PMID: identifiant
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 (20184767)  |
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| titre : |
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Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data. |
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| auteur(s) : |
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Ozren Polašek ( ) 1, 2, Caroline Hayward3, Céline Bellenguez4, Veronique Vitart3, Ivana Kolčić2, Ruth McQuillan1, Vanja Saftić5, Ulf Gyllensten6, James Wilson1, Igor Rudan1, 7, 8, Alan Wright3, Harry Campbell1, Anne-Louise Leutenegger4 |
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| laboratoire : |
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| résumé : |
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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. |
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| domaine : |
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Sciences du Vivant/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique
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langue du texte
intégral : |
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Anglais |
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| ISSN : |
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1471-2164 |
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| type de publication : |
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Articles dans des revues avec comité de lecture |
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| DOI : |
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10.1186/1471-2164-11-139 |
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| Audience : |
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internationale |
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| date de publication : |
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2010 |
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date de publication
électronique : |
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25/02/2010 |
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| volume : |
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11 |
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| numéro : |
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1 |
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| page, identifiant, ... : |
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139 |
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| Descripteur(s) MeSH : |
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Computer Simulation – Consanguinity – Croatia – Genetic Association Studies – Genome – Human – Genotype – Homozygote – Humans – Inheritance Patterns – Likelihood Functions – Polymorphism – Single Nucleotide |
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| contrat, financement : |
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OP was supported by the Public Health Sciences University of Edinburgh PhD Scholarship and the Overseas Research Support Scheme, as well as postgraduate scholarship from the Ministry of Science, Education and Sports of the Republic of Croatia. This study was supported through the grants from the Medical Research Council UK to AFW, HC and IR and the Ministry of Science, Education and Sport of the Republic of Croatia to IR (number 216-1080315-0302). |
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