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

By Curtis P. Van Tassell, T. Smith, Lakshmi K. Matukumalli, Jeremy F. Taylor, Robert D. Schnabel, C. Lawley, C. Haudenschild, S. Moore, W. Warren, Tad Stewart Sonstegard. Nature Methods, 2008

611 citations recorded by the source corpus.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/6328473f2237a157e904cbfb5bad8bc9a15f6b10

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In Genetics

Citations in the corpus

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology (2009, methodology): “Other studies have previously identified a substantial number of SNPs in chickens, using traditional Sanger sequencing [25], in cattle, using Solexa sequences [13] and in pigs, using 454 sequences [23].”
Sequencing technologies and genome sequencing (2011, background): “The GAS program was well implemented to animal genomes with identification of candidate genes and detection of casual quantitative trait nucleotides (QTN) discoveries (for example cattle: Grisart et al. 2001 and pig: Van Laere et al. 2003).”
SNP Discovery via Genomic Reduction, Barcoding, and 454‐Pyrosequencing in Amaranth (2009, methodology): “…large numbers of high-confi dence SNPs. Recently, genomic reduction was successfully used with next-generation sequencing (454-pyrosequencing and Illumina Genome Analyzer) for SNP discovery and allele frequency estimation in cattle (Van Tassell et al., 2008) and pig (Wiedmann et al., 2008).”
Protein model discrimination using mutational sensitivity derived from deep sequencing. (2012, methodology): “Deep sequencing has been successfully used for single-nucleotide polymorphism (SNP) detection (Van Tassell et al., 2008), genome sequencing, and genetic analysis (Bentley et al., 2008; Margulies et al., 2005).”
Genotyping‐by‐Sequencing for Plant Breeding and Genetics (2012, methodology): “…including complexity reduction of polymorphic sequences (van Orsouw et al., 2007) and deep sequencing of reduced representation libraries (van Tassell et al., 2008). h e use of restriction enzymes for targeted reduction of genome complexity combined with NGS was i rst described by Baird et…”
SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing (2013, result): “our research project, which improved the RRL efficiency more than in previous studies [18,20,22,29].”
Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, methodology): “Variations on this method have been used to generate thousands of SNPs for various organisms of agricultural importance (Van Orsouw et al., 2007; Van Tassell et al., 2008; Wiedmann et al., 2008; Amaral et al., 2009; Kerstens et al., 2009; Ramos et al., 2009; Sánchez et al., 2009; Hyten et al., 2010a”
Development and Characterization of a High Density SNP Genotyping Assay for Cattle (2009, methodology): “The RRL SNP produced a higher conversion rate than did any of the other SNP sources which lacked MAF estimates, although with a substantially lower average MAF than when these markers were validated by genotyping the SNP discovery animals [16].”