Many important problems in bioinformatics and genetics require analyses that are NP-complete. For example, one of the basic problems facing researchers that analyze pedigrees—data that represents relationships and genetic traits of a set of individuals—is evaluating whether they are consistent with the Mendelian laws of inheritance. This problem is NP-complete and several specialized algorithms...

A 1024 cpu parallel computer is used to obtain simulated genotypes in the Tristan da Cunha pedigree using random local updating methods. A four-colour theorem is invoked to justify simultaneous updating. Multiple copies of the program are run simultaneously. The results are used to infer the source of the B allele of the ABO blood group that is present in the population.allel, pedigree analysis.

There seems to be no limit to the complexity of computations that genetic linkage analysts want to do. Two primary factors that increase the length of computations are pedigree loops and unknown genotypes. I describe the implementation in FASTLINK of some algorithmic improvements to partly address the problems of pedigree loops and unknown genotypes. LINKAGE is by far the most popular software ...

AIM To analyze mutations in transforming growth factor beta-induced (TGFBI) gene in a Chinese pedigree with Reis-Bücklers corneal dystrophy (RBCD, also known as GCD3). METHODS In a five-generation Chinese family, eight members were identified with RBCD and the rest were unaffected. All members of the family underwent complete ophthalmologic examinations. Exons of TGFBI were amplified by polym...

Genetic Analysis Workshop 18 provided a platform for evaluating genomic prediction power based on single-nucleotide polymorphisms from single-nucleotide polymorphism array data and sequencing data. Also, Genetic Analysis Workshop 18 provided a diverse pedigree structure to be explored in prediction. In this study, we attempted to combine pedigree information with single-nucleotide polymorphism ...

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected sample...

PURPOSE To analyze transforming growth factor beta-induced (TGFBI) gene mutations in a Chinese pedigree with Reis-Bücklers dystrophy (RBCD). METHODS In a four-generation Chinese family with Reis-Bücklers dystrophy, six members were patients and the rest were unaffected. All members of the family underwent complete ophthalmologic examinations. Exons of TGFBI were amplified by polymerase chain ...

PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to 'walk' through family ties by point-and-clicking on per...

We have developed algorithms for the likelihood estimation of additive genetic models for quantitative traits on large pedigrees. The approach uses the expectation L-maximization (EM) algorithm, but avoids intensive computation. In this paper, we focus on extensions of previous work to the case of multivariate data. We exemplify the approach by analyses of bivariate data on a four-generation, 9...

Single Step methods combine pedigree relationships and marker genotypes in a single conceptual and streamlined framework based on extending animal model BLUP to include marker genotypes. The extension can be done because genotypes at markers follow covariances described by the pedigree. This results in a relationship matrix that combines pedigree and markers, called H. Fitting H in Henderson’s ...