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

Autor:	McDaniel JH; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA., Patel V; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA., Olson ND; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA., He HJ; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA., He Z; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA., Cole KD; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA., Schmitt A; Arima Genomics, Inc., 6354 Corte Del Abeto Suite B, Carlsbad, CA 92011, USA., Sikkink K; Arima Genomics, Inc., 6354 Corte Del Abeto Suite B, Carlsbad, CA 92011, USA., Sedlazeck FJ; Human 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., Doddapaneni H; Human Genome Sequencing Center, Baylor College of Medicine, OneBaylor Plaza, Houston, Texas 77030, USA., Jhangiani SN; Human Genome Sequencing Center, Baylor College of Medicine, OneBaylor Plaza, Houston, Texas 77030, USA., Muzny DM; Human Genome Sequencing Center, Baylor College of Medicine, OneBaylor Plaza, Houston, Texas 77030, USA., Gingras MC; Human Genome Sequencing Center, Baylor College of Medicine, OneBaylor Plaza, Houston, Texas 77030, USA., Mehta H; Human Genome Sequencing Center, Baylor College of Medicine, OneBaylor Plaza, Houston, Texas 77030, USA., Paulin LF; Human Genome Sequencing Center, Baylor College of Medicine, OneBaylor Plaza, Houston, Texas 77030, USA., Hastie AR; Bionano Genomics., Yu HC; Bionano Genomics., Weigman V; BioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713., Rojas A; BioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713., Kennedy K; BioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713., Remington J; BioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713., Gonzalez I; BioSkryb Genomics, 2810 Meridian Pkwy, ste110, Durham, NC 27713., Sudkamp M; Applications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA 92121, USA., Wiseman K; Applications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA 92121, USA., Lajoie BR; Applications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA 92121, USA., Levy S; Applications Development Laboratory, Element Biosciences, 10055 Barnes Canyon Rd, San Diego, CA 92121, USA., Jain M; Genome Technology Laboratory, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA., Akeson S; Genome Technology Laboratory, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA., Narzisi G; New York Genome Center, New York, NY 10013, USA., Steinsnyder Z; New York Genome Center, New York, NY 10013, USA., Reeves C; New York Genome Center, New York, NY 10013, USA., Shelton J; New York Genome Center, New York, NY 10013, USA., Kingan SB; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Lambert C; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Bayabyan P; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Wenger AM; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., McLaughlin IJ; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Adamson A; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Kingsley C; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Wescott M; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Kim Y; PacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA., Paten B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., Park J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., Violich I; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., Miga KH; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., Gardner J; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., McNulty B; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA., Rosen G; Ecological and Evolutionary Signal-processing and Informatics (EESI) Lab, College of Engineering, Drexel University, Philadelphia, PA, USA., McCoy R; Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA., Brundu F; Illumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA., Sayyari E; Illumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA., Scheffler K; Illumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA., Truong S; Illumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA., Catreux S; Illumina, Inc., DRAGEN, 5200 Illumina Way, San Diego, CA, 92122, USA., Hannah LC; National Cancer Institute, Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Institutes of Health, 9609 Medical Center Dr, Rockville, MD 20850, USA., Lipson D; Ultima Genomics Inc., 4425 Technology Dr, Fremont, CA 94538, USA., Benjamin H; Ultima Genomics Inc., 4425 Technology Dr, Fremont, CA 94538, USA., Iremadze N; Ultima Genomics Inc., 4425 Technology Dr, Fremont, CA 94538, USA., Soifer I; Ultima Genomics Inc., 4425 Technology Dr, Fremont, CA 94538, USA., Eacker S; Phase Genomics, Inc. Seattle, WA, USA., Wood M; Phase Genomics, Inc. Seattle, WA, USA., Cross E; KromaTiD, 1880 Industrial Circle, Suite A, Longmont, Colorado 80501, USA., Husar G; KromaTiD, 1880 Industrial Circle, Suite A, Longmont, Colorado 80501, USA., Gross S; KromaTiD, 1880 Industrial Circle, Suite A, Longmont, Colorado 80501, USA., Vernich M; KromaTiD, 1880 Industrial Circle, Suite A, Longmont, Colorado 80501, USA., Kolmogorov M; Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA., Ahmad T; Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA., Keskus A; Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA., Bryant A; Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA., Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA., Trow J; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA., Proszynski J; Weill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY 10021, USA., Hirschberg JW; Weill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY 10021, USA., Ryon K; Weill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY 10021, USA., Mason CE; Weill Cornell Medicine, Physiology and Biophysics and WorldQuant Initiative, 1300 York Avenue, New York, NY 10021, USA., Wagner J; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA., Xiao C; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA., Liss AS; Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA., Zook JM; Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2024 Oct 18. Date of Electronic Publication: 2024 Oct 18.
DOI:	10.1101/2024.09.18.613544
Abstrakt:	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 thirteen 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. 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 mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology. Competing Interests: Competing interests A.S. and K.S. are employees of Arima Genomics. L.F.P. from BCM, was sponsored by Genentech Inc until September 2023. F.J.S from BCM, received research support from Illumina, ONT and Pacbio. A.R.H and H-C.Y. are employees of Bionano Genomics and own stock shares and options of Bionano Genomics, Inc. V.W., K.K., J.R., and I.G. are employees of BioSkryb Genomics. M.S., K.B., B.R.L. and S.L. are employees of Element Biosciences. S.B.K., C.L., P.B., A.M.W., I.J.M., A.A., C.K., M.W., and Y.K. are employees and shareholders of PacBio, Inc. D.L., H.B., N.I., and I.S. are employees and shareholders of Ultima Genomics. S.E. and M.W. are employees of Phase Genomics. E.C., G.H., S.G., and M.V. are employees of KromaTiD, Inc, E.C. is also a shareholder. F.B., E.S., K.S., S.T. and S.C. are employees of Illumina, Inc. All other authors have no competing interests.
Databáze:	MEDLINE
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