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Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.
Teer, Jamie K; Bonnycastle, Lori L; Chines, Peter S; Hansen, Nancy F; Aoyama, Natsuyo; Swift, Amy J; Abaan, Hatice Ozel; Albert, Thomas J; Margulies, Elliott H; Green, Eric D; Collins, Francis S; Mullikin, James C; Biesecker, Leslie G.
Afiliación
  • Teer JK; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Genome Res ; 20(10): 1420-31, 2010 Oct.
Article en En | MEDLINE | ID: mdl-20810667
ABSTRACT
Massively parallel DNA sequencing technologies have greatly increased our ability to generate large amounts of sequencing data at a rapid pace. Several methods have been developed to enrich for genomic regions of interest for targeted sequencing. We have compared three of these

methods:

Molecular Inversion Probes (MIP), Solution Hybrid Selection (SHS), and Microarray-based Genomic Selection (MGS). Using HapMap DNA samples, we compared each of these methods with respect to their ability to capture an identical set of exons and evolutionarily conserved regions associated with 528 genes (2.61 Mb). For sequence analysis, we developed and used a novel Bayesian genotype-assigning algorithm, Most Probable Genotype (MPG). All three capture methods were effective, but sensitivities (percentage of targeted bases associated with high-quality genotypes) varied for an equivalent amount of pass-filtered sequence for example, 70% (MIP), 84% (SHS), and 91% (MGS) for 400 Mb. In contrast, all methods yielded similar accuracies of >99.84% when compared to Infinium 1M SNP BeadChip-derived genotypes and >99.998% when compared to 30-fold coverage whole-genome shotgun sequencing data. We also observed a low false-positive rate with all three methods; of the heterozygous positions identified by each of the capture methods, >99.57% agreed with 1M SNP BeadChip, and >98.840% agreed with the whole-genome shotgun data. In addition, we successfully piloted the genomic enrichment of a set of 12 pooled samples via the MGS method using molecular bar codes. We find that these three genomic enrichment methods are highly accurate and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data.
Asunto(s)

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Genoma Humano / Análisis de Secuencia de ADN / Análisis de Secuencia por Matrices de Oligonucleótidos / Diabetes Mellitus Tipo 2 Tipo de estudio: Diagnostic_studies / Evaluation_studies / Prognostic_studies Límite: Humans Idioma: En Revista: Genome Res Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2010 Tipo del documento: Article País de afiliación: Estados Unidos

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Genoma Humano / Análisis de Secuencia de ADN / Análisis de Secuencia por Matrices de Oligonucleótidos / Diabetes Mellitus Tipo 2 Tipo de estudio: Diagnostic_studies / Evaluation_studies / Prognostic_studies Límite: Humans Idioma: En Revista: Genome Res Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2010 Tipo del documento: Article País de afiliación: Estados Unidos