title: Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.
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%.
authors.affiliation: Affymetrix, Inc., 3380 Central Expressway, Santa Clara, California 95051, USA.
authors.forename: Hajime
authors.initials: H
authors.lastname: Matsuzaki
authors.forename: Shoulian
authors.initials: S
authors.lastname: Dong
authors.forename: Halina
authors.initials: H
authors.lastname: Loi
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Di
authors.forename: Guoying
authors.initials: G
authors.lastname: Liu
authors.forename: Earl
authors.initials: E
authors.lastname: Hubbell
authors.forename: Jane
authors.initials: J
authors.lastname: Law
authors.forename: Tam
authors.initials: T
authors.lastname: Berntsen
authors.forename: Monica
authors.initials: M
authors.lastname: Chadha
authors.forename: Henry
authors.initials: H
authors.lastname: Hui
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Yang
authors.forename: Giulia C
authors.initials: GC
authors.lastname: Kennedy
authors.forename: Teresa A
authors.initials: TA
authors.lastname: Webster
authors.forename: Simon
authors.initials: S
authors.lastname: Cawley
authors.forename: P Sean
authors.initials: PS
authors.lastname: Walsh
authors.forename: Keith W
authors.initials: KW
authors.lastname: Jones
authors.forename: Stephen P A
authors.initials: SP
authors.lastname: Fodor
authors.forename: Rui
authors.initials: R
authors.lastname: Mei
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D005820:Genetic Testing / Q000379:methods; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid