ArticlePloS one2013
cgaTOH: extended approach for identifying tracts of homozygosity.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Genome-wide analysis reveals differential admixture dynamics and historical demographic contractions in African cattle.Scientific reports · 2026Article
- Genomic diversity and selection signatures in Asian Zebu Cattle: insights into adaptation and genetic erosion.Scientific reports · 2025Article
- Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep.Animals : an open access journal from MDPI · 2022Article
- Population structure, inbreeding and admixture in local cattle populations managed by community-based breeding programs in Burkina Faso.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2021Article
- Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe.Genetics, selection, evolution : GSE · 2021Article
- Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight.Horticulture research · 2021Article
- A Mix of Old British and Modern European Breeds: Genomic Prediction of Breed Composition of Smallholder Pigs in Uganda.Frontiers in genetics · 2021Article
- A detailed characteristics of bias associated with long runs of homozygosity identification based on medium density SNP microarrays.Journal of genomics · 2020Article
- Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds.Frontiers in genetics · 2020Article
- A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types.Animals : an open access journal from MDPI · 2019Article
- Timing and Extent of Inbreeding in African Goats.Frontiers in genetics · 2019Article
- Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances.Genetics, selection, evolution : GSE · 2018Article
- Article
- GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification.Bioinformatics (Oxford, England) · 2017Article
- The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle.Journal of applied genetics · 2016Article
- Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors.Genetics, selection, evolution : GSE · 2013Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Identification of disease variants via homozygosity mapping and investigation of the effects of genome-wide homozygosity regions on traits of biomedical importance have been widely applied recently. Nonetheless, the existing methods and algorithms to identify long tracts of homozygosity (TOH) are not able to provide efficient and rigorous regions for further downstream association investigation. We expanded current methods to identify TOHs by defining "surrogate-TOH", a region covering a cluster of TOHs with specific characteristics. Our defined surrogate-TOH includes cTOH, viz a common TOH region where at least ten TOHs present; gTOH, whereby a group of highly overlapping TOHs share proximal boundaries; and aTOH, which are allelically-matched TOHs. Searching for gTOH and aTOH was based on a repeated binary spectral clustering algorithm, where a hierarchy of clusters is created and represented by a TOH cluster tree. Based on the proposed method of identifying different species of surrogate-TOH, our cgaTOH software was developed. The software provides an intuitive and interactive visualization tool for better investigation of the high-throughput output with special interactive navigation rings, which will find its applicability in both conventional association studies and more sophisticated downstream analyses. NCBI genome map viewer is incorporated into the system. Moreover, we discuss the choice of implementing appropriate empirical ranges of critical parameters by applying to disease models. This method identifies various patterned clusters of SNPs demonstrating extended homozygosity, thus one can observe different aspects of the multi-faceted characteristics of TOHs.
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