Abstract 3420: Integrative tumor profiling beyond panel sequencing
Authors: Lau Corine K. , Harley Alena S. , Choppa Paul , Cooc Janine , Kyshtoobayeva Ainura , Jun Natalia , Dayrit Mark , Delport Wayne , Saldivar Mark , Jun Yop , Trivedi Raaj , Gylfe Alexandra E. , Lacey Travis R. , Cohen Ezra , Bloom Kenneth , Shinbrot Eve 
Published: August 2019

Abstract
Introduction: Targeted cancer therapies rely on the identification of biomarkers specific to the tumors. Next generation sequencing (NGS) based genomic profiling has informed clinical decision making by identifying somatic alterations such as single nucleotide variants (SNVs), small insertion and deletion mutations (indels), structural variations, tumor mutation burden (TMB), and microsatellite instability (MSI) status. Here, we describe an integrative approach to characterize the genomic complexity of solid tumors using whole genome sequencing (WGS), whole exome sequencing (WES), whole transcriptome sequencing (RNAseq), and tumor only panel sequencing.
Methods: We report on WES for 84 paired tumor normal samples in a variety of tumor types including breast, colon, head and neck, melanoma, cervical, thyroid, glioblastoma, lung, pancreatic, prostate, appendiceal, cholangiocarcinoma, and kidney. A subset of these samples were also sequenced with high depth tumor only gene panel. WGS and RNAseq data were included in the analysis for additional 14 tumor normal pairs. Somatic alteration assessments included SNV, indels, MSI status, TMB, mutational signatures, copy number variations, gene fusions and structural variations.
Results: Analysis using tumor normal WES and RNAseq identified both clinically relevant genes as well as mutational processes. We found a high percentage of germline mutations were misidentified as somatic variants using tumor only panels, further highlighting the importance of paired tumor normal sequencing. In some cases, the putative driver gene or the variant in a cancer gene identified by WES was not included in panel sequencing. For example, mutations in FOXA1 gene were recently implicated as clinically relevant resistance and metastasis marker. Exome wide mutational signature analysis also identified BRCA (Cosmic sig 3) signature in tumors with no alterations in BRCA1/2 genes. WGS analysis and fusion gene detection revealed novel fusion genes as well as important structural alterations. Examples include a novel BRAF fusion in a cholangiocarcinoma devoid of other known driver mutations, a novel NTRK3 fusion partner in a glioblastoma tumor, and numerous tandem duplications in an ovarian cancer.
Conclusion: In contrast to tumor only gene panels, tumor and matched normal whole exome assay examines the entire coding portion of the genome without the limitations of a predefined gene list. This allows for detection of mutations in recently identified cancer drivers, ability to reliably distinguish somatic variants from clonal hematopoiesis or other germline variants, calculate genome wide mutational patterns including TMB, MSI, and identify the underlying mutational processes such as genomic signatures. The addition of WGS sequencing allows the identification of clinically relevant genomic rearrangements and novel structural variations.
Citation Format: Corine K. Lau, Alena S. Harley, Paul Choppa, Janine Cooc, Ainura Kyshtoobayeva, Natalia Jun, Mark Dayrit, Wayne Delport, Mark Saldivar, Yop Jun, Raaj Trivedi, Alexandra E. Gylfe, Travis R. Lacey, Ezra Cohen, Kenneth Bloom, Eve Shinbrot. Integrative tumor profiling beyond panel sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3420.