Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

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dc.contributor.authorCeballos, Francisco C.
dc.contributor.authorHazelhurst, Scott
dc.contributor.authorRamsay, Michèle
dc.date.accessioned2024-09-23T07:15:47Z
dc.date.available2024-09-23T07:15:47Z
dc.date.issued2018
dc.description.abstractBackground: Runs of Homozygosity (ROH) are genomic regions where identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. Results: Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. By allowing heterozygous SNPs per window, using the PLINK homozygosity function and non-parametric analysis, we were able to obtain non-significant differences in number ROH, mean ROH size and total sum of ROH between data sets using the different technologies for almost all populations. Conclusions: By allowing 3 heterozygous SNPs per ROH when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using SNP array and WGS low coverage technologies.
dc.description.sponsorshipNational Research Foundation (NRF).
dc.description.submitterPM2024
dc.facultyFaculty of Science
dc.identifier0000-0001-7113-7387
dc.identifier0000-0002-0581-149X
dc.identifier0000-0002-4156-4801
dc.identifier.citationCeballos, F.C., Hazelhurst, S. & Ramsay, M. Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data. BMC Genomics 19, 106 (2018). https://doi.org/10.1186/s12864-018-4489-0
dc.identifier.issn1471-2164 (online)
dc.identifier.other10.1186/s12864-018-4489-0
dc.identifier.urihttps://hdl.handle.net/10539/41041
dc.journal.titleBMC Genomics
dc.language.isoen
dc.publisherBMC
dc.relation.ispartofseriesVol. 19; No. 106
dc.rights© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.
dc.schoolSchool of Molecular and Cell Biology
dc.subjectRuns of Homozygosity
dc.subjectROH
dc.subjectSNP array data
dc.subjectWGS low coverage data
dc.subject.otherSDG-17: Partnerships for the goals
dc.titleAssessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data
dc.typeArticle
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