probes spanning all the breakpoints that are sometimes
spread over several kilobases of intronic DNA. Ideally, probe
systems should detect both reciprocal partners of the translocation
without the need to include the breakpoint region. Finally,
difficulties arise in identifying variant forms of translocations.
For example, some translocations are accompanied by deletions
within the genetic regions involved in the translocation. Such
deletions can effect both the sensitivity and precision of the
method by weakening, or completely removing, probe binding sites.
Other rearrangements are accompanied by secondary translocations
involving additional chromosomes. In some split-signal
arrangements, such secondary translocations can go entirely
undetected.
[0089] C. FISH Utilizing Signal Segregation Approach
[0090] 1. General
[0091] FISH methods can also be performed using a segregating
signal approach that differs from the foregoing split signal
approach. Such methods utilize first and second sets of probes
hybridizing to first and second chromosomes that are susceptible to
undergoing a reciprocal translocation with one another. Each set of
probes comprises at least one proximal probe and at least one
distal probe. The proximal probe or probes occurs on the
centromeric side of all known breakpoints associated with the
translocation and are referred to as proximal break point probes
(PBPs), or simply proximal probes. The distal probe or probes
occurs on the telomeric side of all known breakpoints associated
with the translocation and are referred to as distal break point
probes (DBPs), or simply distal probes. Neither the proximal nor
the distal probes hybridize to any region within any of the known
breakpoints. In some methods, the proximal and distal probes
hybridize to regions that are at least 10 kb, 50 kb, 100 kb or 200
kb away from the outermost known centromeric break point and the
known outermost telomeric break point, respectively. In some
methods, all known break points associated with a translocation on
a particular chromosome are within a gene, and the proximal and
distal probes are both located outside the gene. In some methods,
the proximal and distal probes hybridize to regions of chromosomal
DNA extending no further than 1 Mb from the outermost known
centromeric and telomeric breakpoints associated with the
translocation. The region, however, can be a shorter distance from
the breakpoint(s) (e.g., up to about 800 kb, 600 kb, 400 kb, 200
kb, 100 kb, 50 kb, 25 kb 10 kb, 5 kb, 1 kb and 0.5 kb) and longer
distances (e.g., up to about 1.2 Mb, 1.4 Mb, 1.6 Mb, 1.8 Mb, 2 Mb
and 4 Mb), including any integer within the foregoing ranges,
provided the region is sufficiently long to allow for specific
hybridization between the probe and region.
[0092] The length of proximal and distal probes and corresponding
regions of chromosomal DNA bound by the probes can vary. In some
methods, the length of chromosomal DNA bound by distal or proximal
probe(s) varies from 10 kb to 1000 kb. In other methods, the length
of chromosomal DNA bound by distal or proximal probe(s) varies from
100 kb to 300 kb and in still other methods is about 200 kb. In
certain methods, the distal probe or probes do not hybridize to a
single contiguous region of chromosomal DNA but rather to several
regions interspersed by repeat sequences for which corresponding
probes sequences have been removed. In such methods, the region of
chromosomal DNA bound by such probes is that between the outermost
regions of chromosomal DNA to which the probes hybridize (i.e.,
including intervening repeating segments not bound by the probe).
In general, signal strength increases within increasing length of
probes, and lengths of the order of 200 kb are typically
utilized.
[0093] FIGS. 1A and 1B illustrate the differences between the
segregating signal and split signal approaches. As can be seen, in
the segregating signal approach (FIG. 1B), the probe binding site
is not "split" due to spanning a breakpoint involved in the
translocation; consequently, there is no loss of signal strength
and sensitivity is increased.
[0094] By analyzing the hybridization pattern, the original first
and second chromosomes, and derivative chromosomal forms that
result from reciprocal translocation between the two chromosomes,
can be identified and distinguished. The methods can also identify
nonreciprocal translocations of DNA from the first or second
chromosome to a third chromosome. The methods can also identify
deletions occurring concurrent with translocations. The methods can
be performed on both interphase and metaphase cells, although in
some methods there are differences in the information that can be
extracted from the resulting hybridization pattern.
[0095] Hybridization patterns can have any a number of arrangements
of labels indicating the presence of various chromosomes and
translocation events. In the two color S-FISH strategy,
translocation between the first and second chromosomes is indicated
by a co-localization of spots of first and second label.
Co-localization means that spots of the labels appear significantly
closer to each other than to other spots of label. Often (but not
necessarily) co-localizing spots of label intersect like two
circles of a Venn diagram. In such cases, the co-localization is
manifested by first label, second label and first and second label
superimposed. If colocalizing spots do not intersect, then
colocalization is indicated by the proximity of two spots relative
to that of other spots in the same hybridization pattern. For
metaphase chromosomes, colocalization can be seen from the two
spots being located on the same chromosome. If the translocation
between first and second chromosomes is reciprocal, then two
derivative chromosomes result, and this is indicated by two
separate colocalizations of first and second label in the
hybridization pattern. If the cell is in metaphase, one can
distinguish between the two derivative chromosomes based on the
locations of colocalizing label. Thus, if a colocalization of first
and second labels has first label in the centromeric region of a
derivative chromosome and second label in the telomeric region,
then one knows that the derivative chromosome is formed from the
first chromosome, with the centromeric region originating from the
first chromosome and the telomeric region from the second
chromosome. Conversely, if a colocalization of first and second
labels has second label in the centromeric region of a derivative
chromosome and first label in the telomeric region, then one knows
that the derivative chromosome formed from the second chromosome,
with the centromeric region originating from the second chromosome
and the telomeric region from the first chromosome region. The
ability of the present methods to detect simultaneously both
derivative chromosomes significantly reduces or eliminates the
probability of scoring false positive cells, a considerable problem
plaguing current detection methods.
[0096] The hybridization pattern can include a spot of first label
without second label and a spot of second label without first label
in addition to colocalizing spots of first and second label. Such
spots signify the presence of untranslocated forms of the first and
second chromosomes. Occasionally, a pattern can be obtained having
four colocalizing spots of first and second label and no spots of
first label with spots of second label. Such a pattern signifies
that both pairs of chromosomes in a diploid cell have undergone a
reciprocal translocation resulting in four derivative
chromosomes.
[0097] If the cells being analyzed are in metaphase, the
hybridization pattern can sometimes include a spot of either first
or second label on a third chromosome different from either the
first or second chromosome. Such a pattern signifies that the first
or second chromosome has undergone a nonreciprocal translocation
with a third chromosome, whereby the third chromosome has acquired
a telomeric segment from the first or second chromosome. Such
nonreciprocal translocations can occur in combination with, or
separate from, reciprocal translocations. Therefore, a spot of
first or second label on a third chromosome can be observed in
combination with either colocalization of first and second label on
reciprocally translocated chromosomes, or with first label without
second label on the first chromosome and second label without first
label on the second chromosome.
[0098] The pattern of hybridization can also indicate the presence
of deletions. Deletions are typically associated with poor
prognosis, thus making unambiguous identification of such changes
highly important. Through F-FISH analysis, deletions are readily
detectable through loss of a label normally present in the signal
pattern. Since each label directly indicates the location of the
origin of the probe generating it, the missing label directly
identifies the region of deletion.
[0099] Generally, deletions of chromosomal material coincident with
a translocation or translocation-like rearrangement can take one of
two forms. Macro-deletions, such as those depicted in FIG. 2D and
FIG. 3D, typically appear to be a consequence of an aborted
translocation where chromosomal material is lost instead of
exchanged, or is exchanged non-reciprocally. Such macro-deletions
result in a loss of all chromosomal material distal and/or proximal
to a known breakpoint involved in the translocation event.
[0100] The second type of deletion, a micro-deletion, differs from
a macro-deletion in two respects. First, micro-deletions, as the
name implies, are typically very much smaller in size when compared
to a macro-deletion. Second, micro-deletions occur proximal
(centromeric), or distal (telomeric), to known breakpoints.
Micro-deletions can result from at least two possible mechanisms.
In one mechanism, a nuclease acts on the unprotected chromosomal
stub left without a telomeric structure following a macro-deletion
or translocation event can effect a deletion. A second possible
mechanism is that previously unmapped breakpoint(s) exist proximal
or distal to all known breakpoints and what is characterized as a
micro-deletion is actually the product of a translocation or
translocation-like event involving the unmapped breakpoint.
[0101] Macro-deletions can be detected by the presence of fewer
spots of label than expected. For example, if a cell is diploid and
no deletions occur, with the two color S-FISH method one expects to
see two spots of first label and two spots of second label. With
the F-FISH method, in the absence of deletions, one expects to see
two sets of two fused spots, the fused spots of the first set
consisting of first and second labels and the fused spots of the
second set consisting of third and fourth labels. If the
hybridization pattern contains fewer spots, then one can conclude
that a deletion has occurred. If the missing spot is of first
label, then one can conclude that a segment from the first
chromosome has been lost, and likewise if the missing spot is of
the second label one can conclude that a segment of the second
chromosome has been lost. If the cell is in metaphase, one can tell
more precisely from the hybridization pattern which chromosome, and
where within the chromosome, the loss of the segment has
occurred.
[0102] Micro-deletions can be detected by comparing the intensities
of different spots of label, usually of the same type. Reduced
intensity of one spot relative to another of the same label
indicates a deletion, and the magnitude of the reduction is related
to the extent of the deletion. This correlation exists because the
intensity of the signal produced by a labeled (e.g. fluorophore)
probe is proportional to the degree of hybridization between the
probe and its chromosomal binding site. Thus, for example, if a
hybridization pattern contains colocalizing spots of first label
(indicating an untranslocated form of the first chromosome) and
colocalizing spots of first and second label (indicating a
derivative chromosome formed by translocation between the first and
second chromosomes), one can compare the intensity of the spots
arising from first label or associated with the untranslocated and
derivative chromosomes. Determining that the intensity of first
label on the derivative chromosome is less than the intensity of
label associated with the untranslocated chromosome indicates that
the derivative chromosome has undergone a deletion.
[0103] 2. Exemplary S-FISH Analyses
[0104] The foregoing principles are illustrated by FIGS. 2A-D
utilizing two color S-FISH methods. FIG. 2A shows regions from
human chromosomes 22 and 9 containing the BCR and ABL genes that
contain breakpoints for a reciprocal translocation. The probes
shown in this figure lie outside of all known breakpoints and in
fact outside the BCR and ABL genes. FIG. 2A shows the hybridization
pattern in a normal cell. There are four spots, two spots
displaying each label, the spots occurring in co-localizing pairs
that at least partially intersect. FIG. 2B shows derivative
chromosomes that result from reciprocal translocation of
chromosomes 22 and 9. Der(22) contains the centromeric region from
chromosome 22 and the telomeric region from chromosome 9, thus
creating the BCR/ABL oncogene whose expression product disrupts
normal cell growth and promotes a cancerous state. Der(9) contains
the centromeric region from chromosome 9 and the telomeric region
from chromosome 22. The hybridization pattern resulting from this
translocation contains two colocalizing spots of first label (open
bar) and second label (single hatched bar) (corresponding to
der(22) and der(9); designated by the letter "A" in FIG. 2B) and
two spots (one of first label and one of second label)
corresponding to untranslocated chromosomes 22 and 9.
[0105] FIG. 2C shows an example of derivative chromosomes resulting
from a variant, nonreciprocal translocation involving chromosomes
1, 9, and 22. Chromosome der(22) consists of the regions of
chromosome 22 centromeric to the translocation breakpoint, and a
telomeric region from chromosome 9. Chromosome der(1) consists of
chromosome 1, to which the telomeric region of chromosome 22 has
been attached. Chromosome der(9) is chromosome 9 which has
undergone a nonreciprocal translocation of the region telomeric to
the translocation breakpoint located in the ABL gene. The effect of
this nonreciprocal translocation on chromosome 9, is a deletion of
the telomeric region of the chromosome arm. When the variant
nonreciprocal translocation of FIG. 2C occurs in diploid cells, at
least three spots of each label can be observed in the
hybridization pattern. The pattern contains two spots, one each of
first and second label, corresponding to untranslocated chromosomes
22 and 9. Colocalizing spots of first and second labels, noted by
the letter "A" in FIG. 2C, correspond to the derivative chromosome
22, der(22). The single spot of second label (single hatched
pattern), noted by the letter "B" in FIG. 2C, corresponds to
der(9); the single spot of first label (open pattern), noted by the
"C" in FIG. 2C, corresponds to der(1). One interpretation of the
variant translocation result depicted in FIG. 2C is that a
reciprocal translocation between chromosomes 9 and 22 was
initiated, but at some point deviated from the common reciprocal
exchange of telomeric regions between the two chromosomes.
Chromosome 22 received the telomeric region of chromosome 9,
forming der(22), but the translocation mechanism transferred the
telomeric region of chromosome 22 to chromosome 1, forming der(1),
instead of attaching it to the breakpoint lesion on chromosome
9.
[0106] A similar mechanism explains the macro-deletion of
chromosome 9 depicted in FIG. 2D. Once again, a reciprocal
translocation event was initiated by cleavage of chromosome 9 at a
breakpoint within the ABL gene. Instead of translocating the
telomeric region of chromosome 9 to chromosome 22, chromosome 22
was left intact and the cleaved telomeric region of chromosome 9
subsequently lost, thus leaving chromosome 9 as a derivative
chromosome, der(9), carrying a macro-deletion. The resulting
hybridization pattern for a diploid cell possessing a chromosome
with this macro-deletion is depicted in FIG. 2D. The pattern
comprises spots of first label (open pattern) corresponding to the
untranslocated pair of chromosome 22 homologues. There are also two
discrete spots of second label (single hatched pattern) in the
pattern. One second label spot corresponds to the untranslocated
chromosome 9 homologue. The other second label spot is of lower
intensity and corresponds to the der(9) containing the
macro-deletion.
[0107] 3. Exemplary F-FISH Analyses
[0108] In a variation of the above methods, distal and proximal
probes of each probe set can be differentially labeled. Such
methods are referred to as F-FISH methods. The differential labels
of distal and proximal probes hybridizing to the first and second
chromosome can be viewed as subtypes of the first and second labels
described above. However, for simplicity, the proximal and distal
probes hybridizing to the first chromosome are now referred to as
having first and second labels, respectively, and the proximal and
distal probes hybridizing to the second chromosome are referred to
as having third and fourth labels, respectively. Methods employing
four differentially labeled probe sets are sometimes referred to as
F-FISH in distinction from methods employing two differentially
labeled probe sets that are sometimes referred to as being
S-FISH.
[0109] F-FISH probes are particularly useful for analyzing
interphase cells. Because each section of the chromosome bearing
the breakpoint of interest hybridizes to a different label, one can
characterize an interphase chromosomal preparation simply by
analyzing the proximity of the probe signals emitted by each label.
Using the F-FISH strategy, one can distinguish both the nature of
the rearrangement and precisely which chromosomes participated in
the rearrangement event, even in interphase systems.
[0110] Hybridization patterns can give any number of arrangements
of labels indicating particular chromosomes and any rearrangements
those chromosomes may have undergone. Untranslocated chromosomes
are indicated by a colocalization of first and second label or
colocalization of third and fourth label. More specifically, a
colocalization of first and second label corresponds to an
untranslocated first chromosome, and colocalization of third and
fourth label corresponds to an untranslocated second chromosome.
Co-localization is possible because the label for each probe set is
unique to the probe set and PBP's are retained on the original
chromosome, even after that chromosome has undergone a
rearrangement.
[0111] A translocation between the first and second chromosomes is
indicated by a co-localization of spots of first and fourth label
or second and third label. A colocalization of first and fourth
label corresponds to the first rearranged chromosome. The
translocated first chromosome having an arm comprised of the
centromeric region of the first chromosome and the telomeric region
of the second chromosome. Correspondingly, a colocalization of
second and third label corresponds to the second rearranged
chromosome. The translocated second chromosome having an arm
comprised of the centromeric region of the second chromosome and
the telomeric region of the first chromosome.
[0112] The hybridization pattern can include isolated spots of
first, second, third and fourth label in addition to
co-localization of spots of first or third label with spots of
fourth or second label. Isolated spots of this type indicate the
presence of either a macro-deletion or a variant translocation of
the telomeric region of the first or second chromosome to a third
chromosome. More specifically, isolated spots of second or fourth
label are indicative of variant translocations comprised of a
transfer of the telomeric region beyond the breakpoint of the first
or second chromosome to a third chromosome. An isolated second spot
corresponds to the transfer of the telomeric region beyond the
breakpoint of the first chromosome, to a third chromosome.
Similarly, an isolated fourth spot corresponds to the transfer of
the telomeric region beyond the breakpoint of the second
chromosome, to a third chromosome.
[0113] Isolated spots of first and third label are indicative of
macro-deletions of telomeric regions of the first or second
chromosome. An isolated spot of first label corresponds to a first
chromosome which has undergone a macro-deletion in the telomeric
region beyond the translocation breakpoint. Similarly, an isolated
spot of third label corresponds to a second chromosome which has
undergone a macro-deletion in the telomeric region beyond the
translocation breakpoint.
[0114] The F-FISH strategy also enables the detection of
micro-deletions by comparing the intensities of different spots of
label of the same type. Reduced intensity of one spot relative to
another of the same label indicates a deletion, and the magnitude
of the reduction is related to the extent of the deletion. This
correlation exists because the intensity of the signal produced by
a labeled fluorescent probe is proportional to the degree of
hybridization between the probe and its chromosomal binding site.
For example, if a hybridization pattern contains colocalizing spots
of first and second label (indicating an untranslocated form of the
first chromosome) and colocalizing spots of first and fourth label
(indicating a derivative chromosome formed by translocation between
the first and second chromosomes), one can compare the intensity of
the first label spots from the untranslocated and derivative
chromosomes. Determining that the spot of label on a derivative
chromosome has less intensity than the same spot of label on an
untranslocated chromosome indicates the derivative chromosome has
undergone a deletion. The same analysis can be done by comparing
isolated spots of any label type with a spot of the same label type
on an untranslocated chromosome. The F-FISH strategy allows
micro-deletion detection to be made for both interphase and
metaphase chromosomes, although metaphase preparations are
preferred because the labels are much more discrete when the
chromatin is condensed.
[0115] The principles of the F-FISH strategy are illustrated
schematically in FIGS. 3A-3D, which shows identical rearrangements
to those depicted in FIGS. 2A-2D for the S-FISH strategy with
chromosomes 9 and 22 containing the ABL and BCR genes,
respectively. Both ABL and BCR contain multiple breakpoints where
chromosomal rearrangements can occur. The probes shown in FIGS. 3A
lie outside all known breakpoints and in fact lie outside the ABL
and BCR genes themselves. FIG. 3A also indicates that each probe
has a unique label, which allows for independent identification of
both centromeric and telomeric regions of each chromosome in both
interphase and metaphase preparations. The hybridization pattern in
a normal diploid cell using the F-FISH strategy is shown in FIG.
3A. There are two spots of each label in the normal pattern, with
first and second labels (open and stippled pattern, respectively)
colocalizing and corresponding to chromosome 22, and third and
fourth labels (single hatched and double hatched patterns,
respectively) colocalizing and corresponding to chromosome 9.
[0116] FIG. 3B shows derivative chromosomes that result from
reciprocal translocation of chromosomes 22 and 9. Der(22) contains
the centromeric region from chromosome 22 and the telomeric region
from chromosome 9 and der(9) contains the centromeric region from
chromosome 9 and the telomeric region from chromosome 22. The
resulting hybridization pattern contains co-localizing spots of
first and second label corresponding to the untranslocated
chromosome 22, and colocalizing spots of third and fourth label
corresponding to untranslocated chromosome 9. The hybridization
pattern also contains two additional sets of colocalized labels
corresponding to derivative chromosomes formed by the reciprocal
translocation event. One of these sets is comprised of first and
fourth label (open and double hatched pattern, respectively) and
corresponds to a derivative chromosome 22, der(22). The second of
these sets of co-localizing spots is comprised of second and third
labels (stippled and single hatched pattern, respectively) and
corresponds to a derivative chromosome 9, der(9).
[0117] FIG. 3C shows three derivative chromosomes formed by a
variant, non-reciprocal translocation. The hybridization pattern
resulting from this rearrangement in diploid cells contains five
sets of spots. One set of spots consists of first and second labels
colocalizing and corresponding to chromosome 22. A second set of
spots consists of third and fourth labels colocalizing and
corresponding to chromosome 9. A third set of spots consists of a
first label (open pattern) colocalizing with a fourth label (double
hatched pattern) and corresponds to a derivative chromosome,
der(22), comprised of the centromeric region of chromosome 22 and
the telomeric region of chromosome 9. The pattern also contains two
isolated spots of label. One of these isolated spots is of third
label (single hatched pattern). In these examples, third label is
associated with the PBP of chromosome 9, and will always correspond
to chromosome 9 or a derivative of that chromosome. Whenever a spot
of third label is observed isolated from all other spots, it
corresponds to a der(9) where the chromosome 9 has undergone a
macro-deletion in the chromatin telomeric to a known breakpoint.
Because the second and fourth labels always migrate with the
chromatin telomeric to a known breakpoint, an isolated spot of
either of these labels indicates that chromatin telomeric to a
known breakpoint has been translocated to a third chromosome. Thus,
the isolated spot of second label (stippled pattern) contained in
the hybridization pattern corresponds to a variant translocation to
a third chromosome, in this case chromosome 1.
[0118] FIG. 3D illustrates the hybridization pattern produced by a
macrodeletion of one of the labeled chromosomes. When such a
deletion occurs in diploid cells, four sets of spots are produced.
Two sets of spots consist of first and second labels (open and
stippled pattern, respectively) colocalizing and corresponding to
the homologous pair of chromosome 22. A third set of spots consists
of third and fourth labels (single hatched and double hatched
pattern, respectively) colocalizing and corresponding to chromosome
9. The hybridization pattern contains a fourth isolated spot of
third label (single hatched pattern) corresponding to a der(9),
which consists of chromosome 9 from which a section of the
telomeric region has been lost as the result of a macrodeletion.
Using this strategy, micro- and macro-deletions encroaching into
the binding regions of first and third probes can be detected.
Micro-deletions are detected by the presence of labels emitting at
a reduced intensity, while the complete absence of label from the
pattern is indicative of a macro-deletion.
[0119] 4. The t(11;14)(q13; q32) Translocation in Mantle Cell
Lymphoma
[0120] The section describes in more detail how the S-FISH and
F-FISH segregated signal approaches can be utilized for the
detection of the t(11;14)(q13; q32) translocation associated with
Mantle Cell Lymphomas. With reference now to FIGS. 5A and 5B, the
t(11;14)(q13; q32) translocation results from breakpoints that
occur within the JH region of the immunoglobulin heavy chain gene
(IGH) on chromosome 14q32; whereas, in more than 80% of the cases,
the breakpoints on chromosome 11 q are clustered in a region known
as the major translocation cluster (MTC), (Rimokh et al., 1990;
Williams et al., 1993; Vandenberghe et al., 1992). Additional
breakpoints have been identified in the region between MTC and the
BCL1 gene known as minor translocation cluster regions 1 & 2
(mTC1 & mTC2). This region spans about 120 kb upstream of the
CCND1 gene at 11q13 (de Boer et al., 1993; Rimokh et al., 1993)
(see FIG. 5A). In FIG. 5A, vertical bars indicate the approximate
positions of the breakpoint region. The CCND1 gene and the
different coding regions of the IGH genes are shown as open
boxes.
[0121] With the two color S-FISH segregating signal approach
provided herein, the labeled probes utilized to detect the
t(11;14)(q13; q32) translocation are selected to hybridize with
segments of chromosomes 11 and 14 that flank the breakpoints. In
this particular detection scheme, two probes are utilized for each
chromosome, with probes that hybridize to the same chromosome
bearing the same label and probes that bind to the different
chromosomes bearing different labels. In the example shown in FIG.
5A, the probes are differentially labeled (e.g., probes for
chromosome 11 are labeled with a green fluorophore), while probes
for chromosome 14 are labeled with a red fluorophore). By utilizing
probes that are differentially labeled for the different
chromosomes, the probes can be readily distinguished from one
another.
[0122] Representative probes that bind to segments flanking the
breakpoints are shown in FIG. 5A with open horizontal bars
indicating binding locations for chromosome 11 probes (i.e., probes
1 and 2 labeled, for example, with a green fluorophore) and single
hatched bars indicating the binding locations for chromosome 14
probes (i.e., probes 3 and 4 labeled, for example, with a red
fluorophore). Of course, other probes for each chromosome can be
utilized, provided the probes hybridize to segments that flank the
known breakpoint regions.
[0123] Thus, the probes derived from the most proximal region of
the translocation breaks will not segregate for all rearrangements
within the BCL1 and IGH genes. In contrast, the probes derived from
the region distal to the proximal breakpoints do segregate to the
reciprocal chromosomes.
[0124] FIGS. 5B and 5D illustrate how the probes become segregated
between the two chromosomes as a consequence of the rearrangement
that occurs with cleavage occurring at the MTC. In normal
interphase chromosomes that have not undergone rearrangement,
probes 3 and 4 (single hatched pattern) generate a red signal,
whereas probes 1 and 2 (open pattern) generate a green signal when
the two color S-FISH strategy is used. The close proximity of the
two probes on each chromosome results in one signal rather than two
distinct signals on each chromosome. However, t(11;14)(q13; q32)
positive nuclei (i.e., nuclei in which the translocation has
occurred) display two fusing or co-localizing green and red signals
(combination of open and single hatched pattern); these
co-localizing signals identify the der(14) and der(11) chromosomes
and arise because the distal probes on each chromosome segregate to
the reciprocal chromosome as a consequence of the
translocation.
[0125] FIG. 5C illustrates identical events as described above for
the S-FISH strategy, with the exception that the interphase
patterns are generated by a four color F-FISH strategy. As
described in detail supra, in the F-FISH strategy each set of
probes carries a unique label allowing specific chromosomal regions
from particular chromosomes to be identified in both interphase and
metaphase preparations. In FIG. 5C, first label is represented by
the stippled pattern and binds to chromosome 11 centromeric to all
known breakpoints in the BCL1 gene.
[0126] The open pattern represents the second label which binds to
chromosome 11 in a position telomeric to all known breakpoints in
the BCL1 gene. The double hatched pattern represents the third
label which binds to chromosome 14 telomeric to the known
breakpoint region found in the IGH gene; the single hatched pattern
represents fourth label which binds chromosome 14 centromeric to
the known breakpoint region found in the IGH gene.
[0127] The normal interphase hybridization pattern shows four sets
of colocalized spots representing the untranslocated forms of
chromosomes 11 and 14. The sets of spots consisting of colocalized
first and second label correspond to chromosome 11 and the sets of
spots consisting of colocalized third and fourth label correspond
to chromosome 14. The tumor interphase hybridization pattern for
the t(11;14)(q13; q32) translocated chromosomes represents a
classic reciprocal translocation pattern using the F-FISH strategy.
As in the normal interphase hybridization pattern, the tumor
interphase hybridization pattern consists of four sets of
colocalizing spots of label. Two of these sets of spots represent
the normal homologues for chromosomes 11 and 14 (colocalized spots
of first and second label correspond to chromosome 11, and
colocalized spots of third and fourth label correspond to
chromosome 14). The remaining two sets of spots correspond to
derivative chromosomes formed from a reciprocal translocation
between chromosomes 11 and 14. Specifically, the colocalized first
and third label spots (stippled and double hatched patterns)
correspond to a der(11) chromosome consisting of the centromeric
region of chromosome 11 and the telomeric region of chromosome 14.
Colocalized spots of second and fourth label (open and single
hatched patterns) correspond to the a der(14) chromosome consisting
of the centromeric region of chromosome 14 and the telomeric region
of chromosome 11.
[0128] As is illustrated by a comparison of the tumor interphase
fields of FIG. 5B and FIG. 5C, the two color S-FISH strategy only
allows a determination of the presence of two rearranged
chromosomes from the presence of the two identical co-localizing
signals. Using the S-FISH strategy, it is impossible to determine
the identity of particular rearranged chromosomes. The F-FISH
strategy improves upon this S-FISH result by allowing
identification of specific derivative chromosomes based upon the
unique probe labels recognizing each breakpoint-flanking region of
each rearranged chromosome, even when the chromosomes are in
interphase.
[0129] Aspects of the segregating signal approach as utilized to
detect the t(11;14)(q13; q32) translocation are described in
greater detail in Example 3.
[0130] 5. The t(14;18)(q32; q21) Translocation in Follicular
Lymphoma
[0131] This section describes the application of the signal
segregating approach to the t(14;18)(q32; q21) translocation
utilizing S-FISH and F-FISH. This section also describes an
analysis in which the probes for at least one chromosome not only
flank the breakpoint(s) involved in the translocation, but also
bind outside the gene involved in the translocation, which is
contrary to conventional FISH methods. This particular
translocation is strongly correlated with two types of B-cell
non-Hodgkin's lymphoma (NHL), FL and DLBCL, and results in the
juxtaposition of the BCL2 gene on chromosome 18q21 with the
immunoglobulin heavy chain (IGH) gene on chromosome 14q32.
[0132] FIG. 6A presents a schematic representation of the genomic
organization of BCL2 and IGH genes. The vertical lines of FIG. 6A
indicate the approximate positions of the breakpoint regions. Open
boxes represent the three BCL2 exons and the different coding
segments of the IGH gene. The horizontal bars indicate the
approximate position of the chromosome to which the probes anneal.
As shown in FIG. 6A, probes 1 and 2 anneal to regions outside the
BCL2 gene. Probes 3 and 4 bind to the indicated regions of the IGH
gene.
[0133] FIG. 6B is a schematic representation of the expected
pattern of signals by two color FISH (i.e., S-FISH) in normal and
tumor interphase nuclei. For chromosomes that have not undergone
translocation, probes 1 and 2 (open pattern) together generate a
green signal, while probes 3 and 4 (single hatched pattern)
generate a red signal. Once hybridized to the chromosome, the
probes are sufficiently close to one another such that distinct
signals are not observed. Nuclei in which the t(14;18)(q32; q21)
translocation has occurred, however, display two fusion or
co-localizing green and red signals (combination of open and single
hatched pattern) identifying the der(14) and der(18) chromosomes,
due to the fact that labels are segregated to the rearranging
chromosomes.
[0134] FIG. 6C illustrates identical events as described above for
the two color S-FISH strategy, with the exception that the
interphase patterns are generated by a four color F-FISH strategy.
In FIG. 6C, a first label is represented by the stippled pattern
and binds to chromosome 18 centromeric to the BCL2 gene and
flanking all known breakpoints associated with the BCL2 gene. The
open pattern represents the second label which binds to chromosome
18 in a position telomeric to the BCL2 gene and all known
breakpoints associated with the BCL2 gene. The double hatched
pattern represents third label which binds chromosome 14 telomeric
to the known breakpoint region found in the IGH gene. The single
hatched pattern represents fourth label which binds chromosome 14
centromeric to the known breakpoint region found in the IGH
gene.
[0135] The normal interphase hybridization pattern shows four sets
of colocalized spots representing the untranslocated forms of
chromosomes 18 and 14. The sets of spots consisting of colocalized
first and second label correspond to chromosome 18 and the sets of
spots consisting of colocalized third and fourth label correspond
to chromosome 14. The tumor interphase hybridization pattern for
the t(14;18)(q32; q21) translocated chromosomes represents a
classic reciprocal translocation pattern using the F-FISH strategy.
As in the normal interphase hybridization pattern, the tumor
interphase hybridization pattern consists of four sets of
colocalizing spots of label. Two of these sets of spots represent
the normal homologues for chromosomes 18 and 14 (colocalized spots
of first and second label correspond to chromosome 18 and
colocalized spots of third and fourth label correspond to
chromosome 14). The remaining two sets of spots correspond to
derivative chromosomes formed from a reciprocal translocation
between chromosomes 18 and 14. Specifically, the colocalized first
and third label spots (combined stippled and double hatched
pattern) correspond to a der(18) chromosome consisting of the
centromeric region of chromosome 18 and the telomeric region of
chromosome 14. Colocalized spots of second and fourth label
(combined open and single hatched pattern) correspond to a der(14)
chromosome consisting of the centromeric region of chromosome 14
and the telomeric region of chromosome 18.
[0136] The probe locations utilized for chromosome 18 illustrate
that the signal segregating approach is effective when the probes
are located a considerable distance from the translocation
breakpoints, in this case outside the gene (BCL2) containing the
translocation breakpoints.
[0137] 6. Automated Detection of the t(14;18)(q32; q21)
Translocation in Follicular Lymphoma
[0138] Although currently there are several methods available for
diagnosing chromosomal translocations, they are not sensitive
enough to detect the translocation in a small number of tumor cells
present in a large pool of normal cells. Thus, they are not
efficient for monitoring patients undergoing chemotherapy or bone
marrow transplantation. For example, routine PCR analysis fails to
recognize almost 25% of breakpoints in MBR and MCR breakpoint
analysis (Vaandrager et al., 2000). Long distance PCR analysis may
be used with greater sensitivity, but it is technically more
demanding and is not suitable for routine analysis in clinical
laboratory settings. In addition PCR, and other current methods for
detecting chromosomal rearrangements, do not readily lend
themselves to automated scoring of cells.
[0139] By facilitating automatic scoring of tumor cells containing
chromosomal rearrangements, the methods described herein reduce
both the cost and the time required to make diagnostic
determinations for a variety of disease states involving such
rearrangements. The probes described herein flank all known
translocation breakpoints and are not disturbed by translocation
events. This property ensures maximum probe hybridization and
signal intensity. By rendering the probes repeat sequence-free (see
infra), probe binding specificity is also significantly enhanced,
lowering background signals frequently plaguing FISH techniques.
These features markedly enhance signal selectivity, virtually
eliminating false positive cells, which is critical for accurate
diagnosis using automated techniques.
[0140] The typical automated process for detection of
translocations incorporating the methods described herein includes
several steps. These steps are depicted in FIGS. 11A-E for a cell
that has undergone the t(14;18)(q32; q21) translocation. FIG. 11A
is a schematic representation of the genomic organization of BCL2
and IGH genes located on chromosomes 18 and 14, respectively.
Vertical lines indicate approximate positions of the breakpoint
regions. The three BCL2 exons and the different coding segments of
the IGH gene are shown as open boxes. Open and single hatched bars
indicate the approximate positions of the two color S-FISH probes
used in this example. Note that the probes flank all known
breakpoints on their respective chromosomes. Probes 1 and 2 (open
bars) bind to chromosome 18 in centromeric and telomeric flanking
regions, respectively. Probes 3 and 4 (single hatched bars) bind to
chromosome 14 in telomeric and centromeric flanking regions,
respectively. Cells to be screened by the method are counterstained
with DAPI (allowing nuclei to be identified) and contacted with
fluorescently-labeled probes constructed as described herein. The
scanning equipment first establishes the focal plane of the nuclei
at a reduced number of grid positions within the scan area. The
slide is then scanned, preferably at a high frame rate. Within each
camera field of view, the counterstain image (DAPI) is captured and
analyzed to identify nuclei. Such a DAPI-stained nucleus is
depicted in FIG. 11B. Shape features of DAPI-stained nuclei are
then available, allowing for rejection of clusters and damaged
nuclei.
[0141] If one or several nuclei are found within the camera field
of view, the fluorescent probes binding to the chromosomes is
detected as illustrated in FIG. 11E. In FIG. 11E, four sets of
spots can be seen. The single discrete dark grey spot in the center
of the field corresponds to an untranslocated chromosome 14. The
single discrete light grey spot in the bottom left of the field
corresponds to an untranslocated chromosome 18. Two sets of spots
consist of fused light and dark grey spots (uppermost sets of spots
in FIG. 11E). These two sets of fused spots correspond to
derivative chromosomes that have undergone a translocation with one
another.
[0142] Once such a nucleus is detected, a fluorescence filter
(e.g., FITC, Rhodamine) is changed to acquire individual S-FISH
probe signals. FIG. 11C illustrates the use of a filter that
removes the probe signals generated by probes 3 and 4, allowing for
the detection of the signals generated by probes 1 and 2. Only
three light grey spots can be seen. These three light grey spots
correspond to the untranslocated copy of chromosome 18 (binding
both probes 1 and 2), and the signals generated by probes 1 and 2
on the respective translocated derivative chromosomes. The spatial
orientation of the three light grey signals in FIG. 11C is
identical to that of the three light grey signals present in the
unfiltered frame in FIG. 11E. Thus, by comparing the filtered image
in FIG. 11C to the unfiltered image in FIG. 11E, the identity of
the chromosomes corresponding to each spot can be ascertained.
[0143] Similarly, FIG. 11D illustrates the use of a filter that
removes the probe signals generated by probes 1 and 2, allowing for
the detection of the signals generated by probes 3 and 4. Only
three dark grey spots can be seen. These three dark grey spots
correspond to the untranslocated copy of chromosome 14 (binding
both probes 3 and 4), and the signals generated by probes 3 and 4
on the respective translocated derivative chromosomes. The spatial
orientation of the three dark grey signals in FIG. 11D is identical
to that of the three dark grey signals present in the unfiltered
frame in FIG. 11E. Thus, by comparing the filtered image in FIG.
11D to the unfiltered image in FIG. 11E, the identity of the
chromosomes corresponding to each spot can be ascertained.
[0144] Determination of suitable, labeled nuclei can be made
manually or automatically by the scanning equipment. Once detected
by either method, a series of images from different focal planes is
captured and combined to an extended focus image (z-stack). If
probes labeled with different fluorochromes are hybridized, an
extended focus image is generated for each fluorochrome/filter
combination. For strong signals, a lower magnification can be used
to increase scanning speed.
[0145] The scanning equipment can also analyze the image texture
within the nuclei in each color plane and extract numerous
features. For example, it identifies spots based on their relative
intensity, size, form factor and proximity. The user can select
criteria and parameters the spots have to meet to be counted,
including minimum or maximum size, minimum contrast, intensity,
etc. In addition, spot co-localization in different color planes is
analyzed to detect fusion signals. The system can be trained to
make such identifications with a set of selected cells that reflect
the morphometric characteristics of the current specimen. The
minimum and maximum distance between red and green signals will be
the determining criteria for the fusion or colocalizing signals in
the automated platform.
[0146] An image for each analyzed cell is stored and displayed in a
gallery for user verification at the end of the analysis. Any of
the measured features can be presented as histograms and scatter
plots and the like, which can be used to select subpopulations for
display, analysis or relocation, immediately after the scan, after
having performed additional assays, or even in real time during the
scanning procedure.
[0147] Aspects of the automated two color S-FISH approach, as
utilized to detect the t(14;18)(q32; q21) translocation, are
described in greater detail in Example 6.
[0148] 7. Detection of the t(8;14)(q24; q32) Translocation
Associated with Burkitt's Lymphoma
[0149] This section describes the use of S-FISH and F-FISH to
detect the t(8;14)(q24;32) translocation. As noted supra, this
particular translocation has been found in 100% of Burkitt's
lymphoma (BL) cases and in about 15% of other high grade B-cell
lymphomas (Offit et al., 1991; 1992; Gaidano et al., 1993). The
variant forms of this t(8;14) translocation, t(8;22)(q24; q11) and
t(2;8)(p11; q24), have been identified in acute lymphoblastic
leukemia, (Rabbitts 1994). The molecular consequence of the
t(8;14)(q24; q32) translocation is the deregulation of the MYC
proto-oncogene; this deregulation results from the replacement of
the regulatory region of MYC gene by the heavy chain constant
region of IGH. However, the locations of the breakpoints within the
MYC gene are variable. Further details regarding the t(8;14)(q24;
q32) translocation associated with Burkitt's Lymphoma (BL) are
presented infra in Example 4.
[0150] FIG. 7A is a schematic representation of the genomic
organization of MYC and IGH genes. The vertical lines of FIG. 7A
indicate the approximate positions of the breakpoint regions. Open
boxes represent the three MYC exons and the different coding
segments of the IGH gene. The horizontal bars indicate the
approximate position of the chromosome to which the probes anneal.
As shown in FIG. 7A, probe 1 anneals to a region outside the MYC
gene and probe 2 anneals to a region within the MYC gene spanning
exon 2, but telomeric to all the known breakpoints. Probes 3 and 4
bind to the indicated regions of the IGH gene.
[0151] FIG. 7B is a schematic representation of the expected
pattern of signals by two color FISH (S-FISH) in normal and tumor
interphase nuclei. For chromosomes that have not undergone
translocation, probes 1 and 2 (open bars) together generate a green
signal, while probes 3 and 4 (single hatched bars) generate a red
signal. Once hybridized to the chromosome, the probes are
sufficiently close to one another such that distinct signals are
not observed. Nuclei in which the t(8;14)(q24; q32) translation has
occurred, however, display two fusion or co-localizing green and
red signals identifying the der(8) and der(14) chromosomes
(combined open and single hatched pattern), due to the fact that
signals are segregated to the rearranging chromosomes.
[0152] FIG. 7C illustrates identical events as described above for
the two color S-FISH strategy, with the exception that the
interphase patterns are generated by a four color F-FISH strategy.
In FIG. 7C, first label is represented by the stippled pattern and
binds to chromosome 8 centromeric to the MYC gene and flanking all
known breakpoints associated with the MYC gene. The open pattern
represents the second label which binds to chromosome 8 in a
position telomeric to all known breakpoints associated with the MYC
gene. The double hatched pattern represents the third label which
binds chromosome 14 telomeric to the known breakpoint region found
in the IGH gene; the single hatched pattern represents the fourth
label which binds chromosome 14 centromeric to the known breakpoint
region found in the IGH gene.
[0153] The normal interphase hybridization pattern shows four sets
of colocalized spots representing the untranslocated forms of
chromosomes 8 and 14. The sets of spots consisting of colocalized
first and second label correspond to chromosome 8 and the sets of
spots consisting of colocalized third and fourth label correspond
to chromosome 14. The tumor interphase hybridization pattern for
the t(8;14)(q24; q32) translocated chromosomes represents a classic
reciprocal translocation pattern using the F-FISH strategy. As in
the normal interphase hybridization pattern, the tumor interphase
hybridization pattern consists of four sets of colocalizing spots
of label. Two of these sets of spots represent the normal
homologues for chromosomes 8 and 14 (colocalized spots of first and
second label correspond to chromosome 8, and colocalized spots of
third and fourth label correspond to chromosome 14). The remaining
two sets of spots correspond to derivative chromosomes formed from
a reciprocal translocation between chromosomes 8 and 14.
Specifically, the colocalized first and third label spots (combined
stippled and double hatched pattern) correspond to a der(8)
chromosome consisting of the centromeric region of chromosome 8 and
the telomeric region of chromosome 14. Colocalized spots of second
and fourth label (combined open and single hatched pattern)
correspond to the a der(14) chromosome consisting of the
centromeric region of chromosome 14 and the telomeric region of
chromosome 8.
[0154] 8. The t(9;22)(q34; q11) Translocation in Chronic Myeloid
Leukemia
[0155] This section discusses how F-FISH can be used to detect a
wide variety of rearrangements associated with the t(9;22)(q34;
q11) Translocation. Cytogenetically, this translocation is the
hallmark of chronic myelogenous leukemia (CML) affecting 95% of
patients by the presence of a reciprocal translocation between
chromosome regions 9q34 and 22q11 which results in Philadelphia
chromosome (Ph) (De Klein et al., 1982; Nowell et al., 1960; Rowley
1973). The presence of Ph chromosome is also identified in 5% of
children and 20% of adults with acute lymphoblastic leukemia (ALL)
(Hagemeijer, 1987). At the molecular level, the translocation
results in the activation of ABL oncogene on chromosome 9q34, which
becomes fused to the 5' end of the BCR gene on chromosome 22q11.
The different breakpoints are clustered in both BCR and ABL genes.
In BCR, the majority of the breakpoints occur in the major
breakpoint cluster region (M-BCR) within a region of 5.8 kb between
exons 12-16 of the entire BCR gene (Heisterkamp et al., 1983; Mills
et al., 1991). In a subset of CML and ALL cases, the breakpoints
are further proximal to M-BCR region termed m-BCR. A third
breakpoint cluster region termed .mu.-BCR, was identified distal to
exon 19 (Pane et al., 1996). In the ABL gene, the breakpoints may
occur anywhere within a region larger than 300 kb proximal to exon
Ib, between exons Ib and Ia or distal to exon Ia. Regardless of the
different breakpoints in ABL gene, the exon a2 is fused to the
truncated BCR gene (Melo, 1996). The BCR/ABL fusion results in the
production of fusion proteins of three different sizes, (p210,
p190, and p230) depending upon the utilization of M-BCR, m-BCR and
.mu.-BCR breakpoints, respectively (Faderl et al., Maurer et al.,
1991).
[0156] Currently, the clinical heterogeneity of CML cases in the
presentation of clinical symptoms and progression is not well
understood. Recently, it was shown that a subset (9%) of CML cases
and a subset of ALL cases had large deletions adjacent to the
translocation breakpoints on the der(9) chromosome (Sinclair et
al., 1999, Kolomietz et al., 2001) and on der(22) chromosome
(Palanisamy, unpublished data). Patients with deletions had a
shorter survival time and high relapse following bone marrow
transplantation. Similar deletions were also found in cases of AML
M4 with inv(16) and cases with MLL gene translocations. Such losses
due to submicroscopic deletions are implicated in altered clinical
behavior and are not detectable by conventional G-band analysis.
Currently available probes do not reproducibly detect such
deletions and are not thoroughly validated for such analysis (Mohr
et al., 2001). The probes and methods described herein offer a
highly sophisticated and sensitive means for detecting deletions on
both derivative chromosomes.
[0157] Detection of a variety of such rearrangements associated
with CML are catalogued in Table 2 and the corresponding
hybridization patterns depicted in FIG. 4. FIG. 4 Panel B
illustrates the t(9;22)(q34; q11) translocation. The remaining
panels of the figure depict the numerous alternative rearrangements
that have been shown to occur in conjunction with the
translocation, including the detection of deletions affecting
specific chromosomes illustrated in Panels C, E and F. Panel D
further illustrates how the F-FISH system is capable of detecting
duplication of one of the rearranged chromosomes and, more
specifically, identifying precisely which chromosomes have been
duplicated. TABLE-US-00002 TABLE 2 Chromosomal rearrangements found
associated with Chronic Myeloid Leukemia Cell type Signal Pattern
Inference A. Normal Normal 9, 22 No translocation B. Tumor Normal
9, 22, der(9) der(22) Translocation positive C. Tumor Normal 9, 22,
der(22) Ph+, deletion of BCR/ ABL region on der(9) D. Tumor Normal
9, 22 der(9), der(22) .times. 2 der(9), double Ph+ E. Tumor Normal
9, 22, der(22), der 9 Ph+, deletion of BCR w/o telomeric region of
22 region on der(9) F. Tumor Normal 9, 22, der(22), der 9 Ph+,
deletion ABL w/o centromeric region of 9 region on der(9) G. Tumor
Normal 9, 22, der(9) Deletion of BCR/ABL region on der(22) H. Tumor
Normal 9, 22, der(9), der 22 Deletion of ABL region w/o telomeric
region of 9 on der(22) I. Tumor Normal 9, 22, der(9), der 22
Deletion of BCR region w/o centromeric region of 22 on der(22) J.
Tumor Normal 9, 22, der(22), isolated Variant translocation spots
ABL centromeric and BCR telomeric regions
[0158] Based on F-FISH analysis, the current inventors have
identified at least ten possible signal patterns excluding
amplification (Table 2). Abnormal signal patterns other than the
listed patterns may be possible with the addition or loss of one of
more of same signals due to copy number changes for the
corresponding chromosomes.
[0159] Panel A of FIG. 4 represents the hybridization pattern in
normal cells. There are two sets of colocalizing spots in the
normal hybridization pattern. One set consists of spots of first
label (proximal probe represented by stippled pattern) colocalizing
with second label (distal probe represented by double hatched
pattern) and corresponding to chromosome 22. The second set
consists of spots of third label (proximal probe represented by
single hatched pattern) colocalizing with fourth label (distal
probe represented by open pattern) and corresponding to chromosome
9.
[0160] The hybridization pattern in Panel B of FIG. 4 shows four
sets of colocalizing spots and indicates that a reciprocal
translocation has taken place between chromosomes 9 and 22. The
hybridization pattern shows one set of colocalizing spots
consisting of first label colocalizing with second label and
corresponding to untranslocated chromosome 22. The second set of
colocalizing spots consists of third label colocalizing with fourth
label and corresponding to untranslocated chromosome 9. The third
set of colocalizing spots consists of a first label and a fourth
label and corresponds to a derivative chromosome 22 containing a
centromeric region from chromosome 22 and a telomeric region from
chromosome 9, i.e., the Philadelphia chromosome described supra.
The fourth set of colocalizing spots consists of a second label and
a third label and corresponds to a derivative chromosome 9
containing a centromeric region from chromosome 9 and a telomeric
region from chromosome 22.
[0161] Panel C of FIG. 4 displays three sets of colocalizing spots.
The first set consists of spots of first and second labels and
corresponds to chromosome 22. The second set consists of spots of
third and fourth labels and corresponds to chromosome 9. The third
set consists of spots of first and fourth label and corresponds to
the Philadelphia chromosome (der(22)). The Philadelphia chromosome
could only have resulted from a translocation involving chromosomes
9 and 22. The hybridization pattern displays the der(22),
(Philadelphia chromosome) but not the corresponding der(9), which
would have been comprised of the centromeric region of chromosome 9
and the telomeric region of chromosome 22. The absence of der(9)
indicates at the very least that the BCR/ABL region of the der(9)
chromosome has been deleted, or that the entire der(9) chromosome
has been deleted.
[0162] The hybridization pattern in Panel D of FIG. 4 displays five
sets of colocalizing spots. One set consists of first label
colocalizing with second label and corresponds to chromosome 22.
The second set consists of third label colocalizing with fourth
label and corresponds to chromosome 9. The third set consists of
second label colocalized with third label and corresponds to a
der(9) chromosome formed through a reciprocal translocation with
chromosome 22. Analysis of the remainder of the hybridization
pattern of Panel D illustrates the power of the F-FISH strategy to
characterize cells with additional copies of one or both of the
rearranged chromosomes, as is sometimes the case with cancer. There
are three spots of first label in the hybridization pattern,
indicating three copies of chromosome 22 (or a derivative of that
chromosome), rather than the two found in diploid cells. As
indicated supra, one of these first labels colocalizes with the
second label and corresponds to an untranslocated chromosome 22.
The other two first labels, however, colocalize with the fourth
label to form the der(22) Philadelphia chromosome. The Philadelphia
chromosome can only be formed through a translocation between
chromosomes 9 and 22, yet only one of the third label spots
corresponds to a der(9) and the other third label spot is
colocalized with a fourth label spot corresponding to an
untranslocated chromosome 9. This additional Philadelphia
chromosome was likely formed by non disjunction in an earlier
mitotic event.
[0163] Panel E of FIG. 4 shows a hybridization pattern of four sets
of spots. One set consists of a spot of first label colocalizing
with second label and corresponds to chromosome 22. The second set
consists of colocalizing spots of third label and fourth label and
corresponds to chromosome 9. The third set of spots consists of
first label colocalizing with fourth label and corresponds to a
der(22) chromosome formed through a reciprocal translocation with
chromosome 9. The fourth spot is an isolated spot of third label.
This isolated spot corresponds to a der(9) formed as part of the
translocation event creating the der(22) chromosome, but during the
translocation, the telomeric region of chromosome 22 was lost and
not joined at the breakpoint of der(9). This left der(9) with a
macrodeletion in its telomeric region, including the BCR gene
region.
[0164] Panel F of FIG. 4 shows a hybridization pattern of four sets
of spots. One set consists of spots of colocalizing first label and
second label and corresponds to chromosome 22. The second set
consists of spots of colocalizing third label and fourth label and
corresponds to chromosome 9. The third set of spots consists of
first label colocalizing with fourth label and corresponds to a
der(22) chromosome formed through a reciprocal translocation with
chromosome 9. The fourth spot is an isolated spot of second label.
This isolated spot corresponds to a der(9) chromosome formed as
part of the translocation event creating the der(22) chromosome,
but during the translocation, the centromeric region of chromosome
9 combining the ABL gene region was deleted and the telomeric
region from chromosome 22 joined. This pattern is not due to a
variant translocation to a third chromosome because there is no
isolated spot of the third label (der(9)) with a macrodeletion in
the telomeric region) as would be expected in such a variant
translocation.
[0165] Panel G of FIG. 4 shows a hybridization pattern of three
sets of spots. One set consists of spots of first label
colocalizing with second label and corresponds to chromosome 22.
The second set consists of spots of third label colocalizing with
fourth label and corresponds to chromosome 9. The third set of
spots consists of second label colocalizing with third label and
corresponds to a der(9) chromosome formed through a reciprocal
translocation with chromosome 22. In this hybridization pattern,
the der(22) which should have been formed by the translocation
forming the der(9) chromosome noted supra is missing. This
indicates that either the BCR/ABL region of the der(22) chromosome
has been deleted to an extent such that label cannot bind, or the
der(22) chromosome is missing entirely.
[0166] Panel H of FIG. 4 shows a hybridization pattern of four sets
of spots. One set consists of colocalizing spots of first label and
second labels and corresponds to chromosome 22. The second set
consists of spots of third label colocalizing and fourth label and
corresponds to chromosome 9. The third set of spots consists of
second label colocalizing with third label and corresponds to a
der(9) chromosome formed through a reciprocal translocation with
chromosome 22. The fourth spot is an isolated spot of first label.
This isolated spot corresponds to a der(22) chromosome formed as
part of the translocation event creating the der(9) chromosome
noted supra; however, the translocation resulted in a loss of the
ABL gene region of the der(22) chromosome and the telomeric region
of chromosome 9 was lost and never joined to chromosome 22.
[0167] Panel I of FIG. 4 shows a hybridization pattern of four sets
of spots. One set consists of spots of colocalizing first label and
second label and corresponds to chromosome 22. The second set
consists of spots of colocalizing third label and fourth label and
corresponds to chromosome 9. The third set of spots consists of
second label colocalizing with third label and corresponds to a
der(9) chromosome formed through a reciprocal translocation with
chromosome 22. The fourth spot is an isolated spot of fourth label.
This isolated spot corresponds to a der(22) chromosome formed as
part of the translocation event creating the der(9) chromosome, but
during the translocation the centromeric region of chromosome 22
was lost during the transfer of the telomeric region from
chromosome 9 to form the der(22) chromosome.
[0168] Panel J of FIG. 4 shows a hybridization pattern of five sets
of spots. One set consists of spots of colocalizing first label and
second label and corresponds to chromosome 22. The second set
consists of spots of colocalizing third label and fourth label and
corresponds to chromosome 9. The third set of spots consists of
first label colocalizing with fourth label and corresponds to a
der(22) chromosome formed through a reciprocal translocation with
chromosome 9. The fourth spot is an isolated spot of third label.
This isolated spot corresponds to a der(9) chromosome formed as
part of the translocation event creating the der(22) chromosome,
but the translocation was variant, with the telomeric region of
chromosome 22 never being transferred to chromosome 9 in the
translocation. Instead, the telomeric region of derivative
chromosome 9 was transferred to a third chromosome as indicated by
the isolated fourth label spot. This hybridization pattern is not
due to polyploidy and a chromosomal deletion because there are only
two spots of each label present in the pattern, indicative of a
diploid chromosomal preparation.
[0169] 9. Probe Detection and the use of pseudo-colors.
[0170] Probe labels of the present invention comprise all agents
that can be detected physically or chemically and can be associated
with the probes described herein. For example, probes of the
present invention are preferably constructed with nucleic acids
comprising labels of one or more fluorescent compounds that are
typically conjugated to the base moiety. Other methods of the
present invention utilize radioactive probes, each emitting
particles of a characteristic energy and/or decay rate. Still other
methods utilize probes comprising distinctive antigens that can be
differentially detected by histochemical means.
[0171] The present invention also enables the detection of any
given probe signal to be transformed to an alternative format
easing display and/or interpretation. For example, a radioactive
probe signal can be transformed into a colored light pattern
displayed on a cathode ray tube; fluorescent probe emissions can be
transformed into a digital representation; the digital
representation can be transformed into a graphical computer
printout and so forth. Other methods allow probes having different
signal characteristics to be used together. For example, one method
uses two probes differentially labeled with fluorescent compounds
and two probes differentially labeled with radioactive isotopes.
Although different detectors are used to monitor the positions of
the respective probe sets, the data from the different detectors is
gathered and transformed to present the data on a common display in
the form of differentially colored spots. Typically, such
transformations are performed by a software-driven computer.
[0172] Some methods of the present invention are capable of
differentiating between signal intensities or color hues, thereby
further increasing probe signal diversification. For example, one
method can distinguish between bright red and dull red. Another
method can distinguish between differences in the specific activity
of probes labeled with a radioactive isotope. Additional methods
comprise differential detection of different isotopes.
[0173] A useful aspect achieved from the use of pseudo-colors is
the ability to resolve fusion signals. For example, in multi-color
FISH assays, such as the F-FISH assay described in the present
invention, there are a multitude of fusion signals that can result
from the juxtapositioning of two or more probes. In the present
methods, such fusion signals would typically be artifactual,
resulting from random aspects inherent in chromosomal positioning
during fixation. Using pseudo-colors, such artifactual fusion
signals can often be resolved into the component signals, as a
given fusion signal can only be formed through certain
combination(s) of the labels used in the experiment. Another
example of using pseudo-colors in the analysis process involves
probes differentially radio-labeled. Even when such probes
completely overlap, detection mechanisms common in the art are
capable of distinguishing the radiation emitted by each probe based
upon the energy of the particles emitted. In displaying the raw
data, components of the fusion signal can therefore also be
communicated, aiding in analysis.
[0174] The use of pseudo-colors also aids in data storage as all
probe data, regardless of the nature of the probe label, can be
stored in a common format.
IV. Additional FISH Methods for Detecting Deletions
[0175] In addition to the foregoing methods for detecting
deletions, another general approach can be utilized to detect
chromosomal deletions, including deletions that are associated with
rearrangements (e.g., translocations) between two chromosomes.
Similar to the segregating signal approaches discussed above, some
deletion detection methods that are provided herein utilize a
nucleic acid probe that hybridizes to a chromosomal region (binding
region) that is either centromeric or telomeric to all known
breakpoints associated with a particular translocation and which at
least partially spans the region at which the deletion occurs.
Thus, the probe does not hybridize to any region that includes any
of the known breakpoints associated with the translocation. The
probe is labeled with a detectable label to facilitate detection.
In certain methods, the breakpoint region(s) associated with the
translocation of interest are located within a gene, and the probe
is designed to have a sequence such that the region to which it
binds is located entirely outside the gene in which the breakpoints
are located.
[0176] When analyzing a chromosomal sample, the probe is contacted
with a chromosomal preparation. The probe hybridizes to the
chromosomes that contain the binding region (or a portion thereof)
to which the probe hybridizes. In a diploid cell, assuming there is
not a complete deletion of the binding region, the probe binds to
the two chromosomes that contain at least a portion of the binding
region. A deletion from the binding region can be determined by
detecting signal from the label associated the two chromosomes to
which the probe is bound. If there is a partial deletion, then the
signal from label on one chromosome has a lower intensity than
signal from the other chromosome. If there is total deletion of the
binding region, then label is only detected on a single chromosome.
As noted supra, for a micro-deletion in which part of the binding
site is retained, the magnitude of signal reduction is related to
the extent of the deletion.
[0177] This general approach for detecting chromosomal deletions
can be utilized independently or in combination with either the
signal splitting or signal segregating approaches. The use of this
deletion detection method with the split signal approach is useful
because it enables detection of deletions which otherwise would
have been impossible to detect. An example of the use of this
deletion detection methodology in combination with a split signal
approach is illustrated in FIGS. 13A-13C. FIG. 13A shows a first
and second chromosome having genes A and B, respectively, prior to
translocation and any deletion. The first chromosome includes a
region susceptible to deletion as part of a translocation.
Consistent with the signal segregating methodology described supra,
a first probe bearing a first label and a second probe bearing a
second label are selected to span the breakpoints of gene A and
gene B, respectively. A third probe bearing a third label at least
partially spans the region of the first chromosome at which a
deletion can occur, but hybridizes to a region that is located
entirely centromeric to the breakpoint. The interphase field for
such a chromosomal arrangement from a diploid cell contains two
colocalizing spots of first and third label corresponding to
untranslocated chromosome 1 and two separate spots of second label
corresponding to untranslocated chromosome 2.
[0178] The arrangement of the three labeled probes following a
translocation that does not involve a deletion is illustrated in
FIG. 13B. In this situation, a colocalized spot of first and third
label and a separate spot of second label correspond to
untranslocated first and second chromosomes, respectively. A
colocalizing spot consisting of first, second and third label
corresponds to the derivative chromosome 1. A fourth spot
consisting of colocalizing first and second label arises from the
derivative chromosome 2.
[0179] The arrangement of probes and the hybridization pattern
arising from a translocation of the first and second chromosomes
and a complete deletion of the probe 3 binding site is depicted in
FIG. 13C. In this instance, the pattern includes a spot of
colocalizing first and third label and a spot of second label
indicative of untranslocated first and second chromosomes,
respectively. The pattern also includes two spots of colocalizing
first and second label corresponding to the derivative chromosome 1
and derivative chromosome 2. A spot containing colocalizing first,
second and third label is not observed because of the deletion.
[0180] In the case of a deletion of only a fraction of the probe 3
binding site, a spot of colocalizing first, second and third label
is observed in the interphase field. The intensity of the third
label signal arising from this spot is reduced relative to the
third label signal arising from third label hybridized to
untranslocated first chromosome. The extent of the deletion can be
assessed from the degree to which the third label signal is
reduced.
[0181] While the foregoing examples have been discussed with
respect to the hybridization pattern arising in an interphase
field, it should be understood that these methods can also be
utilized with metaphase chromosomes. Further, those of skill in the
art will appreciate that analogous methods to those just described
can be performed using the signal segregating approach described
herein. When the deletion detection method is utilized in
combination with the signal segregating approach, the probe
utilized to facilitate detection of the deletion is still selected
to hybridize to a region that is entirely centromeric or telomeric
to the breakpoints involved in the translocation of interest and,
in some instances, is further located outside the gene in which the
breakpoints occur. The deletion detection probe is further selected
such that it does not hybridize to a region that interferes with
the ability of the distal or proximal probes to bind to the same
chromosome to which it binds. As discussed above, the signal
segregating approach is able to detect deletions even without a
separate deletion detection probe. Thus, this probe can be utilized
to augment the existing capability of the segregating signal
approach.
V. Rendering FISH Probes Repeat Sequence Free
[0182] A. General
[0183] Recent advances in molecular genetics and genome analysis
have resulted in the availability of a variety of reagents that can
be used to generate DNA probes, e.g., yeast artificial chromosome
(YACs) bacterial artificial chromosomes (BACs) and P1 artificial
chromosomes (PACs). Well-developed YAC/BAC/PAC maps are available
for most of the chromosomal regions involved in cancer
translocations. However, artifacts in signals have traditionally
been a source of problems with FISH analyses.
[0184] Such artifacts arise from two sources. One is non-specific
binding of labeled DNA to protein in intact fixed nuclei. This can
be partly overcome by treating the nuclei with proteolytic enzymes
such as proteinase K or trypsin. With the recent advances in
imaging technology, computer processing of images can also be
utilized to reduce the background fluorescence arising from
non-specific hybridization.
[0185] The second source of artifacts is non-specific cross
hybridization of probes containing repeat sequences to
complementary repeat sequences in the genome. Various suppression
methods have traditionally been utilized to address this problem.
One such approach involves pre-annealing labeled probes with
unlabeled DNA that contains only repeat sequences (repeat DNA),
such that probes with repeat segments bind to the repeat DNA, thus
allowing such probes to be partially separated from probes without
repeat sequences. Typically, the repeat DNA utilized is human Cot-1
DNA or total human genomic DNA. The unbound probes collected after
a suppression step includes fewer probes with repeats. However,
this particular approach, while helpful in reducing the number of
copies of probes with repeat sequences, nonetheless does not
adequately address the issue. The problem is that for any given
probe present in multiple copies, often the suppression step fails
to bind up all the copies of the probe. Thus, even after the
suppression step, although one may have reduced the number of
copies of any given probe, it is probable, in fact likely, that
additional copies of such probes remain in solution. Consequently,
with conventional suppression steps, the complete suppression of
all repeat sequences is difficult. Furthermore, in suppression
steps, a considerable amount of unique sequences may also reanneal,
thus resulting in reduced signal intensity during hybridization.
Hence, avoiding the suppression step in a hybridization experiment
can improve signal intensity and specificity.
[0186] The methods described herein utilize a different approach
for addressing the non-specific cross hybridization problem, an
example of which is summarized in FIG. 8. In general, the approach
involves cloning a plurality of sequences that flank all the known
breakpoints for a particular translocation of interest. The
resulting cloned sequences are then contacted with one or more
repeat sequences to allow probes containing complementary repeat
segments to hybridize to the repeat sequences. Clones of sequences
that fail to anneal to the repeat sequences are selected and used
in the detection and identification of the translocation of
interest. With this approach, the problems associated with
traditional methods involving hybridization of probes to repeat
sequences are avoided. Conventional approaches simply result in the
enrichment of a population of probes for those lacking repeat
sequences. However, as described above, even for those probes that
hybridize to the repeat sequence, frequently other copies of the
same probe remain that have not hybridized to the repeat
sequence.
[0187] The methods described herein, however, can substantially
avoid this problem. With the present method, one determines if any
given cloned probe anneals to the repeat sequence. If so, such a
probe is not utilized as a probe in a FISH assay since it contains
repeat sequences. By utilizing a binary detection scheme (i.e., a
scheme in which one determines whether a given clone hybridizes to
repeat sequence or not) to identify probes that contain repeat
sequences, one can readily identify potential probes to utilize (or
exclude) in the detection of any given translocation. This method
avoids the problem of the conventional approach. Any binding of a
cloned probe to the repeat sequence is an indication that
particular clone includes repeat sequences and should not be used
in the further development of probes. Hence, unlike certain
conventional suppression approaches, one can essentially eliminate
particular probes that have repeat sequences.
[0188] As depicted in FIG. 8, the method by which the claimed
probes are constructed yields probes that are comprised of
stretches of DNA homologous to portions of the probe binding
region, of at least a minimum size, and completely free of repeat
sequence DNA. As depicted schematically in FIGS. 9A and 9B, the
stretches of DNA from which the probe is constructed are typically
not contiguous, being interspersed between both repeat sequences
(the dark bands in FIGS. 9A and 9B) and cloned sequences deemed too
short to be included in the probe. It should also be noted that the
order in which the clones are ligated together to make the probe
need not reflect the order in which the clones appear in the
chromosomal DNA. For example, in FIG. 9A, the sequences making up
the probe are aligned "A", "B", and "C" in the chromosome, but
their relative positions in the probe are "B", "A", "C". The
consequence of this construction is that one is afforded a
heterogenous set of probes, each containing one or more stretches
of DNA homologous to a subregion of a probe binding region. This
approach allows for multiple copies of probe to bind specifically
to a much greater expanse of DNA without the difficulties created
by background recognition of repeat sequences found in the prior
art.
[0189] An additional aspect of the probe construct is that it
facilitates mapping of deletions that encroach into the probe
binding region. As a deletion removes part of the probe binding
region, subregions that previously supported probe hybridization
are removed. Such an occurrence is depicted in FIG. 9B. This
decrease in probe hybridization necessarily decreases the amount of
label associated with the probe binding region. The loss of label
from the probe binding region, in turn, lowers the intensity of the
signal produced. By comparing the signal intensity emitted by a
chromosome carrying such a deletion with the signal intensity
emitted from the analogous site on a homologous chromosome which
has not undergone such a deletion, the extent of the deletion into
the probe binding region can be estimated.
[0190] By utilizing the segregating probe approach as disclosed
herein, in combination with methods for generating probes that are
free of repeat sequences, three important criteria are met. First,
as the probes hybridize to chromosome regions flanking all the
breakpoints, the signal is not "split" between derivative
chromosomes after a translocation event, as occurs when probes span
the translocation breakpoint. This feature allows for the
identification of both derivative chromosomes (as well as
chromosomes that have not undergone translocation) and ensures the
signal intensity generated by the probe is maintained on the
derivative chromosomes. Second, as the probes produced are free of
repeat sequences, they will not recognize homologous repeat
sequences found throughout the genome. This feature of the methods
decreases background noise caused by spurious hybridization of
probes to repeat sequences and significantly lessens the
possibility of generating a false positive signal pattern. Third,
by reducing background noise and increasing overall probe signal,
the probe constructs described herein facilitate automated cell
scoring methods, making the diagnosis and evaluation of diseases
involving chromosomal rearrangements, including cancer,
routine.
[0191] B. Methodology
[0192] The methods begin by initially identifying regions of DNA
that can serve as potential probes for detecting a translocation of
interest. This is done using a database of gene sequences (e.g.,
GenBank, http://www.ncbi.nlm.nih.gov/) to identify segments of DNA
that flank all the known breakpoints for a particular reciprocal
translocation of interest. The regions examined are those that
typically fall within less than 1 Megabase (Mb) of a potential
breakpoint, or within the regions listed supra. Once such regions
have been identified, primer sequences located upstream and
downstream of these regions are selected using the same databases.
These primers can be used to isolate the potential probe sequences
from a variety of libraries. Typically, the libraries that are
screened are BAC, YAC or PAC libraries that are commercially
available (e.g., PAC and BAC libraries are available from Incyte
Genomics of St. Louis, Mo.; a YAC library is available from
Research Genetics, Huntsville, Ala.). A variety of different
screening methods can be utilized to screen the libraries to
identify which clone includes the potential probe sequences. Often
the screening process is accomplished by conducting PCR with the
primers just described. Positive clones (e.g., a BAC clone that
generates amplified product) are then isolated according to
standard techniques. A variety of hybridization methods for
libraries arranged in nylon membrane filters can be screened using
the primer sequences.
[0193] The isolated clones are subsequently characterized and
validated by determining their specificity and sensitivity in
normal and tumor interphase and metaphase cells. Typically, this
involves initially fixing test cells to a support (e.g., microscope
glass slides) and then permeabilizing the cells with an appropriate
permeabilizing solution (hybridization solution). A solution
containing the fluorescent labeled probes is then contacted with
the cells and the probe is allowed to hybridize with chromosomes.
Excess probe is washed away and the presence of hybridized probe
detected. Those clones that exhibit the desired selectivity (i.e.,
clones that hybridize only to the appropriate normal and derivative
chromosomes) and sensitivity are isolated for further analysis.
[0194] Those clones isolated in the preceding step are then
completely or partially digested with one or more restriction
enzymes to generate a population of overlapping nucleic acid
fragments. The resulting fragments are subcloned into vectors
(e.g., plasmids) using shotgun ligation (Sambrook and Russel,
2001). The result is a library of subclones from individual clones.
The size of the insert of each subclone is checked. This can be
accomplished by various size-based separation procedures, but
typically is done by agarose gel electrophoresis. Prior to
subcloning, the insert size for each clone will be estimated by
pulsed field gel electrophoresis. (Schwartz and Cantor, 1984).
[0195] The resulting subdlones are then screened to remove clones
that have repeat sequences. In certain methods, the size separated
inserts are transferred to a support suitable for conducting
hybridization experiments. Such transfers can be performed, for
example, by transferring the inserts to a nitrocellulose filter or
nylon membranes by capillary transfer. The resulting filter is then
contacted with a solution containing labeled nucleic acids (e.g.,
radioactively labeled) having repeat sequences. A variety of
different types of nucleic acids including repeat sequences can be
utilized in this step. Suitable repeat sequences include Human
Cot-1 DNA, which is a fraction of total genomic DNA enriched for
repeat sequences. The goal in this step is to identify subdlones
that include repeat sequences. As indicated supra, the suppression
methods described herein are designed to substantially reduce the
number of probes that have repeat sequences to achieve increased
specificity. Consequently, clones that do not hybridize with the
nucleic acid including the repeat sequences are selected to obtain
a population of subdlones in which the number having repeat
sequence is substantially reduced; subdlones that do hybridize to
the repeat sequences are discarded.
[0196] To further ensure that subclones identified as being free of
repeat sequences do in fact not contain repeat sequences, each of
the negative clones are reconfirmed by Southern analysis. In
particular, Southern blots are conducted using total human genomic
DNA. These blots are performed by digesting total human genomic DNA
with the same restriction enzymes utilized in the sub-cloning step.
Each of the repeat-free subdlones should yield a single hybridizing
fragment of its own size, thus confirming its size, repeat-free
status and freedom of artifacts.
[0197] Those subclones passing the reconfirmation test are
religated by blunt end ligation to obtain a single, larger repeat
clone (typically less than 5 kb in length). Finally, the religated
clones are tested by FISH for their specificity and sensitivity.
Clones utilized for further analyses are those that hybridize only
to the chromosomes or derivative chromosomes involved in the
translocation of interest. Once hybridized, probes based upon such
clones should also generate bright, easily detectable signals.
[0198] Each of the foregoing probe preparation steps is described
in greater detail in Example 1 infra and summarized in FIG. 8. The
utility of the approach just described would not have been
predicted in advance because one might conclude that all probes
might have sufficient repeat sequences such that at the conclusion
of the process no probes would be left. However, this in fact has
not proved to be the case. The identified single BAC, P1 or YAC
clone is known to contain large portion of repeat sequences.
Additional clones can be generated by chromosome walking on either
side of the first clone utilizing the end sequences of the first
clone. This process can be accomplished by sequencing the ends of
the first clone and selecting primers from the sequences to screen
a genomic library.
[0199] C. Final Probe Characteristics
[0200] 1. Size
[0201] In general the length of the probe is selected to be
sufficient to maintain specificity but is sufficiently short to
avoid difficulties in preparing the probe. As indicated supra, the
probe is also selected to anneal at a region flanking all of the
known breakpoints for any given translocation. Usually the probe is
more than 5 KB, but can be larger. For example, the probe can be 6,
7, 8, 9 or 10 KB or more in length, or any integer between the
foregoing sizes.
[0202] 2. Synthesis
[0203] Once appropriate probes have been identified and confirmed
to have the desired specificity and sensitivity, probes can be
prepared by growing large-scale cultures and DNA prepared by
standard alkaline lysis method (Sambrook and Russel, 2001).
Alternative methods for the preparation of probe DNA includes PCR
amplification of utilizing degenerate oligonucleotide primers
(DOP-PCR) method are described by Telenius et al., (1992).
[0204] 3. Labeling
[0205] Labels can be attached to the probes in a variety of ways.
One option involves chemical modification of a nucleic acid by
substituting a derivatized base for a naturally occurring base.
Adducts can also be formed which, after hybridization, render the
nucleic acid detectable by immunochemical stains or affinity labels
(e.g., biotin/avidin). For example, certain indirect labeling
methods involve the incorporation of a hapten (e.g., biotin,
digoxigenin) into the DNA by enzymatic reactions. Following
hybridization of the probe to the chromosome, a label is attached
to the hybrid through the use of immunological methods, in
particular the use of a labeled antibody that specifically binds to
the antigen incorporated into the probe. Such methods are discussed
further, for example, by Tchen et al. (1984) Proc. Natl. Acad. Sci.
81:3466-3470; and Langer et al. (1981) Proc. Natl. Acad. Sci
78:6633-6637. Another option is to label the probes directly
through the incorporation of labeled nucleotide during synthesis of
the probe. Such an approach is described in greater detail in
Example 2 below. Further methods are discussed by Smith et al.
(1985) Nucleic Acids Research 13:2399-2412; and Connolly et al.
(1985) Nucl. Acids Res. 13:4485-45. Still another option is to
attach the label via a linker attached to a modified nucleotide
(see, e.g., U.S. Pat. No. 5,491,224). Multiple different labels can
be attached to a probe. For example, combinatorial fluorescence
methods can be utilized in which various combinations of dyes are
utilized (see, e.g., Ried et al. (1992) Proc. Natl. Acad. Sci. USA
89:1388-92 and U.S. Pat. No. 5,817,462).
[0206] A variety of suitable dyes are available. Certain methods
utilize fluorescent molecules as labels, as a number of commercial
instruments have been developed for the detection of fluorescent
labeled nucleic acids. A variety of fluorescent molecules can be
used as labels including, for example, fluorescein and fluorescein
derivatives, rhodamine and rhodamine derivatives, naphthylamine and
naphthylamine derivatives, cyanine and cyanine derivatives,
benzamidizoles, ethidiums, propidiums, anthracyclines,
mithramycins, acridines, actinomycins, merocyanines, coumarins,
pyrenes, chrysenes, stilbenes, anthracenes, naphthalenes,
salicyclic acids, benz-2-oxa-1-diazoles (also called
benzofurazans), fluorescamines and bodipy dyes.
[0207] While the in situ hybridization methods described herein
typically utilize fluorescent labels, other labels can be used.
Other suitable labels include, but are not limited to,
chromophores, molecules that emit chemiluminescence, radioisotopes,
electron dense particles, enzymes, cofactors, substrates for
enzymes and ligands having specific binding partners (e.g.,
avidin/biotin).
VI. Methods of Use
[0208] The foregoing methods for generating probes free of repeats
can be utilized to generate repeat-free probes that can be utilized
in a variety of FISH approaches, including the segregating (both
S-FISH and F-FISH methods) and split signal approaches described
supra. The segregating approach is preferred because of the
increase in sensitivity the approach provides. The methods can also
be utilized to develop probes for the detection of virtually any
chromosomal translocation.
[0209] Methods utilizing probes designed as described herein
typically involve (a) fixing a chromosome sample to obtain a
chromosome spread; (b) treating the fixed sample to make the target
DNA more accessible to the probes; (c) contacting the treated
sample with probes prepared as described herein appropriate for the
translocation being detected and allowing the probes to hybridize
with the target sites; (d) washing the hybridization complexes with
rinse solutions to remove unhybridized probes; and (e) detection of
probes that have hybridized to the target sites.
[0210] A variety of suitable fixatives are available for preparing
the chromosomal spread. Examples of such fixatives include, but are
not limited to, acid acetone solutions, various aldehyde solutions
(e.g., formaldehyde, paraformaldehyde and glutaraldehyde) and acid
alcohol solutions. Examples of specific chromosomal fixatives are
discussed, for example, by Trask, et al. (1985) Science
230:1401-1402.
[0211] Treating the chromosomal spread with an agent or agents that
remove proteins from the chromosomes can enhance the ability of
probes to access target sites in the chromosomes. Agents useful for
performing such removal include certain enzymes (e.g., pronase or
proteinase K, trypsin and pepsin) and mild acid. Deproteinization
is performed with an enzyme concentration and for a time period
that increases accessibility to allow for hybridization between
probe and target sites; however, the period is sufficiently short
to prevent a loss of morphological detail that renders subsequent
chromosomal identification difficult. An alternative is to
deproteinize chromosomes by mild acid extraction. Thus, certain
deproteinization methods involve treating the chromosomal spread
with 0.02-0.2 N HCl followed by high temperature (e.g., 70.degree.
C.) washes. An optional pretreatment with RNase can be utilized to
remove residual RNA from the chromosomal spread.
[0212] The chromosomal spread is then denatured so the probes can
bind to the target sites in the chromosomes. Various denaturation
conditions can be utilized. Certain denaturation methods include
incubation in the presence of high pH, low pH, high temperature
and/or various organic solvents (e.g., formamide,
tetraalkylammonium halides). Denaturants are usually removed prior
to contacting the chromosomal spread with the probes using
established washing procedures. For example, when formamide is used
as a fixing agent, common washes involve a series of ice-cold
ethanol rinses at 70%, 80% and 90% ethanol.
[0213] The denatured chromosomal spread is then contacted with
probes prepared according to the methods described herein.
Hybridization is conducted under conditions and for a time period
sufficient for the repeat-free probes to hybridize with the
complementary sequences in the chromosomes. Optimal hybridization
conditions depend upon several factors such as salt concentration,
incubation time between probes and chromosomal spreads and
concentration, composition and length of the probes as will be
appreciated by those of ordinary skill in the art.
[0214] Once probes have annealed to their complementary sequences,
any unbound probes can be washed away. The resulting hybridization
complexes are spectrally analyzed to detect such complexes. A
variety of different optical analyses can be utilized to detect the
complexes. Spectral detection methods are discussed, for example,
in U.S. Pat. No. 5,719,024, and by Schroeck, E. et al. (1996)
Science 273:494-497; and Speicher, R. M., et al. (1996) Nature
Genetics 12:368-375.
[0215] Further guidance regarding general FISH procedures are
discussed, for example, Gall and Pardue (1981) Methods in
Enzymology 21:470-480; Henderson (1982) International Review of
Cytology 76:1-46; Angerer, et al. (1985) in "Genetic Engineering:
Principles and Methods" (Setlow and Hollaender, Eds), Plenum Press,
New York.
[0216] The following examples are provided to illustrate certain
aspects of the methods and probes disclosed herein. Accordingly,
these examples should not be construed so as to limit the scope of
the appended claims.
EXAMPLE 1
Experimental Design
I. General
[0217] The general experimental strategy for developing probes to
be utilized in FISH assays utilizing the signal segregation
approach described supra involves the following steps: (1)
generation of probes by screening a library (e.g., a PAC or BAC
library) to identify probes that flank breakpoints for a
translocation of interest; (2) testing the probes for chimerism and
signal quality on normal metaphase and interphase nuclei; (3)
testing the probes for detection of the translocation in nuclei
from metaphase and interphase nuclei derived from multiple tissues;
and (4) testing the probes on follow-up samples to ensure the
probes have the appropriate sensitivity and specificity.
II. Screening of Human Genomic BAC or PAC Library and Probe
Confirmation Testing
[0218] A. Screening BAC Library.
[0219] In some of the following examples, the clones utilized to
prepare the probes are obtained by screening a human genomic BAC
library, either by PCR or probe hybridization methods according to
the manufacturer's protocols (Incyte Genomics, St. Louis, Mo.).
[0220] B. Screening PAC Library.
[0221] In some of the other examples, clones are obtained from a
PAC library. A PAC library was constructed by ligating a Sau3A1
partially digested human genomic DNA to the BamH1 cloning site of
the PAC vector. The ligation mixture was electrophoretically
introduced to NS3516 bacterial cells to create a 16.5 KB plasmid
containing a genomic insert having an average size of 120 kb. The
PAC library was constructed by arraying each clone into micro titer
dishes. The entire library is arrayed in 321 micro titer dishes.
Each dish contains 384 wells in 24 columns and 16 rows. DNA
prepared from each dish is combined individually in blocks of ten
to create assay pools. A total of 32 upper pools are generated by
combining 10 dishes. Thus, upper pool 1 contains clones pooled from
plates 1-10. This pattern continues through upper pool 32 that
contain clones from plates 311-321.
[0222] The 32 upper pools are screened by 32 individual PCR
reactions using the described primers designed from the regions
described in the following examples. These PCR reactions identify
one of the upper pools that contain 10 plate pools. The next round
of 10 PCR reactions is performed to identify one of the 10 plate
pools. The last experiment of 40 PCR reactions identifies the well
within the plate that contains the clone of interest. This
experiment will be done for each of the primers individually to
screen the library.
[0223] C. Rendering the Probes Repeat Sequence Free.
[0224] The identified clones are purified of probes that contain
repeat sequences according the methods set forth supra. This
increases the specificity of the remaining clones for the sequences
of interest.
[0225] D. Testing Probes for Chimerism and Signal Quality on Normal
Metaphase and Interphase Nuclei.
[0226] Each BAC clone or its derived pool probes is tested for
chimerism, cross-hybridization, and signal strength on metaphase
and interphase nuclei from PHA-stimulated and cultured mononuclear
blood cells from multiple (e.g., five) normal individuals.
[0227] E. Testing the Probes for Detection of Translocations in
Metaphase and Interphase Nuclei Derived from Multiple Tissues.
[0228] The probes are tested in biopsy samples from patients with
lymphomas from the various translocations comprising peripheral
blood, lymph node, bone marrow, and other tissues, as described in
the experimental methods sections in Example 2. Pre-set criteria
for accepting and rejecting normal versus translocation cells are
established and adhered to in conducting the analyses. For each
tissue type, at least 15 cases are tested.
[0229] F. Testing the Probes on Follow-up Bone Marrow Samples.
[0230] In order to detect residual tumor cells, post treatment
(chemotherapy, bone marrow transplantation) samples from 15 cases
are similarly analyzed using the probes disclosed infra.
[0231] G. Preparation of BAC/PAC DNA.
[0232] Following successful isolation of BAC and/or PAC clones,
large-scale preparation of DNA for each clone is made following
established protocols and/or the protocol described in the
manufacturer's BAC and PAC manuals (e.g., Incyte Genomics, St.
Louis, Mo.).
EXAMPLE 2
Experimental Protocols
I. Preparation of Nuclei from Different Tissue Types
[0233] General methods for preparing nuclei from a variety of
tissue sources are described by Heim and Mitelman (1995); ACT
manual (1991); and Verma and Babu (1989). Additional disclosure for
isolation methods for specific tissue types is provided in the
following sections.
[0234] A. Nuclei and metaphase chromosomes from normal
individuals
[0235] Heparinized peripheral blood samples collected from normal
individuals are set up for the preparation of nuclei to be used in
control studies. Briefly, 0.5 to 1.0 ml of peripheral blood is
inoculated to 10 ml of RPMI-1640 medium supplemented with 15% fetal
bovine serum and 1% L-glutamine and streptopenicillin. 0.2 ml of (1
mg/ml) phytohemagglutinin is added and the cultures incubated at
37.degree. C. for 72 hours. One hour prior to harvest, 2 ml (1
.mu.g/ml) of colcemid solution is added and incubated for 1 hour at
37.degree. C. The cultures are harvested by treating cells with
pre-warmed hypotonic solution (0.075M KCl) for 15-20 minutes and
fixed with 3:1 methanol acetic acid fixative. The slides are made
following air drying method.
[0236] B. Lymph node and other tissue biopsies
[0237] The tissues are minced thoroughly in 2-3 ml of growth medium
in order to get a single cell suspension and washed with growth
medium and direct harvest is made following hypotonic treatment
(0.075M KCl) and methanol acetic acid (3:1) fixations. The slides
are made following air drying method.
[0238] C. Bone marrow samples
[0239] Clot free bone marrow aspirates are used to prepare nuclei
by direct harvest method. Initially the cells are treated with
hypotonic solution (0.075M KCl) and followed by methanol acetic
acid (3: 1) fixation. The slides are made following air-dry
method.
[0240] D. Paraffin embedded tissue
[0241] One to three (25-50 .mu.M) thick sections cut from paraffin
embedded blocks are treated with xylene to remove paraffin and
washed in absolute alcohol to remove xylene. The sections are
rehydrated by passing through a series of 95%, 70%, 50% alcohol and
finally suspended in water. The cells are dissociated by treating
with 0.5% pepsin in 0.9% sodium chloride (pH 1.5) at 40.degree. C.
The digestion is halted by adding PBS (without Ca and Mg), which
alters the pH and consequently stops the activity of pepsin. Nuclei
are stored in PBS at 4.degree. C. until further use.
II. Probe Labeling and Hybridization
[0242] Probes utilized for FISH analysis are labeled by standard
nick translation methods using commercially available nick
translation kits (GIBCO-BRL) according to the manufacturer's
instructions or by using other non-enzymatic methods of labeling
(Kreatech Diagnostics, Netherlands). Probe labeling by utilizing
modified nucleotides and (Fluorescein coupled with dNTP's, Texas
red or Rhodamine conjugated dNTP's) incorporation of fluorescent
dyes to DNA probes by chemical methods are utilized to obtain green
and red colored signals, respectively. The labeling of probes are
not limited to green and red colors; multiple colors, as many as
four different colors, can be utilized by labeling each probe with
single color. Following labeling reactions, the unincorporated
nucleotides are separated by passage through Sephadex G-50 columns.
The samples are precipitated with absolute alcohol and resuspended
in hybridization mixture (50% formamide, 2.times.SSC, 10% dextran
sulphate, 1% Denhardts) and stored at -20.degree. C. until further
use. Approximately 200 ng of each probe is used for
hybridization.
[0243] Prior to hybridization, the slides are pretreated by
incubating with 2.times.SSC for one hour at 37.degree. C. followed
by passing through 70%, 80% and 100% alcohol for dehydration. The
slides are denatured at 70.degree. C. in denaturing solution (70%
Formamide, 2.times.SSC) and passed through cold ethanol series.
Simultaneously, the probes are denatured and placed on slides and
hybridized overnight at 37.degree. C. Post hybridization washes are
performed at 45.degree. C. in prewarmed 2.times.SSC solution twice
followed by one room temperature wash in 2.times.SSC. The slides
are counterstained with antifade solution containing 4,6-diamino
2-phenylindole (DAPI, Oncor, Gaithersburg, Md.).
III. Scoring of FISH signals
[0244] In order to define the diagnostic threshold of assays for
the detection of translocations utilizing the probes developed by
the methods described herein, FISH analysis on interphase nuclei
from normal individuals are investigated utilizing probes labeled
with a green fluorophore for one chromosome involved in the
translocation and probes labeled with red fluorophores for the
other chromosome (other colors can be utilized). For each control
and tumor specimen, at least 500 nuclei are analyzed following
stringent criteria. In control specimens, cells are scored as
normal when two separate green and red signals are observed. For
closely placed red and green signals, the distance between each
signal should be at least twice the size of one signal, and is
considered a normal pattern. Similarly, a fusion or co-localizing
signal is scored when the distance between red and green signals is
less than one signal size. In tumor specimens, the same stringent
criteria are followed when normal cells are encountered. Tumor
cells are scored only when two clear fusion signals and a single
red and green signal are observed. The same criteria are followed
for all different tissue types.
IV. Quality control
[0245] For each batch of DNA preparation, test hybridization is
performed for each clone on normal metaphase chromosomes for their
specificity. Different hybridization experiments are carried out
using varying amount of probes to evaluate the optimum probe
concentration to obtain strong hybridizing signals, on all
different tissue types, which can be observed and scored directly
under a microscope.
EXAMPLE 3
Detection of the t(11;14)(q13; q32) Translocation in Mantle Cell
Lymphoma
I. Background
[0246] As indicated above, the Mantle Cell Lymphoma (MCL) is a
subtype of Non-Hodgkin's lymphoma (NHL) originating from pre-immune
B-cells in the mantle zone of the primary follicles in secondary
lymphoid organs. (Weisenburger 1992; Raffeld et al, 1991; Banks et
al., 1992). The t(11;14)(q13; q32) translocation has been
identified as the consistent cytogenetic abnormality in 70% to 90%
of MCLs (Tsujimoto et al., 1984; Williams et al., 1991; Coignet et
al., 1996).
[0247] As can be seen from FIG. 5A, the BCL1 gene is organized in a
centromere to telomere (5'-3') orientation on chromosome band 11q13
spanning about 15 kb of the genomic region with five exons
(Motokura et al., 1993). The t(11;14)(q13; q32) translocation does
not disrupt the BCL1 gene open reading frame that contains 295
amino acids. The BCL1 gene is located 130 kb telomeric to the major
translocation cluster region. In the majority of cases, the BCL1
breakpoints are clustered within a 63 base pair region of the major
translocation cluster (MTC) of the BCL1 locus. Several studies have
shown that breakpoints can occur telomeric of the MTC in a region
about 120 kb between MTC and CCND1 gene and these studies have
identified two minor cluster regions called mTC1 and mTC2.
[0248] The IGH locus is on chromosome 14q32 and is organized in a
telomere to centromere orientation. It consists of a set of V, D,
and J region segments that rearrange and join to create the active
IGH V domain. The V region spans about 1100 kb upstream of the JH
region. The D region lies between V and J segments. A more complex
C region within about 200 kb contains 11 C region segments. The
position of all genes within IGH region is shown in FIG. 5A.
[0249] The t(11;14)(q13; q32) translocation breakpoint in the IGH
gene has been found to occur within or directly adjacent to a JH
segment. In most instances (more than 80%), the breakpoints on
chromosome 11q are clustered in a region known as the major
translocation cluster (MTC), (Rimokh et al., 1990; Williams et al.,
1993; Vandenberghe et al., 1992). Additional breakpoints are
located between MTC and the BCL1 gene within regions referred to as
minor translocation cluster regions 1 & 2 (mTC1 & mTC2).
These clusters span about 120 KB upstream of the CCND1 gene at
11q13 (de Boer et al., 1993; Rimokh et al., 1993).
[0250] Since MCLs are morphologically highly heterogeneous, its
classification as a distinct entity was a controversial subject for
several years. Due to its morphologic variations, MCLs have been
classified as small lymphocytic lymphoma/chronic lymphocytic
leukemia (SLL/CLL) and follicular center cell lymphomas of both
follicular and diffuse type (Raffeld et al., 1991). Recent studies
have identified a characteristic pattern of antigen expression in
MCL that are different from typical SLL/CLL cases, despite their
morphologic heterogeneity, the MCL is diagnosed by CD5+, CD43+ and
CD23- expression pattern by immunohistochemistry which has helped
to define MCL as distinct disease entity (Harris et al., 1994).
[0251] Although MCLs have been known to have distinct antigen
expression patterns, identification of malignant lymphocytes or MCL
cells is difficult for pathologists. In addition, due to the
dispersed nature of the breakpoints on chromosome 11q13,
conventional molecular studies, such as Southern blotting and PCR,
are not useful for detecting all the breakpoints. By Southern blot
analysis about 50% of the MCL cases have been found to have
rearrangements. This analysis requires multiple probes covering the
entire 120 kb breakpoint cluster region. Recent studies have
indicated additional breakpoints in the region 20 kb centromeric to
the MTC locus (Galiege-Zouitina et al, 1994; Wlodarska et al.,
1993). PCR is also of limited value because of difficulties in
quantification and its tendency to generate spurious or false
positive results due to amplification of DNA sequences from dead
tumor cells or even from free DNA lysed still present in the
specimen.
II. Experimental Design:
[0252] A. Probe Generation
[0253] 1. Probes for BCL1 Region
[0254] Probe 1: A BAC clone proximal to the MTC region (probe 1,
FIG. 5A) of the BCL1 locus on 11q 13 is generated by using the
following primers: F-5'AAGGTGTGAGGATCACTGG3' (SEQ ID NO:1);
R-5'AGCTCATGGGGGCTATT3' (SEQ ID NO:2) derived from the D11S1337
(http://carbon.wi.mit.edu) by screening a BAC library. In the
nuclei carrying the translocation, this probe remains on the
der(11) chromosome and generates a fusion or co-localizing signal
in combination with the IGH probe from region 3.
[0255] Probe 2: A BAC clone telomeric to the BCL1 gene region
(probe 2, FIG. 5A) is generated by using the following primers:
F-5'TTTCTGGGTGTGTCTGAAT3' (SEQ ID NO:3); R-5'ACACAGTTGCTCT AAAGGG
T3' (SEQ ID NO:4) derived from the FGF3 gene. In the nuclei
carrying the translocation, this probe segregates to the der(14)
chromosome in translocations involving all the MTC, mTC1 and mTc2
breakpoints within the BCL1 locus on 11q13, and results in a fusion
or co-localizing signal with the IGH probe from region 4.
[0256] 2. Probes for IGH Region
[0257] Probe 3: A BAC clone covering the probe 3 region of the IGH
gene (FIG. 5A) is generated using the following primers derived
from the sub-telomeric V region of the IGH gene to screen the BAC
library: F-5'TGTTTGAAGAAGGGAGTCGT3' (SEQ ID NO:5);
R-5'CCCACTCCATGTCTTCTGTT3' (SEQ ID NO:6). In the nuclei carrying
the translocation, this probe segregates to the der(11) chromosome
and generate a fusion or colocalizing signal in combination with
probe 1.
[0258] Probe 4: A BAC clone covering the probe 4 region of the IGH
gene (FIG. 5A) is generated using the following primers derived
from the C.alpha. region to screen the library:
F-5'CCACTCAGTGTGACCTGGAGCGAA3' (SEQ ID NO:7); R-5'CTCCCCTGGCTTTTC
TGGAACTGG3' (SEQ ID NO:8). In the nuclei carrying the
translocation, this probe remains on the der(14) chromosome and
generates a fusion or co-localizing signal in combination with the
relevant BCL1 probe.
[0259] 3. Screening of Human Genomic BAC Library and PCR Detection
of the t(11;14)(q13; q32) Translocation
[0260] A human genomic BAC library is screened according to the
screening methods described supra, including Example 1, utilizing
the primers described in the preceding paragraph to identify BAC
clones harboring the sequences of interest. Clones so identified
are subsequently purified of probes that contain repeat sequences,
tested for chimerism, cross-hybridization, and signal strength, and
then subjected to follow-up testing as further described in Example
1.
III. Results
[0261] The BCL1 and IGH region probes were tested on normal and
tumor metaphase and interphase cells. The BCL1 probe was labeled
green and the IGH probe labeled red. In normal interphase nuclei
and metaphase chromosomes, the probes exhibited unambiguous signals
with no cross-hybridization to any other chromosomal regions. They
were then tested on metaphase and interphase nuclei of tumors in
which t(11;14)(q13; q32) translocations were identified by G-band
karyotype analysis.
[0262] Normal (control) interphase nuclei show the expected two red
and two green signals. In the tumor metaphase and interphase
nuclei, the der(14) and der(11) chromosomes are identified by two
co-localizing yellow signal. Thus, the two fusion signals observed
confirm the presence of t(11;14)(q13; q32) translocation in the
specimen analyzed.
EXAMPLE 4
Detection of the t(8;14)(q24; q32) Translocation Associated with
Burkitt's Lymphoma
I. Background
[0263] As stated supra, this particular translocation has been
found in 100% of Burkitt's lymphoma (BL) cases and in about 15% of
other high grade B-cell lymphomas (Offit et al., 1991; 1992;
Gaidano et al., 1993). The variant forms of this t(8;14)
translocation, t(8;22)(q24; q11) and t(2;8)(p11; q24), have been
identified in acute lymphoblastic leukemia, (Rabbitts 1994). The
molecular consequence of the t(8;14)(q24; q32) translocation is the
deregulation of the MYC proto-oncogene; this deregulation results
from the replacement of the regulatory region of MYC gene by the
heavy chain constant region of IGH. However, the locations of the
breakpoints within the MYC gene are variable.
[0264] As shown in FIG. 7A, the MYC gene is organized in a
centromere to telomere (5'-3') orientation on chromosome 8q24.1. It
contains three exons (represented by open boxes) of which the
coding region starts at nucleotide 16 of exon 2. The breakpoints
(represented by vertical bars) are scattered over 300 kb of the
genomic region on either side of the MYC gene in 8q24. The
distribution of the breakpoints have been classified into three
categories, class I, II, and III depending on the position within
and outside the gene.
[0265] Breakpoints in the first exon or intron of MYC gene are in
class I, breakpoints immediately upstream of the gene are in class
II, and the distant breakpoints are in class III. The class I and
II breakpoints are prevalent among the sporadic cases of BL,
whereas the class III breakpoints are predominant among endemic
African cases of BL. The class III breakpoints are dispersed over
300 KB upstream of the gene, whereas in variant translocations, the
breakpoints are scattered over a region of 300 KB downstream of MYC
gene (Zeidler et al., 1994). In some BL cases, the MYC gene is
structurally altered while in other cases, it is structurally
normal, with no change in the regulatory region (Showe et al.,
1987). Given the dispersed nature of the breakpoints over several
kilobases in the MYC region, the conventional methods for detecting
the rearrangement, including G banding, Southern blotting and
polymerase chain reaction (PCR), suffer from the technical
limitations described supra.
[0266] The IGH locus is on chromosome 14q32 and is organized in a
telomere to centromere orientation (FIG. 7A). It consists of a set
of V, D, and J region segments that rearrange and join to create
the active IGH V domain. The V region spans about 1100 kb upstream
of the JH region. The D region lies between V and J segments. A
more complex C region within about 200 kb contains 11 C region
segments. Open boxes represent the position of all genes within IGH
region. The t(8;14)(q24; q32) translocation breakpoints in the IGH
gene occur directly adjacent to a C.mu. region (represented by
vertical bars).
II. Experimental
[0267] A. General
[0268] The general strategy for developing probes to be utilized to
FISH assays to detect the t(8;14)(q24; q32) translocation is the
same as that described in Example 1. Certain probe generation
methods as provided herein are designed to prepare probes that bind
to the segments of chromosomes 8 and 14 shown in FIG. 7A. Such
probes can be utilized to conduct FISH assays in the signal
segregation mode described herein. Two probes labeled with a green
fluorophore are derived from the MYC gene at segments corresponding
to the open bars shown (probes 1 and 2); another set of two probes
labeled with a red fluorophore are derived from segments
corresponding to the single hatched bars of the IGH gene (probes 3
and 4). Probes derived from the most proximal region of the
translocation breaks do not segregate to the reciprocal
chromosomes. Since the probe signal is not split, there is no loss
of signal strength. In contrast, the probes derived from the region
distal to the proximal breakpoints will segregate to the reciprocal
chromosomes. These features provide for enhanced sensitivity.
[0269] Thus, when used to label chromosomes from normal and tumor
nuclei, probes 1 and 2 together generate a green signal on
chromosome 8, while probes 3 and 4 together generate a red signal
on normal copies of chromosome 14. Probes 1 and 2 and probes 3 and
4 are close enough to one another on the chromosomes such that
distinct signals are not obtained for each of the probes. The
t(8;14)(q24; q32) positive nuclei, however, display two fusing or
co-localizing green and red signals identifying the der(8) and
der(14) chromosome due to the fact that signals are segregated to
the rearranging chromosomes (see FIG. 7A).
[0270] B. Probe Generation
[0271] 1. Probes for MYC Region
[0272] Probe 1: A BAC clone centromeric to all the three classes of
breakpoints in the MYC region are generated using the following
primers F5'GGCAAATTG GTTTAAGTGGA3' (SEQ ID NO:9);
R5'ACAGGGGAATGGTTAACTGG3' (SEQ ID NO:10) derived from WI-1120
(http://carbon.wi.mit.edu:). In nuclei carrying the translocation,
this probe remains on the der(8) chromosome and generates a fusion
or co-localizing signal in combination with the IGH probe from
region 3 (FIG. 7A).
[0273] Probe 2: A BAC clone telomeric (Probe 2 in FIG. 7A) to all
the breakpoints in the MYC gene is generated from the exon 2 region
of MYC gene using the following primers: F5'-ATGCCCCTCAA
CGTTAGCTTC3' (SEQ ID NO:11); R5'-CAGAGTCGCTGCTGGTGGT3' (SEQ ID NO:
12). In the nuclei carrying the translocation, this probe
segregates to the der(14) chromosome in all three class types of
breakpoints (i.e., breakpoints involving the first intron, the
first exon, or further centromeric region breakpoints) and results
in a fusion or co-localizing signal with IGH probe from region 4
(see FIG. 7A).
[0274] 2. Probes for IGH Region
[0275] Probe 3: A BAC clone covering the probe 3 region of the IGH
gene (see FIG. 7A) is generated using the following primers derived
from the sub-telomeric V region of the IGH gene to screen the BAC
library: F-5'TGTTTGAAGAAGGGAGTCGT3' (SEQ ID NO:13);
R-5'CCCACTCCATGTCTTCTGTT3' (SEQ ID NO:14). In the nuclei carrying
the translocation, this probe segregates to the der(11) chromosome
and generates a fusion or co-localizing signal in combination with
probe 2.
[0276] Probe 4: A BAC clone covering the probe 4 region of the IGH
gene (see FIG. 7A) is generated using the following primers derived
from the Ca region to screen the library: F-5'CCACTCAGTGTG
ACCTGGAGCGAA3' (SEQ ID NO:15); R-5'CTCCCCTGGCTTTTCTGG AACTGG3' (SEQ
ID NO:16). In the nuclei carrying the translocation, this probe
remains on the der(14) chromosome and generates a fusion or
co-localizing signal in combination with the probe 2.
[0277] 3. Screening of Human Genomic BAC Library and PCR Detection
of the t(8;14)(q24; q32) Translocation
[0278] Utilizing the primers just described, a human genomic BAC
library is screened according to the screening methods set forth in
Example 1. Clones so identified are subsequently purified of probes
that contain repeat sequences, tested for chimerism,
cross-hybridization, and signal strength, and then subjected to
follow-up testing as further described in Example 1.
III. Results
[0279] The MYC and JH-C.alpha. probes were tested on normal and
tumor metaphase and interphase cells. The MYC probe was labeled
with a green fluorophore and the IGH probe labeled with a red
fluorophore. In normal interphase nuclei and tumor metaphase
chromosomes, the probes exhibited unambiguous signals with no
cross-hybridization to any other chromosomal regions. They were
then tested on metaphase and interphase nuclei of tumors in which
t(8;14)(q24; q32) translocations were identified by G banding.
[0280] Normal (control) interphase nuclei show the expected two red
and two green signals. In the tumor metaphase and interphase
nuclei, the der(14) and der(8) chromosomes are identified by two
co-localizing yellow signal.
EXAMPLE 5
Detection of the t(14;1 8)(q32; q21) Translocation in Follicular
B-Cell Lymphoma
I. Background
[0281] The t(14;18)(q32; q21) translocation has been found to
characterize about 60% of B-cell Non-Hodgkin's Lymphoma. The
evidence also indicates that the translocation plays a significant
role in indolent follicular and diffuse aggressive large cell
lymphomas. It results in the juxtaposition of the BCL2 gene on
chromosome 18 with the immunoglobulin heavy chain (IGH) gene on
chromosome 14 resulting in over expression of BCL2 and neoplastic
proliferation of B-cells. Approximately 25% of FL transform to DLCL
(Offit and Chaganti, 1992). This translocation can be used as a
diagnostic and prognostic marker.
[0282] The BCL2 gene is organized in a telomere to centromere
(5'-3') orientation on chromosome band 18q21 (FIG. 6A). It covers
approximately 400 kb of genomic region. It has three exons (open
boxes). A large untranslated first exon is followed by a 220 bp
intron I, a 581 bp exon 2, a 370 KB intron II, and a 5.4 KB
untranslated exon III. The t(14;18)(q32; q21) translocation does
not disrupt the BCL2 open reading frame that contains 239 amino
acids. There are three reported breakpoint regions within the BCL2
gene. Approximately 70% of the breaks are clustered within a major
breakpoint region (MBR) in the 3' noncoding region of the gene and
approximately 25% are clustered in a minor cluster region (MCR)
about 25 kb 3' of the gene (FIG. 6A). A third breakpoint with very
low frequency has also been reported 5' to the other two
breakpoints (Tsujimoto et al., 1987; Mikraki et al., 1991). The
MBR, MCR, and 5' breakpoints in the BCL2 gene are not associated
with differences in prognosis or clinical outcome.
[0283] As shown in FIG. 6A, the IGH locus is on chromosome 14q32
and is also organized in a telomere to centromere orientation. It
consists of a set of V, D, and J region segments that rearrange and
join to create the active IGH V domain. The V region spans about
1100 kb upstream of the JH region. The D region lies between V and
J segments. A more complex C region within about 200 kb contains 11
C region segments. The position of all genes within the IGH region
is shown in FIG. 6A (open boxes). The t(14;18)(q32; q21)
translocation breakpoints (vertical bars) in the IGH gene always
occur within or directly adjacent to a JH segment (Cleary and
Sklar, 1985; Tsujimoto et al., 1985; Bakhshi et al., 1985). The
t(14;18)(q32; q21) translocation joins the 3' non coding region of
the BCL2 to the JH segment of the IGH gene.
II. Experimental Design
[0284] A. General
[0285] The general strategy for developing probes to be utilized
with FISH assays to detect the t(14;18)(q32; q21) translocation is
the same as that described in Example 1. Certain probe generation
methods are designed to prepare probes that bind to the segments of
chromosomes 14 and 18 as shown in FIG. 6A. Such probes can be
utilized to conduct FISH assays in the signal segregation mode
described herein.
[0286] B. Probe Generation for Probes Shown in FIG. 6A
[0287] 1. Primers from the Region Centromeric to BCL2 gene:
[0288] Probe 1: A BAC clone covering the probe 1 region of the BCL2
gene was generated using the following primers from the region
centromeric to BCL2 gene to screen the library: F-5'CTTGCCTCCTAAGCC
AGTTG3' (SEQ ID NO:17); R-5'TGGATTCATTTCTGATCCA3' (SEQ ID NO:18).
This probe always remained on the der(18) chromosome in nuclei with
translocations involving all three breakpoints to generate fusion
or co-localizing signal resulting from the segregation of probe 3
from 14q32 to 18q21.
[0289] 2. Primers from the Region Telomeric to BCL2 gene:
[0290] Probe 2: A BAC clone covering the probe 2 region-of the BCL2
gene was generated using primers from the region telomeric to BCL2
gene: F-5'TGGCCAGCAGCAGTGTCAAATAG3' (SEQ ID NO:19);
R-5'GGTGATCGTTAGGACTCCCA3' (SEQ ID NO:20). This probe segregates to
the der(14) chromosome in translocations involving all three
breakpoints within the BCL2 gene and results in a fusion or
co-localizing signal with probe 4.
[0291] 3. Primers from the Region Telomeric to IGH-J Gene:
[0292] Probe 3: A BAC clone covering the probe 3 region of the IGH
gene was generated using the following primers derived from the
sub-telomeric region of chromosome 14q: F-5'TGTTTGAAGAAGGGAGTCGT3'
(SEQ ID NO:21); R-5'CCCA CTCCATGTC TTCTGTT3' (SEQ ID NO:22). In the
nuclei carrying this translocation, the probe segregates to the
der(18) chromosome and generates a fusion or co-localizing signal
in combination with probe 1 in t(14;18)(q32; q21) cases.
[0293] 4. Primers from the Region Centromeric to IGH-J Gene
[0294] Probe 4: A BAC clone covering the probe 4 region of the IGH
gene was generated using the following primers derived from the
C.alpha. region: F-5'CCCTGGACGCTTTTCAAATA3' (SEQ ID NO:23);
R-5'GACTCAGGCAAGGACAAAGC3' (SEQ ID NO:24). In the nuclei carrying
the translocation, this probe will remain on the der(14) chromosome
and generate a fusion or co-localizing signal in combination with
probe 2 from 18q21 region in t(14;18)(q32; q21) cases.
[0295] C. Screening of Human Genomic BAC Library and PCR Detection
of the t(14;18)(q32; q21) Translocation
[0296] A human genomic PAC library is screened utilizing the
primers described in the preceding section according to the
screening methods set forth in Example 1. Clones so identified are
subsequently purified of probes that contain repeat sequences,
tested for chimerism, cross-hybridization, and signal strength, and
then subjected to follow-up testing as further described in Example
1.
III. Results
[0297] A. Probe Testing
[0298] The BCL2 and JH-C.alpha. probe were tested on normal and
tumor metaphase and interphase cells. The BCL2 probe was labeled
with a green fluorophore and the IGH probe labeled with a red
fluorophore. In normal metaphase and interphase nuclei they
exhibited unambiguous signals with no cross-hybridization to any
other chromosomal regions. They were then tested on metaphase and
interphase nuclei tumors cells in which a t(14;18)(q32; q21)
translocation was identified by G band karyotype analysis.
[0299] Normal (control) interphase nuclei show the expected two red
and two green signals. In the tumor metaphase and interphase
nuclei, the der (14) and der(18) chromosomes are identified by two
co-localizing yellow color. In all cases, the translocation was
identified both at metaphase and at interphase.
EXAMPLE 6
Detection of the t(14;18)(q32; q21) Translocation in Follicular
B-Cell Lymphoma using the Metasystems Image Scanning Platform
I. Experimental Design
[0300] A. General
[0301] Probe DNA is prepared from BAC libraries and labeled using
the direct label method. The labeled probes are then hybridized to
cells derived from peripheral blood lymphocytes and scored using
the Metasystems Image Scanning Platform.
[0302] B. MetaSystems Image Scanning Platform
[0303] Automated detection and counting of FISH signals in a large
number of interphase nuclei is demanding both from a physics and an
optical standpoint; the signals are small, contrast is often
inconsistent, and 3-D analysis is required due to the thickness of
the nuclei. The MetaCyte Automated Bio-Imaging System (Meta System
Group, Inc., schematically depicted in FIG. 12A) was developed to
fill the gap between flow cytometers, which are rapid but
inflexible, and microscope based imaging systems for brightfield,
which are not automated (Weber, 1992, Huber, 1995, Salomaa, 1997).
The system consists of the following components: 1) Carl Zeiss Axio
Plan 2 MOT fluorescence microscope, 2) scanning 8-position stage,
3) PC Pentium III Processor, 4) Jai camera, 5) camera interface, 6)
stage control, 7) trackball and mouse, and 8) printer. The focus
analysis begins with a slide set-up loaded onto the microscope. The
slide is scanned as the stage is moved and the image is captured.
Following scanning of the entire slide, a gallery is created. Based
on the criterion set up for positive or negative, the image
analysis either results in a positive or negative signal. If
negative, the slide is rescanned for rare event analyses. If
positive, there is a filter change for the appropriate fluorescent
signal and 5-7 planes are captured and analyzed.
[0304] Standard slide preparation techniques are used (DAPI
counterstain, same preparation techniques as used for manual
interactive analysis). The system is easy to operate; no
slide-specific calibration, adjustments of gain, offset or system
parameters are required. There is walk away/overnight operation for
8 slides (standard or 100 slides with optional tray changer).
Access to microscope and specimen is unrestricted. Adaptive
detection algorithms and automatic exposure control function
compensate for non-uniform staining conditions. Several markers can
be detected simultaneously. The standard light source covers a wide
spectrum from UV to near IR. Real time image gallery for
interactive review, control and verification of scan results is
available. Documentation, on screen review and relocation of any
individual object is straightforward. 500 to 1000 cells per minute
can be scanned for routine FISH spot counting (up to 1,000 cells
per second for rare cell detection). Results from successive scans
can be combined after re-staining the slide, e.g., for
phenotype-genotype correlation.
[0305] C. Automated Slide Scanning
[0306] The scanning process includes several steps depicted in FIG.
11 and discussed in detail supra. Briefly, MetaCyte first
establishes the focal plane of the nuclei at a reduced number of
grid positions within the scan area. Subsequently, MetaCyte scans
the slide with a speed of up to 4 images/sec. Within each camera
field of view, the counterstain image (DAPI) is captured and
analyzed to identify nuclei. Shape features can be available to
reject clusters and damaged nuclei. If one or several nuclei are
found within the camera field of view, the fluorescence filter
(FITC, Rhodamine) is changed to acquire FISH signals. A series of
images from different focal planes is captured and combined to an
extended focus image (z-stack). Where probes labeled with different
fluorochromes are hybridized, an extended focus image is generated
for each fluorochrome/filter combination. The resolution is
typically 0.35 .mu.m (0.17 .mu.m pixel size). For strong signals, a
lower magnification can be used to increase scanning speed.
[0307] The MetaCyte apparatus comprises an adaptive spot counting
algorithm, part of a classifier, which analyzes the image texture
within the nuclei in each color plane and extracts over 20
features. It identifies spots based on their relative intensity,
size, form factor and proximity. The user can select criteria and
parameters the spots have to meet to be counted, including minimum
or maximum size, minimum contrast, intensity, etc. In addition,
spot co-localization in different color planes is analyzed to
detect fusion signals. Classifiers are user trainable with a set of
selected cells that reflect the morphometric characteristics of the
current specimen. The minimum and maximum distance between red and
green signals will be the determining criteria for the fusion or
colocalizing signals in the automated platform. A scoring sheet is
defined with a spreadsheet page for each cell that enables the
review of scan results and markers for corrections of the automated
interpretation by the human operator.
[0308] The system stores an image for each analyzed cell to be
displayed in a gallery for user verification at the end of the
analysis. Any of the measured features can be presented as
histograms and scatter plots which can be used to select
subpopulations for display, analysis or relocation, immediately
after the scan, after having performed additional assays, or even
in real time during the scanning procedure.
[0309] D. Materials and Methods
[0310] 1. Probe Generation for Probes Shown in FIG. 11A
[0311] a. BAC DNA Preparation
[0312] Mini-prep method: 5 ml overnight cultures for each clone are
set up in LB medium containing 12.5 .mu.g/ml of chloramphenicol and
incubated at 37.degree. C. for 14-16 hours with constant shaking.
Cells are spun down in a microfuge tube and resuspended in 100
.mu.l of chilled solution I (50 mM glucose, 20 mM Tris-Cl, pH 8.0,
10 mM EDTA, pH 8.0). 200 .mu.l of freshly prepared solution II
(0.2N NaOH, 1% SDS) is added and mixed gently and kept on ice. 15
.mu.l of solution III (Potassium acetate, 3M potassium and 5 M
acetate) is added and mixed gently. The tubes are spun and the
supernatant collected in a new microfuge tube and mixed with 1 ml
of 100% ethyl alcohol at room temperature. The tubes are spun for
10 minutes at room temperature and the supernatant discarded. The
pellet is washed in 70% ethanol, air-dried and resuspended in 30
.mu.l of TE. A 5 .mu.l aliquot is then tested on agarose gel.
[0313] Alternatively, the BCL2 and JH-C.alpha. probes for the
present example can take the form of those described for use in
example 5, supra.
[0314] b. Probe Labeling
[0315] All the probes included for FISH analysis are labeled by
nick translation (GIBCO-BRL) according to manufacturer's
instructions. Modified nucleotides conjugated with direct
fluorochromes, fluorescein 12-dUTP and Rhodamine 5-dUTP, (Sigma,
MO) are utilized to obtain green and red color signals,
respectively. Following labeling reactions, the unincorporated
nucleotides are separated by passing through Sephadex G-50 columns.
The probe DNA is precipitated with absolute alcohol and dissolved
in hybridization mixture (50% formamide, 2.times.SSC, 10% dextran
sulphate, 1% Denhardt's solution) and stored at -20.degree. C.
until further use. Approximately 200 ng of each probe is used for
hybridization.
[0316] 2. Preparation of Nuclei from Patients: (Verma and Babu
1989)
[0317] Heparinized peripheral blood or bone marrow samples
collected from individuals suspected of suffering from Follicular
B-Cell Lymphoma are used for chromosomal preparation. Briefly, 0.5
to 1.0 ml of peripheral blood is inoculated to 10 ml of RPMI-1640
medium supplemented with 15% fetal bovine serum and 1% L-glutamine
and streptopenicillin. 0.2 ml of (1 mg/ml) phytohemagglutinin is
then added and the cultures incubated at 37.degree. C. for 72
hours. One hour prior to harvest, 0.2ml (10 .mu.g/ml) of colcemid
solution is added and incubated for 1 hour at 37.degree. C. The
cultures are harvested by treating cells with pre-warmed hypotonic
solution (0.075M KC1) for 15-20 minutes and fixed with 3:1 methanol
acetic acid fixative. Standard air-dried slides will be
prepared.
[0318] 3. Hybridization of Probes to Chromosomes
[0319] Prior to hybridization, slides containing chromosomes are
pretreated by incubating with 2.times.SSC for one hour at
37.degree. C. followed by passing through 70%, 80% and 100% alcohol
for dehydration. The slides are denatured at 70.degree. C. in
denaturing solution (70% formamide, 2.times.SSC) and passed through
cold ethanol series. Simultaneously, the probes are denatured and
placed on slides and hybridized overnight at 37.degree. C. Post
hybridization washes are performed at 45.degree. C. in prewarmed
2.times.SSC solution twice, followed by one room temperature wash
in 2.times.SSC. The slides are then counterstained with antifade
solution containing 4', 6'-diamidino-2-phenylindole dihydrochloride
(DAPI) (Vysis, Downers Grove, Ill.).
[0320] 4. Slide Analysis
[0321] a. Manual Image Analysis
[0322] The cells are scored directly under microscope using triple
band pass filter for the simultaneous visualization of red, green
and blue colors. The green and red fluorescence intensities of the
hybridization signals and DAPI staining patterns are captured with
a cooled charge-coupled device camera (CCD) attached to a Olympus
B.times.60 microscope and processed using ISIS software
(Metasystems) for recording purposes.
[0323] Scoring criteria are determined by first defining the
diagnostic threshold of the method for detecting t(14;18)(q32;
q21). For each set of control and tumor specimens, at least 300
nuclei are analyzed following stringent criteria. In control
specimens, cells are scored as normal when two separate green and
red signals are observed. For closely placed red and green signals,
the distance between each signal is at least twice the size of one
signal, which will be considered a normal pattern. Similarly, a
fusion or co-localizing signal is scored when the distance between
red and green signals is less than one signal size.
[0324] In tumor specimens, the same stringent criteria is followed
as when normal cells are encountered. Tumor cells are scored
positive only when two clear fusion signals and single red and
green signals are observed. A comparison with manual slide
evaluation methods is periodically performed to assess the
efficiency of the system including the speed and the ability to
correctly measure and count.
[0325] Cells carrying t(14;18) are identified by the presence of
two fusion signals and one green and one red signal and the normal
cells are identified with two separate green and red signals. In
this method, the following signal patterns are scored for positive
and negative cells:
[0326] 1) cells with two fusion, one green and one red
signal--t(14;18)(q32; q21) carrying cells 2) cells with one fusion,
one green, and one red signal--normal cell with false positive
signal 3) two separate green and two separated signal--normal cell
4) two fusion signals--normal cell with two false positive
signals
[0327] b. Automated Slide Scanning
[0328] Each slide is tested for signal quality and contrast and
have an area of suitable hybridization marked before scanning. At
least one test slide from each series is scanned with different
sensitivity settings. To ensure accurate scoring, automated results
are periodically evaluated by a comparison to the manual image
analysis describes supra. A limit of 1,000 cells is set for all
slides where results are compared with manual slide evaluation.
After each scan all included cells as displayed in the image
gallery are reviewed. They are scored first using the image gallery
only using the same scoring criteria detailed for manual image
analysis, supra.
[0329] For blood samples deficient in peripheral B-cells, the
sample is pre-enriched by sorting out cells expressing B-cell
surface markers using either magnetic separation or FACS.
II. Results
[0330] The BCL2 and JH-C.alpha. probe were tested on normal and
tumor metaphase and interphase cells. The BCL2 probe was labeled
with a green fluorophore and the IGH probe labeled with a red
fluorophore. Automatic scanning of peripheral blood samples was
performed, creating a gallery of tentatively translocation positive
images and a scoring sheet comprised of statistical data for the
sample. In this manner, the Metacyte system affords the clinician
the opportunity to review any putatively positive results through a
manual evaluation of images stored in the gallery. FIG. 11B-11E
depicts one such result. The steps in the process leading to the
result are detailed below and illustrated in the flow diagram of
FIG. 12B.
[0331] FIG. 11B depicts a DAPI-stained nucleus as imaged using the
Metacyte system. An aspect of the system is that it can detect
shape features of DAPI-stained nuclei, allowing for rejection of
clusters and damaged nuclei.
[0332] The system first scans the system looking for suitable DAPI
stained nuclei for analysis. Once found, a fluorescence filter
(e.g., FITC, Rhodamine) is changed to acquire the signal from one
set of S-FISH probe signals. FIG. 11C illustrates the use of a
filter which removes the probe signals generated by probes 3 and 4,
allowing for the detection of the signals generated by probes 1 and
2. Only three light grey spots can be seen. These three light grey
spots correspond to the untranslocated copy of chromosome 18
(binding both probes 1 and 2), and the signals generated by probes
1 and 2 on the respective translocated derivative chromosomes. The
system automatically changes its focal plane through the sample
from 5 to 7 times, storing an image of the sample at each focal
plane. This technique ensures accurate diagnosis by producing a
series of images defining the sample in three dimensions.
[0333] The system then undergoes a second fluorescence filter
change to pick up the second set of signals, an image of which is
presented in FIG. 11D. Only three dark grey spots can be seen.
These three dark grey spots correspond to the untranslocated copy
of chromosome 14 (binding both probes 3 and 4), and the signals
generated by probes 3 and 4 on the respective translocated
derivative chromosomes. Again, the system automatically changes its
focal plane through the sample from 5 to 7 times, storing an image
of the sample at each focal plane.
[0334] The system then takes one final set of images while changing
focal planes with a filter in place which cuts out the DAPI signal
but allows the signals from both sets of FISH probes to pass. An
image from this set is depicted in FIG. 11E.
[0335] Using both interphase and metaphase cells, the automated
methods accurately categorized cells as positive or negative for
the t(14;18)(q32; q21) translocation. This example illustrates the
power of the methods described herein to produce clear, unambiguous
FISH patterns from both tumor and normal cells, suitable for
automated image analysis. These techniques facilitate the rapid
processing of clinical samples, making diagnosis of Follicular
B-Cell Lymphoma, and other NHL's, routine.
EXAMPLE 7
Detection of the t(9;22)(q34.1; q11.2) Translocation and
Associated
Deletions Common to Chronic Myeloid Leukemia (CML)
I. Background
[0336] The BCR/ABL oncogene is expressed at all stages of CML. The
chronic phase is characterized by the expansion of terminally
differentiated neutrophils and as the disease progresses and enters
the acute phase (blast crisis) it is characterized by maturation
arrest with expansion of undifferentiated myeloid or lymphoid
progenitor cells. During disease progression additional genetic and
molecular changes have been acquired which forms the basis for
resistance to treatment, particularly ST1571 (Druker et al., 2001;
Gorre et al., 2001). Although several sporadic incidences of
secondary chromosomal changes have been reported in CML their
clinical correlation has not been clearly established as it has
been shown for deletions on the rearranged chromosome. It has also
been shown that the deletion on der(9) chromosome are known to
occur at the time of t(9;22)(q34.1; q11.2) translocation event
itself (Sinclair et al., 2000). The strong association of deletions
with altered prognosis indicates the importance to detect the
deletions along with translocation. In addition to chemotherapy,
allogenic bone marrow transplantation (BMT) and peripheral blood
stem cell transplantation are also therapies of choice for CML
because of their ability to attain sustained suppression or
elimination of CML cells. However, regardless of the different
modalities in therapy a significant proportion of CML cases relapse
after bone marrow transplants. These treatments require regular
follow-up for recurrence of cancer in bone marrow and blood. The
most definitive method currently in use for this purpose is
karyotype analysis by G-banding. Although this method is precise,
it is labor intensive and will not detect small deletions
associated with CML. In addition, 50% of follow-up specimens do not
yield results due to hypocellularity of marrow samples and poor
cell proliferation in vitro. Other methods of translocation
detection include Southern blotting; PCR and RT-PCR to detect gene
rearrangements and fusion transcripts, but these methods have
sensitivity and specificity issues. For use in detecting
rearrangements, Southern blotting requires the presence of at least
5-10% tumor cells. PCR is difficult to quantitate and prone to
false positive results from amplification of DNA sequences in dead
tumor cells or in free DNA from lysed cells still present in the
specimen. Quantitative RT-PCR is a new method of choice for
monitoring disease after treatment but this method is not suitable
for deletion detection. The strong association of CML deletions
with treatment outcome warrants the need for the development of
sensitive FISH probes to evaluate the presence of deletions at
diagnosis. Molecular methods are laborious and time consuming for
such analysis.
[0337] II. Probe Design and Construction PCR screening of a human
genomic BAC library (Incyte Genomics, St. Louis, Mo.) is performed
to isolate clones covering the BCR and ABL gene regions. The
primers for the screen are selected using the NCBI database
sequence information. Suitable BAC clone sequences for FISH probe
construction are selected. Criteria for sequence selection in this
particular example comprise ensuring that the selected sequences
span about 500 kb on either side of all known t(9;22)(q34.1; q11.2)
translocational breakpoints associated with CML (although shorter
sequences can be used as an alternative).
[0338] A. Probe Labeling
[0339] For F-FISH analysis the centromeric region probes for BCR
and ABL genes are labeled with Cyanin-5-dUTP (Yellow) and Texas red
dUTP (Red) (PerkinElmer Life Sciences, Boston, Mass.) respectively,
and the telomeric region probes for BCR and ABL genes are labeled
with Fluorescein 12-dUTP (Green) and Coumarin-5-dUTP (Blue)
(PerkinElmer Life Science, Boston, MA) respectively. For two color
FISH analysis the ABL and BCR region probes are labeled with
Fluorescein 12-dUTP (Green) and Texas Red--dUTP (Red) labels
respectively.
[0340] The recipe for the labeling reaction consists of; a total of
50 ng each of four-color (F-FISH) probe dissolved in a
hybridization buffer containing 50% Formamide, 2.times.SSC,
10.times.Dextran sulphate and 1% Denhardt's solution. Slides
carrying chromosomal samples for analysis are denatured at
75.degree. C. for 2 minutes and dehydrated in 70%, 80% and 100%
ethanol followed by air-drying. The probe mixture is denatured at
75.degree. C. for 8 minutes, applied to the slides and incubated
overnight at 37.degree. C. Post hybridization washes are then
preformed in 50% formamide, 2.times.SSC at 45.degree. C. (2.times.)
for 10 minutes each and washed twice in 2.times.SSC (45.degree.
C.). Finally, slides are briefly rinsed in distilled water, air
dried and counterstained with DAPI.
[0341] Techniques for hybridizing probes to chromosomes are
described in Example 6 and are commonly known in the art.
[0342] B. Image Scanning
[0343] Alternative scanning and analysis techniques described
elsewhere in this application are also amenable to the F-FISH
analysis described in this example and may be substituted for those
described here.
[0344] FISH images are captured and analyzed using a mega pixel
JAI-CCD camera attached to Axioplan-2IE (ZEISS, Germany) microscope
controlled by In situ Imaging System (ISIS) image processing
software (Metasystems Group, Belmont Mass.). Analysis may be
performed manually, or the process can be automated through the
MetaSystems Image Scanning Platform described in Example 6
III. Results
[0345] Probes developed for performing the signal segregation
analysis are labeled by the two-label system to conduct a
preliminary screening of a panel of 70 unselected CML samples. Of
the 70 cases; 59 were known to have standard t(9;22) (q34.1; q11.2)
translocation, 8 possessed variant translocations, two cases
displayed the Ph chromosome and one case showed amplification of
BCR/ABL fusion region. Of the 70 cases, 59 had t(9;22)(q34.1;
q11.2), 8 had variant translocations, two cases showed additional
Ph chromosomes and K562 cell line with high level amplification of
BCR/ABL fusion region. Of the 59 cases with t(9;22)(q34.1; q11.2),
12 cases were identified as having deletions, and 4 of the 8 cases
with variant translocations were also found to have a deletion. Of
the 12 cases with t(9;22)(q34.1; q11.2), 4 cases had deletions of
both the BCR and ABL regions on der(9) chromosome, and 1 case had a
deletion of the ABL and BCR regions on der(22) chromosome. In two
cases deletion of the BCR region on der(9) was observed, and
deletion of ABL sequences alone was observed in 4 cases. In one
case, deletion of the ABL region on der(22) was observed. The
incidence of deletions was higher in cases with variant
translocations (50%) than in the cases with the t(9;22)(q34.1;
q11.2) translocation (20%). Of the 8 cases with variant
translocations, 4 cases were found to have deletions. These
included deletions in regions of BCR (1 case), ABL (1 case) and
both ABL and BCR (2 cases). In specimens with atypical signal
patterns metaphase cells were analyzed to confirm the origin of the
chromosome suffering a deletion and those chromosomes undergoing
variant translocations.
[0346] From the preliminary screening, specimens for a) normal, b)
standard t(9;22)(q34.1; q11.2) translocation, c) deletion on
der(9), d) deletion on der(22), and e) variant translocation were
selected and subjected to F-FISH analysis. The signal patterns
obtained from the F-FISH analysis are schematically depicted in
FIG. 4.
[0347] As shown in FIG. 4A, in normal interphase nuclei, the two
copies of chromosome 9 and two copies of 22 are identified
unambiguously by a two-label signal for each chromosome such that
there a four distinct labels. Similarly, in tumor cells (FIG. 4B),
in addition to one copy each of normal 9 and 22, the der(9) and
der(22) are each identified by entirely different two-label signal
patterns unique to the respective chromosomes. This four-color
F-FISH approach thus allows interpretation of the various signal
patterns found in analysis of chromosomal rearrangements associated
with CML through analysis of interphase cells alone.
[0348] The studies described in the foregoing examples establish
that clear and unambiguous signals can be obtained utilizing a
segregated signal approach to detect translocations. While analyses
utilizing such signals can be conducted with two probes that
together recognize one of the two derived chromosomes, by using
four probes (two for each chromosome that together flank the
breakpoint) one can simultaneously detect both normal and
translocated chromosomes.
EXAMPLE 8
Removal of Repeat Sequences from a BAC clone
I. Step 1: Size Estimation by Pulsed Field Gel Electrophoresis
(PFGE)
[0349] 100 ng of BAC DNA was digested with Not1 restriction enzyme
to release the insert and vector DNA as separate fragments, which
were resolved by pulsed field gel electrophoresis using the CHEF DR
II apparatus (BIORAD). The following gel run parameters were used
for PFGE: 0.5.times.TBE buffer recirculating at 14.degree. C., 1%
pulsed field certified agarose, initial switch time 1 sec., final
switch time 6 seconds at 6 volts/cm, with an angle at 120.degree.
for 18 hours. Appropriate size markers were used. Following
electrophoresis, the gel was stained with ethidium bromide for 15
minutes and visualized under a UV transilluminator for
documentation. Two bands were identified, one corresponding to
insert (200 kb) and the smaller fragment corresponding to the
vector (7.0 kb).
II. Restriction Digestion of BAC Clone 543:
[0350] Initially the BAC DNA was digested with EcoRI and HindIII.
These digests yielded many larger fragments in the size range of
6-20 kb and few smaller fragments. Southern hybridization with
radiolabeled Cot-1 DNA probe showed very few smaller fragments free
of repeat sequences. Thus, PstI was selected for subdloning the BAC
inserts, because PstI yielded fragments in the size range of 500 bp
to 6 kb and also many fragments were identified to be free of
repeat sequences. The clone 543 selected an example here was
identified with approximately 40 fragments, using PstI digestion,
in the size range of 200 bp-6 kb.
III. Subcloning
[0351] One microgram of BAC DNA was digested with PstI to
completion. Similarly p-Bluscript SK-plasmid vector was also
digested with PstI. Dephosphorylation of the digested plasmid
vector with calf intestinal alkaline phosphatase (CIAP) was done
prior to ligation to the insert DNA. The dephosphorylated vector
DNA was ethanol precipitated and resuspended in TE buffer. For
ligation, the insert and vector DNA in the ratio of
2:1(insert:vector) were mixed and the reaction was continued at
4.degree. C. overnight (Shotgun ligation). The ligation mixture was
transformed into competent cells of XL1-Blue MRF' host bacteria and
plated on selective media containing tetracycline-chloramphenicol
to select for colonies that contained the inserts. Ninety-nine
white bacterial colonies were selected and grown in a 5 ml culture
overnight.
IV. Preparation of Mini Prep DNA
[0352] DNA from the 5 ml overnight culture was prepared by a
standard alkaline lysis method (Sambrook and Russel, 2001). Plasmid
DNA was digested with PstI and electrophoresis was performed to
identify DNA samples with inserts. Ninety of the selected colonies
were found to contain inserts of varying size.
V. Preparation of Glycerol Stock
[0353] Glycerol stock for all the colonies with inserts were made
by mixing 800 .mu.l of bacterial culture and 200 .mu.l of 80%
glycerol and stored at -80.degree. C.
VI. Identification of Repeat Free Clones
[0354] All the insert-containing clones were size selected and run
on an agarose gel. The DNA on the agarose gel was transferred to
nylon membrane and hybridized with radiolabeled (p.sup.32) Human
Cot-1 DNA (Invitrogen, Rockvill, Md.). Of all the 90 clones with
inserts, all 40 of the unique sized clones were identified. Among
the 90 clones hybridized with radiolabled probe, only 28 clones
were found to contain repeat sequences. The rest of the clones were
free of repeats. Among all the repeat free clones, unique size
clones were selected for preparation of large scale DNA to be used
as a probe for FISH hybridization.
[0355] The same approach can be used to select the repeat free
fragments from each BAC clone selected for a translocation
detection probe.
[0356] It is understood that the examples and embodiments described
herein are for illustrative purposes only and that various
modifications or changes, such as utilization of individual colors
for each probe, in light thereof will be suggested to persons
skilled in the art and are to be included within the spirit and
purview of this application and scope of the appended claims. All
publications, patents and patent applications cited herein are
hereby incorporated by reference in their entirety for all purposes
to the same extent as if each individual publication, patent or
patent application were specifically and individually indicated to
be so incorporated by reference.
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Sequence CWU 1
1
24 1 19 DNA Artificial Sequence Description of Artificial
Sequenceprobe 1 for BCL1 region proximal to MTC region primer F 1
aaggtgtgag gatcactgg 19 2 17 DNA Artificial Sequence Description of
Artificial Sequenceprobe 1 for BCL1 region proximal to MTC region
primer R 2 agctcatggg ggctatt 17 3 19 DNA Artificial Sequence
Description of Artificial Sequenceprobe 2 for BCL1 region telomeric
to BCL1 gene region primer F 3 tttctgggtg tgtctgaat 19 4 19 DNA
Artificial Sequence Description of Artificial Sequenceprobe 2 for
BCL1 region telomeric to BCL1 gene region primer R 4 acacagttgc
tctaaaggg 19 5 20 DNA Artificial Sequence Description of Artificial
Sequenceprobe 3 for IGH region sub-telomeric V region of IGH gene
primer F 5 tgtttgaaga agggagtcgt 20 6 20 DNA Artificial Sequence
Description of Artificial Sequenceprobe 3 for IGH region
sub-telomeric V region of IGH gene primer R 6 cccactccat gtcttctgtt
20 7 24 DNA Artificial Sequence Description of Artificial
Sequenceprobe 4 for IGH region Calpha region primer F 7 ccactcagtg
tgacctggag cgaa 24 8 24 DNA Artificial Sequence Description of
Artificial Sequenceprobe 4 for IGH region Calpha region primer R 8
ctcccctggc ttttctggaa ctgg 24 9 11 DNA Artificial Sequence
Description of Artificial Sequenceprobe 1 for MYC region
centromeric to all three classes of breakpoints in MYC region
primer F 9 gtttaagtgg a 11 10 20 DNA Artificial Sequence
Description of Artificial Sequenceprobe 1 for MYC region
centromeric to all three classes of breakpoints in MYC region
primer R 10 acaggggaat ggttaactgg 20 11 21 DNA Artificial Sequence
Description of Artificial Sequenceprobe 2 for MYC region telomeric
to all three classes of breakpoints in MYC region from exon 2
region of MYC gene primer F 11 atgcccctca acgttagctt c 21 12 19 DNA
Artificial Sequence Description of Artificial Sequenceprobe 2 for
MYC region telomeric to all three classes of breakpoints in MYC
region from exon 2 region of MYC gene primer R 12 cagagtcgct
gctggtggt 19 13 20 DNA Artificial Sequence Description of
Artificial Sequenceprobe 3 for IGH region sub-telomeric V region of
IGH gene primer F 13 tgtttgaaga agggagtcgt 20 14 20 DNA Artificial
Sequence Description of Artificial Sequenceprobe 3 for IGH region
sub-telomeric V region of IGH gene primer R 14 cccactccat
gtcttctgtt 20 15 24 DNA Artificial Sequence Description of
Artificial Sequenceprobe 4 for IGH region Calpha region primer F 15
ccactcagtg tgacctggag cgaa 24 16 24 DNA Artificial Sequence
Description of Artificial Sequenceprobe 4 for IGH region Calpha
region primer R 16 ctcccctggc ttttctggaa ctgg 24 17 20 DNA
Artificial Sequence Description of Artificial Sequenceprobe 1 for
region centromeric to BCL2 gene primer F 17 cttgcctcct aagccagttg
20 18 19 DNA Artificial Sequence Description of Artificial
Sequenceprobe 1 for region centromeric to BCL2 gene primer R 18
tggattcatt tctgatcca 19 19 23 DNA Artificial Sequence Description
of Artificial Sequenceprobe 2 for region telomeric to BCL2 gene
primer F 19 tggccagcag cagtgtcaaa tag 23 20 20 DNA Artificial
Sequence Description of Artificial Sequenceprobe 2 for region
telomeric to BCL2 gene primer R 20 ggtgatcgtt aggactccca 20 21 20
DNA Artificial Sequence Description of Artificial Sequenceprobe 3
for region telomeric to IGH-J gene from sub-telomeric region of
chromosome 14q primer F 21 tgtttgaaga agggagtcgt 20 22 20 DNA
Artificial Sequence Description of Artificial Sequenceprobe 3 for
region telomeric to IGH-J gene from sub-telomeric region of
chromosome 14q primer R 22 cccactccat gtcttctgtt 20 23 20 DNA
Artificial Sequence Description of Artificial Sequenceprobe 4 for
region centromeric to IGH-J gene from Calpha region primer F 23
ccctggacgc ttttcaaata 20 24 20 DNA Artificial Sequence Description
of Artificial Sequenceprobe 4 for region centromeric to IGH-J gene
from Calpha region primer R 24 gactcaggca aggacaaagc 20
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References