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The distribution and functional relevance analysis of runs of homozygosity (ROHs) in Chinese Han female population

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Abstract

Extended homozygosity is a genomic region in which the copies inherited from parents are identical, and has obvious inter-individual differences in length and frequency. Runs of homozygosity (ROHs), regarded as a type of structure variations, may have potential capacity in regulating gene transcription. To learn more about the genome-wide distribution of ROH regions in humans and understand the potential roles, this study applied ROH-based approach to quantify and characterize ROHs in 41 Chinese Han female subjects, and test potential associations between ROHs and mRNA expressions by eQTL analysis to ascertain whether ROHs are relevant to gene transcription in peripheral blood mononuclear cells (PBMCs). 10,884 ROH regions were identified in human genome. The average cumulative length of ROH regions was 217,250 ± 20,241 kb. The number of core segments in each chromosome generally matched the total length of corresponding chromosome, i.e., the longer the chromosome, the more the core segments. Genes located in the core regions of ROH were significantly enriched in multiple basic metabolism pathways. A total of 226 cis-eQTLs and 178 trans-eQTLs were identified. The cis-effect size was mainly concentrated at ± 0.5; and the trans-effect size was mainly concentrated at −1.5 and 1.0. Genes with eQTL effects were significantly enriched in functions related to protein binding, cytosol, nucleoplasm, nuclear membrane, protein binding and citrate metabolic process. This study described comprehensive distributions and characteristics of ROH in Han female Chinese, and recognized the significant role of ROH associated with gene transcription in human PBMC.

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Authors and Affiliations

  1. Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People’s Republic of China

    Yi-Hua Lu, Bing-Hua Wang, Wei Xia, Xing-Bo Mo, Long-Fei Wu, Xiao-Wei Zhu, Pei He, Fang-Fei Xie, Xin Lu, Fei-Yan Deng & Shu-Feng Lei

  2. Department of Epidemiology and Health Statistics, School of Public Health, Nantong University, Nantong, 226019, Jiangsu, People’s Republic of China

    Yi-Hua Lu

  3. Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People’s Republic of China

    Yi-Hua Lu, Bing-Hua Wang, Wei Xia, Xing-Bo Mo, Long-Fei Wu, Xiao-Wei Zhu, Pei He, Fang-Fei Xie, Xin Lu, Fei-Yan Deng & Shu-Feng Lei

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  1. Yi-Hua Lu
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  2. Bing-Hua Wang
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  3. Wei Xia
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  4. Xing-Bo Mo
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  8. Fang-Fei Xie
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  9. Xin Lu
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  10. Fei-Yan Deng
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Corresponding authors

Correspondence to Fei-Yan Deng or Shu-Feng Lei.

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Funding

The study was supported by Natural Science Foundation of China (81502868, 81541068, 81473046, 31271336, 81373010, 31401079, and 81401343), the Natural Science Foundation of Jiangsu Province (BK20130300, BK20150346), the Natural Science Research Project of Jiangsu Provincial Higher Education (16KJA330001), the Startup Fund from Soochow University (Q413900112, Q413900712), and a Project of the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Conflict of interest

None of the authors has any conflict of interest to disclose.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. The study was approved by Institutional Research Ethic Board at the Soochow University. Informed consent was obtained from all individual participants included in the study.

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Communicated by S. Hohmann.

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Lu, YH., Wang, BH., Xia, W. et al. The distribution and functional relevance analysis of runs of homozygosity (ROHs) in Chinese Han female population. Mol Genet Genomics 293, 197–206 (2018). https://doi.org/10.1007/s00438-017-1378-1

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  • DOI: https://doi.org/10.1007/s00438-017-1378-1

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