Haplotype blocks (bins) were constructed using LDselect (Christopher S. Carlson and Deborah A. Nickerson, Seattle, Washington, USA), a software package that provides computation of linkage disequilibrium (LD) statistics and population haplotype patterns from genotype data [ 45].
Haplotype blocks were constructed using Haploview, version 4.2 (Broad Institute of MIT and Harvard, Cambridge, MA, USA), a software package that provides computation of linkage disequilibrium (LD) statistics and population haplotype patterns from genotype data [ 16].
The computation of exact linkage scores (LOD or non-parametric) in linkage analysis is of great importance.
Whenever the pedigree is too complex, and the number of selectors needed to determine the inheritance in the pedigree is too large, current methods can not utilize the HMM backbone, and exact computation of the linkage scores is not computationally feasible.
Our space reduction enables exact linkage computations and we demonstrate order of magnitude experimental speedups when performing computations across 6000 genomic locations, as used by standard SNP panels for linkage analysis.
Previously, only approximate scores could be computed for this pedigree on a standard PC and software for exact linkage computations such as Merlin (Abecasis et al., 2002) failed as reported by Albers et al. (2008).
One can precompute many of the terms needed in the formulas and the remaining computations are small compared to the total computation time used in linkage programs.
The database software, Microsoft SQL Server 2008 (Microsoft, Redmond, WA, USA), was used for data linkage, processing and computation.
Explicating these conditions facilitates the discovery of novel equivalence classes that reduce the computational cost of likelihood computations, as we show for genetic linkage analysis.
The linkage process involved the computation of a score for each potential match.
