Verified Genomic Reference Samples for Testing Low to Very Low AF Small Variants in OncoPanels and Liquid Biopsy Assays
2021 AMP Reference Forum Presentation by Wendell Jones
Although reference samples with known ground truth regarding variants have been around for a while (NIST genome-in-a-bottle samples, HapMap samples, etc.), none have variants in large number (thousands) that are also low-frequency (like somatic variants observed in cancer).
This presentation, given at the 2021 AMP Reference Forum, discusses, highlights results from an effort by the FDA-led Sequencing and Quality Controls Phase 2 (SEQC2) consortium to characterize tens of thousands of low frequency variants in the DNA companion to Agilent’s Universal Human Reference RNA, an already established reference sample. This DNA reference sample and the sequence data generated from it are useful in multiple contexts: determining general limits of detection of oncopanel and liquid biopsy assays; proficiency testing; genomic oncology assay development, evaluation, and validation; complex biomarker evaluation (eg. Tumor Mutational Burden); and bioinformatic variant-calling pipeline development.
Download and review the presentation to learn more.