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Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.
Zaboli, Ghazal; Ameur, Adam; Igl, Wilmar; Johansson, Åsa; Hayward, Caroline; Vitart, Veronique; Campbell, Susan; Zgaga, Lina; Polasek, Ozren; Schmitz, Gerd; van Duijn, Cornelia; Oostra, Ben; Pramstaller, Peter; Hicks, Andrew; Meitinger, Tomas; Rudan, Igor; Wright, Alan; Wilson, James F; Campbell, Harry; Gyllensten, Ulf.
Afiliación
  • Zaboli G; Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, SciLifeLab Uppsala, Uppsala University, Uppsala, Sweden.
Eur J Hum Genet ; 20(1): 77-83, 2012 Jan.
Article en En | MEDLINE | ID: mdl-21811304
ABSTRACT
We have used targeted genomic sequencing of high-complexity DNA pools based on long-range PCR and deep DNA sequencing by the SOLiD technology. The method was used for sequencing of 286 kb from four chromosomal regions with quantitative trait loci (QTL) influencing blood plasma lipid and uric acid levels in DNA pools of 500 individuals from each of five European populations. The method shows very good precision in estimating allele frequencies as compared with individual genotyping of SNPs (r(2) = 0.95, P < 10(-16)). Validation shows that the method is able to identify novel SNPs and estimate their frequency in high-complexity DNA pools. In our five populations, 17% of all SNPs and 61% of structural variants are not available in the public databases. A large fraction of the novel variants show a limited geographic distribution, with 62% of the novel SNPs and 59% of novel structural variants being detected in only one of the populations. The large number of population-specific novel SNPs underscores the need for comprehensive sequencing of local populations in order to identify the causal variants of human traits.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Análisis de Secuencia de ADN / Polimorfismo de Nucleótido Simple / Sitios de Carácter Cuantitativo / Mutación INDEL / Variación Estructural del Genoma Tipo de estudio: Diagnostic_studies / Etiology_studies / Incidence_studies / Observational_studies / Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Eur J Hum Genet Asunto de la revista: GENETICA MEDICA Año: 2012 Tipo del documento: Article País de afiliación: Suecia

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Análisis de Secuencia de ADN / Polimorfismo de Nucleótido Simple / Sitios de Carácter Cuantitativo / Mutación INDEL / Variación Estructural del Genoma Tipo de estudio: Diagnostic_studies / Etiology_studies / Incidence_studies / Observational_studies / Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Eur J Hum Genet Asunto de la revista: GENETICA MEDICA Año: 2012 Tipo del documento: Article País de afiliación: Suecia