Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array

AUTOR(ES)

Matsuzaki, Hajime

FONTE

Cold Spring Harbor Laboratory Press

RESUMO

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilizedto investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, andwas further driven by strict empirical measurements of accuracy, reproducibility, andaverage call rate, which we estimate to be >9.5%, >99.9%, and>95%, respectively. With average heterozygosity of 0.38 andgenome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers.

Documentos Relacionados

• Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
• Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay
• Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data
• Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis
• MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays