SNP Array Analysis Detects Genomic Alterations Associated with High-Risk Disease in Neuroblastoma

s 423 SNP Array Analysis Detects Genomic Alterations Associated with High-Risk Disease in Neuroblastoma Karen J. Ouyang , Andres Morales , Gordana Raca , Susan L. Cohn b Departments of Medicine, University of Chicago, Chicago, IL; Pediatrics, University of Chicago, Chicago, IL Neuroblastoma is the most frequent extracranial malignant tumor of childhood. There is remarkable heterogeneity in its clinical presentation, where some tumors regress spontaneously and others progress relentlessly, even with intensive multimodal treatment. Currently, clinical and biologic markers are not sufficient for an accurate prediction of prognosis and response to therapy. Recent studies have shown that tumors with whole chromosome gains or losses have a good prognosis, whereas tumors with segmental imbalances have a poor prognosis. Here we present single nucleotide polymorphism (SNP) array analysis of 2 retrospective cases that were included in the low-risk group at diagnosis based on the accepted clinical-biological criteria, but eventually progressed and presented with metastatic relapse. SNP array results revealed high levels of segmental alterations in both samples. A total of 16 and 8 chromosomal breakpoints, respectively, were identified. The first case showed numerous segmental aneuploidies, including several specific abnormalities (11q rearrangement and duplication of 17q) previously correlated with progressive disease. In addition to regions of segmental aneuploidy, the second case showed striking segmental amplifications on chromosome 12q (with additional 18 chromosome breakpoints), including multiple genes (like CDK4 and MDM2) that have previously been implicated in cancer. Amplifications of the same regions of 12q have previously been noted in the literature as a rare but recurrent abnormality in neuroblastoma, associated with an aggressive phenotype. In both patients, the information about the unfavorable genomic profile may have been helpful in predicting recurrence. Together with previously published data, these cases illustrate how the genomic profile at diagnosis, which can be easily investigated using whole-genome array testing, provides important prognostic information in neuroblastoma, and could help to improve current therapeutic stratification schemes. Conflict of Interest: None. Recurrent Genetic Alterations in Hepatitis C-associated Hepatocellular Carcinoma Detected by CGH+SNP Array Yajuan Liu, Yang Zhou, Matthew Yeh University of Washington, Department of Pathology, Seattle, WA Hepatocellular carcinoma (HCC) is one of the most common malignant neoplasms and represents the third leading cause of cancer-related death worldwide. The incidence of HCC is increasing in theUnited States and Europe,mostly because of the high prevalence of HCV infection. Unlike DNA virus HBV that can be directly oncogenic and lead to HCC through integration of the viral genome into the host genome, HCV is a positive-strand RNA virus that replicates in the cytoplasm and has little potential for integration of its genome into host DNA. It is generally believed that the presence of cirrhosis determines the increased risk for HCC in individuals with HCV infection. To understand the underlying genetic alterations in HCV-associated HCC, microarray studies for characterization of DNA copy number alterations in the setting of cirrhosis have been conducted.We extracted DNA from FFPE tissues and used CCMC 180K CGH+SNP array to scan the whole genome for gene copy number gains and losses and LOH in 15 paired samples of HCV-infected HCC and 1 HCV and HBV coinfectedHCC. Both cancer tissues and nearby cirrhotic non-tumor tissues were processed for genetic characterization. Our results showed that, in general, gain of the long arm (q) of chromosome 1 was one of the most common aberrations observed. Some recurrent gains and losses of chromosomes and genes detected in 15 pairs of HCC and non-tumor tissues will be discussed. The genetic similarity between the tumor sampleswasevaluated using hierarchical clustering analysis of CGH data. The result showed that chromosomal abnormalities partitioned well with HCC and mostly not found in non-tumor tissue, whereas some aberrations at gene levelwere also found in non-tumor tissues. The implication of the findings in hepatocarcinogenesis and subtypingHCCbased on the underlying genetic cause will be discussed. Conflict of Interest: None. Validation of Karyotypic Abnormalities in Human Pluripotent Stem Cells: Cytogenetic Progression in WA09 Mirrors Cancer Benjamin S. Nisler , Seth M. Taapken , Kimberly Leonhard , Erik McIntire , Karen Dyer Montgomery a,b Cytogenetics Laboratory, WiCell Research Institute, Madison WI; Stem Cell and Regenerative Medicine Center, University of Wisconsin, Madison WI Human embryonic stem cell (hESC) line WA09 (H9) was karyotyped during long-term culture to assess cytogenetic stability. Chromosome analysis at passage 33 revealed an inverted duplication of chromosome 12p. At passage 71, the duplication of 12p was present in 2 copies, accompanied by trisomy 14 and an unbalanced translocation 15;17. This progression of abnormalities is similar to that observed in some hematologic cancers. CGH and SNP analysis, using Agilent’s SurePrint G3 Human Genome CGH+SNP Microarray Kit: 4x180K array, confirmed and further characterized the karyotypic abnormalities. In addition, a gain on chromosome5qwas identified in both early and late passages. At passage 71, a gain at 20q11.21 was seen. This CNV is reported to confer selective advantage to hESCs in long-term culture. Use of Agilent’s SureFISH probes resolved the rearrangements found in karyotype analysis and confirmed copy number variations found in CGH+SNPanalysis. SureFISHprobesETV6 confirmed the inverted duplication of 12p and TRIM52 showed that the gain at 5q was translocated to the abnormal 12p. The SureFISH probe for CASC3 on chromosome 17q confirmed an unbalanced translocation to chromosome15p andDNMT3BandMAPRE1on chromosome20q helped to define that copy number gain. Conflict of Interest: None. Genomic Loss of Heterozygosity (LOH) in Pediatric Ovarian Germ Cell Tumors (OGCT) Maxine J. Sutcliffe , Rudolfo Ortega , Doris P. Dumont , Hardeo Panchoosingh , Samuel Laden c All Children’s Hospital, St. Petersburg, FL; University of South Florida, Tampa, FL; St. Joseph’s Children’s Hospital, Tampa, FL