Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.
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%.
Matsuzaki
Hajime
H
Affymetrix, Inc., 3380 Central Expressway, Santa Clara, California 95051, USA.
Dong
Shoulian
S
Loi
Halina
H
Di
Xiaojun
X
Liu
Guoying
G
Hubbell
Earl
E
Law
Jane
J
Berntsen
Tam
T
Chadha
Monica
M
Hui
Henry
H
Yang
Geoffrey
G
Kennedy
Giulia C
GC
Webster
Teresa A
TA
Cawley
Simon
S
Walsh
P Sean
PS
Jones
Keith W
KW
Fodor
Stephen P A
SP
Mei
Rui
R
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