LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data

Background: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulatio...

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Main Authors: Guo, Jing, Chen, Hao, Yang, Peng, Lee, Yew Ti, Wu, Min, Przytycka, Teresa M., Kwoh, Chee Keong, Zheng, Jie
Other Authors: School of Computer Science and Engineering
Format: Article
Language:English
Published: 2018
Subjects:
MHC
Online Access:https://hdl.handle.net/10356/86205
http://hdl.handle.net/10220/45252
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-862052020-03-07T11:48:54Z LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data Guo, Jing Chen, Hao Yang, Peng Lee, Yew Ti Wu, Min Przytycka, Teresa M. Kwoh, Chee Keong Zheng, Jie School of Computer Science and Engineering 1000 Genomes Project MHC Background: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. Method: To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. Conclusion: To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. MOE (Min. of Education, S’pore) Published version 2018-07-26T06:43:36Z 2019-12-06T16:18:01Z 2018-07-26T06:43:36Z 2019-12-06T16:18:01Z 2018 Journal Article Guo, J., Chen, H., Yang, P., Lee, Y. T., Wu, M., Przytycka, T. M., et al. (2018). LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data. BMC Medical Genomics, 11(S2), 27-. https://hdl.handle.net/10356/86205 http://hdl.handle.net/10220/45252 10.1186/s12920-018-0351-0 en BMC Medical Genomics © 2018 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. 8 p. application/pdf
institution Nanyang Technological University
building NTU Library
country Singapore
collection DR-NTU
language English
topic 1000 Genomes Project
MHC
spellingShingle 1000 Genomes Project
MHC
Guo, Jing
Chen, Hao
Yang, Peng
Lee, Yew Ti
Wu, Min
Przytycka, Teresa M.
Kwoh, Chee Keong
Zheng, Jie
LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data
description Background: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. Method: To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. Conclusion: To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system.
author2 School of Computer Science and Engineering
author_facet School of Computer Science and Engineering
Guo, Jing
Chen, Hao
Yang, Peng
Lee, Yew Ti
Wu, Min
Przytycka, Teresa M.
Kwoh, Chee Keong
Zheng, Jie
format Article
author Guo, Jing
Chen, Hao
Yang, Peng
Lee, Yew Ti
Wu, Min
Przytycka, Teresa M.
Kwoh, Chee Keong
Zheng, Jie
author_sort Guo, Jing
title LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data
title_short LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data
title_full LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data
title_fullStr LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data
title_full_unstemmed LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data
title_sort ldsplitdb : a database for studies of meiotic recombination hotspots in mhc using human genomic data
publishDate 2018
url https://hdl.handle.net/10356/86205
http://hdl.handle.net/10220/45252
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