Abstract 2253: Identifying pathogenic germline variants in 1,172 cancer patients utilizing a novel variant phasing tool and strict public database curation
Authors: Polley Amanda , Vaske Charles , Benz Steve , Soon-Shiong Patrick , Rabizadeh Shahrooz , Sanborn J Zachary 
Published: August 2018

The identification of pathogenic or likely pathogenic (P/LP) germline variants in cancer patients is vital in assessing potential genetic causes of cancer risk, as well as incidental rare disease risk. However, sequencing limitations, lack of pedigree data, and unreliable phenotypic data can hinder the discovery of these putative causal germline variants. In order to improve the identification of such variants, we have developed a germline analysis pipeline that phases variants and identifies rare P/LP variants utilizing data from the GnomAD and ClinVar databases.

In order to ensure our pipeline is annotating variants with accurate phenotypic data, we rate the quality of submitters to ClinVar based on their submission history. This history includes review status, agreement between population frequencies and stated clinical significance, and the quality of supporting evidence provided. The variant-phenotype relationship data extracted from ClinVar is valuable in directing us towards cancer-contributing variants, as well as incidental disease risk. However, there are many discrepancies between various institutions' assertion criteria submitted to ClinVar. Many variant entries in ClinVar are submitted as P/LP, yet a large number of these submissions lack evidence or criteria supporting the variant's clinical significance. Our pipeline identifies low-quality submissions, allowing for the inclusion of only high-quality P/LP variant annotations.

In addition to recognizing known P/LP variants from the ClinVar archive, our pipeline provides additional identification of potentially pathogenic novel germline variants via haplotype phasing. Haplotype phasing of germline variants is vital when determining the impact of multiple heterozygous variants within the same gene, but it is difficult to perform such phasing outside of family studies. Our pipeline utilizes normal DNA, tumor DNA, and tumor RNA to predict the phase of variants without the need for full pedigree information.

The pipeline was tested on 1,172 patient samples, with the goal of phasing clinically-associated cancer genes and discovering rare P/LP germline variants. We were able to phase variants in over 50% of the patients, allowing us to identify the nature of compound heterozygosity as it relates to disease risk in these patients. Additionally, our pipeline identified at least 1 high-quality ClinVar P/LP variant per patient in over 25% of the patients. In the vast majority of patients, we were able to identify rare homozygous germline variants. Gene panels specific to cancer type can be used to further investigate which rare variants most likely factor in the patient's disease. Based on these results, as well as our analysis of ClinVar, we assert the need for deep introspection of ClinVar submissions and highlight the utility of RNA data in variant phasing.

Citation Format: Amanda Polley, Charles Vaske, Steve Benz, Patrick Soon-Shiong, Shahrooz Rabizadeh, J Zachary Sanborn. Identifying pathogenic germline variants in 1,172 cancer patients utilizing a novel variant phasing tool and strict public database curation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2253.