SNP-specific extraction of haplotype-resolved targeted genomic regions

The availability of genotyping platforms for comprehensive genetic analysis of complex traits has resulted in a plethora of studies reporting the association of specific single-nucleotide polymorphisms (SNPs) with common diseases or drug responses. However, detailed genetic analysis of these associa...

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Bibliographic Details
Published in:Nucleic acids research 2008-09, Vol.36 (15), p.e94-e94
Main Authors: Dapprich, Johannes, Ferriola, Deborah, Magira, Eleni E, Kunkel, Mark, Monos, Dimitri
Format: Article
Language:English
Subjects:
Alleles
DNA - isolation & purification
Genomics - methods
Haplotypes
Histocompatibility Antigens Class I - genetics
HLA-B Antigens - genetics
HLA-C Antigens - genetics
Humans
Major Histocompatibility Complex
Methods Online
Microsatellite Repeats
Polymorphism, Single Nucleotide
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Summary:The availability of genotyping platforms for comprehensive genetic analysis of complex traits has resulted in a plethora of studies reporting the association of specific single-nucleotide polymorphisms (SNPs) with common diseases or drug responses. However, detailed genetic analysis of these associated regions that would correlate particular polymorphisms to phenotypes has lagged. This is primarily due to the lack of technologies that provide additional sequence information about genomic regions surrounding specific SNPs, preferably in haploid form. Enrichment methods for resequencing should have the specificity to provide DNA linked to SNPs of interest with sufficient quality to be used in a cost-effective and high-throughput manner. We describe a simple, automated method of targeting specific sequences of genomic DNA that can directly be used in downstream applications. The method isolates haploid chromosomal regions flanking targeted SNPs by hybridizing and enzymatically elongating oligonucleotides with biotinylated nucleotides based on their selective binding to unique sequence elements that differentiate one allele from any other differing sequence. The targeted genomic region is captured by streptavidin-coated magnetic particles and analyzed by standard genotyping, sequencing or microarray analysis. We applied this technology to determine contiguous molecular haplotypes across a ∼150 kb genomic region of the major histocompatibility complex.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkn345