Ascertainment of Recurrent Translocations by Chromosomal Microarray Analysis

s 421 Detection and characterization of recurrent translocations play an important role in the diagnosis and treatment of hematological disorders. Chromosomal microarray analysis (CMA) is a powerful tool to detect copy number changes in hematological disorders. One of the limitations of CMA platforms currently in use is that truly balanced chromosome rearrangements cannot be detected. However, some chromosomal rearrangements have cryptic losses or gains at the breakpoints which may be detected by microarray. In addition, recurrent balanced translocations followed by gain or loss of one of the derivative chromosomes can be detected by CMA, and recurrent interstitial deletions resulting in gene fusions may also be detected by microarray. We reviewed over 50 cases where a high-density SNP-oligo microarray was used to detect chromosome aberrations in hematologic cases. The high density design combined with allele detection and good probe performance allowed for precise identificationofbreakpointson the rearrangedchromosomes,whichwas critical for detection and interpretation of the translocations. Many of the suspected recurrent translocations were also confirmed by FISH, which can potentially be used as markers in subsequent studies. Several cases will be discussed in detail in this study. Conflict of Interest: None. Evaluation of SureFISHtm DNA-FISH Probes for Validation of Array-CGH Aberrations Linda I. Barenboim, Jane Houldsworth Cancer Genetics, Inc., Rutherford, NJ Currently in a diagnostic setting, genomic copy number changes detected by array-CGH must be validated by an independent technique, most commonly FISH. Given the multiple aberrations observed in cancer genomes, SureFISH repeat-free oligonucleotide probes (Agilent Technologies) offer an alternative to BACbased probes with respect to cost and time, though their performance has as yet to be assessed on a variety of tissue types. We investigated the performance of three SureFISH combination probes on peripheral blood (PB), bonemarrow (BM), liquid biopsy cervical specimen (LBCS), and formalin fixed paraffin embedded (FFPE) breast tissue. Initially, hybridization conditions were optimized for each of the tissues based on a routine procedure used for BAC-based probes and the manufacturer’s recommendations. SureFISH ABL1 and BCR probes were hybridized to PB, BM (known to be positive for the ABL1/ BCR rearrangement), and FFPE where optimal signal quality and background were obtained using a 24-hour hybridization rather than 6-hour. Wash conditions were as recommended, with the exception of FFPE, where temperatures were decreased. Following the modifications, all hybridizations were considered acceptable for use in a clinical diagnostic setting despite the relatively smaller signal size compared with BAC-based probes. The second probe combination (chromosomes 13, 18, and 21) assessed was hybridized to PB, BM, and LBCS with similar findings. A custom probe for regions on chromosomes 3, 5, 7, and 20 was evaluated on PB and LBCS but optimization was required to balance probe concentrations with respect to signal strengths and fluorochrome. Hybridization signals could be accurately scored using an automated system. In conclusion, we have shown that SureFISH probes can be successfully used on a variety of specimen types that would be encountered in a clinical cytogenetics laboratory performing array-CGH, but requires some technical optimization. Conflict of Interest: The authors are employees of Cancer Genetics, Inc., Rutherford, NJ. The HEL Erythroleukemia Cell Line as a Test Case for Detailed Description of a Complex Karyotype by Combining SNP Array with Multiple FISH Approaches Ruth N. MacKinnon , Adrian Zordan , Meaghan Wall , Lynda J. Campbell a,b Victorian Cancer Cytogenetics Service, Melbourne, Australia; Department of Medicine, St. Vincent’s Hospital, University of Melbourne The HEL cell line is an erythroleukemia cell line that is used by many laboratories to study cell biology and differentiation. Several karyotypes have been published but these have many uncertainties. Using a combination of SNP array, array CGH, single locus FISH, multicolor FISH, and multicolor banding, we have produced a detailed karyotype which defines the breakpoints and structure of most of the abnormal chromosomes. We used SNP array data to identify the breakpoints of unbalanced translocations identified by M-FISH. Because the karyotype is very complex, there were still many ambiguities. Most of these could be clarified using M-BAND or locus-specific FISH probes selected using SNParray copy number data. Selected use of centromere probes identified the centromeres present in some abnormal chromosomes, including dicentric chromosomes. Using this combined approach we deduced that some complex rearrangements had occurred via the formation of dicentric chromosomes and subsequent breakage-fusion-bridge events. This included the production of a der(9) with concomitant amplification of JAK2, MLL, and the 20q11.2 region, which is amplified in some cases of del(20q) acute myeloid leukemia. B allele frequency data provided by SNP array enabled the aberrations involving different homologs of a chromosome to be distinguished in many instances. By combining SNP array data with various FISH techniques, karyotype abnormalities can be described more completely than by microarray alone. This approach takes advantage of advanced microarray karyotyping without losing information on translocation partners, dicentric chromosomes, and mechanisms of karyotype evolution that may be relevant to understanding cancer evolution in a research setting. Conflict of Interest: None. SESSION 2: SOLID TUMORS Analysis of Esophageal Adenocarcinoma Using Combined aCGH e SNP (CCMC v2+EA) Microarray Platform Ausaf Ahmad , Santhoshi Bandla , Tony E. Godfrey , M. Anwar Iqbal a Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY; Department of Surgery, University of Rochester, Rochester, NY; The James P. Wilmot Cancer Center, University of Rochester, Rochester, NY Esophageal adenocarcinoma (EAC) is one of the most common cancers with very poor survival rates. We applied custom designed aCGH e SNP microarray platform (4 180K, CCMC