Abstract 2570: An integrated germline analysis platform for comprehensive clinical cancer genomics.
Authors: Van Allen Eliezer M. , Wagle Nikhil , Keizun Adam , Kryukov Gregory , McKenna Aaron , Huang Franklin , Hiller Elaine , Rainville Irene , Auclair Daniel , Ambrogio Lauren , Gray Stacy , Joffe Steven , Getz Gad , Garber Judy , Garraway Levi 
Published: August 2014

Abstract
Background: In order to apply massively parallel sequencing for use in clinical oncology, we have created algorithms to identify clinically actionable somatic alterations within an individual patient's tumor exome. To fully implement comprehensive clinical sequencing for cancer patients, a parallel platform for analyzing germline genetic variants is necessary to identify 1) clinically relevant cancer risk, non-cancer disease risk, and pharmacogenomics variants, and 2) germline variants related to clinically relevant somatic alterations.
Methods: Databases consisting of genes known to undergo germline alterations that may inform disease risk or pharmacogenomic variation were created by review of publically available resources (e.g. Cancer Gene Census) and augmented with literature review and expert opinion. Whole exome sequencing of normal DNA from prospectively acquired individual patient germline samples was performed using established Broad Institute pipelines for hybrid capture and variant calling. Population frequencies of all non-synonymous variants represented in our clinical germline databases were assessed with Exome Variant Server data, and all variants were cross-referenced with published lists of possibly pathogenic germline variants (e.g. HGMD). Variants with a population frequency of less than 1% that were also present in our clinical germline databases were assigned for high priority review. Integration of germline alterations with somatic data was implemented by computationally searching for germline non-synonymous variants in somatically altered clinically actionable cancer genes or pathways of such genes. All findings were incorporated into a novel web-based decision support system to maximize interpretation access for clinical genetic specialists who determined final classification of the variants.
Results: Application of the germline analysis platform to whole exome sequencing data from twelve prospectively acquired clinical patient samples identified a median of 7 [range: 4-10] high priority germline variants warranting subsequent review from among thousands of variants per patient. Integrative analysis of one patient with EGFR mutant lung adenocarcinoma revealed a non-synonymous germline variant in EGFR at another site warranting further exploration.
Conclusions: Our germline analysis platform facilitates prospective clinical interpretation of germline genomic variants by prioritizing and representing alterations of potential clinical significance. The platform also integrates germline variants with clinically actionable somatic alterations for enhanced understanding of potential disease drivers at the individual patient level. Implementation of clinical cancer sequencing with germline analyses may directly impact patient care and deepen our understanding of the role of germline variants in cancer epidemiology.
Citation Format: Eliezer M. Van Allen, Nikhil Wagle, Adam Keizun, Gregory Kryukov, Aaron McKenna, Franklin Huang, Elaine Hiller, Irene Rainville, Daniel Auclair, Lauren Ambrogio, Stacy Gray, Steven Joffe, Gad Getz, Judy Garber, Levi Garraway. An integrated germline analysis platform for comprehensive clinical cancer genomics. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2570. doi:10.1158/1538-7445.AM2013-2570