A new method for haplotype inference including full-sib information

التفاصيل البيبلوغرافية
العنوان: A new method for haplotype inference including full-sib information
المؤلفون: Henner Simianer, Qin Zhang, Xiang Dong Ding
المصدر: Genetics. 177(3)
سنة النشر: 2007
مصطلحات موضوعية: Male, Linkage disequilibrium, Genotype, Word error rate, Close relatives, Biology, Investigations, 03 medical and health sciences, 0302 clinical medicine, Haplotype inference, Statistics, Genetics, Animals, Humans, Computer Simulation, Nuclear family, 030304 developmental biology, Linkage (software), 0303 health sciences, Likelihood Functions, Models, Genetic, Haplotype, Pedigree, Haplotypes, Female, 030217 neurology & neurosurgery, Algorithms, Alternative strategy
الوصف: Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families, can be an alternative strategy in determining linkage phase and estimating haplotype frequencies. In the case of no possibility to obtain genotypes for parents, and only full-sib information being used, a new approach is suggested to infer phase and to reconstruct haplotypes. We present a maximum-likelihood method via an expectation-maximization algorithm, called FSHAP, using only full-sib information when parent information is not available. FSHAP can deal with families with an arbitrary number of children, and missing parents or missing genotypes can be handled as well. In a simulation study we compare FSHAP with another existing expectation-maximization (EM)-based approach (FAMHAP), the conditioning approach implemented in FBAT and GENEHUNTER, which is only pedigree based and assumes linkage equilibrium. In most situations, FSHAP has the smallest discrepancy of haplotype frequency estimation and the lowest error rate in haplotype reconstruction, only in some cases FAMHAP yields comparable results. GENEHUNTER produces the largest discrepancy, and FBAT produces the highest error rate in offspring in most situations. Among the methods compared, FSHAP has the highest accuracy in reconstructing the diplotypes of the unavailable parents. Potential limitations of the method, e.g., in analyzing very large haplotypes, are indicated and possible solutions are discussed.
تدمد: 0016-6731
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e11ba3f85d8cd8f745d9d79dc94d499d
https://pubmed.ncbi.nlm.nih.gov/17947415
Rights: OPEN
رقم الانضمام: edsair.doi.dedup.....e11ba3f85d8cd8f745d9d79dc94d499d
قاعدة البيانات: OpenAIRE