Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference

We have developed a software package (LIden) for identifying linked regions using high-density SNP genotype data. We focus on handling the case where the genotype data for the whole chromosome of one of the parents in a nuclear family is missing. We use the minimum recombinant model for haplotype inference in pedigrees. Several local optimization algorithms are used to infer the haplotype of each individual and determine the linked regions based on the inferred haplotype data. We have developed a more flexible method to combine nuclear families to further refine (reduce the length of) the linked regions.Our new package (LIden) is efficient software for linked region detection using high-density SNP genotype data. LIden can handle some important cases where the existing programs do not work well. In particular, the new package can handle many cases where the genotype data of one of the two parents is missing for the entire chromosome. The running time of the program is O(mn), where m is the number of members in the family and n is the number of SNP sites in the chromosome. LIden is specifically suitable for handling big sized families. This research also demonstrates another practical use of the minimum recombinant model for haplotype inference in pedigrees.The software package can be downloaded at http://www.cs.cityu.edu.hk/~lwang/software/Link webcite.With the completion of the human genome sequencing project and the development of HapMap project [1], our understanding of human genomic sequences has been extended dramatically. Due to the development of SNP genotyping technology, genotyping of hundreds of thousands of single nucleotide polymorphism (SNP) markers in a high-throughput format has become a routine job in many labs.Compared to classical genotyping methods mainly using microsatellite markers, SNP genotyping is faster and easier. It provides complete coverage of the genome and much more information on covered regions. Linkage analysis is a method to identi