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Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data
BACKGROUND: 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 genealo...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848240/ https://www.ncbi.nlm.nih.gov/pubmed/20184767 http://dx.doi.org/10.1186/1471-2164-11-139 |
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author | Polašek, Ozren Hayward, Caroline Bellenguez, Celine Vitart, Veronique Kolčić, Ivana McQuillan, Ruth Saftić, Vanja Gyllensten, Ulf Wilson, James F Rudan, Igor Wright, Alan F Campbell, Harry Leutenegger, Anne-Louise |
author_facet | Polašek, Ozren Hayward, Caroline Bellenguez, Celine Vitart, Veronique Kolčić, Ivana McQuillan, Ruth Saftić, Vanja Gyllensten, Ulf Wilson, James F Rudan, Igor Wright, Alan F Campbell, Harry Leutenegger, Anne-Louise |
author_sort | Polašek, Ozren |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: Simulation data suggested that multi-point FEstim is the method most strongly correlated to true homozygosity-by-descent. Correlation coefficients between the homozygosity-by-descent estimates were high but only for inbred individuals, with nearly absolute correlation between single-point measures. CONCLUSIONS: Deciding who is really inbred is a methodological challenge where multi-point approaches can be very helpful once the set of SNP markers is filtered to remove linkage disequilibrium. The use of several different methodological approaches and hence different homozygosity measures can help to distinguish between homozygosity-by-state and homozygosity-by-descent in studies investigating the effects of genomic autozygosity on human health. |
format | Text |
id | pubmed-2848240 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-28482402010-04-01 Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data Polašek, Ozren Hayward, Caroline Bellenguez, Celine Vitart, Veronique Kolčić, Ivana McQuillan, Ruth Saftić, Vanja Gyllensten, Ulf Wilson, James F Rudan, Igor Wright, Alan F Campbell, Harry Leutenegger, Anne-Louise BMC Genomics Research Article BACKGROUND: 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. RESULTS: Simulation data suggested that multi-point FEstim is the method most strongly correlated to true homozygosity-by-descent. Correlation coefficients between the homozygosity-by-descent estimates were high but only for inbred individuals, with nearly absolute correlation between single-point measures. CONCLUSIONS: Deciding who is really inbred is a methodological challenge where multi-point approaches can be very helpful once the set of SNP markers is filtered to remove linkage disequilibrium. The use of several different methodological approaches and hence different homozygosity measures can help to distinguish between homozygosity-by-state and homozygosity-by-descent in studies investigating the effects of genomic autozygosity on human health. BioMed Central 2010-02-25 /pmc/articles/PMC2848240/ /pubmed/20184767 http://dx.doi.org/10.1186/1471-2164-11-139 Text en Copyright ©2010 Polašek et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Polašek, Ozren Hayward, Caroline Bellenguez, Celine Vitart, Veronique Kolčić, Ivana McQuillan, Ruth Saftić, Vanja Gyllensten, Ulf Wilson, James F Rudan, Igor Wright, Alan F Campbell, Harry Leutenegger, Anne-Louise Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data |
title | Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data |
title_full | Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data |
title_fullStr | Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data |
title_full_unstemmed | Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data |
title_short | Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data |
title_sort | comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848240/ https://www.ncbi.nlm.nih.gov/pubmed/20184767 http://dx.doi.org/10.1186/1471-2164-11-139 |
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