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