We will apply next-generation sequencing (NGS) technology to assess the genome-wide pattern of structural variation within large (>20 kbp), complex regions of segmental duplication. Combining read-depth and a single-base unique nucleotide (SUN) identifier map, we will generate absolute estimates of diploid copy-number and sequence content for duplicated regions and gene families. We propose to analyze all 2,000 individuals being analyzed as part of the 1000 Genomes Project and to validate regions by a combination of array comparative genomic hybridization (arrayCGH), clone-based sequencing and FISH-based approaches.
This aim will provide the first genotypic assessment of copy and content of these complex regions facilitating future disease association studies.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Program Projects (P01)
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Ethical, Legal, Social Implications Review Committee (GNOM)
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University of Washington
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Watson, C T; Steinberg, K M; Graves, T 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
Huddleston, John; Ranade, Swati; Malig, Maika et al. (2014) Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res 24:688-96
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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
Itsara, Andy; Vissers, Lisenka E L M; Steinberg, Karyn Meltz et al. (2012) Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing. Am J Hum Genet 90:599-613
Hormozdiari, Fereydoun; Alkan, Can; Ventura, Mario et al. (2011) Alu repeat discovery and characterization within human genomes. Genome Res 21:840-9

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