Abstract 5287: Heterogeneity of mutation calling and annotation: a survey of cancer next-generation sequencing initiatives by the Global Alliance for Genomics and Health (GA4GH)
Authors: Vis Daniel J. , Lewin Jeremy , Siu Lillian , Liao Rachel , Zenklusen Jean Claude , Calvo Fabien , Szepessy Edit , Vivancos Ana , Wirta Valtteri , Madhavan Subha , Park Keunchil , Tan Daniel , Laskin Janessa , Brammer Melissa , Dias-Neto Emmanuel , Tolcher Anthony , Hudson Thomas J. , Sawyers Charles , Lawler Mark , Voest Emile E. 
Published: July 2016

Although genomic data sharing is widely endorsed, practical barriers exist. For example, annotation and calling of mutations vary significantly with the method used. This poses clear challenges in data harmonization and sharing. In this setting, GA4GH conducted a survey of Cancer Next Generation Sequencing (NGS) initiatives globally to chart the technical implementation of genomic programs.

A total of 59 of 108 invited initiatives responded (response rate = 55%) via a web-based survey. In total, 63% of programs share their data, and 10% are partially sharing or planning to share. Most initiatives were North American (33%) or European (28%) based. Of the 59 respondents, 51 responded to queries on technical aspects of their NGS program (Table 1). For diagnostic application, 67% employ a small panel (&lt;50 genes), 55% a medium panel (50-250 genes), 45% a large panel (251-1000 genes); only 22% indicated they (also) use whole exome sequencing (WES). Diagnostic programs tend to favor panels and deep sequencing, while research programs favor WES/WGS. Overall, mutation and copy number calls were stored centrally in a single project database (96% and 92% respectively), with lower rates for raw data (BAM files, 86%) and histological data (75%). Somatic mutations were identified primarily via GATK (57%), Samtools (49%), Varscan (47%), MuTect (40%); all but 7 initiatives used combinations of these tools. Mutational variants were annotated by Cosmic (73%), PolyPhen (66%), and dbSnp (64%). Germline samples were used as control in only 62% of initiatives.

In conclusion, the majority of initiatives use an ensemble of tools for calling and annotating mutational variants. Harmonization efforts on gene panel composition and the standardization of tools (eg, methods, application program interfaces (APIs)) are urgently needed to prevent continued generation of isolated data silos that hamper NGS-enabled advances in precision medicine. Primary purpose of test% Diagnostic (n = 9)% Research (n = 22)% Diagnostic & Research (n = 20)OrganizationCentralized testing22%64%30%Unique sample identifiers89%77%70%Certification ISO/CLIA/NE88%45%65%Initiative &gt; 1000 Patients33%36%35%SequencingSequencing depth 50-250x0%55%80%Sequencing depth &gt;250x100%45%20%Panel sequencing89%68%60%Whole Exome/Genome Sequencing22%77%65%SamplesFresh frozen (FF)11%23%15%Formalin Fixed Paraffin Embedded (FFPE)44%27%20%FFPE or FF44%50%65%Germline as control22%68%65%

Citation Format: Daniel J. Vis, Jeremy Lewin, Lillian Siu, Rachel Liao, Jean Claude Zenklusen, Fabien Calvo, Edit Szepessy, Ana Vivancos, Valtteri Wirta, Subha Madhavan, Keunchil Park, Daniel Tan, Janessa Laskin, Melissa Brammer, Emmanuel Dias-Neto, Anthony Tolcher, Thomas J. Hudson, Charles Sawyers, Mark Lawler, Emile E. Voest. Heterogeneity of mutation calling and annotation: a survey of cancer next-generation sequencing initiatives by the Global Alliance for Genomics and Health (GA4GH). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5287.