ArticlebioRxiv : the preprint server for biology2025
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.
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Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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85 authors.
Jennifer H McDanielMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA.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.
Zhiyong HeMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA.ORCID 0000-0002-8000-1040
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.ORCID 0009-0002-4650-2826
Kristin SikkinkArima Genomics, Inc., 6354 Corte Del Abeto Suite B, Carlsbad, CA 92011, USA.ORCID 0000-0002-0805-0622
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, USA.ORCID 0000-0001-6040-2691
Harsha DoddapaneniHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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.
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.
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.
Hung-Chun YuBionano Genomics.
Victor WeigmanBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713.ORCID 0000-0003-2699-9142
Alison RojasBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713.ORCID 0000-0003-1889-9221
Katie KennedyBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713.
Jamie RemingtonBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713.
Isai Salas-GonzálezBioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713.
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 BayabyanPacBio, 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.
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.
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.
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.
Tanveer AhmadCancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
Ayse KeskusCancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
Asher BryantCancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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.
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 XiaoNational 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 LissDepartment of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA.ORCID 0000-0002-4040-9172
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA.ORCID 0000-0003-2309-8402
Funding
NIH Cloud Platform Interoperability Administrative Coordinating CenterOT2OD034190 · OD · RESEARCH TRIANGLE INSTITUTE · PI ROBBINS, ELIZABETH · 2022 to 2023
$16.9MDockstore: 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
$4.5MFunction and fitness consequences of human genetic variationR35GM133747 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Rajiv Champion McCoy · 2019 to 2026
$3.3MCommercialization of a rapid, automated Hi-C platform for sensitive genomic profiling of multiple cancer sample typesR44HG014126 · NHGRI · CANTATA BIO LLC · PI MUNDING, ELIZABETH · 2024 to 2025
$2.0MAdvanced 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
$508kNCI NIH HHS U01 CA253405NHGRI NIH HHS R01 HG011274NHGRI NIH HHS R44 HG014126NHGRI NIH HHS U24 HG011853NIGMS NIH HHS R35 GM133747NIH HHS OT2 OD034190NIH HHS S10 OD028587
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 to be 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, and Hi-C, and karyotyping. In future publications, 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,
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.