Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays

Hajime Matsuzaki; Shoulian Dong; Halina Loi; Xiaojun Di; Guoying Liu; Earl Hubbell; Jane Law; Tam Berntsen; Monica Chadha; Henry Hui; Geoffrey Yang; Giulia C Kennedy; Teresa A Webster; Simon Cawley; P Sean Walsh; Keith W Jones; Stephen P A Fodor; Rui Mei

doi:10.1038/nmeth718

Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays

Nat Methods. 2004 Nov;1(2):109-11. doi: 10.1038/nmeth718.

Authors

Hajime Matsuzaki¹, Shoulian Dong, Halina Loi, Xiaojun Di, Guoying Liu, Earl Hubbell, Jane Law, Tam Berntsen, Monica Chadha, Henry Hui, Geoffrey Yang, Giulia C Kennedy, Teresa A Webster, Simon Cawley, P Sean Walsh, Keith W Jones, Stephen P A Fodor, Rui Mei

Affiliation

¹ Affymetrix, Inc., 3380 Central Expressway, Santa Clara, California 95051, USA.

PMID: 15782172
DOI: 10.1038/nmeth718

Abstract

We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.

Publication types

Evaluation Study
Validation Study

MeSH terms

Algorithms*
Chromosome Mapping / methods*
DNA Mutational Analysis / methods*
Genetic Testing / methods
Genome, Human
Genotype
Humans
Oligonucleotide Array Sequence Analysis / instrumentation
Oligonucleotide Array Sequence Analysis / methods*
Polymorphism, Single Nucleotide / genetics*
Reproducibility of Results
Sensitivity and Specificity
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Sequence Homology, Nucleic Acid