| JONES, W., B.S. GONG, N. NOVORADOVSKAYA, D. LI, R. KUSKO, T.A. RICHMOND, D.J. JOHANN, H. BISGIN, S.M.E. SAHRAEIAN, P.R. BUSHEL, M. PIROOZNIA, K. WILKINS, M. CHIERICI, W.J. BAO, L.S. BASEHORE, A.B. LUCAS, D. BURGESS, D.J. BUTLER, S. CAWLEY, C.J. CHANG, G.C. CHEN, T. CHEN, Y.C. CHEN, D.J. CRAIG, A. DEL POZO, J. FOOX, M. FRANCESCATTO, YT FU, C. FURLANELLO, K. GIORDA, K.P. GRIST, M.J. GUAN, Y.Y. HAO, S. HAPPE, G. HARIANI, N. HASELEY, J. JASPER, G. JURMAN, D.P. KREIL, P. LABAJ, K. LAI, J.Y. LI, Q.Z. LI, Y.L. LI, Z.G. LI, Z.C. LIU, M.S. LOPEZ, K. MICLAUS, R. MILLER, V.K. MITTAL, M. MOHIYUDDIN, C. PABON-PENA, B.L. PARSONS, F.J. QIU, A. SCHERER, T.L. SHI, S. STIEGELMEYER, C. SUO, Nikola TOM, D. WANG, Z.N. WEN, L.H. WU, W.Z. XIAO, C. XU, Y. YU, J.Y. ZHANG, Y.F. ZHANG, Z.H. ZHANG, Y.T. ZHENG, C.E. MASON, J.C. WILLEY, W.D. TONG, L.M. SHI and J. XU. A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency. GENOME BIOLOGY. LONDON: BIOMED CENTRAL LTD, 2021, vol. 22, No 1, p. 111-148. ISSN 1474-760X. Available from: https://dx.doi.org/10.1186/s13059-021-02316-z. |
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@article{1782163,
author = {Jones, W. and Gong, B.S. and Novoradovskaya, N. and Li, D. and Kusko, R. and Richmond, T.A. and Johann, D.J. and Bisgin, H. and Sahraeian, S.M.E. and Bushel, P.R. and Pirooznia, M. and Wilkins, K. and Chierici, M. and Bao, W.J. and Basehore, L.S. and Lucas, A.B. and Burgess, D. and Butler, D.J. and Cawley, S. and Chang, C.J. and Chen, G.C. and Chen, T. and Chen, Y.C. and Craig, D.J. and Del Pozo, A. and Foox, J. and Francescatto, M. and Fu, YT and Furlanello, C. and Giorda, K. and Grist, K.P. and Guan, M.J. and Hao, Y.Y. and Happe, S. and Hariani, G. and Haseley, N. and Jasper, J. and Jurman, G. and Kreil, D.P. and Labaj, P. and Lai, K. and Li, J.Y. and Li, Q.Z. and Li, Y.L. and Li, Z.G. and Liu, Z.C. and Lopez, M.S. and Miclaus, K. and Miller, R. and Mittal, V.K. and Mohiyuddin, M. and PabonandPena, C. and Parsons, B.L. and Qiu, F.J. and Scherer, A. and Shi, T.L. and Stiegelmeyer, S. and Suo, C. and Tom, Nikola and Wang, D. and Wen, Z.N. and Wu, L.H. and Xiao, W.Z. and Xu, C. and Yu, Y. and Zhang, J.Y. and Zhang, Y.F. and Zhang, Z.H. and Zheng, Y.T. and Mason, C.E. and Willey, J.C. and Tong, W.D. and Shi, L.M. and Xu, J.},
article_location = {LONDON},
article_number = {1},
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},
language = {eng},
issn = {1474-760X},
journal = {GENOME BIOLOGY},
title = {A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency},
url = {https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02316-z.pdf},
volume = {22},
year = {2021}
}
TY - JOUR
ID - 1782163
AU - 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.
PY - 2021
TI - A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
JF - GENOME BIOLOGY
VL - 22
IS - 1
SP - 111
EP - 111
PB - BIOMED CENTRAL LTD
SN - 1474760X
KW - COPY NUMBER VARIATIONS
KW - SOMATIC MUTATIONS
KW - QUALITY-CONTROL
KW - INDEL DETECTION
KW - READ ALIGNMENT
KW - EXOME
KW - ACCURATE
KW - DISCOVERY
KW - FRAMEWORK
KW - DATABASE
UR - https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02316-z.pdf
N2 - 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.
ER -
JONES, W., B.S. GONG, N. NOVORADOVSKAYA, D. LI, R. KUSKO, T.A. RICHMOND, D.J. JOHANN, H. BISGIN, S.M.E. SAHRAEIAN, P.R. BUSHEL, M. PIROOZNIA, K. WILKINS, M. CHIERICI, W.J. BAO, L.S. BASEHORE, A.B. LUCAS, D. BURGESS, D.J. BUTLER, S. CAWLEY, C.J. CHANG, G.C. CHEN, T. CHEN, Y.C. CHEN, D.J. CRAIG, A. DEL POZO, J. FOOX, M. FRANCESCATTO, YT FU, C. FURLANELLO, K. GIORDA, K.P. GRIST, M.J. GUAN, Y.Y. HAO, S. HAPPE, G. HARIANI, N. HASELEY, J. JASPER, G. JURMAN, D.P. KREIL, P. LABAJ, K. LAI, J.Y. LI, Q.Z. LI, Y.L. LI, Z.G. LI, Z.C. LIU, M.S. LOPEZ, K. MICLAUS, R. MILLER, V.K. MITTAL, M. MOHIYUDDIN, C. PABON-PENA, B.L. PARSONS, F.J. QIU, A. SCHERER, T.L. SHI, S. STIEGELMEYER, C. SUO, Nikola TOM, D. WANG, Z.N. WEN, L.H. WU, W.Z. XIAO, C. XU, Y. YU, J.Y. ZHANG, Y.F. ZHANG, Z.H. ZHANG, Y.T. ZHENG, C.E. MASON, J.C. WILLEY, W.D. TONG, L.M. SHI and J. XU. A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency. \textit{GENOME BIOLOGY}. LONDON: BIOMED CENTRAL LTD, 2021, vol.~22, No~1, p.~111-148. ISSN~1474-760X. Available from: https://dx.doi.org/10.1186/s13059-021-02316-z.
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