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...

Let $D$ be a finite and simple digraph with vertex set $V(D)$‎.‎A signed total Roman $k$-dominating function (STR$k$DF) on‎‎$D$ is a function $f:V(D)rightarrow{-1‎, ‎1‎, ‎2}$ satisfying the conditions‎‎that (i) $sum_{xin N^{-}(v)}f(x)ge k$ for each‎‎$vin V(D)$‎, ‎where $N^{-}(v)$ consists of all vertices of $D$ from‎‎which arcs go into $v$‎, ‎and (ii) every vertex $u$ for which‎‎$f(u)=-1$ has a...

The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR repeat units. These methods do not allow for the full resolution of STR base composition that sequencin...

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...

BACKGROUND Molecular haplotyping is a developing technology with great potential for use in clinical diagnostics. We describe a haplotyping method that uses PCR combined with hybridization probes. METHODS We designed a LightCycler assay that uses fluorescence resonance energy transfer hybridization probes to haplotype the poly(TG) and polyT (TG-T) tract in the IVS-8 region of the CFTR gene. T...

MOTIVATION In genetic studies of complex diseases, haplotypes provide more information than genotypes. However, haplotyping is much more difficult than genotyping using biological techniques. Therefore effective computational techniques have been in demand. The individual haplotyping problem is the computational problem of inducing a pair of haplotypes from an individual's aligned SNP fragments...

The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the haplotypes to be embedded in a perfect phylogeny evolutionary tree, a well-known biologically-motivated data structure. For PH we extend recent work of [16] by ...

To analyze the function of DNA, researchers have to obtain each haplotype, the genetic constitution of an individual chromosome, of an individual for analysis. Due to the significant efforts required in collecting haplotypes, the descriptions of one conflated pair of haplotypes called genotypes are usually collected. Since the genotype data contains insufficient information to identify the comb...