Abstract

PROJECT 3 This project's goal is to resolve the sequence structure of 20 complex genomic regions where common genome structural variation is associated with disease. In collaboration with Chris Amemiya, we propose to construct large-insert clone (BAC) libraries (10-fold coverage) from 18 reference genomes from the 1000 Genomes Project. We will target regions and individuals identified from Projects 1 and 2, retrieve and characterize BACs, and use next-generation sequencing (NGS) lllumina clone pooling strategy sequence to resolve haplotypes of these regions. As part of our collaboration with Washington University Genome Sequencing Center (WUGSC), we will select haplotype-resolved tiling paths for complete high-quality sequencing. The results of this work will provide common high-quality alternate haplotypes of biomedical relevance to be integrated into the human reference genome.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Program Projects (P01)
Project #
5P01HG004120-07
Application #
8489318
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Project Start
Project End
Budget Start
2013-07-01
Budget End
2014-06-30
Support Year
7
Fiscal Year
2013
Total Cost
$176,820
Indirect Cost
$57,152

  Institution

Name
University of Washington
Department
Type
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195

  Publications

Eslami Rasekh, Marzieh; Chiatante, Giorgia; Miroballo, Mattia et al. (2017) Discovery of large genomic inversions using long range information. BMC Genomics 18:65
Watson, Corey T; Steinberg, Karyn Meltz; Graves, Tina A et al. (2015) Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes Immun 16:24-34
Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa et al. (2014) Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513:409-13
Huddleston, John; Ranade, Swati; Malig, Maika et al. (2014) Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res 24:688-96
Stong, Nicholas; Deng, Zhong; Gupta, Ravi et al. (2014) Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res 24:1039-50
Antonacci, Francesca; Dennis, Megan Y; Huddleston, John et al. (2014) Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat Genet 46:1293-302
Steinberg, Karyn Meltz; Schneider, Valerie A; Graves-Lindsay, Tina A et al. (2014) Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res 24:2066-76
Nuttle, Xander; Itsara, Andy; Shendure, Jay et al. (2014) Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing. Nat Protoc 9:1496-513
Mueller, Michael; Barros, Paula; Witherden, Abigail S et al. (2013) Genomic pathology of SLE-associated copy-number variation at the FCGR2C/FCGR3B/FCGR2B locus. Am J Hum Genet 92:28-40
Nuttle, Xander; Huddleston, John; O'Roak, Brian J et al. (2013) Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions. Nat Methods 10:903-9

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