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Title: ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis
Authors: Przytycka, Teresa M.
Zheng, Jie
Chen, Hao
Yang, Peng
Guo, Jing
Kwoh, Chee Keong
Keywords: Meiotic recombination hotspot
Individual recombination strength
Issue Date: 2015
Source: Chen, H., Yang, P., Guo, J., Kwoh, C. K., Przytycka, T. M., & Zheng, J. (2015). ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis. BMC Genomics, 16(Suppl 12), S1-.
Series/Report no.: BMC Genomics
Abstract: Background: Meiotic recombination hotspots play important roles in various aspects of genomics, but the underlying mechanisms for regulating the locations and strengths of recombination hotspots are not yet fully revealed. Most existing algorithms for estimating recombination rates from sequence polymorphism data can only output average recombination rates of a population, although there is evidence for the heterogeneity in recombination rates among individuals. For genome-wide association studies (GWAS) of recombination hotspots, an efficient algorithm that estimates the individualized strengths of recombination hotspots is highly desirable. Results: In this work, we propose a novel graph mining algorithm named ARG-walker, based on random walks on ancestral recombination graphs (ARG), to estimate individual-specific recombination hotspot strengths. Extensive simulations demonstrate that ARG-walker is able to distinguish the hot allele of a recombination hotspot from the cold allele. Integrated with output of ARG-walker, we performed GWAS on the phased haplotype data of the 22 autosome chromosomes of the HapMap Asian population samples of Chinese and Japanese (JPT+CHB). Significant cis-regulatory signals have been detected, which is corroborated by the enrichment of the well-known 13-mer motif CCNCCNTNNCCNC of PRDM9 protein. Moreover, two new DNA motifs have been identified in the flanking regions of the significantly associated SNPs (single nucleotide polymorphisms), which are likely to be new cis-regulatory elements of meiotic recombination hotspots of the human genome. Conclusions: Our results on both simulated and real data suggest that ARG-walker is a promising new method for estimating the individual recombination variations. In the future, it could be used to uncover the mechanisms of recombination regulation and human diseases related with recombination hotspots.
ISSN: 1471-2164
DOI: 10.1186/1471-2164-16-S12-S1
Schools: School of Computer Engineering 
Rights: © 2015 Chen et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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