Construction of fine SNP haplotypes and haplotype blocks in 5 genes in the centromere of chromosome 15 in Chinese Han subjects

Huang, Weijun; Li, Caixia; Yang, Keqin; Sun, Jiandong; Zhou, Yan; Fang, Jian; Wang, Yiming

doi:10.1007/bf03184035

Cited by 4 publications

(1 citation statement)

References 13 publications

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“…The full animal model included fixed effects of marker genotype, birth year, season of birth (spring vs. fall), age of dam, sire, farm, sex, and random effects (permanent environment, animal, and residual). The effects associated with season of birth, age of dam, sire, farm, and sex were not matched in the linear model, as the preliminary statistical analyses indicated that these effects do not have a significant influence on the variability of traits in the analyzed population [9]. The reduced animal model and SPSS software (version 18.0) were used to analyze the relationship between the genotypes and traits.…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Bovine HSD17B8 gene and its relationship with growth and meat quality traits

Chen

et al. 2015

Science Bulletin

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Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Bovine HSD17B8 gene and its relationship with growth and meat quality traits

Chen

et al. 2015

Science Bulletin

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High resolution linkage disequilibrium and haplotype maps for the genes in the centromeric region of chromosome 15 in Tibetans and comparisons with Han population

Huang

Labu

et al. 2006

CHINESE SCI BULL

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Genetic variations and their functional implications have been one of the focuses in recent genome research. With the release of the HapMap by the International Consortium, and the availability of the ultra-high-volume genotyping platform, it will soon be possible to use genome-wide association approach to identify genetic variations responsible for complex traits/diseases. While the power of this approach is generally agreed, it is a debated issue as to how much population difference should be exploited, and how best it should be applied. To address this issue we have sequenced 7 genes in the centromeric region of chromosome 15, investigated their SNPs, SNP frequencies, tagSNPs, LD structures, and haplotypes in 50 Tibetan subjects, and compared them with those from the Han population. Genetic diversities between the two populations were also quantified. Our results show that the overall genetic variation between the two populations is very little, but there are differences, primarily in allele frequencies, which is a dominating factor for haplotypes and tagSNPs. In general Tibetans have longer LD and less diversity in the region studied. These data provide genetic evidence for the close relationship between the two populations, and support the idea that all populations are fundamentally the same, but also indicate population variations, particularly in allele frequency, should be taken into account in complex traits/ diseases analysis. Data obtained in this investigation not only help us understand the genome region, but also provide road maps for variation study in the genes/ region in Tibetan population.

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A method for haplotype inference in general pedigrees without recombination

Wang

Qiu

et al. 2007

CHINESE SCI BULL

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The abundance of single nucleotide polymorphisms (SNPs) makes the haplotype-based method instead of single-maker-oriented method the main approach to association studies on QTL mapping. The key problem in haploptype-based method is how to reconstruct haplotypes from genotype data. Directly assaying haplotypes in diploid individuals by experimental methods is too expensive, therefore the in silico haplotyping-determination methods are the major choice at the present. This paper presents a rapid and reliable algorithm for haplotype reconstruction for tightly linked SNPs in general pedigrees. It is based on six rules and consists of three steps. First, the parental origins of alleles in offspring are assigned conditional on genotypes in parent-offspring trios; second, the redundant haplotypes are eliminated based on the six rules; and finally, the most likely haplotype combinations are chosen via maximum likelihood method. Our method was verified and compared with PEDPHASE by simulated data with different pedigree sizes, numbers of loci, and proportions of missing genotypes. The result shows that our algorithm was superior to PEDPHASE in terms of computing time and accuracy of haplotype estimation. The computing time for 100 runs was 10-15 times less and the accuracy was 4%-10% higher than PEDPHASE. The result also indicates that our method was very robust and was hardly affected by pedigree size, number of loci, and proportion of missing genotypes.haplotyping, rule-based algorithm, general pedigree, no recombination, SNP With the completion of the Human Genome Project, millions of single nucleotide polymorphisms (SNPs) have become a powerful tool to identify genetic variants in the human genome, which can be used to fine map gene or quantitative trait loci (QTLs) in short haplotype blocks. Many studies show that haplotypes may provide more power and higher precision than single marker in gene mapping [1 -4] . The key problem in haploptypebased method is how to reconstruct haplotypes. Directly assaying haplotypes in diploid individuals by experimental methods is too expensive; therefore in silico haplotyping-determination methods are the major choice at the present [2] . Genotype data used in haplotyping can be divided into two categories: pedigree data and population data. Since pedigree information can reduce phase ambiguity and improve the efficiency of haplotype determination, and pedigree data can be colleted easily in livestock population, more attention is paid to pedigree data than population data for haplotype inference in livestock population. Therefore, in this paper we only deal with the haplotype inference with pedigree data.There are two categories of computational methods for haplotype inference in general pedigrees: statistical methods [5,6] and ruled-methods [7][8][9] . Statistical methods have some good qualities, such as inferring haplotype configurations with likelihood estimations. But these methods need more assumptions, or can only handle small data sets, or require complete data [2] . On the...

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Construction of fine SNP haplotypes and haplotype blocks in 5 genes in the centromere of chromosome 15 in Chinese Han subjects

Cited by 4 publications

References 13 publications

Bovine HSD17B8 gene and its relationship with growth and meat quality traits

Bovine HSD17B8 gene and its relationship with growth and meat quality traits

High resolution linkage disequilibrium and haplotype maps for the genes in the centromeric region of chromosome 15 in Tibetans and comparisons with Han population

A method for haplotype inference in general pedigrees without recombination

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