Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/86205
Title: LDSplitDB : a database for studies of meiotic recombination hotspots in MHC using human genomic data
Authors: Guo, Jing
Chen, Hao
Yang, Peng
Lee, Yew Ti
Wu, Min
Przytycka, Teresa M.
Kwoh, Chee Keong
Zheng, Jie
Keywords: 1000 Genomes Project
MHC
Issue Date: 2018
Source: 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-.
Series/Report no.: BMC Medical Genomics
Abstract: 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.
URI: https://hdl.handle.net/10356/86205
http://hdl.handle.net/10220/45252
DOI: http://dx.doi.org/10.1186/s12920-018-0351-0
Rights: © 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.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCSE Journal Articles

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