ArticleScientific data2025
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.
Erratum issuedAbstract readDataset
In one paragraph
Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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19citing papers in PubMed
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Who cites it
19 citing papers in PubMed.
- Small variant calling in the era of long-read sequencing.Nature reviews. Genetics · 2026Review
- Pileup-hi: an ultra-high-throughput, customizable alignment pileup program for large datasets.Bioinformatics (Oxford, England) · 2026Article
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.NAR genomics and bioinformatics · 2026Article
- nf-core/pacsomatic: a scalable somatic analytic pipeline using PacBio HiFi data.Bioinformatics (Oxford, England) · 2026Article
- Pansoma, a machine learning tool for identifying somatic variants using pangenome graphs.bioRxiv : the preprint server for biology · 2026Article
- Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- cyberDMR: accurate and robust identification of differentially methylated regions from WGS-derived methylomes.BMC biology · 2026Article
- A complete human pancreatic cancer genome.bioRxiv : the preprint server for biology · 2026Article
- SVScope improves somatic structural variations detection via graph-genome optimization.Genome biology · 2026Article
- Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.Cell genomics · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Benchmarking major somatic structural variant callers on the HG008 genome.Frontiers in genetics · 2026Article
- Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq.bioRxiv : the preprint server for biology · 2025Article
- Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes.bioRxiv : the preprint server for biology · 2025Article
- Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions.Nature communications · 2025Article
- Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions.bioRxiv : the preprint server for biology · 2025Article
- Flexible, production-scale, human whole genome sequencing on a benchtop sequencer.BMC genomics · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
Corrections and comments
- Erratum issued
- Update of
Authors and funding
85 authors.
Jennifer H McDanielMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA. jennifer.mcdaniel@nist.gov.ORCID 0000-0003-1987-0914
Vaidehi PatelMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA.ORCID 0009-0001-0511-6649
Nathan D OlsonMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA.ORCID 0000-0003-2585-3037
Hua-Jun HeMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA.ORCID 0000-0002-8000-1040
Zhiyong HeMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA.ORCID 0009-0002-4650-2826
Kenneth D ColeMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA.
Alexander A GoodenMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA.
Anthony SchmittArima Genomics, Inc., 6354 Corte Del Abeto Suite B, Carlsbad, CA, 92011, USA.
Kristin SikkinkArima Genomics, Inc., 6354 Corte Del Abeto Suite B, Carlsbad, CA, 92011, USA.ORCID 0000-0002-0805-0622
Fritz J SedlazeckDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.ORCID 0000-0001-6040-2691
Harsha DoddapaneniHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.ORCID 0000-0002-2433-633X
Shalini N JhangianiHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.ORCID 0000-0002-6674-0074
Donna M MuznyHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.
Marie-Claude GingrasHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.ORCID 0000-0003-2570-6360
Heer MehtaHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.ORCID 0000-0002-5357-2112
Sairam BeheraHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.ORCID 0000-0002-9047-0203
Luis F PaulinHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.ORCID 0000-0003-2567-3773
Alex R HastieBionano Genomics, San Diego, USA.
Hung-Chun YuBionano Genomics, San Diego, USA.
Victor WeigmanBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC, 27713, USA.ORCID 0000-0003-2699-9142
Alison RojasBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC, 27713, USA.ORCID 0000-0003-1889-9221
Katie KennedyBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC, 27713, USA.
Jamie RemingtonBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC, 27713, USA.
Isai Salas-GonzálezBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC, 27713, USA.ORCID 0000-0002-0347-5058
Mitch SudkampApplications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA, 92121, USA.ORCID 0009-0003-0905-7775
Kelly WisemanApplications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA, 92121, USA.
Bryan R LajoieApplications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA, 92121, USA.
Shawn LevyApplications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA, 92121, USA.
Miten JainGenome Technology Laboratory, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA.ORCID 0000-0002-4571-3982
Stuart AkesonGenome Technology Laboratory, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA.
Giuseppe NarzisiNew York Genome Center, New York, NY, 10013, USA.ORCID 0000-0003-1118-8849
Zoe SteinsnyderNew York Genome Center, New York, NY, 10013, USA.
Catherine ReevesNew York Genome Center, New York, NY, 10013, USA.ORCID 0000-0002-9942-8909
Jennifer SheltonNew York Genome Center, New York, NY, 10013, USA.
Sarah B KinganPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Christine LambertPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Primo BaybayanPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Aaron M WengerPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.ORCID 0000-0003-1183-0432
Ian J McLaughlinPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.ORCID 0009-0008-6863-2975
Aaron AdamsonPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Christopher KingsleyPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Melanie WescottPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Young KimPacBio, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0000-0001-8863-3539
Jimin ParkUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0000-0002-4702-382X
Ivo ViolichUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Karen H MigaUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0000-0002-3670-4507
Joshua GardnerUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID 0000-0003-4386-0628
Brandy McNultyUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Gail L RosenEcological and Evolutionary Signal-processing and Informatics (EESI) Lab, College of Engineering, Drexel University, Philadelphia, PA, USA.ORCID 0000-0003-1763-5750
Rajiv McCoyDepartment of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.ORCID 0000-0003-0615-146X
Francesco BrunduIllumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA.ORCID 0000-0003-2133-1426
Erfan SayyariIllumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA.ORCID 0009-0004-7008-4032
Konrad SchefflerIllumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA.ORCID 0000-0002-6041-8367
Sean TruongIllumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA.ORCID 0009-0005-7584-2688
Severine CatreuxIllumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA.ORCID 0009-0008-1813-1240
Lesley Chapman HannahNational Cancer Institute, Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Institutes of Health, 9609 Medical Center Dr, Rockville, MD, 20850, USA.ORCID 0009-0004-6050-1701
Doron LipsonUltima Genomics Inc., 4425 Technology Dr, Fremont, CA, 94538, USA.
Hila BenjaminUltima Genomics Inc., 4425 Technology Dr, Fremont, CA, 94538, USA.
Nika IremadzeUltima Genomics Inc., 4425 Technology Dr, Fremont, CA, 94538, USA.ORCID 0000-0002-4977-204X
Ilya SoiferUltima Genomics Inc., 4425 Technology Dr, Fremont, CA, 94538, USA.
Gat KriegerUltima Genomics Inc., 4425 Technology Dr, Fremont, CA, 94538, USA.
Stephen EackerPhase Genomics, Inc, Seattle, WA, USA.
Mary WoodPhase Genomics, Inc, Seattle, WA, USA.
Erin CrossKROMATID, 1880 Industrial Circle, Suite A, Longmont, Colorado, 80501, USA.
Greg HusarKROMATID, 1880 Industrial Circle, Suite A, Longmont, Colorado, 80501, USA.
Stephen GrossKROMATID, 1880 Industrial Circle, Suite A, Longmont, Colorado, 80501, USA.
Michael VernichKROMATID, 1880 Industrial Circle, Suite A, Longmont, Colorado, 80501, USA.
Mikhail KolmogorovCancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.ORCID 0000-0002-5489-9045
Tanveer AhmadCancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
Ayse G KeskusCancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.ORCID 0000-0002-3934-8587
Asher BryantCancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.ORCID 0009-0005-9132-782X
Francoise Thibaud-NissenNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA.
Jonathan TrowNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA.
Jacqueline ProszynskiWeill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY, 10021, USA.
Jeremy Wain HirschbergWeill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY, 10021, USA.
Krista RyonWeill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY, 10021, USA.
Christopher E MasonWeill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY, 10021, USA.ORCID 0000-0002-1850-1642
Mital S BhaktaDovetail Genomics, part of Cantata Bio, 100 Enterprise Way, Suite A101, Scotts Valley, CA, 95066, USA.
J Zachary SanbornDovetail Genomics, part of Cantata Bio, 100 Enterprise Way, Suite A101, Scotts Valley, CA, 95066, USA.
Elizabeth M MundingDovetail Genomics, part of Cantata Bio, 100 Enterprise Way, Suite A101, Scotts Valley, CA, 95066, USA.
Justin WagnerMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA.ORCID 0009-0003-8903-0504
Chunlin Xiao *National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA.ORCID 0000-0001-8702-4889
Andrew S Liss *Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.ORCID 0000-0002-4040-9172
Justin M Zook *Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, 20899, USA. justin.zook@nist.gov.ORCID 0000-0003-2309-8402
Funding
NIH Cloud Platform Interoperability Administrative Coordinating CenterOT2OD034190 · OD · RESEARCH TRIANGLE INSTITUTE · PI ROBBINS, ELIZABETH · 2022 to 2023
$16.9MVAST Center: Viromes Across Space(s) and TimeU54AG089334 · NIA · STANFORD UNIVERSITY · PI Christopher Edward Mason · 2025 to 2026
$13.3MProject 4 Green-DavisP01CA272295 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI Christopher Edward Mason · 2024 to 2026
$9.3MDockstore: The Community Platform for Reproducible Biomedical Workflows and ApplicationsU24HG011853 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Jonathan Lawson, Benedict Paten · 2021 to 2026
$5.7MTelomere-to-telomere assemblies of human genomesR01HG011274 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Karen Hayden Miga · 2020 to 2026
$4.5MBAF complex deregulation in lymphomaR01CA266279 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Michael Richard Green, Christopher Edward Mason · 2022 to 2026
$3.4MFunction and fitness consequences of human genetic variationR35GM133747 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Rajiv Champion McCoy · 2019 to 2026
$3.3MAI-based AML risk stratification using next generation cytogenomicsR44CA278140 · NCI · PHASE GENOMICS, INC. · PI EACKER, STEPHEN MATTHEW · 2023 to 2024
$2.0MA next-generation method for cytogenomics using Hi-C proximity ligation sequencingR44HD104323 · NICHD · PHASE GENOMICS, INC. · PI EACKER, STEPHEN MATTHEW · 2020 to 2022
$1.9MAdvanced development of Lancet, an emerging tool for complex variant calling in cancer genomicsU01CA253405 · NCI · NEW YORK GENOME CENTER · PI NARZISI, GIUSEPPE · 2021 to 2023
$1.5MShared Sequel II Systems at BCM HGSCS10OD028587 · OD · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2020 to 2020
$508kNational Science Foundation (NSF) 1919691National Science Foundation (NSF) 1936791NCI NIH HHS P01 CA272295NCI NIH HHS R01 CA266279NCI NIH HHS R44 CA278140NCI NIH HHS U01 CA253405NHGRI NIH HHS R01 HG011274NHGRI NIH HHS U24 HG011853NIA NIH HHS U54 AG089334NICHD NIH HHS R44 HD104323NIGMS NIH HHS R35 GM133747NIH HHS OT2 OD034190NIH HHS S10 OD028587United States Department of Commerce | National Institute of Standards and Technology (NIST) 60NANB20D166U.S. Department of Health & Human Services | National Institutes of Health (NIH) OT2OD034190U.S. Department of Health & Human Services | National Institutes of Health (NIH) R35GM133747U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01CA253405U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG011274U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U24HG011853
Abstract
The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic variants. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.
Indexed as
Carcinoma, Pancreatic DuctalGenome, HumanPancreatic NeoplasmsCell Line, TumorHumansWhole Genome Sequencing
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