A detailed characteristics of bias associated with long runs of homozygosity identification based on medium density SNP microarrays

Tomasz Szmatoła , Artur Gurgul , Igor Jasielczuk , Weiwei Fu , Katarzyna Ropka-Molik

Abstract

In the present study, runs of homozygosity (ROH) detected with the use of a standard bovine 54k single nucleotide polymorphism (SNP) genotyping assay and two different ROH detection approaches, based on 50 (M1) or 15 (M2) consecutive SNPs, were compared with results of whole genome sequencing. Both microarray-based methods accurately recognised medium-sized ROH, however, it was found that M2 method seemed to better than M1 identify short ROH, but highly overestimated their number, leading to numerous false positive calls. Moreover, long ROH identified with microarray data tended to break into shorter segments in sequencing data because of the presence of regions with high heterozygosity within the ROH sequences. This may indicate, that these long ROH are formed by closely positioned shorter homozygous segments that may be of older origin or may be created by two similar but not identical haplotypes, showing minor internal recombination signs. Such finding also suggests that at least some of the results of previous studies in regard to long ROH may be biased leading to inaccurate estimations of genomes autozygosity via ROH classification into length categories.
Author Tomasz Szmatoła (VET) - The National Research Institute of Animal Production
Tomasz Szmatoła,,
- University Centre for Veterinary Medicine UJ-UR
, Artur Gurgul (VET / CfEaIM) - The National Research Institute of Animal Production
Artur Gurgul,,
- Center for Experimental and Innovative Medicine
, Igor Jasielczuk (VET) - The National Research Institute of Animal Production
Igor Jasielczuk ,,
- University Centre for Veterinary Medicine UJ-UR
, Weiwei Fu - College of Animal Science and Technology, Northwest A&F University, Yangling
Weiwei Fu,,
-
, Katarzyna Ropka-Molik - The National Research Institute of Animal Production
Katarzyna Ropka-Molik,,
-
Journal seriesJournal of Genomics, ISSN 1839-9940, (N/A 100 pkt)
Issue year2020
Vol8
Pages43-48
Publication size in sheets0.5
Keywords in Englishruns of homozygosity, autozygosity, microarray, next generation sequencing
DOIDOI:10.7150/jgen.39147
URL https://www.jgenomics.com/v08p0043.pdf
Languageen angielski
LicenseJournal (articles only); author's original; Uznanie Autorstwa (CC-BY); after publication
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A detailed characteristics of bias associated with long runs of homozygosity identification based on medium density SNP microarrays of 06-05-2020
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Score (nominal)100
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