Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Li Tai Fang; Bin Zhu; Yongmei Zhao; Wanqiu Chen; Zhaowei Yang; Liz Kerrigan; Kurt Langenbach; Maryellen de Mars; Charles Lu; Kenneth Idler; Howard Jacob; Yuanting Zheng; Luyao Ren; Ying Yu; Erich Jaeger; Gary P Schroth; Ogan D Abaan; Keyur Talsania; Justin Lack; Tsai-Wei Shen; Zhong Chen; Seta Stanbouly; Bao Tran; Jyoti Shetty; Yuliya Kriga; Daoud Meerzaman; Cu Nguyen; Virginie Petitjean; Marc Sultan; Margaret Cam; Monika Mehta; Tiffany Hung; Eric Peters; Rasika Kalamegham; Sayed Mohammad Ebrahim Sahraeian; Marghoob Mohiyuddin; Yunfei Guo; Lijing Yao; Lei Song; Hugo Y K Lam; Jiri Drabek; Petr Vojta; Roberta Maestro; Daniela Gasparotto; Sulev Kõks; Ene Reimann; Andreas Scherer; Jessica Nordlund; Ulrika Liljedahl; Roderick V Jensen; Mehdi Pirooznia; Zhipan Li; Chunlin Xiao; Stephen T Sherry; Rebecca Kusko; Malcolm Moos; Eric Donaldson; Zivana Tezak; Baitang Ning; Weida Tong; Jing Li; Penelope Duerken-Hughes; Claudia Catalanotti; Shamoni Maheshwari; Joe Shuga; Winnie S Liang; Jonathan Keats; Jonathan Adkins; Erica Tassone; Victoria Zismann; Timothy McDaniel; Jeffrey Trent; Jonathan Foox; Daniel Butler; Christopher E Mason; Huixiao Hong; Leming Shi; Charles Wang; Wenming Xiao; Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium

doi:10.1038/s41587-021-00993-6

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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Journal article

Peer reviewed

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Li Tai Fang, Bin Zhu, Yongmei Zhao, Wanqiu Chen, Zhaowei Yang, Liz Kerrigan, Kurt Langenbach, Maryellen de Mars, Charles Lu, Kenneth Idler, …

Nature biotechnology, Vol.39(9), pp.1151-1160

2021

DOI: https://doi.org/10.1038/s41587-021-00993-6

PMCID: PMC8532138

PMID: 34504347

Abstract

Benchmarking

Breast Neoplasms - genetics

Cell Line, Tumor

Datasets as Topic

DNA Mutational Analysis - standards

Germ Cells

High-Throughput Nucleotide Sequencing - standards

Humans

Mutation

Reference Standards

Reproducibility of Results

Whole Genome Sequencing - standards

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.

Details

Title: Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
Authors/Creators: Li Tai Fang - Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
Bin Zhu - National Institutes of Health
Yongmei Zhao - Frederick National Laboratory for Cancer Research
Wanqiu Chen - Loma Linda University
Zhaowei Yang - First Affiliated Hospital of Guangzhou Medical University
Liz Kerrigan - ATCC (American Type Culture Collection), Manassas, VA, USA
Kurt Langenbach - ATCC (American Type Culture Collection), Manassas, VA, USA
Maryellen de Mars - ATCC (American Type Culture Collection), Manassas, VA, USA
Charles Lu - Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
Kenneth Idler - Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
Howard Jacob - Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
Yuanting Zheng - Fudan University
Luyao Ren - Fudan University
Ying Yu - Fudan University
Erich Jaeger - Illumina Inc., Foster City, CA, USA
Gary P Schroth - Illumina Inc., Foster City, CA, USA
Ogan D Abaan - Illumina Inc., Foster City, CA, USA
Keyur Talsania - Frederick National Laboratory for Cancer Research
Justin Lack - Frederick National Laboratory for Cancer Research
Tsai-Wei Shen - Frederick National Laboratory for Cancer Research
Zhong Chen - Loma Linda University
Seta Stanbouly - Loma Linda University
Bao Tran - Frederick National Laboratory for Cancer Research
Jyoti Shetty - Frederick National Laboratory for Cancer Research
Yuliya Kriga - Frederick National Laboratory for Cancer Research
Daoud Meerzaman - Genomics (United Kingdom)
Cu Nguyen - Genomics (United Kingdom)
Virginie Petitjean - Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
Marc Sultan - Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
Margaret Cam - CCR Collaborative Bioinformatics Resource (CCBR), Office of Science and Technology Resources, Center for Cancer Research, Bethesda, MD, USA
Monika Mehta - Frederick National Laboratory for Cancer Research
Tiffany Hung - Genentech
Eric Peters - Genentech
Rasika Kalamegham - Genentech
Sayed Mohammad Ebrahim Sahraeian - Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
Marghoob Mohiyuddin - Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
Yunfei Guo - Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
Lijing Yao - Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
Lei Song - National Institutes of Health
Hugo Y K Lam - Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
Jiri Drabek - European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
Petr Vojta - European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
Roberta Maestro - Centro di Riferimento Oncologico
Daniela Gasparotto - Centro di Riferimento Oncologico
Sulev Kõks - University of Tartu
Ene Reimann - University of Tartu
Andreas Scherer - University of Helsinki
Jessica Nordlund - Uppsala University
Ulrika Liljedahl - Uppsala University
Roderick V Jensen - Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
Mehdi Pirooznia - National Heart Lung and Blood Institute
Zhipan Li - Sentieon (United States)
Chunlin Xiao - National Center for Biotechnology Information
Stephen T Sherry - National Center for Biotechnology Information
Rebecca Kusko - Immuneering Corporation, Boston, MA, USA
Malcolm Moos - Center for Biologics Evaluation and Research
Eric Donaldson - Center for Drug Evaluation and Research
Zivana Tezak - Center for Devices and Radiological Health
Baitang Ning - National Center for Toxicological Research, FDA, Jefferson, AR, USA
Weida Tong - National Center for Toxicological Research, FDA, Jefferson, AR, USA
Jing Li - First Affiliated Hospital of Guangzhou Medical University
Penelope Duerken-Hughes - Loma Linda University
Claudia Catalanotti - 10x Genomics, Pleasanton, CA, USA
Shamoni Maheshwari - 10x Genomics, Pleasanton, CA, USA
Joe Shuga - 10x Genomics, Pleasanton, CA, USA
Winnie S Liang - Translational Genomics Research Institute
Jonathan Keats - Translational Genomics Research Institute
Jonathan Adkins - Translational Genomics Research Institute
Erica Tassone - Translational Genomics Research Institute
Victoria Zismann - Translational Genomics Research Institute
Timothy McDaniel - Translational Genomics Research Institute
Jeffrey Trent - Translational Genomics Research Institute
Jonathan Foox - Weill Cornell Medicine
Daniel Butler - Weill Cornell Medicine
Christopher E Mason - Weill Cornell Medicine
Huixiao Hong - National Center for Toxicological Research, FDA, Jefferson, AR, USA. huixiao.hong@fda.hhs.gov
Leming Shi - Fudan University
Charles Wang - Loma Linda University
Wenming Xiao - Center for Devices and Radiological Health
Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium
Publication Details: Nature biotechnology, Vol.39(9), pp.1151-1160
Publisher: Springer Nature
Grant note: 18IPA34170301 / American Heart Association (American Heart Association, Inc.) HHSN261201500003I / NCI NIH HHS HHSN261201500003C / NCI NIH HHS HHSN261201400008C / NCI NIH HHS P20 GM103466 / NIGMS NIH HHS P30 GM114737 / NIGMS NIH HHS Z99 CA999999 / Intramural NIH HHS S10 OD019960 / NIH HHS P30 CA071789 / NCI NIH HHS
Identifiers: 991005634025107891
Murdoch Affiliation: Personalised Medicine Centre
Language: English
Resource Type: Journal article

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Collaboration types: Industry collaboration; Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.189 Genome Studies; 1.189.310 Population Genetics
Web Of Science research areas: Biotechnology & Applied Microbiology
ESI research areas: Biology & Biochemistry