Genotype Inference

genotype inference Burdick JT, Chen WM, Abecasis GR and Cheung VG (2006). In silico method for inferring genotypes in pedigrees. Nat Genet 38:1002-4. [PDF]

We have developed a genotype inference method that reduces the number of genotyping reactions and increases the power of genome-wide association studies.  Our method combines sparse marker data from a linkage scan and high-resolution SNP genotypes for several individuals to infer genotypes for related individuals.  We illustrate our method’s utility by inferring over 53 million SNP genotypes for 78 children in the Centre d’Etude du Polymorphisme Humain (CEPH) families.  Our method can be used to obtain high-density genotypes in different family structures, including nuclear families commonly used in complex disease gene mapping studies.

The inferred genotypes (using genotypes from HapMap builds 16c1 and 21, and IBD information from Vivian Cheung's lab) are available from the HapMap website.

The software we used to infer those genotypes