WO2013033169A1 - Methods of identifying genomic translocations associated with cancer - Google Patents

Abstract

The invention provides methods for evaluating and detecting translocation mutations in different cancers using SNP array data and in particular by determining copy number variations (CNV) in or close to the genes which are involved in the translocation.

Description

METHODS OF IDENTIFYING GENOMIC TRANSLOCATIONS

ASSOCIATED WITH CANCER

Related Applications

This application claims priority to U.S. Provisional Patent Application No.

61/529,714, filed August 31, 2011, U.S. Provisional Patent Application No. 61/532,409, filed September 8, 2011, and French Patent Application No. 1255627, filed June 15, 2012.

The contents of the aforementioned applications are hereby incorporated herein by reference in their entireties.

Field of Invention

The invention provides methods for evaluating and detecting translocation mutations in different cancers using SNP array data.

Background One of the major goals in cancer research is to identify causal genetic aberrations.

This has led to the identification of several successful therapeutic targets, including BCR-ABL fusion, EGFR amplification/mutation, and HER2 amplification. Among different types of genetic aberrations, chromosomal rearrangements creating oncogenic gene fusions are the hallmark of many haematopoietic malignancies as well as rare bone and soft-tissue tumors (Soda, Choi et al. 2007) (Mertens, Antonescu et al. 2009). Recent reports suggest that many solid tumors also contain gene fusions that confer tumorigenic potential. Multiple methods were developed for identifying gene fusions caused by chromosomal translocations. Traditional methods involve cytogenetic analysis followed by fluorescent in situ hybridization analysis. Recent high-throughput data platforms also provide opportunities to discover novel fusions. For example, expression data based analysis such as Cancer Outlier Profile Analysis (COPA) (MacDonald and Ghosh 2006) identified novel fusions, including TMPRSS2-ERG and TMPRSS2-ETV1 in prostate cancer (Tomlins, Rhodes et al. 2005). Deep sequencing of cDNA libraries led to the discovery of the EML4-ALK fusion in non- small-cell lung cancer (NSCLC) (Soda, Choi et al. 2007), and integrative analysis of high-throughput long- and short-read

transcriptome sequencing identified several gene fusions in prostate cancer cell lines (Maher, Kumar-Sinha et al. 2009). However, since these methods are based on information from RNA transcripts, the fusion identified might be due to alternative splicing, or transcript level re-arrangement. Identifying translocations at the

chromosomal level remains a challenging task.

Chromosomal translocations, by definition, alter genomic sequences, and may generate fusion proteins or dysregulate gene expression. Chromosomal translocations elicit DNA repair processes, which involve mis-repair of double-strand ends. Cloning genomic junctions in various chromosome translocations in leukemia shows that there are deletions, duplications, and insertions at the breakpoints in many translocations (Nickoloff, De Haro et al. 2008). The sizes of deletions and duplications range from a few bp to a few hundred bp. Many fusion genes are also reported to have multiple copies. These will result in copy number variation (CNV) between segments retained in the fusion gene and its neighboring genomic sequences. High density SNP arrays are useful tools, not only to study SNP-based genetic linkage, but also to detect DNA CNV across the whole genome. The current Affymetrix SNP array 6.0 contains 1.8 million markers for genetic variation, and has a median inter-marker distance of less than 700 bases. During the last few years, extensive efforts have been dedicated to SNP array profiling on tumor samples and cell lines. For example, the Sanger Institute has profiled over 800 cancer cell lines on the Affymetrix SNP array 6.0.

Summary of Invention

The disclosure provides, herein, a method for diagnosing a patient suspected of having a gene translocation-associated cancer including the step of detecting the presence of a copy number variation (CNV) breakpoint signature in a gene of a subject, wherein the presence of the signature in the gene is indicative of the subject having the gene translocation-associated cancer. The method can also include a step of determining the nucleic acid sequence of the gene containing the copy number variation breakpoint signature to confirm the presence of an associated gene translocation. The method can also include using first or first or second steps described above for diagnosing the subject as having a gene translocation-associated cancer; and administering to the subject a compound that inhibits the activity of the gene or a polypeptide encoded by the gene if said copy number variation (CNV) breakpoint signature or said associated gene translocation is present thereby treating the patient having the gene translocation- associated cancer.

The disclosure also provides a method for selecting therapy for a patient having a gene translocation-associated cancer, including the steps of determining whether said cancer exhibits a gene having a copy number variation breakpoint signature; and if said cancer exhibits the gene having the copy number variation breakpoint signature, selecting for said patient a therapy that comprises the administration of a compound that inhibits the activity of the gene or a polypeptide encoded by the gene. The method can further include determining the nucleic acid sequence of the gene containing the copy number variation breakpoint signature to confirm the presence of an associated gene translocation.

For any of the methods described above, the copy number variation breakpoint signature can be detected using a single nucleotide polymorphism (SNP) array. For any of the methods described above, the gene translocation-associated cancer can include a balanced or an unbalanced translocation. For any of the methods described above, the copy number variation breakpoint signature can include a region of copy number variation within the boundary of the gene; a region of increased copy number flanked by copy number variation breakpoints; or a region of decreased copy number flanked by copy number variation breakpoints.

For any of the methods described above, the gene can be an oncogene or a proto- oncogene. For example, the gene can be FYN, MMEL1, RAB8A, VAV2, BRAF, ERBB2, ETV6, FLU, MET, NAE1, NTRK3, PVT1, RAB31, RAB3A, RAB40C, or

THRB. For any of the methods described above, the gene can be PVT1, THRB, AKT3, RAB3C, AKAP13, VAV2, ABL2, ERBB4, AKT2, NTRK3, ALK, VAV3, BRAF, KIT, BCL2, EGFR, ERG, ETV6, EWSR1, RET, RUNX1, FER, RAF1, ERBB2, MKRN2, RAB31„RAB5A, RAPGEF1, ETS1, MERTK, KRAS, RAB2A, CRKL, FYN, ABL1, EFCAB2, RAP1A, FLU, RAB40B, ROS1, VAV1, CSF1R, ERBB3, LYN, MYB,

RAB28, RAB40C, TETl, FGFR10P2, RAB10, RABIA, RAB30, RRAS2, TET2, USP6, DEK, MET, RALA, RAPIB, SH3D19, TTC23, SRC, TAF8, ECT2, RAB22A, RAB4A, RAB7A, SKIL, TET3, THRA, TPR, ETS2, ETV7, HEXB, RAB18, RAB27A, RAB38, RAB6A, RALB, TMEM50A, CDON, CSDE1, ENTPD5, MYBL1, NAE1, NTRK1, PDGFB, RAB17, RAB3B, RAB6B, RNASEH2A, SPAG9, SPI1, USP4, FGFR10P, NDUFC2, PEA15, RAB 11A, RAB14, RAB20, RAB23, RAB33B, RAB37, RABL4, SKI, SSPN, WNT3, CRK, ETV3, FLJ10357, FOS, GLI1, GNB2L1, ISY1, KLF6, LCK, LYRM5, MAP3K8, MMEL1, MYBL2, MYCL1, NRAS, PTK6, RAB12, RAB32,

RAB35, RAB39, RAB43, RAB5C, RAB7L1, RAB8A, RAB8B, RABL3, RAP2A, SET, or TMED9. For any of the methods described above, the gene can be the gene can be ERBB4, FER, AKT3, ERG, ABL2, ALK, BCL2, EFCAB2, EGFR, ETS2, ETV6, ETV7, FGFRIOP, ISY1, NTRK3, PDGFB, PVT1, RABIA, RAB27B, RAB40B, RAB6B, RAB7A, RAF1, RAPGEF1, RUNX1, SET, TAF8, THRB, or TMEM50A.

The disclosure also provides an isolated nucleic acid comprising a gene fusion of any of FYN, MMEL1, RAB8A, VAV2, BRAF, ERBB2, ETV6, FLU, MET, NAE1, NTRK3, PVT1, RAB31, RAB3A, RAB40C, or THRB. The disclosure also provides an isolated nucleic acid comprising a gene fusion of any of PVT1, THRB, AKT3, RAB3C, AKAP13, VAV2, ABL2, ERBB4, AKT2, NTRK3, ALK, VAV3, BRAF, KIT, BCL2, EGFR, ERG, ETV6, EWSR1, RET, RUNX1, FER, RAF1, ERBB2, MKRN2,

RAB31„RAB5A, RAPGEF1, ETS1, MERTK, KRAS, RAB2A, CRKL, FYN, ABL1, EFCAB2, RAP1A, FLU, RAB40B, ROS1, VAV1, CSF1R, ERBB3, LYN, MYB, RAB28, RAB40C, TETl, FGFR10P2, RAB10, RABIA, RAB30, RRAS2, TET2, USP6, DEK, MET, RALA, RAPIB, SH3D19, TTC23, SRC, TAF8, ECT2, RAB22A, RAB4A, RAB7A, SKIL, TET3, THRA, TPR, ETS2, ETV7, HEXB, RAB18, RAB27A, RAB38, RAB6A, RALB, TMEM50A, CDON, CSDE1, ENTPD5, MYBL1, NAE1, NTRK1, PDGFB, RAB17, RAB3B, RAB6B, RNASEH2A, SPAG9, SPI1, USP4, FGFRIOP, NDUFC2, PEA15, RAB 11A, RAB14, RAB20, RAB23, RAB33B, RAB37, RABL4, SKI, SSPN, WNT3, CRK, ETV3, FLJ10357, FOS, GLI1, GNB2L1, ISY1, KLF6, LCK, LYRM5, MAP3K8, MMEL1, MYBL2, MYCL1, NRAS, PTK6, RAB12, RAB32, RAB35, RAB39, RAB43, RAB5C, RAB7L1, RAB8A, RAB8B, RABL3, RAP2A, SET or TMED9. The disclosure also provides an isolated nucleic acid comprising a gene fusion of any of ERBB4, FER, AKT3, ERG, ABL2, ALK, BCL2, EFCAB2, EGFR, ETS2, ETV6, ETV7, FGFRIOP, ISY1, NTRK3, PDGFB, PVT1, RABIA, RAB27B, RAB40B, RAB6B, RAB7A, RAF1, RAPGEF1, RUNX1, SET, TAF8, THRB, and TMEM50A. The disclosure also provides a method for detecting the presence of a

chromosomal translocation in a tumor sample including the step of detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the signature in the gene is indicative of a chromosomal translocation.

The disclosure also provides a method for identifying a gene containing a chromosomal translocation in a tumor sample including the step of detecting the presence of a copy number variant breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as containing a chromosomal translocation.

The disclosure also provides a method for identifying a translocation gene fusion including the step of detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as a translocation gene fusion.

The disclosure also provides a method for identifying a gene deletion including the step of detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as a gene deletion.

The disclosure also provides a method for identifying a gene amplification including the step of detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as a gene amplification.

For any of the methods described above, the gene can be a tumor suppressor gene. For any of the methods described above, the gene can be RUNX3, HRPT2, FH, FHIT, RASSF1A, TGFBR2, VHL, hCDC4, APC, NKX3.1, Pl6^mKM, Pl^, PTC, TSC1, BMPR1, PTEN, WT1, MEN1, Ρ5Ί^Άρ2, TIMP3, IGFBP, CDKN2A/pl6^INK4A,

CDKN2B/pl5^INK4B, Pl^, P53, P73, GSTP1, MGMT, CDH1, DAPK, MLH1, THBS1, RB, CASP8, APAF1, or CTMP.

Brief Description of the Drawings

Figure 1 depicts genomic level CNV analysis of BCR and ABL1 genes using Affymetrix SNP 6.0 array® data for eight CML cell lines. Copy number states are divided into the following categories: 0 -homozygous deletion; 1 - heterozygous deletion; 2 - normal diploid; 3 - single copy gain; and 4 - multiple copy gain. Arrows highlight both amplified (blue) and deleted (red) genomic segments. The black arrow indicates the direction of the transcript. Affymetrix Genotyping Console software was used for this analysis.

Figure 2 depicts an Affymetrix Genotyping Console Browser® view of BCR and ABL1 genes for two non-CML cell lines that possess copy number breakpoints in both BCR and ABL1 genes. Copy number states are divided into the following categories: 0 -homozygous deletion; 1 - heterozygous deletion; 2 - normal diploid; 3 - single copy gain; and 4 - multiple copy gain. Arrows highlight both amplified (blue) and deleted (red) genomic segments. The black arrows indicate the direction of the transcript.

Figure 3 depicts an Affymetrix Genotyping Console Browser® view of the segment deletion between TMPRSS2 and ERG in prostate cancer samples. Copy number states are divided into the following categories: 0 -homozygous deletion; 1 - heterozygous deletion; 2 - normal diploid; 3 - single copy gain; and 4 - multiple copy gain. Red arrows demarcate deleted genomic segments, while black arrows designate the directions of the two transcripts.

Figure 4 depicts an Affymetrix Genotyping Console Browser® view of EML4 and ALK genes in six lung cancer cell lines that contain copy number breakpoints in both genes. Copy number states are divided into the following categories: 0 - homozygous deletion; 1 - heterozygous deletion; 2 - normal diploid; 3 - single copy gain; and 4 - multiple copy gain. Arrows highlight both amplified (blue) and deleted (red) genomic segments. Black arrows indicate the directions of the transcripts.

Figure 5 depicts a boxplot view of the numbers of gene-linked copy number breakpoints in 820 cancer cell lines from different cancer origins. The numbers in brackets indicate the number of cell lines mapped to each cancer type. Cancer types with less than 5 cell lines are not included. Y axis: the number of gene-linked copy number breakpoints. Median: bolded line inside the box; 25 percentile: top line of the box; 75 percentile: bottom line of the box; Maximum (excluding outliers): top bar outside of the box; Minimum (excluding outliers): lowest bar outside of the box; Outlier: O Detailed Description of the Invention

The invention provides methods for evaluating and detecting translocation mutations in different cancers using SNP array data. The present invention is based, in part, on the discovery that genomic deletion or duplication at the breakpoint/junction site of a gene fusion event or amplification of a fusion gene during tumorigenesis can be detected by high-resolution SNP arrays.

The methods of the invention were validated by analyzing three well-known genetic fusions in cancer: BCR-ABL1, TMPRSS2-ERG, and EML4-ALK using high density SNP array data from related patient samples and cancer cell lines. The copy number breakpoint near or at the junction of each fusion gene as examined and two aspects were evaluated: (i) whether a deletion or amplification in copy number could be detected, and (ii) the distance relative to the specific fusion junction. Based on the information from the analysis of the validation set, a search tool was developed to identify additional cancer cell lines that contain interesting fusion genes by examining the SNP array data of Sanger's 820 cancer cell lines. The distribution of gene-linked copy number breakpoints in cancer cell lines was also evaluated. The methods of the invention have identified several breakpoints that are associated with particular types of cancer. In particular, breakpoints in the genes FYN, MMEL1, RAB8A, VAV2, BRAF, ERBB2, ETV6, FLU, MET, NAE1, NTRK3, PVT1, RAB31, RAB3A, RAB40C, and THRB are associated with prostate cancer. Breakpoints in the genesPVTl, THRB, AKT3, RAB3C, AKAP13, VAV2, ABL2, ERBB4, AKT2, NTRK3, ALK, VAV3, BRAF, KIT, BCL2, EGFR, ERG, ETV6, EWSR1, RET,

RUNXl, FER, RAFl, ERBB2, MKRN2, RAB31„RAB5A, RAPGEFl, ETSl, MERTK, KRAS, RAB2A, CRKL, FYN, ABL1, EFCAB2, RAP1A, FLU, RAB40B, ROS1, VAV1, CSF1R, ERBB3, LYN, MYB, RAB28, RAB40C, TET1, FGFR10P2, RAB10, RABIA, RAB30, RRAS2, TET2, USP6, DEK, MET, RALA, RAPIB, SH3D19, TTC23, SRC, TAF8, ECT2, RAB22A, RAB4A, RAB7A, SKIL, TET3, THRA, TPR, ETS2, ETV7, HEXB, RAB18, RAB27A, RAB38, RAB6A, RALB, TMEM50A, CDON, CSDE1, ENTPD5, MYBL1, NAE1, NTRK1, PDGFB, RAB17, RAB3B, RAB6B, RNASEH2A, SPAG9, SPI1, USP4, FGFRIOP, NDUFC2, PEA15, RAB11A, RAB14, RAB20, RAB23, RAB33B, RAB37, RABL4, SKI, SSPN, WNT3, CRK, ETV3,

FLJ10357, FOS, GLI1, GNB2L1, ISY1, KLF6, LCK, LYRM5, MAP3K8. MMEL1, MYBL2, MYCL1, NRAS, PTK6, RAB12, RAB32, RAB35, RAB39, RAB43, RAB5C, RAB7L1, RAB8A. RAB8B. RABL3, RAP2A, SET and TMED9 are associated with lung cancer. Breakpoints in the genes ERBB4, FER, AKT3, ERG, ABL2, ALK, BCL2, EFCAB2, EGFR, ETS2, ETV6, ETV7, FGFRIOP, ISY1, NTRK3, PDGFB, PVT1, RAB1A, RAB27B, RAB40B, RAB6B, RAB7A, RAF1, RAPGEF1, RUNX1, SET, TAF8, THRB, and TMEM50A are associated with leukemia.

Examples

The present invention is further illustrated by the following examples which should not be construed as further limiting.

Methods

Gene position on the chromosome

For each gene, the transcript start and end positions, as well as the coding start and end positions, were retrieved from the hgl8 human genome assembly RefGene table. In the case of genes with multiple splice transcripts, the transcript start position was based on the first transcript start site, and the transcript end position was based on the last transcript end site on the chromosome. Genes were excluded from analysis if any of the following criteria were met: (1) transcripts annotations were on different

chromosomes, or on un-assembled segments; (2) genes were on either the X or Y chromosomes; (3) the transcript sequence length was less than 0. Based on the hgl8 RefGene table, 19,642 genes meet the above criteria, and among them, 224 genes were annotated as oncogenes based on Affymetrix "HG-U133_Plus_2.na27.annot.txt" annotation table. For genes with multiple splice transcripts, the start position for the coding sequences was based on the last start site, and the end position was based on the first end site on the chromosome, provided that the resulting coding sequence length was larger than 0. There are total 17,609 genes in the genome that meet these criteria, and 205 genes were annotated as oncogenes. SNP array data analysis

SNP array data were analyzed using Affymetrix Genotyping Console 3.0.2 and Birdseed v2 genotype algorithm. All of the arrays passed quality control requirements, with contrast QC and MAPD values within boundaries. If there were no paired samples, samples were normalized against default Affymetrix normal samples. For the copy number analysis, we used regional GC correction and required 5 markers to be found within the changed region and the size of the region to be at least 100 kb. Genotyping Console Browser (Affymetrix) was used to illustrate copy number changes detected.

SNP array data of 820 cell lines, kindly provided by Sanger Institute, were profiled on the Affymetrix SNP Array 6.0 set.

SNP array data of 38 unique HapMap normal cell lines downloaded from GEO (datasets GSE15096 and GSE17359), were profiled on the Affymetrix SNP Array 6.0 set.

SNP array data of 20 paired prostate tumor samples with matched normal samples were downloaded from GEO (GSE12702), and were profiled on the Affymetrix Mapping 500K Array set. Samples were normalized against the matched normal samples.

SNP array data of 25 GIST cancer samples were downloaded from GEO (dataset GSE20709) and were profiled on the Affymetrix SNP Array 6.0 set.

Searching for genes containing copy number breakpoint

For each sample, a segment reporting file was exported from Affymetrix

Genotyping Console 3.0.2, which contains CNV segment information, including copy number state, chromosome location, start position, and end position. The information was utilized to search for copy number breakpoint in an interested gene.

Simulation

In order to evaluate the probability of finding, by random chance, a start/end point of a CNV segment that falls inside a gene of interest in a specific cell line, a simulation was performed as following:

1. For a defined cell line, extract the information of all CNV segments, such as size, copy number status (gain or loss). 2. Randomly assign the CNV segments, with the defined size, gain/loss status, to a hypothetical human genome, avoiding generating CNV segment overlaps.

3. Examine whether there is a start/end point of a CNV segment that falls inside the gene(s) of interested.

4. Repeat steps 1-3 for 100,000 iterations.

5. Calculate P values based on the number of iterations required to identify a CNV inside the gene(s) of interest based on the above criteria, per 100,000 iterations.

Example 1: BCR-ABL

Examination of CML cell lines with reported Philadelphia chromosome

translocations

The BCR-ABL gene fusion, also referred to as the Philadelphia chromosome or Philadelphia translocation, is the best known chromosomal abnormality resulting from a reciprocal translocation between chromosome 9 and 22. The fusion contains 5 'end sequences from BCR and 3'end sequences from ABL1, which contains the kinase domain. The chimeric BCR-ABL protein has constitutively elevated tyrosine

phosphokinase activity. This abnormal enzymatic activation is critical to the oncogenic potential of BCR-ABL (Kurzrock, Kantarjian et al. 2003). It is found in 95% of the subjects with CML, in 25-30% of ALL patients, and occasionally in AML patients (Kurzrock, Kantarjian et al. 2003).

Among the 820 cell lines that the Sanger Institute profiled, there are eight cell lines that are of CML origin with reported Philadelphia chromosomes: MEG01, K562, BV173, EM2, LAMA84, NALM1, CMLT-1, and KU812. The SNP array data of these cell lines was analyzed and observed that five cell lines (MEG01, K562, BV173, EM2, and LAMA84) contain copy number breakpoints in both the BCR and ABL1 genes

(Figure 1). There are three known breakpoint cluster regions in BCR. The majority of breakpoints in CML patients have been reported to occur between BCR exons 12 to 16. The second breakpoint cluster region, mainly in ALL, lies within an intron between BCR exons 1 and 2, while the third one is located downstream of BCR exon 19 (Uphoff, Habig et al. 1999). In the five CML cell lines in which copy number breakpoints were observed, the breakpoints in BCR all reside between exons 12 to 16, while the breakpoints in ABL1 vary somewhat, but the majority reside within the first intron. As for the CNV, in BCR, the copy number at its 3 'end is lower than that of its 5 'end, while in ABL1, the copy number at its 3'end is always higher than that of its 5'end, thus favoring presence of BCR-ABL fusion protein. As for the other three CML cell lines (NALM1, CMLT-1, and KU812), breakpoints were detected in either BCR, ABL1, or in the neighboring regions. For example, in CMLT-1 cells, a copy number breakpoint was found in ABL1, while in KU812 a micro-deletion was found in ABL1. Of note, CNV were found in the neighbor genes of BCR in all three cell lines. In conclusion, although the number of examples is limited, the copy numbers for sequences that retain in the fusion gene are either remained as normal or increased, but are never decreased; while the copy numbers for sequences that are not in the fusion gene are either lost or remain as normal, but are never increased.

In order to evaluate CNV in the coding regions, especially in the oncogenes, the copy number breakpoint resides within the transcript of the oncogene in these eight CML cell lines was searched. As shown in Table 1, ABL1 contains copy number breakpoints in six out of the eight CML cell lines. The frequency (75%) is the highest compared to other oncogenes. Table 1. Oncogenes that contain copy number breakpoints in eight CML cell lines.

Breakpoint is within the transcript, regardless of the location or whether it was associated with amplification or deletion.

# of CML Cell

HUGO Lines Cell Lines

EM-2_4063#BV-173_4655#K-562_3955#LAMA-

ABL1 6 84_4698#CML-T1_4045#MEG-01_4635

ERBB4 3 K-562_3955#LAMA-84_4698#KU812_4664

FER 3 LAMA-84_4698#KU812_4664#MEG-01_4635

AKT3 2 BV-173_4655#K-562_3955

ERG 2 K-562_3955#LAMA-84_4698

ABL2 1 K-562_3955

ALK 1 LAMA-84_4698

BCL2 1 KU812_4664

EFCAB2 1 BV-173_4655

EGFR 1 LAMA-84_4698

ETS2 1 K-562_3955

ETV6 1 K-562_3955

ETV7 1 K-562_3955

FGFRIOP 1 K-562_3955

ISY1 1 K-562_3955 NTRK3 1 MEG-01_4635

PDGFB 1 K-562_3955

PVT1 1 EM-2_4063

RAB 1A 1 LAMA-84_4698

RAB27B 1 KU812_4664

RAB40B 1 LAMA-84_4698

RAB6B 1 KU812_4664

RAB7A 1 EM-2_4063

RAF1 1 K-562_3955

RAPGEF1 1 LAMA-84_4698

RUNX1 1 LAMA-84_4698

SET 1 LAMA-84_4698

TAF8 1 MEG-01_4635

THRB 1 K-562_3955

TMEM50A 1 K-562_3955

Searching for other cancer cell types with potential BCR- ABLl fusions

The occurance of copy number breakpoints within BCR and ABLl in cancer cells of non-hematopoietic origins was investigated. By analyzing the Sanger 820 cell line panel, two cell lines were identified that contain breakpoints in both BCR and ABLl (Figure 2). The breakpoint within BCR in NCI-H747, a colon cancer cell line, was similar to that of the other CML cell lines, residing between exons 12 to 16. However, in NCI-H1581, a lung cancer cell line, the breakpoint was between exons 1 and 2, similar to that of ALL. In NCI-H747, the CNV was consistent with what was observed in the other CML cell lines: namely, the copy number at 3 'end is lower than that of 5' end for BCR, and the copy number at 3' end is higher than that of 5' end for ABLl. However, in NCI-H1581, the CNV in ABLl is different, with the 3'end (containing the kinase domain) at lower copy number relative to the 5' end. Whether these cell lines contain a functional BCR-ABL fusion is yet to be determined.

To evaluate the random chance to identify copy number breakpoints in both BCR and ABLl genes in a given cell line, simulations were performed by assigning the information of all amplification or loss segments, such as the segment length, copy number status (gain or loss) from either NCI-H1581 or NCI-H747, on a hypothetic genome. For each cell line, the simulation was performed 100,000 times, and no breakpoint was found in both BCR and ABLl in a single case. This suggests that the chance to observe copy number breakpoints in both BCR and ABLl in the two cell lines is unlikely to occur by chance alone. Example 2: TMPRSS2-ERG

Examination of prostate cancer samples and cell lines Recent findings, through a bioinformatics approach (COPA) (MacDonald and

Ghosh 2006), revealed that prostate cancers frequently over-express the ETS family transcription factors ERG and ETV1 as a result of chromosomal rearrangements that lead to the fusion of the 5' end of the androgen-regulated serine protease TMPRSS2 (21q22.2) to the 3' end of either ERG (21q22.3) or ETV1 (7p21.3) (Tomlins, Rhodes et al. 2005). The consequence is the aberrant androgen receptor-driven expression of the potential oncogenes ERG or ETV1. The TMPRSS2-ERG fusion is present at high frequency in moderate to poorly differentiated prostate cancers (35/86, 40.7%) (Rajput, Miller et al. 2007), in contrast to TMPRSS2-ETV1 which is the product of a rare fusion event.

The ability of SNP data to reveal insights about the mechanisms involved in these fusion events in prostate cancer was evaluated. To this end, the SNP array data of 20 paired prostate cancer samples with matched normal samples from GEO was analyzed. Both TMPRSS2 and ERG are on the same chromosome, chromosome 21, and reside on the negative DNA strand with an invervening distance of 2.7 Mb. As shown in Figure 3, three out of 20 samples (15%) contain a segment deletion between TMPRSS2 and ERG. Although the positions of the breakpoints at both TMPRSS2 and ERG are different in the three samples, the final fusions retain the coding sequence of ERG linked to the 5' regulatory sequences of TMPRSS2. In addition, we found that ETV1 was amplified in three of the 10 prostate samples (data not shown).

In order to evaluate CNV in the coding regions, especially in the oncogenes, copy number breakpoints residing within the transcript of the oncogene in these 20 prostate cancer samples were searched. As shown in Table 2, ERG contains copy number breakpoints in three out of the 20 prostate cancer samples. The frequency (15%) is the highest compared to other oncogenes. Table 2. Oncogenes that contain copy number breakpoints in 20 prostate cancer samples. Breakpoint is within the transcript, regardless of the location or whether it was associated with amplification or deletion.

The TMPRSS2-ERG fusion is known to exist in the prostate cell line VCaP (Maher, Kumar-Sinha et al. 2009). However, publicly available SNP array data for this cell line could not be located. Instead, prostate cell lines profiled by Sanger Institute were investigated. Among 820 cancer cell lines, five prostate cancer cell lines are represented: 22RV, BPH-1, DU-145, LNCaP, PC-3. None of these lines possess segmental deletions between TMPRSS2 and ERG, nor is the copy number of ETV1 amplified (data not shown).

Searching for other cancer cell types with the TMPRSS2-ERG fusion

In order to assess whether the TMPRSS2-ERG fusion is unique to prostate cancers, a search was performed to identify other cell line containing segmental deletions between ERG and TMPRSS2. Specifically, a deletion segment was queried for with one end anchored either within TMPRSS2 or between TMPRSS2 and its neighbor RIPK4, and the other end anchored either within the 5' end of ERG or between ERG and its neighbor gene ETS2. This type of deletion has the potential to create a fusion gene that utilizes the promoter of TMPRSS2 and links to the coding of ERG. However, among the 820 cell lines that the Sanger Institute profiled, none contains such deletion. This is suggestive that the TMPRSS2-ERG fusion is restricted to specific subtypes of prostate cancers.

Example 3: EML4-ALK

Examination of lung cancer cell lines

The EML4-ALK fusion was identified in a NSCLC sample by full-length cDNA cloning. It was also detected in other lung cancers with a frequency of 9.1% (3 out of 33) (Soda, Choi et al. 2007). To further evaluate the utility of SNP array data for identifying potential translocations, both EML4 and ALK were examined for potential copy number breakpoints in Sanger's 140 lung cancer cell lines. Among these 140 lung cancer cell lines, six (4%) were found to carry breakpoints for both EML4 and ALK. As shown in Figure 4, most of the copy number breakpoints in EML4 are caused by the amplification of the 5'end of the gene, while breakpoints in ALK are closer to its 3'end. This is consistent with the junctional sequence described for EML4-ALK, in which the 5'end sequence of EML4 is linked to the 3'end sequence of ALK, where the kinase domain resides. A literature search revealed that, among these six lung cancer cell lines, NCIH2228 is reported to contain EML4-ALK fusion that links EML4 exon 6 to ALK exon 20 (Rikova, Guo et al. 2007).

In order to evaluate CNV in the coding regions, especially in the oncogenes, the copy number breakpoints residing within the transcript of the oncogene in these 140 lung cancer cell lines were searched. As shown in Table 3, ALK contains copy number breakpoints in 22 out of the 140 lung cancer cell lines. Its frequency (15.7%) is among the highly ranked but the not the highest compared to other oncogenes. Among the ten oncogenes that have higher copy number breakpoint frequencies than that of ALK, five of them: PVT1 (t(2;8) and t(8;22) in Burkitt lymphoma) (Shtivelman, Henglein et al. 1989), AKT3 (t(l;13)(q44;q32) in microcephaly and agenesis of the corpus callosum) (Boland, Clayton-Smith et al. 2007), VAV2 (t(l;9)(p36.32;q34.2) in cryptic imbalance) (Gajecka, Glotzbach et al. 2006), ABL2 (t(l;12)(q25;pl3) in AML) (Iijima, Ito et al. 2000), and NTRK3 (t(12; 15)(pl3;q25) in salivary gland tumors and AML) (Skalova, Vanecek et al. 2010) (Eguchi, Eguchi-Ishimae et al. 1999), were reported to be involved in reciprocal translocation.

Table 3. Oncogenes that contain copy number breakpoints in 140 lung cancer cell lines. Breakpoint is within the transcript, regardless of the location or whether it was associated with amplification or deletion.

HUGO # of Lung Cell Lines

Cell Lines

PVT1 41 DMS-273_4238#Calu-l_3554#Calu-6_4277#COR-L105_3742#DMS-

114_4227#LCLC-103H_4255#NCI-H1395_3399#NCI-H1563_4211#NCI-

H2228_3820#NCI-H345_4962#NCI-H446_4347#SHP-

77_4328#A549_4999#EPLC-272H_4559#NCI-H 1092_4428#NCI-

H 157_4303#NCI-H 1666_4309#NCI-H 1694_4308#NCI-H 1838_4290#NCI-

H2081_4341#NCI-H209_3380#NCI-H2126_3400#NCI-H520_4975#NCI-

H524_5003#NCI-H526_4337#NCI-H64_4351#NCI-H1155_4952#NCI-

H1355_4439#NCI-H146_4505#NCI-H1650_4292#NCI-H1734_3717#NCI-

H2171_3999#NCI-H250_3661#NCI-H522_3920#NCI-H650_3645#NCI-

H719_3728#NCI-H810_3683#NCI-H82_4355#NCI-N417_4331#SBC-

5_3703#SK-LU-1_4326

THRB 35 DMS-273_4238#LC-lF_4261#NCI-H1792_4298#NCI-H596_4344#COR-

L279_4273#LC-2-ad_4247#NCI-H1437_3435#NCI-H1581_4297#NCI-

Hl 755_3593#NCI-H 1793_4206#NCI-H 1930_3711#NCI-

H2141_4957#NCI-H2228_3820#NCI-H2342_4234#NCI-H345_4962#NCI-

H441_4937#NCI-H446_4347#NCI-H889_3591#BEN_3743#EPLC-

272H_4559#HT-29_3963#IST-SL1_3651#NCI-H128_3423#NCI-

H2029_4346#NCI-H2081 _4341 #NCI-H2107_3667#NCI-

H2126_3400#NCI-H2330_3560#NCI-H774_3674#EKVX_4697#NCI-

H1618_3689#NCI-H250_3661#NCI-H748_4932#NCI-N417_4331#SBC-

5_3703

AKT3 34 DV-90_4562#NCI-H596_4344#COR-L279_4273#NCI-H1648_4312#NCI-

H1703_4294#NCI-H1755_3593#NCI-H2228_3820#NCI-H446_4347#NCI-

H835_3791#Calu-3_3575#EPLC-272H_4559#IST-SLl_3651#NCI-

H1092_4428#NCI-H1993_4354#NCI-H209_3380#NCI-H2107_3667#NCI-

H2126_3400#NCI-H2170_4342#NCI-H526_4337#S Wl 573_4310#ABC-

1_3809#LU-135_4223#LU-139_4276#NCI-H1355_4439#NCI-

H146_4505#NCI-H1618_3689#NCI-H1963_4353#NCI-H2227_4338#NCI-

H2347_4356#NCI-H250_3661#NCI-H322M_4661#NCI-H522_3920#NCI-

H748_4932#NCI-H82_4355

RAB3C 30 C AL- 12T_4626#Calu-6_4277#COR-L279_4273#NCI-H 1299_4266#NCI- H1395_3399#NCI-H1581_4297#NCI-H1623_4293#NCI-

Hl 703_4294#NCI-H 1755_3593#NCI-H2141_4957#NCI-

H2342_4234#NCI-H69_4434#NCI-H889_3591#COLO-668_3773#NCI-

H 1092_4428#NCI-H 1666_4309#NCI-H 1993_4354#NCI-

H2122_3441 #NCI-H2170_4342#NCI-H2330_3560#NCI-

H526_4337#VMRC-LCP_3771#EKVX_4697#LU-139_4276#NCI-

H1417_4944#NCI-H1650_4292#NCI-H2087_3389#NCI-

H322M_4661#NCI-H650_3645#SK-MES-1_4323

AKAP13 I 27 | DMS-273_4238#COR-L279_4273#LC-2-ad_4247#NCI-H1437_3435#NCI-

Hl 623_4293#NCI-H 1770_3420#NCI-H 1930_3711#NCI- H2030_4239#NCI-H2141_4957#NCI-H345_4962#NCI- H889_3591#A549_4999#Calu-3_3575#NCI-H128_3423#NCI- H 1666_4309#NCI-H 1975_3716#NCI-H2170_4342#NCI- H2291_3688#NCI-H520_4975#NCI-H661_4348#A427_4200#NCI- H1417_4944#NCI-H 1618_3689#NCI-H2087_3389#NCI-H727_4339#NCI-

H748_4932#SK-MES-1_4323

VAV2 I 27 I COR-L88_4256#CAL-12T_4626#DMS-114_4227#NCI-H1563_4211#NCI-

H1581_4297#NCI-H2228_3820#NCI-H446_4347#DMS-79_4527#IA- LM_4623#NCI-H 128_3423#NCI-H 1694_4308#NCI-H2029_4346#NCI- H209_3380#NCI-H2107_3667#NCI-H2170_4342#NCI-H460_3979#NCI- H524_5003#PC-14_4279#SW1573_4310#A427_4200#ABC- l_3809#EKVX_4697#NCI O355_4439#NCI-H1417_4944#NCI-

H2171_3999#NCI-H250_3661#NCI-H748_4932

ABL2 I 26 I LC-1F_4261#NCI-H596_4344#NCI-H1395_3399#NCI-H1703_4294#NCI-

H1755_3593#NCI-H1770_3420#NCI-H2228_3820#NCI-H446_4347#NCI- Hl 092_4428#NCI-H 1173_3563#NCI-H 128_3423#NCI-H2009_3428#NCI- H2107_3667#NCI-H2170_4342#NCI-H520_4975#VMRC- LCP_3771#A427_4200#ABC-1_3809#LU-135_4223#LU-139_4276#NCI- H2087_3389#NCI-H2227_4338#NCI-H322M_4661#NCI-

H522_3920#SBC-5_3703#SK-MES-1_4323

ERBB4 I 25 | NCI-H1755_3593#NCI-H1793_4206#NCI-H2141_4957#NCI-

H2342_4234#NCI-H446_4347#NCI-H69_4434#NCI-H889_3591#EPLC- 272H_4559#NCI-H 1092_4428#NCI-H 128_3423#NCI-H 157_4303#NCI- H1694_4308#NCI-H2122_3441#NCI-H510A_3653#NCI-H64_4351#PC- 14_4279#VMRC-LCP_3771#LU- 135_4223#LU- 139_4276#NCI- H146_4505#NCI-H522_3920#NCI-H719_3728#NCI-H727_4339#NCI-

H838_4350#SBC-5_3703

AKT2 I 23 I NCI-H1792_4298#Calu-6_4277#NCI-H1395_3399#NCI-

Hl 581_4297#NCI-H 1623_4293#NCI-H 1930_3711#NCI-H345_4962#NCI- H835_3791#NCI-H889_3591#SHP-77_4328#Calu-3_3575#COLO- 668_3773#HOP-62_3975#HT-29_3963#NCI-H 1092_4428#NCI- H1694_4308#NCI-H526_4337#ABC-1_3809#LU-135_4223#LU-

65_4436#NCI-H 1618_3689#NCI-H 1882_3810#NCI-H2405_4345

NTRK3 I 23 I NCI-H596_4344#DMS-114_4227#NCI-H1437_3435#NCI-

Hl 770_3420#NCI-H 1930_3711#NCI-H2030_4239#NCI- H2141_4957#NCI-H345_4962#NCI-H889_3591#Calu-3_3575#HT- 29_3963#NCI-H 1666_4309#NCI-H 1693_4305#NCI-H 1975_3716#NCI- H2081_4341#NCI-H2170_4342#NCI-H524_5003#NCI-H661_4348#NCI- H1417_4944#NCI-H2087_3389#NCI-H727_4339#NCI-H748_4932#SK-

LU-1_4326

ALK I 22 I LC-1F_4261#NCI-H1648_4312#NCI-H1703_4294#NCI-

H1793_4206#NCI-H2030_4239#NCI-H2228_3820#NCI- H835_3791#A549_4999#EPLC-272H_4559#HOP-62_3975#NCI- Hl 694_4308#NCI-H2009_3428#NCI-H2122_3441#NCI- H2330_3560#NCI-H1355_4439#NCI-H1417_4944#NCI- H2171_3999#NCI-H2227_4338#NCI-H522_3920#NCI-H748_4932#NCI- H82 4355#RERF-LC-MS 4233

VAV3 22 I LC-lF_4261#NCI-H596_4344#Calu-6_4277#COR-L279_4273#DMS- 114_4227#LXF-289_4281#NCI-H1770_3420#NCI-H2141_4957#NCI- H441_4937#A549_4999#BEN_3743#EPLC-272H_4559#NCI-

Hl 694_4308#NCI-H2009_3428#NCI-H2107_3667#HOP-92_4671#LU-

135_4223#NCI-H1355_4439#NCI-H2227_4338#NCI-H250_3661#NCI-

H82_4355#SK-MES-1_4323

BRAF 20 DMS-273_4238#LC-lF_4261#LC-2-ad_4247#NCI-H1623_4293#NCI-

H1770_3420#NCI-H889_3591#EPLC-272H_4559#IA-LM_4623#IST-

SL1_3651#NCI-H 1694_4308#NCI-H2107_3667#PC-

14_4279#S W 1573_4310#VMRC-LCP_3771#NCI-H 1304_3713#NCI-

H2227_4338#NCI-H2405_4345#NCI-H250_3661#RERF-LC-

MS_4233#SBC-5_3703

KIT 20 DMS-273_4238#NCI-H1299_4266#NCI-H1581_4297#NCI- H2141_4957#NCI-H69_4434#A549_4999#Calu-3_3575#EPLC- 272H_4559#LB647-SCLC_3414#NCI-H128_3423#NCI-H157_4303#NCI- H209_3380#NCI-H2107_3667#NCI-H460_3979#S Wl 573_4310#HOP- 92_4671#LK-2_4429#NCI-H2171_3999#SW900_3583#SK-MES-1_4323

BCL2 19 LXF-289_4281#NCI-H1437_3435#NCI-H1926_4296#NCI-

H1930_3711#NCI-H2141_4957#NCI-H2342_4234#NCI-

H441_4937#A549_4999#BEN_3743#DMS-79_4527#NCI-

H128_3423#NCI-H1838_4290#NCI-H378_4983#PC-

14_4279#S W 1573_4310#LU- 139_4276#LU-65_4436#NCI-

H1882_3810#NCI-H838_4350

EGFR 19 DMS-273_4238#LC-lF_4261#Calu-l_3554#DMS-114_4227#LXF- 289_4281 #NCI-H 1703_4294#NCI-H 1770_3420#NCI-H 1793_4206#DMS - 79_4527#IA-LM_4623#NCI-H2081_4341#NCI-H2107_3667#NCI- H2126_3400#NCI-H774_3674#PC-

14_4279#SW1573_4310#EKVX_4697#NCI-N417_4331#SW900_3583

ERG 19 C AL- 12T_4626#NCI-H 1755_3593#NCI-H 1770_3420#NCI-

H1930_3711#NCI-H345_4962#NCI-H835_3791#NCI-H889_3591#SCLC-

21 H_4956#A549_4999#HT-29_3963#NCI-H 1666_4309#NCI-

H 1975_3716#NCI-H2081 _4341 #NCI-H2122_3441#NCI-

H2170_4342#EKVX_4697#NCI-H 1417_4944#NCI-H2227_4338#NCI-

H650_3645

ETV6 19 DMS-273_4238#NCI-H596_4344#Calu-6_4277#COR-L51_4253#LC-2- ad_4247#NCI-H 1437_3435#NCI-H 1581 _4297#NCI-H 1623_4293#NCI- H1793_4206#NCI-H1926_4296#NCI-H2342_4234#NCI-H889_3591#NCI- H1173_3563#NCI-H128_3423#NCI-H2291_3688#NCI- H2330_3560#LCLC-97TM1_3675#LU-139_4276#SW900_3583

EWSR1 19 DMS-273_4238#NCI-H596_4344#LCLC-103H_4255#NCI-

H 1703_4294#NCI-H2141 _4957#A549_4999#NCI-H 128_3423#NCI-

Hl 666_4309#NCI-H 1693_4305#NCI-H2009_3428#NCI-

H2081_4341#NCI-H2330_3560#NCI-H460_3979#NCI-H526_4337#PC-

14_4279#SW1573_4310#VMRC-LCP_3771#NCI-H727_4339#SK-LU-

1_4326

RET 19 DMS-273_4238#CAL-12T_4626#LCLC-103H_4255#NCI- H1930_3711#NCI-H2141_4957#NCI-H835_3791#COLO-668_3773#NCI- H1092_4428#NCI-H157_4303#NCI-H2029_4346#NCI-H2081_4341#NCI- H2107_3667#PC- 14_4279#LU-65_4436#NCI-H 1105_4441#NCI- H 1417_4944#NCI-H 1650_4292#NCI-H 1963_4353#NCI-H2196_3610

RUNX1 18 LC-lF_4261#Calu-l_3554#NCI-H1755_3593#NCI-H2342_4234#NCI- H446_4347#NCI-H835_3791#NCI-H889_3591#Calu-3_3575#HT- 29_3963#NCI-H 1666_4309#NCI-H2170_4342#NCI-H460_3979#NCI- H520_4975#NCI-H524_5003#NCI-H 1417_4944#NCI-H650_3645#NCI- H748_4932#SK-LU-1_4326

FER 17 LC-lF_4261#Calu-6_4277#NCI-H1793_4206#NCI-H2342_4234#NCI-

H345_4962#NCI-H889_3591#SHP-77_4328#HOP-62_3975#IA-

LM_4623#NCI-H2081_4341#NCI-H2122_3441#VMRC-

LCP_3771#EKVX_4697#LK-2_4429#LU-165_4286#NCI-

H650_3645#SBC-5_3703

RAF1 17 LC-lF_4261#COR-L279_4273#LC-2-ad_4247#NCI-H1581_4297#NCI- H2342_4234#NCI-H446_4347#NCI-H835_3791#IST-SL1_3651#NCI-

Hl 173_3563#NCI-H 1694_4308#NCI-H2107_3667#NCI-

H2126_3400#NCI-H 1417_4944#NCI-H 146_4505#NCI-H2087_3389#SBC- l_3665#SBC-5_3703

ERBB2 16 LC-1F_4261#NCI-H596_4344#A549_4999#IA-LM_4623#NCI- H 1666_4309#NCI-H 1694_4308#NCI-H 1838_4290#NCI- H2009_3428#NCI-H2081_4341#NCI-H2122_3441#NCI-H524_5003#NCI- H64_4351#SW1573_4310#UMC-11_4301#A427_4200#LU-139_4276

MKRN2 16 LC-lF_4261#NCI-H596_4344#COR-L279_4273#LC-2-ad_4247#NCI- H1437_3435#NCI-H 1755_3593#NCI-H 1930_3711#NCI- H2141_4957#NCI-H2228_3820#NCI-H2342_4234#EPLC- 272H_4559#HT-29_3963#NCI-H2170_4342#NCI-H 1618_3689#NCI- H250_3661#NCI-H748_4932

RAB31 16 COR-L279_4273#LXF-289_4281#NCI-H441_4937#A549_4999#EPLC- 272H_4559#NCI-H 1173_3563#NCI-H 128_3423#NCI-H2126_3400#NCI- H64_4351#PC-14_4279#SW1573_4310#VMRC-LCP_3771#ABC- 1_3809#COR-L96CAR_3744#LCLC-97TM1_3675#SK-MES-1_4323

RAB5A 16 DMS-273_4238#LC-2-ad_4247#NCI-H1437_3435#NCI-

Hl 581_4297#NCI-H 1755_3593#NCI-H 1930_3711#NCI-

H2228_3820#NCI-H2342_4234#HT-29_3963#NCI-H1173_3563#NCI-

H2126_3400#NCI-H2291_3688#NCI-H2330_3560#NCI-H774_3674#LU-

139_4276#NCI-H748_4932

RAPGEF1 16 DMS-114_4227#NCI-H1563_4211#NCI-H2030_4239#NCI- H2228_3820#NCI-H446_4347#SHP-77_4328#NCI-H2009_3428#NCI- H2291_3688#NCI-H510A_3653#NCI-H524_5003#EKVX_4697#NCI- H 1355_4439#NCI-H 1417_4944#NCI-H 146_4505#NCI- H250_3661#RERF-LC-MS_4233

ETS 1 15 NCI-H 1573_4291#NCI-H 1623_4293#COLO-668_3773#DMS- 79_4527#EPLC-272H_4559#NCI-H 1092_4428#NCI-H 1666_4309#NCI- H2081_4341#NCI-H2126_3400#NCI-H520_4975#ABC-1_3809#NCI- Hl 618_3689#NCI-H2171_3999#NCI-H522_3920#NCI-N417_4331

MERTK 15 NCI-H 1792_4298#NCI-H 1395_3399#NCI-H 1648_4312#NCI- H889_359 l#HOP-62_3975#NCI-H 1092_4428#NCI-H 128_3423#NCI- H1693_4305#NCI-H2009_3428#NCI-H2330_3560#NCI- H510A_3653#NCI-H661_4348#NCI-H522_3920#NCI-H82_4355#SBC- 5_3703

KRAS 14 DMS-273_4238#NCI-H1437_3435#NCI-H2342_4234#SCLC-

21 H_4956#HT-29_3963#NCI-H 1173_3563#NCI-H 128_3423#NCI-

H23_3946#NCI-H460_3979#NCI-H774_3674#A427_4200#LCLC-

97TM1_3675#LU-165_4286#NCI-H748_4932

RAB2A 14 LC-lF_4261#COR-L279_4273#LXF-289_4281#NCI-H1437_3435#NCI- H1563_4211#SCLC-21H_4956#Calu-3_3575#EPLC-272H_4559#IA- LM_4623#NCI-H64_4351#PC-14_4279#NCI-H1355_4439#NCI- H650_3645#SBC-5_3703

CRKL 13 DMS-273_4238#DMS-114_4227#NCI-H1648_4312#NCI- H2228_3820#NCI-H69_4434#NCI-H835_3791#Calu-3_3575#COLO- 668_3773#DMS-79_4527#NCI-H1173_3563#NCI- H2009_3428#S W 1573_4310#NCI-H2347_4356

FYN 13 LC- 1F_4261#CAL- 12T_4626#NCI-H 1299_4266#NCI-H889_359 l#COLO- 668_3773#EPLC-272H_4559#NCI-H1838_4290#NCI-H1975_3716#NCI- H1993_4354#NCI-H2291_3688#NCI-H460_3979#LCLC- 97TM1_3675#NCI-H82_4355

ABL1 12 COR-L88_4256#CAL-12T_4626#LXF-289_4281#NCI-H1581_4297#SHP- 77_4328#DMS-79_4527#NCI-

H460_3979#S W 1573_4310#A427_4200#NCI-H 1734_3717#NCI- H250_3661#NCI-H748_4932

EFCAB2 12 NCI-H596_4344#Calu-6_4277#NCI-H 1703_4294#NCI-H441_4937#NCI- H835_3791#NCI-H1693_4305#NCI-H1993_4354#NCI-H526_4337#PC- 14_4279#LU- 135_4223#NCI-H522_3920#SBC-5_3703 RAP1A 12 C AL- 12T_4626#NCI-H 1770_3420#NCI-H2141 _4957#NCI- H2228_3820#NCI-H835_3791#EPLC-272H_4559#NCI-H2107_3667#NCI- H2126_3400#S W 1573_4310#HOP-92_4671 #KNS -62_4221 #NCI- H522_3920

FLU 11 LXF-289_4281#NCI-H2228_3820#NCI-H835_3791#COR- L23_4214#DMS-79_4527#HT-29_3963#NCI-H1666_4309#NCI- H460_3979#NCI-H 1618_3689#NCI-H748_4932#NCI-N417_4331

RAB40B 11 NCI-H 1648_4312#NCI-H2342_4234#SHP-77_4328#NCI- H1993_4354#NCI-H64_4351#SW1573_4310#EKVX_4697#NCI- H1355_4439#NCI-H2227_4338#NCI-H2405_4345#SK-LU-1_4326

ROS 1 11 NCI-H 1299_4266#NCI-H 1703_4294#NCI-H441_4937#NCI-

H889_3591#SCLC-21H_4956#EPLC-272H_4559#NCI-H1092_4428#NCI-

H1993_4354#NCI-H2081_4341#NCI-H460_3979#SW1573_4310

VAV1 11 NCI-H 1437_3435#NCI-H 1623_4293#NCI-H 1755_3593#Calu-

3_3575#COLO-668_3773#NCI-H1693_4305#RERF-LC-FM_3692#UMC-

11_4301#EKVX_4697#NCI-H719_3728#NCI-H82_4355

CSF1R 10 NCI-H596_4344#Calu-3_3575#HOP-62_3975#IA-LM_4623#NCI-

Hl 173_3563#NCI-H 157_4303#NCI-H2081_4341#NCI-H2122_3441#NCI-

H520_4975#NCI-H 1417_4944

ERBB3 10 NCI-H 1792_4298#NCI-H 1755_3593#NCI-H 1770_3420#NCI- H2342_4234#Calu-3_3575#NCI-H2009_3428#NCI-H2122_3441#NCI- H2126_3400#NCI-H810_3683#SK-LU- 1_4326

LYN 9 DMS-273_4238#LC-1F_4261#NCI-H1930_3711#SCLC-21H_4956#HT-

29_3963#NCI-H2330_3560#NCI-H23_3946#NCI-

H460_3979#SW1573_4310

MYB 9 NCI-H596_4344#DMS-114_4227#NCI-H1437_3435#COLO- 668_3773#EPLC-272H_4559#NCI-H2126_3400#NCI-H 1417_4944#NCI- Hl 650_4292#NCI-H322M_4661

RAB28 9 LXF-289_4281 #NCI-H 1437_3435#NCI-H 1648_4312#NCI-

H1770_3420#NCI-H2342_4234#NCI-H835_3791#EPLC-272H_4559#NCI-

H128_3423#EKVX_4697

RAB40C 9 LCLC-103H_4255#NCI-H1573_4291#Calu-3_3575#COR- L23_4214#EPLC-272H_4559#HOP-62_3975#NCI-H774_3674#NCI- Hl 618_3689#NCI-H2347_4356

TET1 9 NCI-H345_4962#NCI-H835_3791#DMS-79_4527#NCI-

H2107_3667#NCI-H2170_4342#PC- 14_4279#NCI-H522_3920#NCI-

H650_3645#SK-LU-1_4326

FGFR10P2 8 NCI-H596_4344#NCI-H1581_4297#NCI-H889_3591#NCI-

H128_3423#NCI-H2107_3667#NCI-H2291_3688#NCI-H774_3674#NCI-

H82_4355

RAB 10 8 LC-1F_4261#LXF-289_4281#NCI-H2030_4239#NCI-H835_3791#NCI- Hl 694_4308#NCI-H 1355_4439#NCI-H 1417_4944#NCI-H522_3920

RAB 1A 8 NCI-H835_3791#PC-14_4279#VMRC-LCP_3771#ABC-1_3809#NCI- H1417_4944#NCI-H2227_4338#NCI-H322M_4661#SBC-5_3703

RAB30 8 DMS-273_4238#NCI-H1437_3435#NCI-H2141_4957#Calu-3_3575#DMS- 79_4527#HT-29_3963#IA-LM_4623#NCI-H322M_4661

RRAS2 8 LC-lF_4261#NCI-H2342_4234#COLO-668_3773#COR-L23_4214#HT- 29_3963#NCI-H128_3423#NCI-H2227_4338#NCI-H522_3920

TET2 8 Calu-6_4277#NCI-H 1770_3420#NCI-H214 l_4957#NCI-H345_4962#Calu- 3_3575#PC-14_4279#NCI-H748_4932#NCI-H82_4355

USP6 8 NCI-H1437_3435#HT-29_3963#NCI-H1173_3563#PC-14_4279#NCI- H1105_4441#NCI-H650_3645#SBC-5_3703#SW900_3583

DEK 7 NCI-H1573_4291#NCI-H2342_4234#SCLC-21H_4956#COLO- 668_3773#SW1573_4310#NCI-H2227_4338#NCI-H650_3645

MET 7 DMS-273_4238#LCLC-103H_4255#EPLC-272H_4559#IA- LM_4623#NCI-H1092_4428#NCI-H209_3380#LCLC-97TM1_3675

RALA 7 DMS-273_4238#DMS-114_4227#NCI-H1694_4308#NCI- H2009_3428#NCI-H2122_3441#NCI-H661_4348#RERF-LC-MS_4233 RAP IB 7 NCI-H596_4344#NCI-H 1975_3716#NCI-H2126_3400#VMRC- LCP_3771#LCLC-97TM 1_3675#NCI-H 1304_3713#NCI-H 1882_3810

SH3D19 7 DMS - 114_4227#NCI-H 1793_4206#NCI-H 1666_4309#NCI- H1975_3716#NCI-H2107_3667#KNS-62_4221#NCI-H748_4932

TTC23 7 DMS-273_4238#LXF-289_4281#NCI-H345_4962#NCI-H69_4434#ABC- 1_3809#NCI-H748_4932#NCI-N417_4331

SRC 6 LC-1F_4261#LXF-289_4281#COR-L23_4214#NCI-H1693_4305#NCI- H2009_3428#SW900_3583

TAF8 6 NCI-H 1755_3593#SCLC-21 H_4956#IA-LM_4623#NCI- H2107_3667#NCI-H2291_3688#NCI-H520_4975

ECT2 5 DMS-273_4238#CAL-12T_4626#NCI-H1755_3593#NCI- H2342_4234#LCLC-97TM 1_3675

RAB22A 5 NCI-H2030_4239#NCI-H446_4347#HOP-62_3975#NCI-H2122_3441#PC- 14_4279

RAB4A 5 NCI-H596_4344#NCI-H2342_4234#NCI-H2122_3441#ABC-1_3809#SK- MES-1_4323

RAB7A 5 NCI-H446_4347#NCI-H69_4434#A549_4999#LK-2_4429#SK-MES- 1_4323

SKIL 5 NCI-H 1793_4206#UMC- 11_4301#NCI-H250_3661#NCI- H650_3645#NCI-H748_4932

TET3 5 CAL-12T_4626#NCI-H2030_4239#NCI-H2141_4957#NCI- H2126_3400#SBC-5_3703

THRA 5 A427_4200#LU-65_4436#NCI-H 1618_3689#NCI-H650_3645#NCI- H838_4350

TPR 5 Calu-6_4277#LC-2-ad_4247#RERF-LC-FM_3692#LU- 135_4223#LU- 139_4276

ETS2 4 NCI-H1930_3711#NCI-H1173_3563#NCI-H1693_4305#NCI-H522_3920

ETV7 4 NCI-H 1299_4266#NCI-H2030_4239#NCI-H446_4347#COLO-668_3773

HEXB 4 Calu-6_4277#NCI-H1793_4206#NCI-H1173_3563#NCI-H650_3645

RAB 18 4 NCI-H2030_4239#NCI-H 1092_4428#NCI-H 1105_4441#RERF-LC- MS_4233

RAB27A 4 NCI-H 1581 _4297#NCI-H 1623_4293#HT-29_3963#NCI-H 1092_4428

RAB38 4 NCI-H2342_4234#NCI-H157_4303#NCI-H1993_4354#NCI-H748_4932

RAB6A 4 NCI-H 1648_4312#NCI-H214 l_4957#HOP-62_3975#NCI-H 1734_3717

RALB 4 NCI-H 1770_3420#NCI-H2342_4234#NCI-H 128_3423#PC- 14_4279

TMEM50A 4 NCI-H1437_3435#NCI-H2228_3820#NCI-H1666_4309#NCI-H1838_4290

CDON 3 NCI-H446_4347#NCI-H520_4975#NCI-H 1417_4944

CSDE1 3 Calu-3_3575#A427_4200#NCI-H2227_4338

ENTPD5 3 NCI-H 1792_4298#NCI-H 1299_4266#NCI-H 1437_3435

MYBL1 3 NCI-H460_3979#NCI-H510A_3653#NCI-H1355_4439

NAE1 3 C AL- 12T_4626#NCI-H2141 _4957#NCI-H345_4962

NTRK1 3 NCI-H 1770_3420#NCI-H526_4337#NCI-H 1355_4439

PDGFB 3 NCI-H 1173_3563#NCI-H2081_4341#NCI-H748_4932

RAB 17 3 NCI-H526_4337#PC-14_4279#RERF-LC-MS_4233

RAB3B 3 NCI-H1395_3399#NCI-H446_4347#NCI-H650_3645

RAB6B 3 NCI-H 1755_3593#EPLC-272H_4559#EKVX_4697

RNASEH2A 3 NCI-H 128_3423#NCI-H2107_3667#NCI-H 1618_3689

SPAG9 3 COR-L279_4273#A549_4999#HOP-62_3975

SPI1 3 NCI-H 1437_3435#NCI-H 1703_4294#NCI-H2141 _4957

USP4 3 LC-2-ad_4247#NCI-H2107_3667#NCI-H2170_4342

FGFRIOP 2 NCI-H596_4344#NCI-H441_4937

NDUFC2 2 NCI-H1573_4291#NCI-H520_4975

PEA15 2 NCI-H2141 _4957#NCI-H 1693_4305

RAB 11A 2 C AL- 12T_4626#NCI-H748_4932 RAB 14 2 COR-L88_4256#NCI-H250_3661

RAB20 2 NCI-H2141_4957#NCI-H460_3979

RAB23 2 NCI-H 1618_3689#NCI-H748_4932

RAB33B 2 EPLC-272H_4559#NCI-H661_4348

RAB37 2 COLO-668_3773#NCI-H748_4932

RABL4 2 LXF-289_4281#NCI-H146_4505

SKI 2 NCI-H 1648_4312#NCI-H378_4983

SSPN 2 NCI-H460_3979#NCI-H748_4932

WNT3 2 COR-L279_4273#S W 1573_4310

CRK 1 NCI-H2330_3560

ETV3 1 SK-MES-1_4323

FLJ 10357 1 COR-L96CAR_3744

FOS 1 NCI-H 1793_4206

GLI1 1 NCI-H596_4344

GNB2L1 1 COLO-668_3773

ISY1 1 EKVX_4697

KLF6 1 NCI-H345_4962

LCK 1 EKVX_4697

LYRM5 1 NCI-H23_3946

MAP3K8 1 NCI-H 128_3423

MMEL1 1 A549_4999

MYBL2 1 NCI-H526_4337

MYCL1 1 NCI-H378_4983

NRAS 1 NCI-H 157_4303

PTK6 1 NCI-H345_4962

RAB 12 1 NCI-H 1693_4305

RAB32 1 NCI-H1417_4944

RAB35 1 ABC-1_3809

RAB39 1 DMS-114_4227

RAB43 1 NCI-H2170_4342

RAB5C 1 NCI-H2342_4234

RAB7L1 1 NCI-H322M_4661

RAB8A 1 HOP-62_3975

RAB8B 1 NCI-H2030_4239

RABL3 1 VMRC-LCP_3771

RAP2A 1 NCI-H596_4344

SET 1 NCI-H1395_3399

TMED9 1 Calu-3_3575

Searching for additional cancer cell lines with EML4-ALK fusions

Cell lines carrying breakpoints for both EML4 and ALK genes were identified by surveying the entire 820 Sanger cell lines, and identify an additional 18 cell lines that carry copy number breakpoints similar to those of the six lung cell lines were searched for. As shown in Table 4, these cell lines are from different cancer origins, including breast, skin, stomach, and colon. Calculated P values suggest that it is highly unlikely that copy number breakpoints within both EML4 and ALK in there cell lines occur by random chance. This is in agreement with a report indicating that the EML4-ALK fusion is not only found in lung cancer samples, but also in other cancers such as breast and colorectal (Lin, Li et al. 2009). It is worth noting that this fusion sequence was detected by RT-PCR assay in the colon cell line SW1417 (Lin, Li et al. 2009).

Table 4. Additional Sanger's non-lung cancer cell lines that contain breakpoints in both EML4 and ALK genes. P value indicates the random chance for the cell line to contain breakpoints in both EML4 and ALK.

Cell Line Primary Tissue P value

Saos-2 bone 0.002

MDA-MB-468 breast 0.017

UACC-893 breast 0.028

COLO-824 breast 0.004

KNS-42 brain 0.053

DoTc2-4510 cervix 0.042

DEL haematopoietic 0.011

LAMA-84 haematopoietic 0.03

SW403 colon 0.006

SW1417 colon 0.016

OVCAR-5 ovary 0.011

PANC-08-13 pancreas 0.013

A101D skin 0.009

CHL-1 skin 0.006

SK-MEL-5 skin 0.004

SCH stomach 0.008

MKN28 stomach 0.002

639-V urinary 0.009

Identifying oncogenes with copy number breakpoints

A proto-oncogene can become an oncogene as a consequence of a relatively small modification such as mutations or increased expression. Chromosomal rearragement can lead to the increased gene expression, or the expression of a constitutively active hybrid protein (Croce 2008). In order to identify cell lines carrying similar breakpoint as ABLl, the CNV in the oncogenes that were defined by Affymetrix chip annotation across Sanger's 820 cancer cell lines were searched according to the following criteria: (1) The copy number breakpoint resides within the transcript of the oncogene; and (2) the copy number for the coding sequence is either normal (n=2) or amplified, but not deleted. Among the 205 oncogenes annotated by Affymetrix, 26% (54) oncogenes contain copy number breakpoints in at least one cancer cell line (Table 5). This is substantially higher (P value = 0.001) than the genome-wide search, where it was found that 17% (2,945 of out total 17,609) of the genes contain copy number breakpoint in at least one cancer cell line.

Table 5. Oncogenes that contain copy number breakpoints in Sanger's 820 cancer cell lines. Breakpoint is within the transcript, and copy number of the coding region is either remained normal or amplified, but not deleted.

HUGO # of Cell Lines Gene Definition

Sanger

820 Cell

Lines

AKAP1 74 HLE_4269#NB 13_3768#COLO-775_4030#COR- gb:ALl 33427.1 3 L279_4273#GOTO-P3_3906#HCC1806_4283#LC-2- /DB_XREF=gi:6562 ad_4247#MDA-MB-468_4287#NB 17_3807#NCI- 629 /FEA=mRNA

H1437_3435#NCI-H1930_3711#NCI- /CNT=65

H2030_4239#NCI-H2141_4957#NCI-H28_4650#NCI- /TlD=Hs.42506.0

H345_4962#NCI-H747_4537#NCI-H889_3591#OC- /TIER=ConsEnd

314_4554#OE19_4237#OVCAR- /STK=0

3_3935#PSN1_4268#RVH-421_3561#SNU- /UG=Hs.42506

423_4251#SW1088_3888#8305C_3794#A549_4999#C /UG_TITLE=Homo

2BBel_3860#Calu-3_3575#Caov-3_3853#COLO- sapiens mRNA full

205_4688#COLO-800_4701#D-397MG_3654#D- length insert cDNA

423MG_3700#HSC-4_3551#KNS- clone EUROIMAGE

42_3891#LoVo_3839#MDA-MB-157_3714#MEL- 261172

HO_4973#MZl- /DEF=Homo sapiens

PC_4995#NB 10_3790#NB7_3774#NCI- mRNA full length

H 128_3423#NCI-H 1975_3716#NCI-H2170_4342#NCI- insert cDNA clone

H630_3846#NCI-H661_4348#NOS-1_3707#SK-CO- EUROIMAGE

1_4689#SNU- 261172.

387_3903#A427_4200#ACN_3992#COLO- 678_4985#EW-

3_3753#GOTO_4049#HCC 1143_3402#HuH- 28_3721#ITO-II_3702#KOSC-2_4565#KYSE-

274280 /FEA=EST

/CNT=15

/TID=Hs.203213.1

/TIER=Stack

/STK=12

/UG=Hs.203213

/UG_TITLE=ESTs

AKT2 8 NCI-H 1792_4298#Calu-6_4277#HuH-7_4226#KYSE- gb:AA448167

410_4213#G-361 _4658#NCI-H 1092_4428#KOSC- /DB_XREF=gi:2161

2_4565#LU-135_4223 837

/DB_XREF=zw83al

2.sl

/CLONE= IMAGE: 7

82782 /FEA=EST

/CNT=6

/TID=Hs.98325.0

/TIER=ConsEnd

/STK=5

/UG=Hs.98325

/UG_TITLE=ESTs

ERBB2 8 NB6_3799#COLO-680N_3824#MDA-MB- gb:S57296.1

415_3718#NCI-H2081_4341#NCI-H64_4351#UMC- /DB_XREF=gi:2986 l l_4301#LB 1047-RCC_3970#PANC-08-13_3681 93 /GEN=HER2neu receptor

/FEA=mRNA

/CNT=1

/TID=Hs.241524.0

/TIER=ConsEnd

/STK=0

/UG=Hs.241524

/UG_TITLE=HER2 neu receptor { 3 region, alternatively spliced} (human, breast cancer cell line, mRNA Partial,

175 nt)

/DEF=HER2neu receptor {3 region, alternatively spliced} (human, breast cancer cell line, mRNA Partial,

175 nt).

RAPG 8 Becker_4548#NCI-H2030_4239#SHP-77_4328#VA- gb:AU158380

EF1 ES-BJ_3972#NCI-ADR-RES_3984#NCI- /DB_XREF=gi: 1101

H1355_4439#NCI-H146_4505#RERF-LC-MS_4233 9901

/DB_XREF=AU158

380

/CLONE=PLACE20

00176 /FEA=mRNA

/CNT=52

/TID=Hs.9195.0

/TIER=Stack

/STK=17

/UG=Hs.9195

/UG_TITLE=Homo sapiens cDNA

FLJ 13698 fis, clone

PLACE2000176 CDON 6 HLE_4269#A673_3915#NCI- gb:AU151222

H2052_3374#ACN_3992#BFTC-905_3737#KOSC- /DB_XREF=gi: 1101

2_4565 2743

/DB_XREF=AU151 222

/CLONE=NT2RP20

04709 /FEA=mRNA

/CNT=35

/TID=Hs.38034.0

/TIER=Stack

/STK=18

/UG=Hs.38034

/UG_TITLE=Homo sapiens cDNA

FLJ12924 fis, clone

NT2RP2004709

SKIL 6 NCI-H1793_4206#Daoy_3898#LS-411N_3835#NCI- gb:Z19588.1

H250_3661#NCI-H650_3645#SNU-C1_3895 /DB_XREF=gi:3116

23 /FEA=mRNA /CNT=9

/TID=Hs.38783.3

/TIER=ConsEnd

/STK=0

/UG=Hs.38783

/LL=6498

/UG_GENE=SKIL

/DEF=H. sapiens snol mRNA.

/PROD=snoI

CSF1R 5 Hu09_4528#NCI-H596_4344#HSC-2_4525#IST- gb:NM_00521 1.1

MES 1_3596#NCI-H 157_4303 /DB_XREF=gi:4885

158 /GEN=CSF1R /FEA=FLmRNA /CNT=135 /TID=Hs.174142.0 /TIER=FL+ S tack /STK=60

/UG=Hs.174142 /LL=1436

/DEF=Homo sapiens colony stimulating factor 1 receptor, formerly

McDonough feline sarcoma viral (v- fms) oncogene homolog (CSF1R), mRNA.

/PROD=colony stimulating factor 1 receptor, formerlyMcDonoug h feline sarcoma viral (v-fms) oncogene homolog /FL=gb:NM_005211 .1

RAB23 5 Caov-3_3853#IST-MELl_3611#U-2-OS_3844#NCI- gb:AF161486.1

H 1618_3689#NCI-H748_4932 /DB_XREF=gi:6841

495

RABL5 5 D-502MG_3680#Saos-2_3879#SW403_3834#786- gb:AW026449 0_3969#EW-12_3804 /DB_XREF=gi:5879

979

/DB_XREF=wvl3eO 9.xl

/CLONE= IMAGE: 2 529448

/FEA=FLmRNA

/CNT=55

/TID=Hs.61809.0

/TIER=Stack

/STK=14

/UG=Hs.61809

/LL=64792

/UG_GENE=FLJ 14

117

/UG_TITLE=hypoth etical protein FLJ14117

/FL=gb:NM_022777 .1

RALA 5 DMS-273_4238#NCI-H1694_4308#NCI- gb:AV703462

H661_4348#Capan-2_3552#RERF-LC-MS_4233 /DB_XREF=gi: 1072

0789

/DB_XREF=AV703 462

/CLONE=ADBCHG

05 /FEA=mRNA

/CNT=149

/TID=Hs.6906.0

/TIER=Stack

/STK=66

/UG=Hs.6906

/UG_TITLE=Homo sapiens cDNA:

FLJ23197 fis, clone

REC00917

SH3D1 5 HSC-3_4964#NCI-H 1975_3716#NCI- gb:BG285417 9 H2107_3667#KYSE-520_3698#MIA-PaCa-2_3885 /DB_XREF=gi: 1303

7353

/DB_XREF=602409 786F1

/CLONE=IMAGE:4

539428

/FEA=mRNA

/CNT=102

/TID=Hs.24715.0

/TIER=Stack

/STK=28

UG=Hs.24715

/UG_TITLE=Homo sapiens mRNA; cDNA

DKFZp434D0215 (from clone DKFZp434D0215); partial cds

SSPN 5 UACC-893_4299#KYSE-270_4274#NCI- gb:NM_005086.2

H748_4932#SF268_4000#TE-8_3767 /DB_XREF=gi:7669

543 /GEN=SSPN

993

/DB_XREF=wul4aO 5.xl

/CLONE= IMAGE: 2

516912

/FEA=mRNA

/CNT=27

/TID=Hs.156905.0

/TIER=Stack

/STK=12

/UG=Hs.156905

/LL=80312

/UG_GENE=KI A A 1

676

/UG_TITLE=KIAA 1676

THRA 1 OVCAR-5_3926 Cluster Incl.

M24899:Human triiodothyronine

(ear7) mRNA, complete cds

/cds=(411,1883)

/gb=M24899

/gi=537521

/ug=Hs.724

/len=2309

As a comparison, the copy number breakpoints of oncogenes and all genes in normal cell lines, which were converted from the blood samples of healthy donors collected by the International HapMap project was further evaluated. Based on the limited 38 HapMap normal cell line data retrieved from GEO, none of the oncogenes contains copy number breakpoints, while only 0.1% (19 out of total 17,609) of the genes in the genome contain CNV in at least one normal cell line. There is no significant difference between oncogenes versus all genes (P value = 0.638) with regard to the frequency of copy number breakpoints in these normal cell lines.

Genome- wide evaluation of gene-linked copy number breakpoints in cancer cell lines

The initial analyses of oncogenes and broadly evaluate copy number breakpoints across all genes for all 820 of the Sanger cancer cell lines was extended. A gene was considered to contain a copy number breakpoint if the CNV was present within its transcript, regardless of the location or whether it was associated with amplification or deletion. The results of this analysis reveal that the mean value of the number of genes with copy number breakpoints in Sanger's cancer lines is 369, which is much higher than the mean of 25 obtained for HapMap normal cell lines (p <= 4.054e-10). When the numbers of genes containing copy number breakpoints were plotted against cancers of various tissue origins, a significant variability was observed amongst cancer origins. On one end of the spectrum, liver cancers and mesotheliomas possess medians of greater than 600 genes containing copy number breakpoints. In contrast, hematopoietic cancers exhibited a median of 70 genes containing copy number breakpoints (Figure 5).

Discussion In this study, SNP array data has been utilized to evaluate three well known fusion genes that are associated with tumorigenesis for the presence of copy number breakpoints within genomic sequences.

For BCR-ABL1, breakpoints in both BCR and ABL1 were observed in 5 out of 8 CML cell lines. However, it should be noted that for the other three CML cell lines, breakpoints were present in either BCR, ABL1, or in the neighboring genes. Additional searches identified two non-leukemia cancer cell lines that also contain copy number breakpoints in BCR and ABL1. It will be of interest to confirm whether these two cell lines do contain BCR-ABL1 fusions since BCR-ABL1 has only been reported in leukemias to date.

For TMPRSS2-ERG, based on the 20 paired prostate patient samples, the SNP array data reveal that some of the fusions are likely results of genomic sequence deletion. As for other Ets family members, such as ETV1, the altered expression may be due to different genetic mutations, such as gene amplification. Alternatively, the frequency of TMPRSS2-ETV1 translocation fusions may be much lower than for TMPRSS2-ERG. In this limited data set, the samples that contain amplified ETV1 and fusion ERG were mutually exclusive, which implies that the over-expression of one of the Ets genes may contribute to initiation or progression of prostate cancer. Genome wide analysis indicates that none of the 820 Sanger cancer cell lines contain a segment deletion between TMPRSS2 and ERG similar to that observed in the prostate primary cancer samples. There are two possibilities: (1) with only five prostate cancer cell lines in the panel, the number is too small to represent the wide genetic diversity of prostate cancers; (2) TMPRSS2-ERG is unique to prostate cancer, since TMPRSS2 expression is almost exclusively in the prostate with some expression in the GI track. In addition, the fusion is regulated by androgen as TMPRSS2 expression is androgen dependent (Bastus, Boyd et al. 2010) (Mwamukonda, Chen et al. 2010), which provides it a growth advantage only in prostate and not in other tissues. However, it can not ruled out that other fusion transcript mechanisms, such as transcript read-through, which can not be captured by SNP array data at the DNA level. This is all the more possible given that TMPRSS2 and ERG are closely located on the same chromosome, and that read-through fusion transcripts were identified in prostate cancer (Maher, Kumar-Sinha et al. 2009).

For the EML4-ALK fusion, 6 lung cancer cell lines, and 18 cell lines from other cancer origins with copy number breakpoints were identified. This is in agreement with a report by Lin et al., where a RT-PCR assay was used to examine a panel of 124 cell lines from breast cancer, colorectal cancer, and NSCLC for fusion transcripts of EML4- ALK. With this panel, 9 cell lines, including a known positive control (H2228), were identified to harbor the EML4-ALK fusion. Since the detailed information of the 124 cell lines was not available in the publication, it was not possible to compare them with the copy number analysis. However, based on some of the positive and negative cell lines listed in the paper, nine cell lines that were common could be evaluated. Among them, two cell lines (H2228 and SW1417) are positive, and five cell lines (T47D,

CAL120, HCT116, H1299, and H838) are negative supported by both methods. There are two cell lines (H460 and H1975), which were found to contain fusion transcripts, but do not show copy number breakpoints by SNP array data. In the above evaluations, all copy number breakpoints in the coding regions, especially in the oncogenes were also assessed. The frequencies of the copy number breakpoint for ABL1 (75%), ERG (15%) and ALK (15.7%) are high in the eight CML cell lines, 20 prostate cancer samples, and 140 lung cancer cell lines, respectively.

However, the frequency for ERG may be underestimated since the SNP array data of the prostate cancer samples were generated from Affymetrix 500K array Set, whose probe coverage is less than one third of the Affymetrix array 6.0 used for the Sanger panel. In the CML cell lines and prostate cancer samples, the frequencies of copy number breakpoint for ABL1 and ERG, respectively, were ranked top compared to other oncogenes. In the lung cancer cell lines, there are several oncogenes whose copy number breakpoint frequencies are higher than that of ALK. Some of them were reported to be involved in reciprocal translocation in other cancers or developmental diseases. Since the overall frequency of EML4-ALK fusion is low (9.1%) in lung cancers, other mechanisms including other fusions, may possibly be involved in these lung cancer cell lines. In conclusion, analyzing SNP array data for copy number breakpoint frequencies of oncogenes provides a translocation candidate list to be further followed up experimentally.

Genome- wide copy number breakpoint analysis was also performed in the 820 Sanger cell lines. It had identified genes that contain copy number breakpoints in Sanger cancer cell lines, but not in the 38 Hapmap normal cell lines. The top ten genes that are highly linked with copy number breakpoints only in the cancer cell lines were evaluated (Table 6). The genomic sizes of these genes tend to be very large, which may increase the chance for them to link with a copy number breakpoint. Nevertheless, it is interesting to note that five out of the ten genes: MACROD2 (Stephens, McBride et al. 2009), FHIT (Gemmill, West et al. 1998), CNTNAP2 (Belloso, Bache et al. 2007), MAGI2 (Berger, Lawrence et al. 2011), LRP1B (Moller, Kubart et al. 2008), were reported to be involved in genomic sequence re-arrangement/translocation.

Table 6. Top ten genes that contain copy number breakpoints in Sanger's 820 cancer cell lines, and not in 38 Hapmap normal cell lines.

Gene # of Cell Lines Genomic

Sanger Size (Kb) 820

Cell

Lines

RPL21 411 ALL-PO_3996#BC-3_4230#CAPAN-1_3668#COR- 5

L88_4256#DMS-273_4238#DV-90_4562#GA-10-Clone-

20_4570#GAMG_3865#HCC1569_4259#HCC2218_3395#H

CE-T_4531#HLE_4269#HuO9_4528#JAR_4940#KYSE-

70_4246#LC- 1F_4261#LP- l_4693#MOG-G-

CCM_3847#MUTZ- 1 _4662#NCI-H 1792_4298#NCI-

H596_4344#ONS-76_4607#RMG-I_4960#SK-LMS- l_4642#SW948_4599#SW962_4201#U-698-M_4615#UACC-

257_4994#A 101 D_4306#A2058_4313#A375_4643#A673_39

15#AML-193_3759#ATN-l_4651#Becker_4548#CAL-

12T_4626#Calu-l_3554#Calu-6_4277#CMK_3995#COLO-

775_4030#COR-L279_4273#D-263MG_3679#D-

336MG_3650#DB_4217#DBTRG-05MG_3838#DG-

75_4545#DMS-114_4227#DoTc2-4510_4289#EFE-

184_3662#EFM- 19_4564#EM- 2_4063#ES3_3741#ES5_3733#ES8_3757#ETK-1_4550#EW-

1_3815#EW-24_3764#GDM-1_4056#GOTO-P3_3906#HAL-

01_3817#HCC1806_4283#HCC1937_3429#HSC-

2_4525#HuH-7_4226#HuO-3Nl_4945#HUTU-

80_4984#KATOIII_4684#KM-H2_4561#KP-

4_4232#KURAMOCHI_4563#KYSE-510_4203#L-

540_4538#LCLC-103H_4255#LN-405_3849#LNCaP-Clone-

FGC_4649#LS-123_3908#LS-513_4539#LXF-

289_4281#MCF7_4622#MDA-MB- 134-VI_3607#MDA-MB-

468_4287#MRK-nu-l_3586#NCI-H1299_4266#NCI-

H1395_3399#NCI-H1437_3435#NCI-H1522_4304#NCI-

H1563_4211#NCI-H1573_4291#NCI-H1581_4297#NCI-

H 1623_4293#NCI-H 1770_3420#NCI-H 1926_4296#NCI-

H1930_3711#NCI-H2030_4239#NCI-H2052_3374#NCI-

H2141_4957#NCI-H2228_3820#NCI-H2342_4234#NCI-

H345_4962#NCI-H441_4937#NCI-H446_4347#NCI-

H69_4434#NCI-H716_4704#NCI-H835_3791#NCI-

H889_359 l#OAW-42_4515#OC-314_4554#OCUB-

M_4250#OE33_4228#OVCAR-3_3935#OVCAR-

4_3977#PFSK-1_3832#PSN1_4268#RD_3892#RPMI-

8226_4628#RT4_3896#RVH-421_3561#SAS_3574#SCLC-

21H_4956#SHP-77_4328#SJRH30_3883#SJSA-1_3869#SK-

MEL-2_3940#SK-NEP-1_3904#SK-PN-

DW_3867#SNB75_3976#SNU-

475_3861#SW756_4988#SW837_3837#UACC-

62_3988#UACC-812_4967#UACC-893_4299#WERI-Rb- l_4620#YKG-l_4987#ZR-75-

30_4714#8305C_3794#A549_4999#AC0887_3378#AGS_358

4#AM-38_3845#BB65-RCC_3434#BE-

13_3945#BEN_3743#C2BBel_3860#Ca-

Ski_4675#CA46_4657#CAKI-l_3921#CAL-148_3678#Calu-

3_3575#Caov-3_3853#CGTH-W-l_3739#CHL-

1_3559#COLO-205_4688#COLO-668_3773#COLO-

680N_3824#COLO-720E_3842#COLO-792_3615#COLO-

800_4701#COLO-824_3788#D-397MG_3654#D-

423MG_3700#Daoy_3898#DEL_3570#DK-MG_3830#DMS-

79_4527#DOK_3588#EB2_4037#EC-GI-

10_4526#ECC 10_3568#ECC 12_3601 #EFO-21 _4574#EPLC-

272H_4559#GAK_3571#GB-1_3872#GI-1_3852#GMS-

10_4668#GR-

ST_4051#HCC 1599_3375#HCC2157_3403#HCC38_3392#H DLM-2_4955#HOP-62_3975#HPAF-II_3612#Hs-578- T_3930#HSC-4_3551#HT-

29_3963#HT55_4542#HuCCTl_3590#IA-LM_4623#IST- MEL1_3611#IST-MES 1_3596#IST-SL1_3651#IST- SL2_4209#J82_3439#K-562_3955#KALS-1_3827#KINGS- 1_4572#KLE_3729#KMOE-2_4083#KNS-42_3891#L- 428_4535#LB2241-RCC_3422#LB2518-MEL_3445#LS- 1034_3431 #MD A-MB - 157_3714#MD A-MB - 361_4431#MDA-MB-453_4502#MFE-280_3618#MHH-ES- 1_3569#MKN28_3619#ML-2_4070#MN-60_4068#MONO- MAC-6_4040#MZ1 -PC_4995#MZ7- mel_3453#NB 12_3776#NB5_3782#NBsusSR_3647#NCI- H 1048_4433#NCI-H 1092_4428#NCI-H 1173_3563#NCI- Hl 666_4309#NCI-H 1693_4305#NCI-H2009_3428#NCI- H2029_4346#NCI-H2081 _4341 #NCI-H2126_3400#NCI- H2170_4342#NCI-H226_3932#NCI-H2330_3560#NCI- H23_3946#NCI-H2452_3585#NCI-H378_4983#NCI- H460_3979#NCI-H510A_3653#NCI-H524_5003#NCI- H526_4337#NCI-H630_3846#NCI-H64_4351#NCI- H661_4348#NCI-H774_3674#NEC8_4236#NOMO-

1_4047#NOS-1_3707#OS-RC-2_4216#P31-FUJ_4048#PA- l_3826#PANC-03-27_3655#PANC-10-05_3669#PC-

14_4279#PLC-PRF-5_3695#RCM-1_4950#RERF-LC-

FM_3692#RH- 18_3740#RH- 1_3801#RS4-1 l_4637#Saos-

2_3879#SCC- 15_3566#SCC-4_3595#SCC-

9_3557#SCH_3582#SF126_4938#SF539_3980#SK-CO-

1_4689#SK-HEP-1_4639#SK-MEL-5_4009#SK-N-

FI_3666#SNU-387_3903#SNU-449_3913#SUP-

T1_4295#SW1990_3894#SW780_3902#SW872_3851#T84_4

606#T98G_3890#TALL-1_4057#TC-YIK_3696#TE- l_3765#TGW_4081#U-2-OS_3844#VA-ES-

BJ_3972#380_4943#647-V_3778#786-0_3969#A3-

KAW_3562#A427_4200#ABC- 1_3809#B2- 17_4089#B ALL-

1_3960#BCPAP_3646#BFTC-905_3737#BOKU_3684#BT-

20_4218#BT-549_3943#BxPC-3_3797#CAL-

120_3816#CAL-39_3706#CAL-62_3758#CAL-85-

1_3812#Caov-4_3814#Capan-2_3552#COLO-320-

HSR_4553#COLO-678_4985#COLO-741_3874#COR-

L96CAR_3744#CTB-1_3750#D-247MG_3660#D-

538MG_3642#D-566MG_3699#DU-

145_3961#ECC4_4936#EKVX_4697#FADU_4715#FTC-

133_4288#GCIY_3565#GOTO_4049#H4_3843#HCC1143_3

402#HCC2998_4001#HEC-1_3573#HMV-II_4624#IMR-

5_4052#ITO-II_3702#K052_4677#KASUMI-1_4023#KMS-

12-BM_4098#KMS-12-PE_4075#KOSC-2_4565#KP-N-

YS_3725#KU812_4664#KYSE-270_4274#KYSE-

520_3698#LB 1047-RCC_3970#LB831-BLC_3388#LCLC-

97TM1_3675#LS-411N_3835#LU-134-A_4195#LU-

139_4276#MDA-MB-231_3957#MDA-MB-435_3938#MEG-

01_4635#MFH-ino_4928#MHH-NB-

11_4093#MKN7_3671#MLMA_4065#NB 14_3819#NCI-

ADR-RES_3984#NCI-H 1105_4441 #NCI-H 1417_4944#NCI-

Hl 650_4292#NCI-H 1734_3717#NCI-H 1882_3810#NCI-

Hl 963_4353#NCI-H2171_3999#NCI-H2196_3610#NCI-

H2347_4356#NCI-H295_4034#NCI-H508_3857#NCI-

H522_3920#NCI-H650_3645#NCI-H719_3728#NCI-

H727_4339#NCI-H748_4932#NCI-H82_4355#NCI-SNU-

5_4669#NH- 12_4020#no- 10_3944#NUGC-

3_3597#NY_4519#OAW-28_3694#OVCAR-8_3997#Ramos-

2G6-4C10_4327#RO82-W-l_3676#RPMI-8402_4053#S-

117_4282#SBC-1_3665#SBC-

5_3703#SF268_4000#SiHa_3705#SK-MEL-28_3922#SK-

MEL-30_3602#SK-MM-2_4017#SK-N-AS_3900#SK-OV-

3_4713#SKG-IIIa_3649#SN 12C_3919#SNB 19_4004#SNU-

C1_3895#SW13_3831#SW620_3964#T47D_3971#TCCSUP_

3871#TE-10_3784#TE-11_3787#TE-12_3761#TE-

15_4972#TE-5_3781#TE-9_3806#TUR_4659#U-118-

MG_3881#U-87-MG_3763#UM-UC-3_3998#VM-CUB-

1_4245#VMRC-MELG_3756#WSU-NHL_5002#YH-

13_3981#8505C_3690#ES6_3798#HCC 1187_3376#HCC 1395

_3394#HT-1376_3848

MACRO 288 A388_5001#C AS - 1 _4965#D V-90_4562#G A- 10-Clone- 2,058 D2 20_4570#GAMG_3865#HCC1569_4259#HCC2218_3395#H

LE_4269#HT-3_5008#HUH-6- clone5_4215#Hu09_4528#J AR_4940#KU- 19-19_4280#LC- lF_4261#MOG-G-CCM_3847#MUTZ-

1_4662#NB 13_3768#RCC 10RGB_4271#S W948_4599#S W96

2_4201#UACC-257_4994#AU565_4240#BPH-1_3652#BT-

474_3712#Calu-6_4277#CMK_3995#COLO-829_3424#COR- L279_4273#COR-L51_4253#DOTC2-4510_4289#EFE-

184_3662#EFM- 19_4564#EFO-27_4573#ETK- 1_4550#EW-

18_3754#Gp2D_4552#HCC 1806_4283#HCC 1954_3443#HS

C-2_4525#HT- 1197_3850#HTC-C3_370 l#HuH-

7_4226#KATOIII_4684#KM-H2_4561#KP-4_4232#KS-

1_3877#KYSE-410_4213#L-540_4538#LAN-1_4077#LN-

405_3849#LS- 174T_3916#LS-513_4539#MCF7_4622#ME-

180_5005#MFM-223_3576#MRK-nu-

1_3586#NB 17_3807#NCI-H 1299_4266#NCI-

H1437_3435#NCI-H1563_4211#NCI-H1573_4291#NCI-

H 1581 _4297#NCI-H 1703_4294#NCI-H 1770_3420#NCI-

H1793_4206#NCI-H2030_4239#NCI-H2052_3374#NCI-

H2228_3820#NCI-H345_4962#NCI-H446_4347#NCI-

H747_4537#NCI-H835_3791#NCI-SNU-l_4986#OC-

314_4554#OCUB-

M_4250#OE19_4237#OE33_4228#OVCAR-

3_3935#OVCAR-4_3977#PSNl_4268#RT4_3896#RVH-

421_3561#SAS_3574#SHP-77_4328#SK-N-

DZ_3875#SNB75_3976#SNU-

475_3861#SW756_4988#SW837_3837#TYK- nu_4603#UACC-812_4967#UACC-893_4299#YKG- l_4987#ZR-75-30_4714#23132-

87_3550#A704_3897#AGS_3584#CAKI-l_3921#Calu-

3_3575#Caov-3_3853#CGTH-W-l_3739#CHL-l_3559#CHP-

212_3911#COLO-205_4688#COLO-680N_3824#COLO-

684_3599#COLO-720E_3842#CP50-MEL-B_3410#D-

397MG_3654#D-423MG_3700#D-

502MG_3680#Daoy_3898#DOK_3588#ECC10_3568#EFO-

21_4574#EW-11_3823#G-361_4658#GB-1_3872#GI-

1_3852#GI-ME-

N_4041#HCC2157_3403#HCC38_3392#HCC70_4257#HCT-

15_3954#HEL_4090#HPAF-II_3612#Hs-578-T_3930#HT-

144_3617#HT-29_3963#HT55_4542#HuCCTl_3590#IGR-

1_3564#IPC-298_3623#IST-MES 1_3596#IST-SL1_3651#K-

562_3955#KALS-1_3827#KARPAS-

422_4512#KLE_3729#KM12_3949#KMOE-2_4083#KNS-

42_3891#KP-N-S 19s_4031#L-363_4949#LB2241-

RCC_3422#LB2518-MEL_3445#LB771 -HNC_3390#LS-

1034_3431#M059J_3738#MDA-MB-157_3714#MDA-MB-

361_4431#MDA-MB-453_4502#MEL-HO_4973#MG-

63_4544#MMAC-SF_3710#MPP-89_3606#MZ1 -

PC_4995#NB7_3774#NCI-H1048_4433#NCI-

Hl 173_3563#NCI-H 157_4303#NCI-H 1975_3716#NCI-

H2122_3441 #NCI-H2126_3400#NCI-H2170_4342#NCI-

H2291_3688#NCI-H510A_3653#NCI-H520_4975#NCI-

H524_5003#NCI-H526_4337#NCI-H630_3846#NCI-

H64_4351#NEC8_4236#NOS-1_3707#OS-RC-

2_4216#PANC-03-27_3655#RCM- 1_4950#RERF-LC-

FM_3692#RH-1_3801#RPMI-7951_4654#SCC-

9_3557#SCH_3582#SF126_4938#SF539_3980#SK-MEL-

1_3621#SK-MEL-3_3577#SK-MEL-5_4009#SK-MG-

1_4946#SNU-

449_3913#S W 1417_3863#S Wl 573_4310#S Wl 990_3894#S W403_3834#SW684_3887#SW780_3902#T84_4606#TGW_4 081#UMC-11_4301#VA-ES-BJ_3972#VMRC- LCP_3771#647-V_3778#A498_4002#ACN_3992#B2- 17_4089#BHT- 10 l_3793#BT-20_4218#BxPC-3_3797#C AL- 39_3706#CAL-62_3758#Caov-4_3814#Capan- 2_3552#COLO-320-HSR_4553#COR-L96CAR_3744#DU- 145_3961#EKVX_4697#EW- 7_3748#FADU_4715#GCIY_3565#H4_3843#HGC-

27_3622#HN_4569#HOP-92_4671#HuH-28_3721#HuP-

T4_3589#IGROV-1_3990#K5_3686#KNS-62_4221#KP-N-

YS_3725#KYSE-270_4274#KYSE-450_4275#KYSE-

520_3698#LB 1047-RCC_3970#LB831-BLC_3388#LCLC-

97TM1_3675#LK-2_4429#M14_3924#MDA-MB-

435_3938#MKN7_3671#NB 1_3803#NCI-ADR-

RES_3984#NCI-H 1304_3713#NCI-H 1417_4944#NCI-

H1734_3717#NCI-H1882_3810#NCI-H2227_4338#NCI-

H2405_4345#NCI-H295_4034#NCI-H508_3857#NCI-

H650_3645#NCI-H810_3683#NCI-H82_4355#NCI-

H838_4350#NCI-SNU-5_4669#NMC-Gl_3912#no-

10_3944#no- 11_4712#NUGC-3_3597#NY_4519#OVCAR-

5_3926#P12-ICHIKAWA_4084#RERF-LC-

MS_4233#RXF393_3987#S-117_4282#SBC-

5_3703#SF268_4000#SiHa_3705#SK-MEL-30_3602#SK-

MM-2_4017#SN 12C_3919#SNU-C 1 _3895#SNU-

C2B_3901#SW13_3831#SW620_3964#SW626_3884#SW900

_3583#T47D_3971#TCCSUP_3871#TE-12_3761#TE-

8_3767#TE-9_3806#TK10_4008#TUR_4659#VM-CUB-

1_4245#VMRC-

MELG_3756#YAPC_4024#HCC 1395_3394#HCC 1954- BL_3449#HT-1376_3848

FHIT 286 BC-3_4230#CAPAN-1_3668#DMS-273_4238#DV- 1,502

90_4562#GAMG_3865#HCE-T_4531#HT- 3_5008#JAR_4940#KYSE-70_4246#LC-1F_4261#MUTZ- 1_4662#NCI-H 1792_4298#NCI-

H596_4344#Raji_4333#RCC10RGB_4271#SW948_4599#UA

CC-257_4994#A101D_4306#A253_5000#AN3-

CA_3578#AsPC-l_3572#ATN- l_4651#AU565_4240#Becker_4548#BT-474_3712#CAL-

12T_4626#Calu-l_3554#CMK_3995#COLO-

829_3424#COR-L279_4273#D-263MG_3679#DB_4217#DG-

75_4545#DMS-114_4227#DoTc2-4510_4289#EFO-

27_4573#ETK- 1_4550#HCC1806_4283#HD-MY-

Z_4575#HSC-3_4964#HT-1197_3850#HTC-C3_3701#HuO-

3N 1_4945#HUTU-80_4984#KARPAS -

45_4027#KATOIII_4684#KP-4_4232#KYSE-

410_4213#LAN- 1 _4077#LC-2-ad_4247#LCLC-

103H_4255#LNCaP-Clone-FGC_4649#LS - 174T_3916#LS -

513_4539#MCF7_4622#MEL-JUSO_3605#MES-

S A_4992#NCI-H 1299_4266#NCI-H 1437_3435#NCI-

H 1581 _4297#NCI-H 1623_4293#NCI-H 1648_4312#NCI-

Hl 703_4294#NCI-H 1755_3593#NCI-H 1793_4206#NCI-

H1930_3711#NCI-H2141_4957#NCI-H2228_3820#NCI-

H2342_4234#NCI-H28_4650#NCI-H345_4962#NCI-

H441_4937#NCI-H446_4347#NCI-H716_4704#NCI-

H747_4537#NCI-H835_3791#NCI-H889_3591#NCI-

N87_4636#NCI-SNU-l_4986#OC-314_4554#OCUB-

M_4250#OE19_4237#OE33_4228#OVCAR-

3_3935#PSN1_4268#RPMI-8226_4628#RVH-

421_3561#SAS_3574#SH-4_3613#SJRH30_3883#SK-NEP- l_3904#SNU-475_3861#TYK-nu_4603#UACC-

893_4299#YKG-l_4987#23132-87_3550#639-

V_3587#A549_4999#AGS_3584#BB65-RCC_3434#BC- l_4673#BEN_3743#BFTC-909_3786#Ca-Ski_4675#CAKI- l_3921#Calu-3_3575#Caov-3_3853#CHP-134_3854#COLO-

205_4688#COLO-680N_3824#COLO-800_4701#CW-

2_4529#EC-GI- 10_4526#ECC 10_3568#ECC 12_3601#EPLC-

272H_4559#GAK_3571#GB-1_3872#GMS-10_4668#GR- ST_4051#HCT- 15_3954#HEL_4090#HPAF-II_3612#Hs-578-

T_3930#HSC-4_3551#HT-29_3963#HuCCTl_3590#IPC-

298_3623#IST-MES 1_3596#IST-SL1_3651#JEG-3_4687#K-

562_3955#KLE_3729#KM12_3949#KMOE-2_4083#KNS-

42_3891#L-363_4949#LB2241 -RCC_3422#LB2518-

MEL_3445#LB373-MEL-D_3427#LB771 -

HNC_3390#LoVo_3839#LS-1034_3431#M059J_3738#MDA-

MB - 157_3714#MD A-MB -415_3718#MG-

63_4544#MKN 1_3567#MMAC-SF_3710#MPP-

89_3606#NB 10_3790#NB7_3774#NCI-H 1092_4428#NCI-

Hl 173_3563#NCI-H 128_3423#NCI-H 157_4303#NCI-

H 1666_4309#NCI-H 1693_4305#NCI-H 1838_4290#NCI-

H1975_3716#NCI-H2081_4341#NCI-H2107_3667#NCI-

H2122_3441 #NCI-H2126_3400#NCI-H2170_4342#NCI-

H2291_3688#NCI-H23_3946#NCI-H2452_3585#NCI-

H460_3979#NCI-H526_4337#NCI-H630_3846#NCI-

H661_4348#NEC8_4236#NOS-1_3707#OS-RC-

2_4216#PANC-03-27_3655#PLC-PRF-5_3695#RCM-

1_4950#RH-1_3801#RPMI-7951_4654#SCC-15_3566#SCC-

9_3557#SCH_3582#SK-HEP-1_4639#SK-MG-1_4946#SK-

UT-1_5011#SNU-

387_3903#S W 1417_3863#S Wl 573_4310#S Wl 990_3894#S

W403_3834#T84_4606#TE-

1_3765#TGBC11TKB_3556#TGW_4081#VA-ES-

BJ_3972#143B_4036#647-V_3778#A3-KAW_3562#A4-

Fuk_4989#A427_4200#ACN_3992#BALL-l_3960#BFTC-

905_3737#BHT- 10 l_3793#BxPC-3_3797#C AL-

120_3816#CAL-39_3706#CAL-62_3758#CaR-

1_3708#COLO-320-HSR_4553#CRO-AP5_4543#EGI-

1_4018#EKVX_4697#GCIY_3565#H4_3843#HCC1143_340

2#HCT-116_3962#HGC-27_3622#HOP-

92_467 l#HOS_3907#HT_4432#HuH-28_3721#KMS- 12-

BM_4098#KNS-62_4221#KOSC-

2_4565#KU812_4664#KYSE-270_4274#KYSE-

450_4275#KYSE-520_3698#LB 1047-RCC_3970#LB831-

BLC_3388#LK-2_4429#LS-411N_3835#LU-139_4276#LU-

65_4436#M 14_3924#MC-IXC_4019#MDA-MB-

435_3938#MFH-ino_4928#MIA-PaCa-

2_3885#MKN45_3641#MKN7_3671#MLMA_4065#NCI-

ADR-RES_3984#NCI-H 1417_4944#NCI-H 146_4505#NCI-

Hl 618_3689#NCI-H2347_4356#NCI-H250_3661#NCI-

H322M_4661#NCI-H508_3857#NCI-H522_3920#NCI-

H748_4932#NCI-H838_4350#no-11_4712#OMC-

1_3802#OVCAR-5_3926#OVCAR-8_3997#PANC-08-

13_3681#Ramos-2G6-

4C 10_4327#RTSG_4991#RXF393_3987#SBC-

5_3703#SiHa_3705#SK-LU-l_4326#SK-MEL-28_3922#SK-

N-AS_3900#SNU-

C1_3895#SW620_3964#SW626_3884#T47D_3971#TE- 11_3787#TE- 12_3761#TE- 15_4972#TE-5_3781#TE- 8_3767#TGBC24TKB_4078#TUR_4659#U-266_4038#UM- UC-3_3998#VMRC-

MELG_3756#YAPC_4024#HCC 1395_3394#HT- 1376_3848#SK-MES-1_4323

wwox 275 BC-3_4230#CAPAN-1_3668#DV- 1, 112

90_4562#HCC 1569_4259#HCC2218_3395#HCE- T_4531#HUH-6- clone5_4215#HuO9_4528#JAR_4940#MHH-PREB- l_4534#MUTZ-l_4662#NCI-H1792_4298#Raji_4333#SK-

LMS- 1_4642#SW948_4599#SW962_4201#A253_5000#A375_4643

#A673_3915#AC0912_4300#AsPC- l_3572#AU565_4240#Becker_4548#BL-41_4095#BPH- l_3652#CAL-12T_4626#CAL-33_4947#CAL-54_3780#Calu-

1_3554#COLO-775_4030#COLO-829_3424#COR-

L105_3742#COR-L279_4273#D-263MG_3679#EM-

2_4063#EW-

1_3815#HCC 1806_4283#HCC 1937_3429#HCC 1954_3443#H D-MY-Z_4575#HTC-C3_3701#HuH-7_4226#HUTU- 80_4984#KARPAS-299_4546#KM-H2_4561#L- 540_4538#LCLC-103H_4255#LS-

123_3908#MCF7_4622#MDA-MB- 134-VI_3607#MDA-MB-

468_4287#ME- 180_5005#NB4_4082#NB6_3799#NCI-

H 1299_4266#NCI-H 1395_3399#NCI-H 1648_4312#NCI-

Hl 703_4294#NCI-H 1793_4206#NCI-H 1930_3711#NCI-

H2030_4239#NCI-H2228_3820#NCI-H28_4650#NCI-

H441_4937#NCI-H446_4347#NCI-H835_3791#NCI-SNU-

1_4986#NKM-1_4029#OAW-42_4515#OCUB-

M_4250#OE33_4228#OVCAR-3_3935#OVCAR-

4_3977#PSN1_4268#RPMI-8226_4628#SJRH30_3883#SK-

N-DZ_3875#SK-NEP-1_3904#SK-PN-

DW_3867#SW1088_3888#SW756_4988#TYK- nu_4603#UACC-812_4967#UACC-

893_4299#22RV1_3672#23132-

87_3550#A704_3897#AGS_3584#AM-38_3845#BC-

1_4673#BEN_3743#BFTC-

909_3786#BHY_3658#C2BBel_3860#Ca9-22_4966#CAKI- l_3921#Calu-3_3575#Caov-3_3853#COLO-

680N_3824#COLO-792_3615#COLO-800_4701#COR-

L23_4214#CRO-AP2_4939#D-397MG_3654#DJM-

1_3604#DMS-79_4527#DOK_3588#EC-GI-10_4526#EFO-

21_4574#ES7_3813#GAK_3571#GB-1_3872#GI-ME-

N_4041#GR-ST_4051#HCT-15_3954#HOP-62_3975#HPAF-

II_3612#HT-29_3963#HT55_4542#HuCCTl_3590#IM-

9_4069#IPC-298_3623#IST-MES 1_3596#IST-

SL1_3651#JEG-3_4687#K-562_3955#KALS-

1_3827#KM12_3949#L-428_4535#LB2241-

RCC_3422#LB373-MEL-D_3427#LB647-

SCLC_3414#LoVo_3839#LS-1034_3431#MDA-MB-

157_3714#MDA-MB - 175- VII_4425#MDA-MB -

361_4431#MDA-MB-415_3718#MDA-MB-453_4502#MEL-

HO_4973#MKN28_3619#NB 10_3790#NB7_3774#NCI-

Hl 28_3423#NCI-H 157_4303#NCI-H 1975_3716#NCI-

H1993_4354#NCI-H2009_3428#NCI-H2081_4341#NCI-

H2122_3441 #NCI-H2170_4342#NCI-H2330_3560#NCI-

H23_3946#NCI-H460_3979#NCI-H520_4975#NCI-

H524_5003#NCI-H526_4337#NCI-H661_4348#NOS-

1_3707#PANC-10-05_3669#PC-14_4279#PLC-PRF-

5_3695#RERF-LC-FM_3692#RF-48_3579#RH- 18_3740#RH-

1_3801#SCH_3582#SF126_4938#SK-MEL-1_3621#SK-

MEL-3_3577#SK-MG-1_4946#SK-UT-1_5011#SNU-

449_3913#SW1573_4310#SW684_3887#SW872_3851#TC-

YIK_3696#TGBC 11TKB_3556#TGW_408 l#U-2-

OS_3844#U031_4663#A3-KAW_3562#A4-

Fuk_4989#A427_4200#ABC-

1_3809#ACHN_3950#ACN_3992#B2-17_4089#BT-

20_4218#BT-549_3943#BxPC-3_3797#CAL-

120_3816#CAL-39_3706#CAL-62_3758#CAL-85-

1_3812#Caov-4_3814#Capan-2_3552#COLO-320-

HSR_4553#CRO-AP5_4543#DU- 145_3961#ECC4_4936#EW-

16_3792#FADU_4715#GCIY_3565#H4_3843#HC-

1_4022#HCC2998_4001#HCT- 116_3962#HEC- l_3573#HGC-27_3622#HOP-92_4671#HuP-

T4_3589#KASUMI-1_4023#KGN_3644#KNS-

62_4221#KU812_4664#KYSE-450_4275#KYSE-

520_3698#LB 1047-RCC_3970#LOXIMVI_3936#LS-

411N_3835#LU- 139_4276#LU-65_4436#MDA-MB-

231_3957#MKN45_3641#MKN7_3671#NB 14_3819#NB 16_3

829#NCI-ADR-RES_3984#NCI-H1105_4441#NCI-

H1355_4439#NCI-H146_4505#NCI-H1650_4292#NCI-

H1882_3810#NCI-H1963_4353#NCI-H2087_3389#NCI-

H322M_4661#NCI-H508_3857#NCI-H650_3645#NCI-

H727_4339#NCI-H838_4350#NCI-N417_4331#no-

10_3944#NY_4519#OPM-2_4088#OVCAR-

8_3997#REH_4035#RPMI-

8866_4055#RTSG_4991#RXF393_3987#S-117_4282#SBC- 1_3665#SK-N- AS_3900#SN 12C_3919#SNB 19_4004#SNU- C2B_3901#SW13_3831#SW620_3964#TCCSUP_3871#TE- 10_3784#TE- 12_3761 #TE- 15_4972#TE-5_3781 #TE- 8_3767#TE-9_3806#TGBC1TKB_4087#TUR_4659#U- 266_4038#U-87-MG_3763#U251_3994#UM-UC- 3_3998#VM-CUB-1_4245#8-MG-BA_3893#ES6_3798#SK- MES-1_4323

CSMD1 262 A388_5001#BC-3_4230#CAPAN-1_3668#COR- 2,057

L88_4256#D-392MG_3614#DMS-273_4238#DV-

90_4562#HCC 1569_4259#HCC2218_3395#HCE-

T_4531 #HUH-6-clone5_4215#Hu09_4528#KU- 19-

19_4280#KYSE-70_4246#L542_3408#LC-1F_4261#MUTZ- l_4662#NCI-H596_4344#ONS-76_4607#Raji_4333#UACC-

257_4994#A253_5000#A375_4643#AML-

193_3759#AU565_4240#BT-474_3712#C32_4652#CAL-

33_4947#CAL-54_3780#Calu-l_3554#COLO-

775_4030#COR-L105_3742#D-263MG_3679#D-

542MG_3381#DB_4217#DMS-114_4227#DoTc2-

4510_4289#DSH1_4963#EM-2_4063#ES3_3741#EW-

13_3745#EW- 1_3815#EW-24_3764#GDM-

1_4056#HCC1937_3429#HCC1954_3443#HH_4430#HSC-

3_4964#HTC-C3_3701#HUTU-80_4984#KM-H2_4561#KP-

4_4232#LC-2-ad_4247#LCLC- 103H_4255#LN-

405_3849#LS - 123_3908#MCF7_4622#MD A-MB - 134-

VI_3607#MEL-JUSO_3605#MFM-223_3576#MRK-nu-

1_3586#NB 17_3807#NCI-H1437_3435#NCI-

H 1522_4304#NCI-H 1573_4291 #NCI-H 1581 _4297#NCI-

H 1703_4294#NCI-H 1755_3593#NCI-H 1926_4296#NCI-

H1930_3711#NCI-H2052_3374#NCI-H345_4962#NCI-

H716_4704#NCI-H889_3591#OCUB-M_4250#OVCAR-

4_3977#PC-3_3978#PFSK-

1_3832#PSN1_4268#RD_3892#RPMI-

8226_4628#RT4_3896#RVH-421_3561#SAS_3574#SCLC-

21H_4956#SHP-77_4328#SJSA-1_3869#SNU-

423_4251#SNU-475_3861#SW756_4988#TYK- nu_4603#UACC-893_4299#YKG-l_4987#ZR-75-

30_4714#8305C_3794#A172_3859#AM-38_3845#BB65-

RCC_3434#BFTC-909_3786#BHY_3658#CHL-

1_3559#COLO-205_4688#COLO-680N_3824#COLO-

684_3599#COLO-720E_3842#COLO-824_3788#D-

423MG_3700#Daoy_3898#DJM-l_3604#DOK_3588#EC-GI-

10_4526#ECC10_3568#EPLC-272H_4559#EW-11_3823#G-

361_4658#GB-1_3872#GMS-10_4668#HA7- RCC_4667#HCC38_3392#HCC70_4257#HEL_4090#HOP- 62_3975#HSC-4_3551#HT-144_3617#HT-29_3963#HuP- T3_3553#IST-SL2_4209#J82_3439#JEG-3_4687#KALS- l_3827#KLE_3729#KNS-42_389 l#KNS-81 -FD_3704#KP-N- S 19s_4031#LB771 -HNC_3390#MDA-MB-157_3714#MDA- MB-361_4431#MDA-MB-415_3718#MEL-HO_4973#MFE- 280_3618#MG-63_4544#MHH-ES-

1_3569#MKN 1_3567#MKN28_3619#MPP-89_3606#MZ1 -

PC_4995#NB10_3790#NB7_3774#NCI-H128_3423#NCI-

H 1666_4309#NCI-H 1838_4290#NCI-H 1975_3716#NCI-

H2009_3428#NCI-H2081_4341#NCI-H209_3380#NCI-

H2107_3667#NCI-H2122_3441 #NCI-H2126_3400#NCI-

H2452_3585#NCI-H460_3979#NCI-H526_4337#NCI-

H64_435 l#NEC8_4236#NOMO- 1_4047#OS-RC-

2_4216#PANC-03-27_3655#PC-14_4279#RCM-l_4950#RF-

48_3579#RH-1_3801#SCC-15_3566#SCC-

9_3557#SF539_3980#SK-MEL-5_4009#SNU-

449_3913#SW1573_4310#SW684_3887#SW872_3851#TE- l_3765#TGW_4081#U-2-OS_3844#VMRC-LCP_3771#A3-

KAW_3562#A498_4002#ACN_3992#ARH-77_4997#BB30-

HNC_3383#BCPAP_3646#BT-549_3943#CAL-

120_3816#CAL-62_3758#Caov-4_3814#Capan-

2_3552#COLO-741_3874#COR-L96CAR_3744#EGI-

1_4018#EKVX_4697#EW- 12_3804#EW-

22_3735#FADU_4715#HCC1143_3402#HEC-1_3573#HGC-

27_3622#HN_4569#HuP-T4_3589#IGROV-l_3990#IMR-

5_4052#KE-37_4079#KMS-12-PE_4075#KNS-

62_422 l#KOSC-2_4565#KP-N-

YS_3725#KU812_4664#KYSE-520_3698#LK-

2_4429#LOXIMVI_3936#LS 1034-PBL_3446#LU- 134-

A_4195#M14_3924#MDA-MB-231_3957#MEG-

01_4635#MHH-NB-l l_4093#MIA-PaCa-

2_3885#MKN7_367 l#MOLT-4_3956#NCI-

BL2087_3406#NCI-H1105_4441#NCI-H1155_4952#NCI-

H 1355_4439#NCI-H 1417_4944#NCI-H 146_4505#NCI-

Hl 618_3689#NCI-H2087_3389#NCI-H2171_3999#NCI-

H2405_4345#NCI-H250_3661#NCI-H322M_4661#NCI-

H727_4339#NCI-H810_3683#NCI-SNU-

5_4669#N Y_4519#OCI-AML2_4064#OVCAR-

5_3926#RL95-2_3663#R082-W-

1_3676#RTSG_4991#RXF393_3987#SBC-

5_3703#SiHa_3705#SNB 19_4004#SNU-Cl_3895#SNU-

C2B_3901#SW626_3884#T47D_3971#TE-5_3781#TE-

6_3760#TE-9_3806#VMRC-MELG_3756#YAPC_4024#8-

MG-BA_3893#8505C_3690#ES6_3798

CNTNAP 237 ALL-PO_3996#BC-3_4230#CCF-STTG1_3880#D- 2,305 2 392MG_3614#DMS-

273_4238#GAMG_3865#HCC2218_3395#HCE-

T_4531#HLE_4269#HT-3_5008#JAR_4940#KU-19-

19_4280#LC-1F_4261#LP-1_4693#NB 13_3768#NCI-

H596_4344#SK-LMS-1_4642#SW948_4599#UACC-

257_4994#A2058_4313#A253_5000#BT-474_3712#COLO-

775_4030#COR-L105_3742#COR-L279_4273#COR-

L51_4253#DB_4217#DBTRG-05MG_3838#DoTc2-

4510_4289#EFE- 184_3662#ETK-

1_4550#GCT_4958#HCC1937_3429#HSC-3_4964#HTC- C3_370 l#KATOIII_4684#KP-4_4232#KYSE-410_4213#L- 540_4538#LAN-l_4077#LC-2-ad_4247#LS-123_3908#LS- 513_4539#MCF7_4622#MRK-nu-l_3586#NB 17_3807#NCI- H 1299_4266#NCI-H 1581 _4297#NCI-H 1623_4293#NCI- HI 755_3593#NCI-H 1770_3420#NCI-H2052_3374#NCI-

H2141_4957#NCI-H2342_4234#NCI-H835_3791#NCI-

H889_3591#OC-314_4554#PC-3_3978#SHP-77_4328#SK-

MEL-24_4993#SK-MEL-2_3940#SK-N-DZ_3875#SK-NEP-

1_3904#SNB75_3976#SW756_4988#UACC-

62_3988#UACC-812_4967#22RV1_3672#BEN_3743#BFTC-

909_3786#Ca-Ski_4675#CA46_4657#CAKI-l_3921#Caov-

3_3853#CHL-l_3559#CHP-134_3854#COLO-

680N_3824#COLO-684_3599#COLO-720E_3842#CP50-

MEL-B_3410#D-397MG_3654#D-423MG_3700#D-

502MG_3680#D-556MED_3657#DEL_3570#DMS-

79_4527#EB2_4037#ECC 10_3568#ECC 12_360 l#EFO-

21_4574#EPLC-272H_4559#ES7_3813#G-

402_3864#GAK_3571#GI-ME-N_4041#GMS-10_4668#GR-

ST_4051#HA7-RCC_4667#HCC2157_3403#HEL_4090#Hs-

578-T_3930#HT55_4542#IA-LM_4623#IPC-298_3623#IST-

MES 1_3596#IST-SL1_3651#K-

562_3955#KLE_3729#KMOE-2_4083#KP-N-S 19s_4031#L-

428_4535#LAMA-84_4698#LB2241 -RCC_3422#LB771 -

HNC_3390#MDA-MB-175-VII_4425#MEL-HO_4973#MG-

63_4544#MKN1_3567#MMAC-SF_3710#MZ1-

PC_4995#MZ7-mel_3453#NB5_3782#NBsusSR_3647#NCI-

H 1693_4305#NCI-H 1694_4308#NCI-H 1975_3716#NCI-

H1993_4354#NCI-H209_3380#NCI-H2107_3667#NCI-

H2291_3688#NCI-H23_3946#NCI-H460_3979#NCI-

H510A_3653#NCI-H526_4337#NCI-H661_4348#NCI-

H774_3674#NEC8_4236#OS-RC-2_4216#PC- 14_4279#RH- l_3801#RPMI-7951_4654#Saos-2_3879#SCC-4_3595#SCC-

9_3557#SCH_3582#SK-HEP-1_4639#SK-MEL-

3_3577#SNU-

449_3913#SW1573_4310#SW403_3834#T84_4606#T98G_38

90#TGW_4081#TT_3805#U-2-OS_3844#UMC-

11_4301#VMRC-LCP_3771#786-

0_3969#A498_4002#BCPAP_3646#BHT-101_3793#BxPC-

3_3797#Capan-2_3552#CaR-l_3708#COLO-320-

HSR_4553#COR-L96CAR_3744#D-566MG_3699#DU-

145_3961#EGI-1_4018#EoL- 1 -cell_4080#FTC-

133_4288#HCC 1143_3402#HCE-4_3719#HGC-

27_3622#HMV-II_4624#IGROV-1_3990#KYSE-

270_4274#KYSE-450_4275#KYSE-520_3698#LAN-

5_4060#LB831-BLC_3388#LCLC-97TM1_3675#LU-

135_4223#LU- 139_4276#M 14_3924#Malme-

3M_3928#MDA-MB-231_3957#MDA-MB-435_3938#MHH-

NB-l l_4093#MIA-PaCa-2_3885#MKN45_3641#NCI-

H 1155_4952#NCI-H 1417_4944#NCI-H2171 _3999#NCI-

H2196_3610#NCI-H2227_4338#NCI-H2405_4345#NCI-

H250_3661#NCI-H295_4034#NCI-H508_3857#NCI-

H522_3920#NCI-H719_3728#NCI-H727_4339#NCI-

H810_3683#NCI-H82_4355#no-11_4712#OAW-

28_3694#OPM-2_4088#OVCAR-8_3997#RERF-LC-

MS_4233#RXF393_3987#SBC-5_3703#SCCH-

26_409 l#SF268_4000#SiHa_3705#SK-LU- 1_4326#SK-MEL-

28_3922#SNB 19_4004#SNU-

C1_3895#SW13_3831#SW620_3964#T47D_3971#TCCSUP_

3871#TE-11_3787#TE-15_4972#TE-5_3781#TE-

9_3806#TGBC 1 TKB_4087#TK 10_4008#U- 118-

MG_3881#U-87-MG_3763#UM-UC-3_3998#VMRC-

MELG_3756#YAPC_4024#CP66-

MEL_3437#ES6_3798#HCC1395_3394 KIAA168 236 CAPAN-1_3668#DMS-273_4238#HCE- 1,474 0 T_4531#HLE_4269#HT-

3_5008#HuO9_4528#JAR_4940#LC-lF_4261#NCI- H1792_4298#ONS-

76_4607#RCC 10RGB_4271#S W948_4599#UACC- 257_4994#A253_5000#A375_4643#A673_3915#AC0912_43

00#ATN-l_4651#AU565_4240#Becker_4548#BPH- l_3652#Calu-6_4277#COLO-775_4030#COLO- 829_3424#COR-L105_3742#DoTc2-4510_4289#EFE- 184_3662#ETK-l_4550#GCT_4958#Gp2D_4552#HSC- 3_4964#HT-1197_3850#HuH-7_4226#HuO- 3N1_4945#HUTU-80_4984#KATOIII_4684#KM- H2_456 l#KP-4_4232#KYSE-410_4213#LAN- l_4077#LNCaP-Clone-FGC_4649#LS- 174T_3916#LXF- 289_4281#MCF7_4622#MDA-MB- 468_4287#NB 17_3807#NCI-H1437_3435#NCI- H1581_4297#NCI-H1648_4312#NCI-H2141_4957#NCI- H2228_3820#NCI-H345_4962#NCI-H747_4537#NCI- H889_3591#NCI-SNU-l_4986#OC-314_4554#OCUB- M_4250#OE33_4228#OVCAR-4_3977#PC- 3_3978#PSN1_4268#RPMI-8226_4628#SAS_3574#SHP- 77_4328#SK-NEP-1_3904#SNB75_3976#SNU- 475_3861#SW756_4988#SW837_3837#UACC- 62_3988#UACC-812_4967#YKG- 1_4987#23132- 87_3550#A549_4999#AGS_3584#AM-38_3845#BC- l_4673#BFTC-909_3786#Ca-Ski_4675#Calu-3_3575#Caov- 3_3853#COLO-205_4688#COLO-680N_3824#COLO- 800_4701#DJM-1_3604#DOK_3588#ECC10_3568#EPLC- 272H_4559#ES7_3813#G-361_4658#GB-1_3872#GI- 1_3852#GI-ME-

N_404 l#GP5d_4934#HCC 1599_3375#HCC70_4257#HO- 1 - N-1_3664#HPAF-II_3612#HSC-4_3551#HT- 29_3963#J82_3439#JEG-3_4687#KALS-1_3827#KARPAS- 422_4512#KNS-42_3891#LB2241-RCC_3422#LB647- SCLC_3414#LB771-

HNC_3390#LoVo_3839#M059J_3738#MDA-MB- 157_3714#MG-63_4544#MMAC-SF_3710#MZ2- MEL._3825#NCI-H 128_3423#NCI-H 157_4303#NCI- H 1693_4305#NCI-H 1838_4290#NCI-H 1975_3716#NCI- H1993_4354#NCI-H2081_4341#NCI-H209_3380#NCI- H2107_3667#NCI-H2126_3400#NCI-H2330_3560#NCI- H2452_3585#NCI-H526_4337#NCI-H630_3846#NCI- H64_4351#NCI-H661_4348#NOS-1_3707#OS-RC- 2_4216#PANC- 10-05_3669#PC- 14_4279#RF-48_3579#RH- 18_3740#RH-1_3801#SCH_3582#SF539_3980#SK-HEP- 1_4639#SW1417_3863#SW1990_3894#SW403_3834#SW78

0_3902#SW982_3609#T84_4606#T98G_3890#VA-ES- BJ_3972#VMRC-LCP_3771#A3-

KAW_3562#A498_4002#ACN_3992#BT-20_4218#BT- 549_3943#BxPC-3_3797#CAL-39_3706#CAL- 62_3758#Capan-2_3552#CaR-l_3708#COLO-320- HSR_4553#D-566MG_3699#EKVX_4697#EW- 7_3748#FADU_4715#GCIY_3565#HCC1143_3402#HCT- 116_3962#HEC-l_3573#HGC-27_3622#HMV-II_4624#HOP- 92_4671#HuH-28_3721#ITO-II_3702#K052_4677#KMS-12- BM_4098#KNS-62_4221#KOSC- 2_4565#KU812_4664#KYSE-270_4274#KYSE- 450_4275#KYSE-520_3698#LAN-5_4060#LK- 2_4429#LOXIMVI_3936#LU-165_4286#M14_3924#MDA- MB-435 3938#MFH-ino 4928#MIA-PaCa- 2_3885#MKN45_3641#MKN7_3671#MOLT-4_3956#NCI-

ADR-RES_3984#NCI-H1355_4439#NCI-H1650_4292#NCI-

H2171_3999#NCI-H250_3661#NCI-H508_3857#NCI-

H727_4339#NCI-H748_4932#NCI-H810_3683#NCI-

N417_4331#NY_4519#OAW-28_3694#OVCAR-

8_3997#P12-ICHIKAWA_4084#RERF-LC-

MS_4233#RXF393_3987#S-117_4282#SBC-1_3665#SBC-

5_3703#SiHa_3705#SKM-l_4025#SNB 19_4004#SNU-

C1_3895#SNU-

C2B_3901#SW13_3831#SW620_3964#SW900_3583#T47D_

3971#TCCSUP_3871#TE-10_3784#TE-12_3761#TE- 15_4972#TE-6_3760#TE-8_3767#TE-9_3806#UM-UC- 3_3998#VM-CUB-1_4245#YH-

13_3981#YT_4941#8505C_3690#CP66-MEL_3437#CP67- MEL_3736#ES6_3798#SK-MES-1_4323

MAGI2 219 BC-3_4230#CAPAN-1_3668#COLO-679_4711#DMS- 1,436

273_4238#GAMG_3865#HCC1569_4259#HLE_4269#HUH-

6-clone5_4215#LC- 1 F_4261 #LP- 1 _4693#NB 13_3768#NCI-

Hl 792_4298#NCI-H596_4344#SK-LMS - l_4642#SW948_4599#U-698-M_4615#A2058_4313#BL-

41_4095#COLO-829_3424#COR-

L279_4273#DB_4217#DBTRG-05MG_3838#DoTc2-

4510_4289#EFE- 184_3662#EFM-

19_4564#ES3_3741#ES8_3757#GCT_4958#HSC-

2_4525#HSC-3_4964#HTC-C3_3701#KP-4_4232#KYSE-

410_4213#L-540_4538#LC-2-ad_4247#MCF7_4622#MDA-

MB-468_4287#MRK-nu-l_3586#NB 17_3807#NCI-

Hl 623_4293#NCI-H 1755_3593#NCI-H 1793_4206#NCI-

H2052_3374#NCI-H441_4937#NCI-H446_4347#NCI-

H69_4434#NCI-H835_3791#OE33_4228#OVCAR-

4_3977#PC-3_3978#RPMI-8226_4628#RVH-

421_3561#SAS_3574#SF295_3929#SJRH30_3883#SK-MEL-

2_3940#SK-N-DZ_3875#SK-NEP-

1_3904#SNB75_3976#SNU-423_4251#UACC-62_3988#ZR-

75-30_4714#22RVl_3672#8305C_3794#AM-38_3845#Calu-

3_3575#Caov-3_3853#CHL-l_3559#COLO-792_3615#D-

397MG_3654#Daoy_3898#DEL_3570#EB2_4037#EC-GI-

10_4526#EPLC-272H_4559#GMS-

10_4668#HCC2157_3403#HCC38_3392#HEL_4090#HO-1-

N-l_3664#HPAF-II_3612#Hs-578-T_3930#HT-

144_3617#HT55_4542#HuCCTl_3590#IA-LM_4623#IGR-

1_3564#IPC-298_3623#IST-MES 1_3596#IST-SL1_3651#K-

562_3955#KLE_3729#KNS-42_3891#L-363_4949#LAMA-

84_4698#LB2241-RCC_3422#LB373-MEL-

D_3427#M059J_3738#MC116_4524#MDA-MB-

361 _4431 #MD A-MB -415_3718#MFE-280_3618#MG-

63_4544#MKN1_3567#MMAC-SF_3710#MZ1-

PC_4995#NCI-H 1092_4428#NCI-H 157_4303#NCI-

Hl 694_4308#NCI-H 1975_3716#NCI-H2009_3428#NCI-

H2107_3667#NCI-H2126_3400#NCI-H2170_4342#NCI-

H2291_3688#NCI-H2452_3585#NCI-H520_4975#NCI-

H526_4337#NOMO-1_4047#OS-RC-2_4216#PC-

14_4279#RERF-LC-FM_3692#RH- 18_3740#RH-

1_3801#RPMI-7951_4654#SCC-

4_3595#SCH_3582#SF539_3980#SK-HEP-1_4639#SK-MEL- 1_362 l#SNU-449_3913#SR_4006#SUP- T1_4295#SW1417_3863#SW780_3902#SW872_3851#TE- 1_3765#TGW_408 l#U-2-OS_3844#UMC-l 1_4301#VMRC- LCP_3771#786-0_3969#ACN_3992#BB30- HNC_3383#BCPAP_3646#BHT-101_3793#BxPC- 3_3797#CAL-85-l_3812#Capan-2_3552#CaR-l_3708#COR-

L96CAR_3744#CRO-AP5_4543#D-566MG_3699#EGI-

1_4018#EKVX_4697#FTC- 133_4288#HCC 1143_3402#HEC- l_3573#HGC-27_3622#HMV-II_4624#IGROV-

1_3990#IMR-5_4052#KGN_3644#KP-N-YS_3725#KYSE-

270_4274#LB831-BLC_3388#LCLC-97TM1_3675#LS-

411N_3835#LU- 134-A_4195#LU- 135_4223#LU-

65_4436#M14_3924#Malme-3M_3928#MDA-MB-

435_3938#MHH-NB-

11_4093#MKN7_3671#NB 16_3829#NCI-ADR-

RES_3984#NCI-H 1105_4441 #NCI-H 1417_4944#NCI-

H2227_4338#NCI-H2405_4345#NCI-H250_3661#NCI-

H322M_4661#NCI-H522_3920#NCI-H719_3728#NCI-

H727_4339#NCI-H82_4355#no-l l_4712#OPM-

2_4088#OVCAR-8_3997#RERF-LC-

MS_4233#RXF393_3987#SBC-5_3703#SCCH-

26_409 l#SF268_4000#SiHa_3705#SK-LU- 1_4326#SK-MEL-

28_3922#SK-MEL-

30_3602#SN12C_3919#SNB 19_4004#SW13_3831#SW626_3

884#SW900_3583#T47D_3971#TE-

9_3806#TGBC24TKB_4078#TK10_4008#TUR_4659#U-118- MG_3881#U-87-MG_3763#UM-UC-3_3998#VM-CUB- 1_4245#VMRC-MELG_3756#YAPC_4024#ES6_3798#HT- 1376_3848#SK-MES-1_4323

LRP1B 217 CAPAN-l_3668#CAS-l_4965#HUH-6- 1,900 clone5_4215#HuO9_4528#KYSE-70_4246#LC-

1F_4261#ONS-76_4607#RMG-I_4960#SW948_4599#UACC-

257_4994#A 101 D_4306#A2058_4313#A253_5000#A375_46

43#ATN-l_4651#Becker_4548#CAL-12T_4626#CAL-

33_4947#Calu-6_4277#CMK_3995#D-263MG_3679#D-

336MG_3650#DMS-114_4227#DoTc2-4510_4289#EFE-

184_3662#EFM- 19_4564#ES5_3733#HD-MY-Z_4575#HSC-

2_4525#HSC-3_4964#HTC-C3_3701#HuH-7_4226#HuO-

3Nl_4945#KATOIII_4684#KP-4_4232#LAN-

1_4077#MCF7_4622#MDA-MB-468_4287#ME-

180_5005#MEL-JUSO_3605#NCI-H 1299_4266#NCI-

H1563_4211#NCI-H1573_4291#NCI-H1581_4297#NCI-

Hl 623_4293#NCI-H 1755_3593#NCI-H 1770_3420#NCI-

H1793_4206#NCI-H2030_4239#NCI-H2141_4957#NCI-

H2228_3820#NCI-H2342_4234#NCI-H28_4650#NCI-

H69_4434#NCI-H889_3591#OC-

314_4554#OE33_4228#OVCAR-

3_3935#PSN1_4268#RD_3892#SHP-

77_4328#SJRH30_3883#SK-PN-

DW_3867#SNB75_3976#UACC-62_3988#UACC-

812_4967#UACC-893_4299#ZR-75-30_4714#639-

V_3587#8305C_3794#A704_3897#AGS_3584#AM-

38_3845#BEN_3743#BHY_3658#C2BBel_3860#Caov-

3_3853#CGTH-W-l_3739#CHL-l_3559#COLO-

680N_3824#COLO-824_3788#D-397MG_3654#D-

502MG_3680#EB2_4037#EC-GI- 10_4526#EFO-

21_4574#EPLC-272H_4559#G-361_4658#GB-1_3872#GI-

1_3852#HCC2157_3403#HCC38_3392#HCC70_4257#HCT-

15_3954#HOP-62_3975#HPAF-

II_3612#HuCCTl_3590#IGR-l_3564#IST-MES l_3596#JEG-

3_4687#KINGS-1_4572#KNS-42_3891#LAMA-

84_4698#LB771 -HNC_3390#LB996-

RCC_3401#M059J_3738#MDA-MB-157_3714#MDA-MB-

361_4431#MDA-MB-415_3718#MDA-MB-453_4502#MFE-

280_3618#MKN28_3619#NB 12_3776#NB7_3774#NBsusSR _3647#NCCIT_4653#NCI-H 1092_4428#NCI-

Hl 28_3423#NCI-H 157_4303#NCI-H 1694_4308#NCI-

H2122_3441 #NCI-H2126_3400#NCI-H2170_4342#NCI-

H460_3979#NCI-H520_4975#NCI-

H661_4348#NEC8_4236#NOS-1_3707#PC-14_4279#PLC-

PRF-5_3695#RH-1_3801#RPMI-7951_4654#SCH_3582#SK-

CO-l_4689#SK-MG-

1_4946#SW1417_3863#SW1573_4310#SW780_3902#SW98

2_3609#TGBCl lTKB_3556#U-2-OS_3844#UMC-

11_4301#VMRC-LCP_3771#A3-KAW_3562#B2-

17_4089#BT-20_4218#BT-549_3943#BxPC-3_3797#CAL-

85-l_3812#Caov-4_3814#CaR-l_3708#CHP-126_3967#D-

247MG_3660#D-566MG_3699#ECC4_4936#EGI-

1_4018#EW-22_3735#EW-

7_3748#FADU_4715#GCIY_3565#H4_3843#HCE- 4_3719#HCT-116_3962#HEC-l_3573#HGC-27_3622#ITO- II_3702#KNS-62_4221#KU812_4664#KYSE- 270_4274#KYSE-450_4275#KYSE-520_3698#LB 1047- RCC_3970#LOXIMVI_3936#LU- 135_4223#LU- 139_4276#Malme-3M_3928#MC-IXC_4019#MEG- 01_4635#MHH-NB-11_4093#MKN7_3671#NCI- H1304_3713#NCI-H146_4505#NCI-H522_3920#NCI- H719_3728#NCI-H748_4932#NCI-H82_4355#NCI- H838_4350#NCI-N417_4331#NY_4519#OAW- 28_3694#OVC AR-5_3926#OVC AR-8_3997#P 12- ICHIKAWA_4084#PANC-08- 13_3681#RERF-LC- MS_4233#SBC-5_3703#SF268_4000#SK-MEL- 28_3922#SN 12C_3919#SNB 19_4004#SNU- C1_3895#T47D_3971#TE-11_3787#TE-15_4972#TE- 6_3760#TE-

9_3806#TGBC 1 TKB_4087#TGBC24TKB_4078#TK10_4008

#TUR_4659#U251_3994#UM-UC-3_3998#VM-CUB- 1_4245#YH-13_3981#8-MG-BA_3893#HCC1395_3394#SK- MES-1_4323

DLG2 208 BC-3_4230#D-392MG_3614#DMS-273_4238#GA-10-Clone- 2, 173

20_4570#GAMG_3865#HCC1569_4259#HCE-

T_4531#HLE_4269#HT-

3_5008#HuO9_4528#J AR_4940#KU- 19-19_4280#LP-

1_4693#MUTZ- 1_4662#NB 13_3768#RCC 10RGB_4271#SK-

LMS-l_4642#SW962_4201#U-698-

M_4615#A253_5000#A673_3915#BPH- 1_3652#CAL-

12T_4626#CMK_3995#COLO-

775_4030#DB_4217#DSH 1 _4963#EFM- 19_4564#ETK- 1_4550#EW- 13_3745#EW-

1_3815#GCT_4958#HCC1806_4283#HCC1954_3443#HCC2

157-BL_3451#HD-MY-Z_4575#HSC-2_4525#HT-

1197_3850#HTC-C3_3701#HuO-

3N1_4945#KATOIII_4684#KG-1_4645#L-540_4538#LXF-

289_4281#MCF7_4622#MDA-MB- 134-VI_3607#ME-

180_5005#MFE-296_3592#MRK-nu-

1_3586#NB 17_3807#NCI-H1395_3399#NCI-

H1437_3435#NCI-H1573_4291#NCI-H2030_4239#NCI-

H2052_3374#NCI-H2141_4957#NCI-H2228_3820#NCI-

H2342_4234#NCI-H28_4650#NCI-H441_4937#NCI-

H446_4347#NCI-H716_4704#NCI-

H747_4537#OE33_4228#OVCAR-3_3935#RPMI-

8226_4628#RVH-421_3561#SAS_3574#SCLC-

21H_4956#SJRH30_3883#SK-MEL-2_3940#SK-PN-

DW_3867#SNB75_3976#TYK-nu_4603#WERI-Rb-

1_4620#YKG-1_4987#639-V_3587#A172_3859#BFTC- 909_3786#CAKI-l_3921#Calu-3_3575#Caov-

3_3853#CGTH-W-l_3739#CHL-l_3559#COLO-

668_3773#COLO-800_4701#COR-L23_4214#D-

502MG_3680#DMS-79_4527#ECC 12_3601#EPLC-

272H_4559#ES7_3813#G-361_4658#GR-

ST_4051#HCC2157_3403#HOP-62_3975#HPAF-

II_3612#Hs-578-T_3930#HT-144_3617#HT-

29_3963#HT55_4542#IA-LM_4623#IGR-1_3564#IST-

MEL1_3611#IST-MES 1_3596#J82_3439#JEG-

3_4687#KALS - 1_3827#KLE_3729#LB2241 -

RCC_3422#LB373-EBV_3398#LB373-MEL-D_3427#LS-

1034_3431 #MD A-MB - 157_3714#MD A-MB -

361 _4431 #MD A-MB -415_3718#MEL-

HO_4973#MKNl_3567#MMAC-

SF_3710#NBsusSR_3647#NCCIT_4653#NCI-

H 1092_4428#NCI-H 128_3423#NCI-H 157_4303#NCI-

Hl 666_4309#NCI-H 1693_4305#NCI-H23_3946#NCI-

H460_3979#NCI-H630_3846#NEC8_4236#OS-RC-

2_4216#PANC-03-27_3655#Saos-2_3879#SCC-

4_3595#SCC-9_3557#SF126_4938#SF539_3980#SK-MEL-

5_4009#SK-MG- 1_4946#SNU-

387_3903#S W 1417_3863#S Wl 990_3894#S W403_3834#S W

684_3887#TT_3805#U-2-OS_3844#VA-ES-BJ_3972#647-

V_3778#A498_4002#ACN_3992#BT-20_4218#BxPC-

3_3797#CaR-l_3708#COR-L96CAR_3744#DU-

145_3961#EKVX_4697#GCIY_3565#HCC 1143_3402#HEC- l_3573#HGC-27_3622#HMV-II_4624#HuH-

28_3721#K5_3686#KYSE-

450_4275#LOXIMVI_3936#Malme-3M_3928#MDA-MB-

435_3938#MEG-01_4635#MKN45_3641#NB 16_3829#NCI-

ADR-RES_3984#NCI-H 1105_4441 #NCI-H 1417_4944#NCI-

H 1618_3689#NCI-H2171 _3999#NCI-H322M_4661 #NCI-

H522_3920#NCI-H748_4932#NCI-N417_4331#no-

10_3944#OPM-2_4088#OVCAR-5_3926#RXF393_3987#S-

117_4282#SBC-5_3703#SF268_4000#SIMA_4026#SK-LU-

1_4326#SK-MEL-28_3922#SK-MEL-30_3602#SK-MM-

2_4017#SK-N-

AS_3900#SW13_3831#SW620_3964#SW900_3583#T47D_3

971#TE-11_3787#TE-15_4972#TE-5_3781#TE-

9_3806#TGBC24TKB_4078#TK10_4008#UM-UC-

3_3998#VM-CUB-1_4245#VMRC-MELG_3756#8-MG-

BA_3893#HCC1395_3394#SK-MES-1_4323

Many cancer cell lines have extensive in vitro passage histories and therefore may accumulate additional mutations associated with extended laboratory propagation. Cancer cell lines, many of which have defective DNA repair machinery, are particularly susceptible to genetic alterations that confer growth or survival advantages under conventional tissue culture conditions. In order to evaluate whether cancer lines contain greater frequencies of translocation mutations, the gene-linked copy number breakpoints in primary cancer samples was assessed. First, the number of genes containing copy number breakpoints in the 20 paired primary prostate cancer samples was examined. The average value of 74 was significantly lower (t -test with P value <= 0.0001) than the average value (=462) of the five prostate cancer cell lines in the Sanger set.

However, the number for the 20 primary prostate cancer samples may be underestimated due to the low density of SNP array used. Next, a public data set from primary gastrointestinal stromal tumors (GIST) samples that were profiled on the same one million SNP array was examined. In the 25 GIST samples, the average number for the gene linked copy number breakpoint is 239, and it is lower but not significantly different from the average value (=310) of the 20 stomach cancer cell lines in Sanger's set (P > 0.01). In conclusion, based on the initial analysis, there is no significant difference of gene linked copy number breakpoints between primary cancer samples and related cancer cell line.

It was suggested that common chromatin structures at breakpoint cluster regions may lead to chromosomal translocations found in chronic and acute leukemias (Strick, Zhang et al. 2006). These chromatin structural elements include topo II and DNase I cleavage sites, scaffold attachment regions (SARs) and lowest free energy level sites. Such elements have previously been shown to co-localize with genomic breakpoints of chromosome translocation in leukemia, suggesting their potential involvement in nonhomologous recombination (Strick, Zhang et al. 2006); (Zhang and Rowley 2006). SARs, topo II and DNase I sites were found to be dispersed throughout the genome every 60-100kb. It is of interest whether these chromatin structural elements play a role in the progression of other cancer types. Incorporating the genomic positions of those sites together with the copy number breakpoints, will help in better defining the translocation events and delineating the underlying mechanisms. Recent reports in the New England Journal of Medicine demonstrated that the

ALK inhibitor crizotinib yielded a stunning overall response rate of 55% and an estimated 6 month, progression-free survival rate of 72% in NSCLC patients (Choi, Soda et al. 2010) (Kwak, Bang et al. 2010). Remarkably, it took less than three years from the finding of rearrangement of ALK in NSCLC to translate this into a clinic therapy, with the repositioning of an existing ALK inhibitor in development (Gerber and Minna 2010). This prompts the use of genome- wide analysis to identify new gene mutations, which will not only help us to identify potential novel targets for specific cancers in the context of personalized medicine, but also facilitate the repositioning of drugs either already on the market or in development for new purposes. Next-generation sequencing is likely powerful enough to detect different kinds of gene mutations, including new variant and fusion genes. However, generating the data, as well as performing correct gene mapping and alignment, are not trivial tasks and will take time to be practiced in the patient population. The analysis set forth herein demonstrates the utility of SNP array data as a complementary data set to assist in the identification of genetic translocations associated with the tumorigenesis process. High density SNP array profiles have been generated extensively in the past few years. Querying GEO pubic database (http://www.ncbi.nlm.nih.gov/geo/) alone for Affymetrix and Illumina 1 million SNP array profiles have identified -4000 samples, and most of them are cancer related. For The Cancer Genome Atlas project at NCI, the goal is to provide

comprehensive genomic characterization and sequencing to the research community on at least 3,000 new cancer cases by the fall of 2011, which includes high density SNP array profiling. The vast amount data provide us a great resource and opportunity to evaluate the known fusions: for their prevalence in a specific cancer type, as well as the presence and prevalence across different cancers. This type of data also can be used to predict novel fusions for oncogenes and to prioritize the fusion candidates to be validated experimentally. Recently shown by Berger et al., integrative analysis of transcriptomic and SNP array data indicates that there are clear changes in DNA copy number, with well defined breakpoints evident within both partner genes in six out of eight melanoma fusions (Berger, Levin et al. 2010). This further supports the utility of SNP array data in fusion gene identification. In conclusion, thousands of publicly available high-density SNP array datasets have provided useful information regarding genes with aberrant copy numbers. However, little attention has been paid to those genes containing copy number breakpoints, or at the border of a CNV. The data set forth herein, for the first time, demonstrates that genes with copy number breakpoints are represented at much higher level in cancer versus normal cells. References

The following references are hereby incorporated by reference in their entirety: Bastus, N. C, L. K. Boyd, et al. (2010). "Androgen-induced TMPRSS2:ERG fusion in nonmalignant prostate epithelial cells." Cancer Res 70(23): 9544-9548.

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Berger, M. F., M. S. Lawrence, et al. (2011). "The genomic complexity of primary

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Berger, M. F., J. Z. Levin, et al. (2010). "Integrative analysis of the melanoma

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Bioinformatics 22(23): 2950-2951.

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transcript in prostate tumor cells reflects TMPRSS2-ERG fusion status." Prostate

Cancer Prostatic Pis 13(1): 47-51.

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Curr Opin Hematol 15(4): 338-345.

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fusion is increased in moderate to poorly differentiated prostate cancers." J Clin

Pathol 60(11): 1238-1243.

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Shtivelman, E., B. Henglein, et al. (1989). "Identification of a human transcription unit affected by the variant chromosomal translocations 2;8 and 8;22 of Burkitt lymphoma." Proc Natl Acad Sci U S A 86(9): 3257-3260.

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undescribed salivary gland tumor entity." Am J Surg Pathol 34(5): 599-608. Soda, M., Y. L. Choi, et al. (2007). "Identification of the transforming EML4-ALK

fusion gene in non- small-cell lung cancer." Nature 448(7153): 561-566.

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rearrangement in human breast cancer genomes." Nature 462(7276): 1005-1010. Strick, R., Y. Zhang, et al. (2006). "Common chromatin structures at breakpoint cluster regions may lead to chromosomal translocations found in chronic and acute leukemias." Hum Genet 119(5): 479-495.

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Claims

CLAIMS What is claimed is

1. A method for diagnosing a patient suspected of having a gene translocation- associated cancer comprising (a) detecting the presence of a copy number variation breakpoint signature in a gene of a subject, wherein the presence of the signature in the gene is indicative of the subject having the gene translocation- associated cancer.

2. The method of claim 1, further comprising (b) determining the nucleic acid sequence of the gene containing the copy number variation breakpoint signature to confirm the presence of an associated gene translocation.

A method for treating a patient having a gene translocation-associated cancer, comprising: diagnosing the subject as having a gene translocation-associated cancer according to the method of claim 1 or 2; and administering to the subject a compound that inhibits the activity of the gene or a polypeptide encoded by the gene if said copy number variation breakpoint signature or said associated gene translocation is present.

A method for selecting therapy for a patient having a gene translocation- associated cancer, comprising: (a) determining whether said cancer exhibits a gene having a copy number variation breakpoint signature; and (b) if said cancer exhibits the gene having the copy number variation breakpoint signature, selecting for said patient a therapy that comprises the administration of a compound that inhibits the activity of the gene or a polypeptide encoded by the gene.

5. The method of claim 4, further comprising (c) determining the nucleic acid sequence of the gene containing the copy number variation breakpoint signature to confirm the presence of an associated gene translocation.

6. The method of any one of the preceding claims, wherein the copy number variation breakpoint signature is detected using a single nucleotide

polymorphism (SNP) array.

7. The method of any one of the preceding claims, wherein the gene translocation- associated cancer comprises a balanced translocation.

8. The method of any one of the preceding claims, wherein the gene translocation- associated cancer comprises an unbalanced translocation.

9. The method of any one of the preceding claims, wherein the copy number

variation breakpoint signature comprises a region of copy number variation within the boundary of the gene.

10. The method of any one of the preceding claims, wherein the copy number

variation breakpoint signature comprises a region of increased copy number flanked by copy number variation breakpoints.

11. The method of any one of the preceding claims, wherein the copy number

variation breakpoint signature comprises a region of decreased copy number flanked by copy number variation breakpoints.

12. The method of any one of the preceding claims, wherein the gene is an oncogene or a proto-oncogene.

13. The method of any one of the preceding claims, wherein gene is selected from the group consisting of FYN, MMEL1, RAB8A, VAV2, BRAF, ERBB2, ETV6, FLU, MET, NAE1, NTRK3, PVTl, RAB31, RAB3A, RAB40C, and THRB.

14. The method of any one of the preceding claims, wherein gene is selected from the group consisting of PVTl, THRB, AKT3, RAB3C, AKAP13, VAV2, ABL2, ERBB4, AKT2, NTRK3, ALK, VAV3, BRAF, KIT, BCL2, EGFR, ERG, ETV6, EWSR1, RET, RUNX1, FER, RAF1, ERBB2, MKRN2, RAB31„RAB5A, RAPGEF1, ETS1, MERTK, KRAS, RAB2A, CRKL, FYN, ABL1, EFCAB2, RAP1A, FLU, RAB40B, ROS1, VAV1, CSF1R, ERBB3, LYN, MYB, RAB28, RAB40C, TETl, FGFR10P2, RABIO, RABIA, RAB30, RRAS2, TET2, USP6, DEK, MET, RALA, RAP1B, SH3D19, TTC23, SRC, TAF8, ECT2, RAB22A, RAB4A, RAB7A, SKIL, TET3, THRA, TPR, ETS2, ETV7, HEXB, RAB18,

RAB27A, RAB38, RAB6A, RALB, TMEM50A, CDON, CSDE1, ENTPD5, MYBL1, NAE1, NTRK1, PDGFB, RAB17, RAB3B, RAB6B, RNASEH2A, SPAG9, SPIl, USP4, FGFRIOP, NDUFC2, PEA15, RABl lA, RAB14, RAB20, RAB23, RAB33B, RAB37, RABL4, SKI, SSPN, WNT3, CRK, ETV3,

FLJ10357, FOS, GLI1, GNB2L1, ISY1, KLF6, LCK, LYRM5, MAP3K8.

MMEL1, MYBL2, MYCL1, NRAS, PTK6, RAB12, RAB32, RAB35, RAB39, RAB43, RAB5C, RAB7L1, RAB8A, RAB8B, RABL3, RAP2A, SET, and TMED9.

15. The method of any one of the preceding claims, wherein gene is selected from the group consisting of ERBB4, FER, AKT3, ERG, ABL2, ALK, BCL2, EFCAB2, EGFR, ETS2, ETV6, ETV7, FGFRIOP, ISY1, NTRK3, PDGFB, PVT1, RABIA, RAB27B, RAB40B, RAB6B, RAB7A, RAF1, RAPGEF1, RUNX1, SET, TAF8, THRB, and TMEM50A.

16. An isolated nucleic acid comprising a gene fusion of a gene selected from the group consisting of FYN, MMEL1, RAB8A, VAV2, BRAF, ERBB2, ETV6, FLU, MET, NAE1, NTRK3, PVT1, RAB31, RAB3A, RAB40C, and THRB.

17. An isolated nucleic acid comprising a gene fusion of a gene selected from the group consisting of PVT1, THRB, AKT3, RAB3C, AKAP13, VAV2, ABL2, ERBB4, AKT2, NTRK3, ALK, VAV3, BRAF, KIT, BCL2, EGFR, ERG, ETV6, EWSR1, RET, RUNX1, FER, RAF1, ERBB2, MKRN2, RAB31„RAB5A, RAPGEF1, ETS1, MERTK, KRAS, RAB2A, CRKL, FYN, ABL1, EFCAB2, RAP1A, FLU, RAB40B, ROS1, VAV1, CSF1R, ERBB3, LYN, MYB, RAB28,

RAB40C, TETl, FGFR10P2, RAB10, RABIA, RAB30, RRAS2, TET2, USP6, DEK, MET, RALA, RAP1B, SH3D19, TTC23, SRC, TAF8, ECT2, RAB22A, RAB4A, RAB7A, SKIL, TET3, THRA, TPR, ETS2, ETV7, HEXB, RAB18, RAB27A, RAB38, RAB6A, RALB, TMEM50A, CDON, CSDE1, ENTPD5, MYBL1, NAE1, NTRK1, PDGFB, RAB17, RAB3B, RAB6B, RNASEH2A, SPAG9, SPIl, USP4, FGFRIOP, NDUFC2, PEA15, RABl lA, RAB14, RAB20, RAB23, RAB33B, RAB37, RABL4, SKI, SSPN, WNT3, CRK, ETV3,

FLJ10357, FOS, GLI1, GNB2L1, ISY1, KLF6, LCK, LYRM5, MAP3K8.

MMEL1, MYBL2, MYCL1, NRAS, PTK6, RAB12, RAB32, RAB35, RAB39, RAB43, RAB5C, RAB7L1, RAB8A. RAB8B, RABL3, RAP2A, SET, and TMED9.

18. An isolated nucleic acid comprising a gene fusion of a gene selected from the group consisting of ERBB4, FER, AKT3, ERG, ABL2, ALK, BCL2, EFCAB2, EGFR, ETS2, ETV6, ETV7, FGFRIOP, ISY1, NTRK3, PDGFB, PVT1, RAB1A, RAB27B, RAB40B, RAB6B, RAB7A, RAF1, RAPGEF1, RUNX1, SET, TAF8, THRB, and TMEM50A.

19. A method for detecting the presence of a chromosomal translocation in a tumor sample comprising detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the signature in the gene is indicative of a chromosomal translocation.

20. A method for identifying a gene containing a chromosomal translocation in a tumor sample comprising detecting the presence of a copy number variant breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as containing a chromosomal translocation.

21. A method for identifying a translocation gene fusion comprising detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as a translocation gene fusion.

22. A method for identifying a translocation gene fusion comprising detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as a gene deletion.

23. A method for identifying a translocation gene fusion comprising detecting the presence of a copy number variation breakpoint signature in a gene, wherein the presence of the copy number variant breakpoint signature in the gene identifies the gene as a gene amplification.

24. The method of any one of the preceding claims, wherein the gene is a tumor

suppressor gene.

25. The method of any one of the preceding claims, wherein gene is selected from the group consisting of RUNX3, HRPT2, FH, FHIT, RASSFIA, TGFBR2, VHL, hCDC4, APC, NKX3.1, Ρΐβ™⁴, P14^MF, PTC, TSC1, BMPR1, PTEN, WT1,

MEN1, ΡδΊ^², TIMP3, IGFBP, CDKN2A/pl6^INK4A, CDKN2B/pl5

P P1144^MF,, PP5533,, PP7733,, GGiSTP1, MGMT, CDH1, DAPK, MLH1, THBS 1, RB, CASP8, APAF1, and CTMP.