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.

Advanced Biomedical and Computational Sciences Biomedical Informatics and Data Science Directorate Frederick National Laboratory for Cancer Research Frederick MD USA

ATCC Manassas VA USA

Bioinformatics and Computational Biology Core National Heart Lung and Blood Institute National Institutes of Health Bethesda MD USA

Bioinformatics Research and Early Development Roche Sequencing Solutions Inc Belmont CA USA

Biomarker Development Novartis Institutes for Biomedical Research Basel Switzerland

CCR Collaborative Bioinformatics Resource Office of Science and Technology Resources Center for Cancer Research Bethesda MD USA

Center for Biologics Evaluation and Research FDA Silver Spring MD USA

Center for Devices and Radiological Health FDA Silver Spring MD USA

Center for Drug Evaluation and Research FDA Silver Spring MD USA

Center for Genomics Loma Linda University School of Medicine Loma Linda CA USA

Centro di Riferimento Oncologico di Aviano IRCCS National Cancer Institute Unit of Oncogenetics and Functional Oncogenomics Aviano Italy

Computational Genomics and Bioinformatics Branch Center for Biomedical Informatics and Information Technology National Cancer Institute Rockville MD USA

Computational Genomics Genomics Research Center AbbVie North Chicago IL USA

Department of Allergy and Clinical Immunology State Key Laboratory of Respiratory Disease National Clinical Research Center for Respiratory Disease Guangzhou Institute of Respiratory Health 1st Affiliated Hospital of Guangzhou Medical University Guangzhou China

Department of Basic Science Loma Linda University School of Medicine Loma Linda CA USA

Department of Biological Sciences Virginia Tech Blacksburg VA USA

Department of Medical Sciences Molecular Medicine and Science for Life Laboratory Uppsala University Uppsala Sweden

Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA

Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Bethesda MD USA

Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia

European Infrastructure for Translational Medicine Amsterdam the Netherlands

Genentech a member of the Roche group South San Francisco CA USA

Illumina Inc Foster City CA USA

Immuneering Corporation Boston MA USA

IMTM Faculty of Medicine and Dentistry Palacky University Olomouc Czech Republic

Institute for Molecular Medicine Finland University of Helsinki Helsinki Finland

National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda MD USA

National Center for Toxicological Research FDA Jefferson AR USA

Perron Institute for Neurological and Translational Science Nedlands Western Australia Australia

Sentieon Inc Mountain View CA USA

Sequencing Facility Cancer Research Technology Program Frederick National Laboratory for Cancer Research Frederick MD USA

State Key Laboratory of Genetic Engineering Human Phenome Institute School of Life Sciences and Shanghai Cancer Center Fudan University Shanghai China

Translational Genomics Research Institute Phoenix AZ USA

x Genomics Pleasanton CA USA

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