Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls

Abstract

BackgroundCancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types.ResultsWe identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. The samples affected by these technical artifacts include all acute myeloid leukemia and practically all ovarian cancer samples.ConclusionsWe demonstrate how technical artifacts induced by whole genome amplification of DNA can lead to false positive germline-tumor type associations and suggest TCGA whole genome amplified samples be used with caution. This study draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3770-y) contains supplementary material, which is available to authorized users.

Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

“…8072, Integrated analysis of germline and somatic perturbation as it relates to tumor phenotypes). Whole exome (WXS) germline variant calls from 8542 individuals were obtained using GATK v3.5 as described previously [ 20 ]. The samples prepared using whole genome amplification (WGA) were excluded from the analysis due to previous identification of technical artifacts in both somatic and germline variant calls in WGA samples [ 20 , 21 ].…”

“…Whole exome (WXS) germline variant calls from 8542 individuals were obtained using GATK v3.5 as described previously [ 20 ]. The samples prepared using whole genome amplification (WGA) were excluded from the analysis due to previous identification of technical artifacts in both somatic and germline variant calls in WGA samples [ 20 , 21 ]. Somatic mutation calls obtained using MuTect2 were downloaded from GDC as Mutation Annotation Format (MAF) files [ 22 ].…”

Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables

“…As genomic analysis becomes more common in clinical practice, it is critical for the scientific community to understand not only how to accurately model mutations and experimental error but also how to choose an appropriate variant caller and how various aspects of clinical and laboratory workflow can affect the performance of the algorithms they use [ 27 ]. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing alongside diverse biological and clinical features and evaluate their effect on variant caller selection and optimization.…”

Whole-exome sequencing capture kit biases yield false negative mutation calls in TCGA cohorts

“…At the same time, this broad scope makes it more susceptible to measurement errors. For example, Buckley et al found technical artifacts in TCGA germline samples due to whole chromosome amplification resulting in spurious indel calls [ 5 ].…”