Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

Ozren Polasek; Caroline Hayward; Celine Bellenguez; Veronique Vitart; Ivana Kolcić; Ruth McQuillan; Vanja Saftić; Ulf Gyllensten; James F Wilson; Igor Rudan; Alan F Wright; Harry Campbell; Anne-Louise Leutenegger

doi:10.1186/1471-2164-11-139

Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

Ozren Polasek, Caroline Hayward, Celine Bellenguez, Veronique Vitart, Ivana Kolcić, Ruth McQuillan, Vanja Saftić, Ulf Gyllensten, James F Wilson, Igor Rudan, Alan F Wright, Harry Campbell, Anne-Louise Leutenegger

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Abstract / Description of output

Genome-wide homozygosity estimation from genomic data is becoming an increasingly interesting research topic. The aim of this study was to compare different methods for estimating individual homozygosity-by-descent based on the information from human genome-wide scans rather than genealogies. We considered the four most commonly used methods and investigated their applicability to single-nucleotide polymorphism (SNP) data in both a simulation study and by using the human genotyped data. A total of 986 inhabitants from the isolated Island of Vis, Croatia (where inbreeding is present, but no pedigree-based inbreeding was observed at the level of F > 0.0625) were included in this study. All individuals were genotyped with the Illumina HumanHap300 array with 317,503 SNP markers.

Original language	English
Pages (from-to)	139
Journal	BMC Genomics
Volume	11
DOIs	https://doi.org/10.1186/1471-2164-11-139
Publication status	Published - 2010

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10.1186/1471-2164-11-139

Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data
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Polasek, O., Hayward, C., Bellenguez, C., Vitart, V., Kolcić, I., McQuillan, R., Saftić, V., Gyllensten, U., Wilson, J. F., Rudan, I., Wright, A. F., Campbell, H., & Leutenegger, A.-L. (2010). Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data. BMC Genomics, 11, 139. https://doi.org/10.1186/1471-2164-11-139

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abstract = "Genome-wide homozygosity estimation from genomic data is becoming an increasingly interesting research topic. The aim of this study was to compare different methods for estimating individual homozygosity-by-descent based on the information from human genome-wide scans rather than genealogies. We considered the four most commonly used methods and investigated their applicability to single-nucleotide polymorphism (SNP) data in both a simulation study and by using the human genotyped data. A total of 986 inhabitants from the isolated Island of Vis, Croatia (where inbreeding is present, but no pedigree-based inbreeding was observed at the level of F > 0.0625) were included in this study. All individuals were genotyped with the Illumina HumanHap300 array with 317,503 SNP markers.",

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AU - Polasek, Ozren

AU - Hayward, Caroline

AU - Bellenguez, Celine

AU - Vitart, Veronique

AU - Kolcić, Ivana

AU - McQuillan, Ruth

AU - Saftić, Vanja

AU - Gyllensten, Ulf

AU - Wilson, James F

AU - Rudan, Igor

AU - Wright, Alan F

AU - Campbell, Harry

AU - Leutenegger, Anne-Louise

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AB - Genome-wide homozygosity estimation from genomic data is becoming an increasingly interesting research topic. The aim of this study was to compare different methods for estimating individual homozygosity-by-descent based on the information from human genome-wide scans rather than genealogies. We considered the four most commonly used methods and investigated their applicability to single-nucleotide polymorphism (SNP) data in both a simulation study and by using the human genotyped data. A total of 986 inhabitants from the isolated Island of Vis, Croatia (where inbreeding is present, but no pedigree-based inbreeding was observed at the level of F > 0.0625) were included in this study. All individuals were genotyped with the Illumina HumanHap300 array with 317,503 SNP markers.

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JO - BMC Genomics

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Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

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