Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array.
The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to 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, and was further driven by strict empirical measurements of accuracy, reproducibility, and average call rate, which we estimate to be >99.5%, >99.9%, and>95%, respectively [corrected]. With average heterozygosity of 0.38 and genome 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.
Matsuzaki
Hajime
H
Affymetrix, Inc., Santa Clara, California 95051, USA.
Loi
Halina
H
Dong
Shoulian
S
Tsai
Ya-Yu
YY
Fang
Joy
J
Law
Jane
J
Di
Xiaojun
X
Liu
Wei-Min
WM
Yang
Geoffrey
G
Liu
Guoying
G
Huang
Jing
J
Kennedy
Giulia C
GC
Ryder
Thomas B
TB
Marcus
Gregory A
GA
Walsh
P Sean
PS
Shriver
Mark D
MD
Puck
Jennifer M
JM
Jones
Keith W
KW
Mei
Rui
R
D000483:Alleles; D015415:Biomarkers; D002178:Candidiasis, Chronic Mucocutaneous / Q000235:genetics; D017931:DNA Primers / Q000235:genetics*; D015342:DNA Probes / Q000235:genetics / Q000378:metabolism; D005006:Ethnicity / Q000235:genetics; D008040:Genetic Linkage / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics; D015894:Genome, Human; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012107:Research Design / Q000592:standards; D013959:Thyroid Diseases / Q000235:genetics
D015415:Biomarkers; D017931:DNA Primers; D015342:DNA Probes