Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes

Libin Deng; Dake Zhang; Elliott Richards; Xiaoli Tang; Jin Fang; Fei Long; Yan Wang

doi:10.1016/S1673-8527(08)60163-0

Volume 36 Issue 12

Dec. 2009

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Article Navigation > Journal of Genetics and Genomics > 2009 > 36(12): 703-709

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Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes

doi: 10.1016/S1673-8527(08)60163-0

a
Faculty of Basic Medical Science, Nanchang University, Nanchang 330006, China
b
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
c
Graduate School of Chinese Academy of Sciences, Beijing 100049, China
d
Department of Biology, College of Life Sciences, Brigham Young University, Provo UT 84602, USA
e
The Laboratory Center of Medicine, Nanchang University, Nanchang 330006, China

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Corresponding author: E-mail address: wyjxmc@sina.com (Yan Wang)
Received Date: 2009-05-31
Accepted Date: 2009-11-24
Rev Recd Date: 2009-11-12

Available Online: 2009-12-21

Publish Date: 2009-12-20

Abstract

Abstract

Transmission distortion (TD) is a significant departure from Mendelian predictions of genes or chromosomes to offspring. While many biological processes have been implicated, there is still much to be understood about TD in humans. Here we present our findings from a genome-wide scan for evidence of TD using haplotype data of 60 trio families from the International HapMap Project. Fisher's exact test was applied to assess the extent of TD in 629,958 SNPs across the autosomes. Based on the empirical distribution of and further permutation tests, we identified 1,205 outlier loci and 224 candidate genes with TD. Using the PANTHER gene ontology database, we found 19 categories of biological processes with an enrichment of candidate genes. In particular, the “protein phosphorylation” category contained the largest number of candidates in both HapMap samples. Further analysis uncovered an intriguing non-synonymous change in PPP1R12B, a gene related to protein phosphorylation, which appears to influence the allele transmission from male parents in the YRI (Yoruba from Ibadan, Nigeria) population. Our findings also indicate an ethnicity-related property of TD signatures in HapMap samples and provide new clues for our understanding of TD in humans.
- transmission distortion,
- HapMap Project,
- gene ontology

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References(22)

References

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