A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

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Authors	JONES W. GONG B.S. NOVORADOVSKAYA N. LI D. KUSKO R. RICHMOND T.A. JOHANN D.J. BISGIN H. SAHRAEIAN S.M.E. BUSHEL P.R. PIROOZNIA M. WILKINS K. CHIERICI M. BAO W.J. BASEHORE L.S. LUCAS A.B. BURGESS D. BUTLER D.J. CAWLEY S. CHANG C.J. CHEN G.C. CHEN T. CHEN Y.C. CRAIG D.J. DEL POZO A. FOOX J. FRANCESCATTO M. FU YT FURLANELLO C. GIORDA K. GRIST K.P. GUAN M.J. HAO Y.Y. HAPPE S. HARIANI G. HASELEY N. JASPER J. JURMAN G. KREIL D.P. LABAJ P. LAI K. LI J.Y. LI Q.Z. LI Y.L. LI Z.G. LIU Z.C. LOPEZ M.S. MICLAUS K. MILLER R. MITTAL V.K. MOHIYUDDIN M. PABON-PENA C. PARSONS B.L. QIU F.J. SCHERER A. SHI T.L. STIEGELMEYER S. SUO C. TOM Nikola WANG D. WEN Z.N. WU L.H. XIAO W.Z. XU C. YU Y. ZHANG J.Y. ZHANG Y.F. ZHANG Z.H. ZHENG Y.T. MASON C.E. WILLEY J.C. TONG W.D. SHI L.M. XU J.
Year of publication	2021
Type	Article in Periodical
Magazine / Source	GENOME BIOLOGY
MU Faculty or unit	Central European Institute of Technology
Citation
web	https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02316-z.pdf
Doi	http://dx.doi.org/10.1186/s13059-021-02316-z
Keywords	COPY NUMBER VARIATIONS; SOMATIC MUTATIONS; QUALITY-CONTROL; INDEL DETECTION; READ ALIGNMENT; EXOME; ACCURATE; DISCOVERY; FRAMEWORK; DATABASE
Description	BackgroundOncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.ResultsIn reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100x more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.ConclusionThese new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.
Related projects:	Involvement of Czech Translational Medicine Infrastructure to the European Advanced Translational Research Infrastructure in Medicine CEITEC 2020 Comprehensive prognostic and predictive panel for chronic lymphocytic leukemia: a next-generation sequencing tool suitable for clinical practice and study of genetic architecture behind the disease progress