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

Nat Methods. 2004 Nov;1(2):109-11. 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