In this project, we propose to discover, sequence and integrate into the human genome three classes of refractory structural variation. This will include novel insertions not present with the reference sequence, regions of recurrent copy-number variation, and duplicated regions of high sequence diversity. Using an existing fosmid clone resource from 16 reference individuals, we will identify and subclone these regions, generate high-quality sequence commensurate with the human genome, and assess copy-number variation of these regions. We predict that this project will recover and characterize 1,575 loci that will be difficult to fully characterize by other experimental and computational approaches. The advantage of our approach is that it utilizes the entire sequence of the clone to determine the complete context of this variation. Our goal will be to integrate this high-quality sequence into the reference genome as alternate haplotypes that may be annotated and further characterized. This work will, thus, complement ongoing efforts as part of the 1000 Genomes Project and Genome Reference Consortium to comprehensively assess the complete spectrum of human genetic variation.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Program Projects (P01)
Project #
5P01HG004120-07
Application #
8489316
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
$222,409
Indirect Cost
$79,838
Name
University of Washington
Department
Type
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
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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
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
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
Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa et al. (2014) Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513:409-13
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
Watson, Corey T; Steinberg, Karyn M; Huddleston, John et al. (2013) Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am J Hum Genet 92:530-46
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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