Journal article
Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens
L Henden, S Lee, I Mueller, A Barry, M Bahlo
Plos Genetics | PUBLIC LIBRARY SCIENCE | Published : 2018
Open access
Abstract
Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized in analysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections. Using the inferred IBD status at genomic location..
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Awarded by Wellcome Trust
Funding Acknowledgements
This work was supported by National Health and Medical Research Council (NHMRC) Program Grant (APP1054618) and NHMRC Senior Research Fellowship (1002098) to MB and a NHMRC Project Grant (APP1027108) awarded to AB. LH was supported by the John and Patricia Farrant Scholarship and the Australian Postgraduate Award Scholarship. SL was also supported by the Australian Postgraduate Award Scholarship. This work was also supported by Victorian State Government Operational Infrastructure Support and the Australian Government NHMRC IRISS funding. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.