ArticleNature biotechnology2021
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
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Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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85citing papers in PubMed
11.6field-weighted citation impact, top 1% of its field
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Who cites it
85 citing papers in PubMed, 140 citations in OpenAlex.
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- Improving somatic variant calling with long-read technologies and public datasets.Nature biotechnology · 2026Article
- Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.Nature biotechnology · 2026Article
- Somatic likelihood tiering: an interpretable post-calling triage protocol for tumor-only whole-exome variant review.Briefings in bioinformatics · 2026Article
- nf-core/pacsomatic: a scalable somatic analytic pipeline using PacBio HiFi data.Bioinformatics (Oxford, England) · 2026Article
- ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.Nature methods · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- VariantMedium: sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental data.Genome medicine · 2026Article
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs.NAR genomics and bioinformatics · 2026Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.Genome biology · 2026Article
- Improved tumor-only variant calling and mutation burden estimation with VarNet-T.Nature communications · 2026Article
- Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.Cell genomics · 2026Article
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples.Genome research · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.Cell reports methods · 2026Article
- GATES: A Lightweight Tool Automating Pathogenic Variant Discovery From Raw Whole-Exome Sequencing Data.Cancer informatics · 2026Article
- Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA.Nature communications · 2025Article
- The Impact of Variant Calling on Substitution Mutational Signature Inference.bioRxiv : the preprint server for biology · 2025Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
80 authors at 20 institutions in 10 countries.
Li Tai Fang *Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA.ORCID http://orcid.org/0000-0003-3201-5162
Bin Zhu *Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-0172-5516
Yongmei Zhao *Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.ORCID http://orcid.org/0000-0003-0800-4658
Wanqiu ChenCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA.ORCID http://orcid.org/0000-0003-3706-7834
Zhaowei YangCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA.ORCID http://orcid.org/0000-0002-1805-4360
Liz KerriganATCC (American Type Culture Collection), Manassas, VA, USA.
Kurt LangenbachATCC (American Type Culture Collection), Manassas, VA, USA.
Maryellen de MarsATCC (American Type Culture Collection), Manassas, VA, USA.
Charles LuComputational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA.
Kenneth IdlerComputational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA.
Howard JacobComputational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA.
Yuanting ZhengState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
Luyao RenState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
Ying YuState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
Erich JaegerIllumina Inc., Foster City, CA, USA.
Gary P SchrothIllumina Inc., Foster City, CA, USA.ORCID http://orcid.org/0000-0002-3055-056X
Ogan D AbaanIllumina Inc., Foster City, CA, USA.
Keyur TalsaniaAdvanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Justin LackAdvanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Tsai-Wei ShenAdvanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.ORCID http://orcid.org/0000-0001-9644-1748
Zhong ChenCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA.ORCID http://orcid.org/0000-0003-2444-8216
Seta StanboulyCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA.
Bao TranSequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Jyoti ShettySequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Yuliya KrigaSequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Daoud MeerzamanComputational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA.
Cu NguyenComputational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA.
Virginie PetitjeanBiomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Marc SultanBiomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland.
Margaret CamCCR Collaborative Bioinformatics Resource (CCBR), Office of Science and Technology Resources, Center for Cancer Research, Bethesda, MD, USA.
Monika MehtaSequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.ORCID http://orcid.org/0000-0003-3928-3733
Tiffany HungGenentech, a member of the Roche group, South San Francisco, CA, USA.
Eric PetersGenentech, a member of the Roche group, South San Francisco, CA, USA.
Rasika KalameghamGenentech, a member of the Roche group, South San Francisco, CA, USA.
Sayed Mohammad Ebrahim SahraeianBioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA.
Marghoob MohiyuddinBioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA.
Yunfei GuoBioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA.
Lijing YaoBioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA.
Lei SongDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Hugo Y K LamBioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA.
Jiri DrabekIMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
Petr VojtaIMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.ORCID http://orcid.org/0000-0003-0036-1853
Roberta MaestroEuropean Infrastructure for Translational Medicine, Amsterdam, the Netherlands.ORCID http://orcid.org/0000-0002-6642-5592
Daniela GasparottoEuropean Infrastructure for Translational Medicine, Amsterdam, the Netherlands.
Sulev KõksEuropean Infrastructure for Translational Medicine, Amsterdam, the Netherlands.ORCID http://orcid.org/0000-0001-6087-6643
Ene ReimannEuropean Infrastructure for Translational Medicine, Amsterdam, the Netherlands.ORCID http://orcid.org/0000-0002-5410-4433
Andreas SchererEuropean Infrastructure for Translational Medicine, Amsterdam, the Netherlands.ORCID http://orcid.org/0000-0002-4254-7122
Jessica NordlundEuropean Infrastructure for Translational Medicine, Amsterdam, the Netherlands.
Ulrika LiljedahlEuropean Infrastructure for Translational Medicine, Amsterdam, the Netherlands.
Roderick V JensenDepartment of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
Mehdi PiroozniaBioinformatics and Computational Biology Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-4210-6458
Zhipan LiSentieon Inc., Mountain View, CA, USA.
Chunlin XiaoNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0001-8702-4889
Stephen T SherryNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Rebecca KuskoImmuneering Corporation, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6730-5990
Malcolm MoosCenter for Biologics Evaluation and Research, FDA, Silver Spring, MD, USA.
Eric DonaldsonCenter for Drug Evaluation and Research, FDA, Silver Spring, MD, USA.
Zivana TezakCenter for Devices and Radiological Health, FDA, Silver Spring, MD, USA.
Baitang NingNational Center for Toxicological Research, FDA, Jefferson, AR, USA.
Weida TongNational Center for Toxicological Research, FDA, Jefferson, AR, USA.
Jing LiDepartment of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
Penelope Duerken-HughesDepartment of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA, USA.
Claudia Catalanotti10x Genomics, Pleasanton, CA, USA.
Shamoni Maheshwari10x Genomics, Pleasanton, CA, USA.
Joe Shuga10x Genomics, Pleasanton, CA, USA.
Winnie S LiangTranslational Genomics Research Institute, Phoenix, AZ, USA.ORCID http://orcid.org/0000-0002-5698-7735
Jonathan KeatsTranslational Genomics Research Institute, Phoenix, AZ, USA.ORCID http://orcid.org/0000-0003-4375-7399
Jonathan AdkinsTranslational Genomics Research Institute, Phoenix, AZ, USA.
Erica TassoneTranslational Genomics Research Institute, Phoenix, AZ, USA.
Victoria ZismannTranslational Genomics Research Institute, Phoenix, AZ, USA.
Timothy McDanielTranslational Genomics Research Institute, Phoenix, AZ, USA.
Jeffrey TrentTranslational Genomics Research Institute, Phoenix, AZ, USA.ORCID http://orcid.org/0000-0003-0183-4202
Jonathan FooxDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Daniel ButlerDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.ORCID http://orcid.org/0000-0002-1850-1642
Huixiao HongNational Center for Toxicological Research, FDA, Jefferson, AR, USA. huixiao.hong@fda.hhs.gov.ORCID http://orcid.org/0000-0001-8087-3968
Leming ShiState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China. lemingshi@fudan.edu.cn.ORCID http://orcid.org/0000-0002-2981-4150
Charles WangCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA. oxwang@gmail.com.
Wenming XiaoCenter for Devices and Radiological Health, FDA, Silver Spring, MD, USA. wenming.xiao@fda.hhs.gov.ORCID http://orcid.org/0000-0003-4096-9724
Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium
National Institutes of Health · USTranslational Genomics Research Institute · USNational Center for Toxicological Research · USIllumina (United States) · USFrederick National Laboratory for Cancer Research · USCenter for Devices and Radiological Health · USAmerican Type Culture Collection · USLoma Linda University · USNovartis (Switzerland) · CHFudan University · CNAbbVie (United States) · USCenter for Translational Molecular Medicine · NLCornell University · USLa Roche College · USUppsala University · SECenter for Biologics Evaluation and Research · USCentro di Riferimento Oncologico · ITNational Cancer Institute · USOffice of Science · USUniversity of Toledo Medical Center · US
Funding
UH Hilo COP A&RP20GM103466 · NIGMS · UNIVERSITY OF HAWAII AT MANOA · PI HELEN C TURNER · 2012 to 2026
$60.3MUniversity of Hawaii Cancer Center CCSGP30CA071789 · NCI · UNIVERSITY OF HAWAII AT MANOA · PI GERTRAUD MASKARINEC · 1996 to 2026
$56.2MSmall Grants ProgramP30GM114737 · NIGMS · UNIVERSITY OF HAWAII AT MANOA · PI YANAGIHARA, RICHARD · 2015 to 2022
$8.1MHigh Throughput DNA SequencerS10OD019960 · OD · LOMA LINDA UNIVERSITY · PI WANG, CHARLES · 2015 to 2015
$272kAmerican Heart Association (American Heart Association, Inc.) 18IPA34170301Intramural NIH HHS Z99 CA999999NCI NIH HHS HHSN261201400008CNCI NIH HHS HHSN261201500003CNCI NIH HHS HHSN261201500003INCI NIH HHS P30 CA071789NIGMS NIH HHS P20 GM103466NIGMS NIH HHS P30 GM114737NIH HHS S10 OD019960
Abstract
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.
Indexed as
BenchmarkingBreast NeoplasmsCell Line, TumorDatasets as TopicDNA Mutational AnalysisGerm CellsHigh-Throughput Nucleotide SequencingHumansMutationReference StandardsReproducibility of ResultsWhole Genome Sequencing
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