SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Export

@article{citeulike:2439348, abstract = {High-density single-nucleotide polymorphism (SNP) arrays have revolutionized the ability of genome-wide association studies to detect genomic regions harboring sequence variants that affect complex traits. Extensive numbers of validated SNPs with known allele frequencies are essential to construct genotyping assays with broad utility. We describe an economical, efficient, single-step method for SNP discovery, validation and characterization that uses deep sequencing of reduced representation libraries (RRLs) from specified target populations. Using nearly 50 million sequences generated on an Illumina Genome Analyzer from DNA of 66 cattle representing three populations, we identified 62,042 putative SNPs and predicted their allele frequencies. Genotype data for these 66 individuals validated 92\% of 23,357 selected genome-wide SNPs, with a genotypic and sequence allele frequency correlation of r = 0.67. This approach for simultaneous de novo discovery of high-quality SNPs and population characterization of allele frequencies may be applied to any species with at least a partially sequenced genome.}, address = {Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA.}, author = {Van Tassell, Curtis P P. and Smith, Timothy P L P. and Matukumalli, Lakshmi K K. and Taylor, Jeremy F F. and Schnabel, Robert D D. and Lawley, Cynthia Taylor T. and Haudenschild, Christian D D. and Moore, Stephen S S. and Warren, Wesley C C. and Sonstegard, Tad S S.}, citeulike-article-id = {2439348}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nmeth.1185}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nmeth.1185}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18297082}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18297082}, day = {24}, doi = {10.1038/nmeth.1185}, issn = {1548-7105}, journal = {Nat Methods}, keywords = {discovery, library, reduced, representation, snp}, month = {February}, posted-at = {2009-06-11 22:52:32}, priority = {0}, title = {SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.}, url = {http://dx.doi.org/10.1038/nmeth.1185}, year = {2008} }

TY - JOUR ID - citeulike:2439348 L3 - citeulike-article-id:2439348 N2 - High-density single-nucleotide polymorphism (SNP) arrays have revolutionized the ability of genome-wide association studies to detect genomic regions harboring sequence variants that affect complex traits. Extensive numbers of validated SNPs with known allele frequencies are essential to construct genotyping assays with broad utility. We describe an economical, efficient, single-step method for SNP discovery, validation and characterization that uses deep sequencing of reduced representation libraries (RRLs) from specified target populations. Using nearly 50 million sequences generated on an Illumina Genome Analyzer from DNA of 66 cattle representing three populations, we identified 62,042 putative SNPs and predicted their allele frequencies. Genotype data for these 66 individuals validated 92% of 23,357 selected genome-wide SNPs, with a genotypic and sequence allele frequency correlation of r = 0.67. This approach for simultaneous de novo discovery of high-quality SNPs and population characterization of allele frequencies may be applied to any species with at least a partially sequenced genome. JF - Nat Methods SN - 1548-7105 AD - Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA. TI - SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. KW - discovery KW - library KW - reduced KW - representation KW - snp AU - Van Tassell, Curtis P AU - Smith, Timothy P L AU - Matukumalli, Lakshmi K AU - Taylor, Jeremy F AU - Schnabel, Robert D AU - Lawley, Cynthia Taylor AU - Haudenschild, Christian D AU - Moore, Stephen S AU - Warren, Wesley C AU - Sonstegard, Tad S PY - 2008/02/24/ UR - http://dx.doi.org/10.1038/nmeth.1185 ER -