Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

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.

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Publication Details

Journal
Scientific Data
Published
2025-07-16
DOI
https://doi.org/10.1038/s41597-025-05438-2
Citations
5
Primary Topic
Cancer Genomics and Diagnostics
Type
article
Field-Weighted Citation Impact
4.68

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article

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Stuart Akeson, Jimin Park, Elizabeth M. Munding, Zoe Steinsnyder et al.
5 citations
Scientific Data
Cancer Genomics and Diagnostics
4.68
article

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Stuart Akeson, Jimin Park, Elizabeth M. Munding, Zoe Steinsnyder, Brandy McNulty, Luis F. Paulin, Victor Weigman, Alison M. Earley, Melanie P. Wescott, Sairam Behera, Kristin Sikkink, Lesley Chapman Hannah, Miten Jain, Francoise Thibaud-Nissen, Bryan R. Lajoie, Jacqueline Proszynski, J. Zachary Sanborn, Erfan Sayyari, Gail Rosen, Mikhail Kolmogorov, Alex Hastie, Doron Lipson, Jennifer Shelton, Shawn Levy, Stephen Gross, Jonathan Trow, Jamie Remington, Marie‐Claude Gingras, Fritz Joachim Sedlazeck, Severine Catreux, Anthony D. Schmitt, Stephen Eacker, Hung‐Chun Yu, Jennifer McDaniel, Karen H. Miga, Christopher Kingsley, HarshaVardhan Doddapaneni, Nika Iremadze, Hua‐Jun He, Krista Ryon, Justin M. Zook, Ayse G. Keskus, Ilya Soifer, Konrad Scheffler, Benedict Paten, Christine Lambert, Gat Krieger, Francesco Brundu, Heer H. Mehta, Mary Wood, Nathan D. Olson, Alexander A Gooden, Aaron W. Adamson, Ivo Violich, Shalini N. Jhangiani, Hila Benjamin, Jeremy Wain Hirschberg, Chunlin Xiao, Joshua Gardner, Rajiv C. McCoy, Giuseppe Narzisi, Justin Wagner, Andrew Scott Liss, Sarah B. Kingan, Aaron M. Wenger, Christopher E. Mason, Ian J McLaughlin, Primo Baybayan, Isai Salas-González, Catherine Reeves, Kelly Wiseman, Young Kim, Tanveer Ahmad, Kenneth D. Cole, Asher Bryant, Sean Truong, Mitch Sudkamp, Michael Vernich, Erin Cross, Katie Kennedy, Mital S. Bhakta, Vaidehi Patel, Zhiyong He, Donna M. Muzny, Greg Husar
article en
5 citations

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.

Scientific DataVol. 12(1)
Meridian Institute (US), Northeastern University (US), National Institutes of Health (US), Harvard University (US), Johns Hopkins University (US), Illumina (United States) (US), Baylor College of Medicine (US), University of California, Santa Cruz (US), Cornell University (US), Massachusetts General Hospital (US), BioNano Genomics (United States) (US), Arima Genomics (United States) (US), National Center for Biotechnology Information (US), BD Biosciences (United States) (US), ID Genomics (United States) (US), National Cancer Institute (UA), National Cancer Institute (US), KromaTiD (United States) (US), Material Measurement Laboratory (US), New York Genome Center (US), Dovetail Genomics (United States) (US), Department of Health and Human Services (US), Pacific Biosciences (United States) (US), Drexel University (US), Rice University (US)
National Science Foundation, Drexel University, New York Genome Center, National Institutes of Health, National Institute of Standards and Technology, National Human Genome Research Institute, National Cancer Institute, U.S. National Library of Medicine
Industry, innovation and infrastructure
Openalex Percentile: Top 5%
Cancer Genomics and Diagnostics
4.68
DOIOpen Access PDFOpenAlex
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