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Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.
Gustafson, Jonas A; Gibson, Sophia B; Damaraju, Nikhita; Zalusky, Miranda Pg; Hoekzema, Kendra; Twesigomwe, David; Yang, Lei; Snead, Anthony A; Richmond, Phillip A; De Coster, Wouter; Olson, Nathan D; Guarracino, Andrea; Li, Qiuhui; Miller, Angela L; Goffena, Joy; Anderson, Zachery; Storz, Sophie Hr; Ward, Sydney A; Sinha, Maisha; Gonzaga-Jauregui, Claudia; Clarke, Wayne E; Basile, Anna O; Corvelo, André; Reeves, Catherine; Helland, Adrienne; Musunuri, Rajeeva Lochan; Revsine, Mahler; Patterson, Karynne E; Paschal, Cate R; Zakarian, Christina; Goodwin, Sara; Jensen, Tanner D; Robb, Esther; McCombie, W Richard; Sedlazeck, Fritz J; Zook, Justin M; Montgomery, Stephen B; Garrison, Erik; Kolmogorov, Mikhail; Schatz, Michael C; McLaughlin, Richard N; Dashnow, Harriet; Zody, Michael C; Loose, Matt; Jain, Miten; Eichler, Evan E; Miller, Danny E.
Afiliación
  • Gustafson JA; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Gibson SB; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
  • Damaraju N; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Zalusky MP; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Hoekzema K; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Twesigomwe D; Institute for Public Health Genetics, University of Washington, Seattle, WA, USA.
  • Yang L; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Snead AA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Richmond PA; Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
  • De Coster W; Pacific Northwest Research Institute, Seattle, WA, USA.
  • Olson ND; Department of Biology, New York University, New York, NY, USA.
  • Guarracino A; Alamya Health, Baton Rouge, LA, USA.
  • Li Q; Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
  • Miller AL; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
  • Goffena J; Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Anderson Z; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
  • Storz SH; Human Technopole, Milan, Italy.
  • Ward SA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • Sinha M; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Gonzaga-Jauregui C; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Clarke WE; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Basile AO; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Corvelo A; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Reeves C; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Helland A; International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México.
  • Musunuri RL; New York Genome Center, New York, NY, USA.
  • Revsine M; Outlier Informatics Inc., Saskatoon, SK, Canada.
  • Patterson KE; New York Genome Center, New York, NY, USA.
  • Paschal CR; New York Genome Center, New York, NY, USA.
  • Zakarian C; New York Genome Center, New York, NY, USA.
  • Goodwin S; New York Genome Center, New York, NY, USA.
  • Jensen TD; New York Genome Center, New York, NY, USA.
  • Robb E; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • McCombie WR; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Sedlazeck FJ; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
  • Zook JM; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Montgomery SB; Department of Computer Science, Stanford University, Stanford, CA, USA.
  • McLaughlin RN; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
  • Dashnow H; Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA.
  • Zody MC; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
  • Loose M; Department of Computer Science, Rice University, Houston, TX, USA.
  • Jain M; Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
  • Eichler EE; Department of Genetics, Stanford University, Stanford, CA, USA.
  • Miller DE; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
medRxiv ; 2024 Mar 07.
Article en En | MEDLINE | ID: mdl-38496498
ABSTRACT
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos