Mutation Profiling of Clinical Tumor Samples Using Next Generation Sequencing

s 213 Mutation Profiling of Clinical Tumor Samples Using Next Generation Sequencing Liu Liu, Fengqi Chang, Erica Fang, Guangcheng Zhang, Yanchun Li, Marilyn M. Li Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA Cancers are complex genomic diseases caused by diverse genomic alterations. Identification of actionable somatic mutations in patient tumor tissue provides potential targets for therapeutic options, which could be difficult to achieve by conventional molecular techniques. Next Generation Sequencing (NGS) technologies allow sequencing numerous genes simultaneously and provide molecular profiling of cancer genomes. Our lab started offering Next Generation Sequencing (NGS) tests for clinical cancer diagnosis using Ampliseq Cancer Mutation Panel in December 2011. The initial mutation panel covers 749 mutations in 46 key cancer genes, followed by an update version covers 2855 mutations in 50 cancer genes, many of which are clinically actionable mutations that are of diagnostic, prognostic, and therapeutic significance. Since then, we have tested over 300 tumor samples from patients with various cancer types. We identified more than 300 mutations in 29 genes. The overall positive rate was over 65%. The most common tumor types tested were breast cancer, colon cancer, and lung cancer. TP53 gene is the most commonly mutated gene, in which 91 mutations were identified in different tumor samples. We also identified 31 KRAS mutations and predominately in colon cancer. In addition, we identified 36 mutations in PIK3CA with 50% of the mutations in breast cancer. These cancer mutation data have helped oncologists to determine appropriate personalized treatment strategies for their patients. Mutations common in one specific tumor type could be rare in other tumor types. For example, EGFR exon 19 deletion is common in NSCLC, but we detected this deletion in some of our breast and prostate cancers; these patients could benefit from anti-EGFR targeted therapies. Our experience demonstrates that with rigorous laboratory validation and an effective laboratory testing pipeline, NGS technology is an efficient and reliable tool for cancer mutation profiling. High Resolution Genomic Profiling of Metastatic Testicular Teratomas Karen J. Ouyang, Holli Drendel, Jadwiga Szymanska, Oscar Cummings, Lawrence Einhorn, Gail H. Vance Division of Diagnostic Genomics, Department of Medical and Molecular Genetics, Indiana School of Medicine, Indianapolis, IN, USA Testicular germ cell tumors (TGCT) are the most common malignancy in young males between the ages of 15 and 44, with increasing incidence in western industrial countries. Interestingly, the overall incidence has more than doubled over the past 50 years. Teratomas represent a subgroup of TGCTs with immense histologic diversity, consisting of well differentiated, mature tissues only or also including immature, fetal-like tissues. The pathogenic mechanism of this type of tumor remains elusive. To evaluate the genomic profile of this cohort of TGCTs, we performed high resolution SNP array analysis on ten adult metastatic testicular teratoma tumors. An average of 30 aberrations per tumor was observed. Segmental gains/losses with complex patterns were most common at chromosomes 1 and 12, and the X chromosome; while whole chromosome gains/losses were most frequently observed at chromosomes 3, 5, 8, 11, 13, 18, and 21. Furthermore, genomic regions showing loss of heterozygosity (LOH) were overrepresented at chromosomes 5, 9, 11, and 22. Here, we report a comprehensive genomic characterization of metastatic teratomas that may provide insight into the pathogenesis of TGCTs. Microarray Studies in Pediatric T-Cell Acute Lymphoblastic Leukemia/Lymphoma: A Report of Four Cases Jennifer N. Sanmann, Diane L. Pickering, Jadd M. Stevens, Warren G. Sanger Human Genetics Laboratory at the Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA Pediatric T-cell acute lymphoblastic leukemia/lymphoma (T-ALL) is an aggressive malignancy that accounts for nearly 10-15% of newly diagnosed ALL cases per year. Cytogenetic and fluorescence in situ hybridization (FISH) studies have identified recurrent genetic aberrations in pediatric T-ALL, which most commonly include rearrangements of the TCR gene loci and deletions of 6q and 9p. To date, few microarray studies have been reported in cases of pediatric T-ALL. Therefore, we performed microarray studies on bone marrow aspirations from four pediatric cases with confirmed diagnoses of T-ALL following conventional cytogenetic analysis and adjunct FISH testing (when requested). Microarray studies confirmed all abnormalities detected by cytogenetics and/or FISH, which included loss of 9p and rearrangement of 14q11.2 [TRA/TRD]. However, microarray studies also detected additional, significant aberrations in 2/4 (50%) cases. Specifically, microarray studies detected a complex abnormal clone further characterized by del(1p33) [STIL], del(11)(p12p13), and del(14q32.2) [BCL11B] in case 3 and an abnormal clone further characterized by del(7p21.2)x2 (IKZF1), del(9p21.3) [CDKN2A], and del(14q32.33) [IGH] in case 4. These findings suggest that consequential genetic changes are present in patients with pediatric T-ALL that cannot be identified using conventional cytogenetic and FISH methodologies. Thus, high-resolution molecular techniques, such as microarray, play a critical role in the improved delineation of clinically relevant genetic changes in patients with pediatric T-ALL.