Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. Unfortunately, when data entries are missing, as is often the case in real laboratory data, the resulting formal problem IPPH, which...

In this report, we compared haplotyping approaches using families and unrelated individuals on the simulated rheumatoid arthritis (RA) data in Problem 3 from Genetic Analysis Workshop (GAW) 15. To investigate these two approaches, we picked two representative programs: PedPhase and fastPHASE, respectively, for each approach. PedPhase is a rule-based method focusing on the haplotyping constraint...

An efficient rule-based algorithm is presented for haplotype inference from general pedigree genotype data, with the assumption of no recombination. This algorithm generalizes previous algorithms to handle the cases where some pedigree founders are not genotyped, provided that for each nuclear family at least one parent is genotyped and each non-genotyped founder appears in exactly one nuclear ...

Single nucleotide polymorphisms (SNPs) within a gene region have often been studied to determine their effect on phenotype. Although a single base pair change can produce a phenotypic change, phenotype is often influenced by the presence of multiple polymorphisms and their relative positions within a given region. For example, if multiple changes occur in a promoter region, how they influence g...

In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method ca...

Available commercial kits only screen for the most common cystic fibrosis transmembrane conductance regulator (CFTR) mutations causing classic cystic fibrosis and for the Tn variant in IVS8. However, full scanning of CFTR is needed for the diagnosis of patients with cystic fibrosis or CFTR-related disorders (including congenital bilateral absence of the vas deferens) bearing rare mutations. Sta...

For diploid organisms (e.g. humans), each chromosome is present in two non-exact copies and the description of all the data from a single chromosome is called a haplotype. Obtaining haplotype data is important in applications such as analyzing complex diseases, however this is a very difficult problem to solve experimentally and finding mixed genotype data is much less technically difficult and...

The line graph of a G has one node per each edge G, two them being adjacent only when the corresponding edges have in common. In this work, we consider problem finding minimum number to delete so that resulting is graph, which presents an interesting application haplotyping diploid organisms. We propose Integer Linear Programming formulation for problem. compare our approach with other existing...