Abstract 445: A validated genomic reference material with known content applicable to panel assays requiring low frequency variant allele detection
Authors: Wendell Jones, Joshua Xu, Binsheng Gong
Journal: Cancer Research (2019)

Abstract Prospective and GCP testing of tumors for important somatic variants in cancer is becoming more commonplace. Currently, there is a lack of a reliable and perpetual publicly available genomic material that can be used across a wide range of genomic testing methods for assessing the potential accuracy of a given test. A great variety of the next-gen sequencing (NGS) methods and processes currently in place now or in the future will have heterogeneous genomic targets, limits of detection, input material, and cost requirements. The variety of these tests extends from small panels (targeting 10 or more genes) to larger panels (targeting &amp;gt; 100 genes) to comprehensive tests (several hundred genes or WES/WGS). There is considerable variability in the sensitivity requirements of various assays with some designed to detect variant allele frequencies (VAF) of 10% or more while others wish to detect VAF &amp;lt; 1%. In addition, the testing itself has several layers of complexity: 1) the size and complex nature of the human genome; 2) the additional complexity of the damaged genome in cancer cells; 3) the amount and origin of the input material; and 4) the complex instruments and software algorithms necessary to proficiently perform the tests. The SEQC2 consortium has extensively evaluated and documented a pooled cell line reference material that has &amp;gt; 40,000 known variants with the great majority having allele frequencies &amp;lt; 10% in the standard pool. This effort evaluated DNA pooled from 11 cell lines, 10 of which are from distinct cancers, used for generating RNA material for the Universal Human Reference RNA (UHRR). This consortium defined ground truth (primarily SNVs, Indels) for each cell line using related and orthogonal genomic testing methods (multiple platforms, enrichment methods, and software algorithms) so that the content of various standardized admixtures and pools of the material will be known. The final results were validated by additional sequencing of the individual pools and through ddPCR testing of a large number of identified variants. The result is a series of reference materials with a large number and variety of validated variants at various VAF, suitable for a wide range of testing, including variants with VAF &amp;lt; 1%. These materials can be used as an ongoing reference material when developing new assays, conducting proficiency and reproducibility tests, or for quality control purposes when running regulated assays (positive and negative control variants). Citation Format: Wendell Jones, Joshua Xu, Binsheng Gong, Onco-panel Working Group of the Sequencing QualityControl Phase 2 (SEQC2) Consortium. A validated genomic reference material with known content applicable to panel assays requiring low frequency variant allele detection [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 445.