Whole-genome genotyping with the single-base extension assay

Nat Methods. 2006 Jan;3(1):31-3. doi: 10.1038/nmeth842.


We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scalability, throughput and accuracy of the system by resequencing homozygous loci from our 100k Human-1 Genotyping BeadChip.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA Primers / chemistry*
  • Genome, Human / genetics*
  • Genomics / economics
  • Genomics / methods*
  • Genotype
  • Humans
  • Nucleotides / chemistry
  • Polymorphism, Single Nucleotide*
  • Reproducibility of Results
  • Sensitivity and Specificity


  • DNA Primers
  • Nucleotides