title: SNP-specific extraction of haplotype-resolved targeted genomic regions.
abstract: 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 approximately 150 kb genomic region of the major histocompatibility complex.
authors.affiliation: Generation Biotech, Lawrenceville, NJ 08648, USA. jdapprich@generationbiotech.com
authors.forename: Johannes
authors.initials: J
authors.lastname: Dapprich
authors.forename: Deborah
authors.initials: D
authors.lastname: Ferriola
authors.forename: Eleni E
authors.initials: EE
authors.lastname: Magira
authors.forename: Mark
authors.initials: M
authors.lastname: Kunkel
authors.forename: Dimitri
authors.initials: D
authors.lastname: Monos
mesh_terms: D000483:Alleles; D004247:DNA / Q000302:isolation & purification; D023281:Genomics / Q000379:methods*; D015235:HLA-B Antigens / Q000235:genetics; D015236:HLA-C Antigens / Q000235:genetics; D006239:Haplotypes; D015395:Histocompatibility Antigens Class I / Q000235:genetics; D006801:Humans; D008285:Major Histocompatibility Complex; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide
chemical_list: D015235:HLA-B Antigens; D015236:HLA-C Antigens; D015395:Histocompatibility Antigens Class I; C099187:MHC class I-related chain A; D004247:DNA