Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches. Carothers, A., D., Rudan, I., Kolcic, I., Polasek, O., Hayward, C., Wright, A., F., Campbell, H., Teague, P., Hastie, N., D., & Weber, J., L. Annals of human genetics, 70(Pt 5):666-76, 9, 2006.
Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches. [link]Website  abstract   bibtex   
We have used genealogies and genomic polymorphisms to estimate individual inbreeding coefficients (F) in 50 subjects with an expected range (based on recent genealogies) of F from 0.0 to 0.0625. The estimates were based on two approaches, using genotypes respectively from 410 microsatellite markers (410-STR panel) and from 10,000 SNPs (10K-SNP panel). The latter was performed in a sub-sample of 15 individuals. We concluded that for both marker panels measures of inbreeding based on the excess of homozygosity over Hardy-Weinberg expectation were not closely correlated with 4-5 generation genealogical F-values. For the 10K-SNP panel we found two alternative measures which correlated more closely with F, based respectively on standard errors and on paired homozygosity of nearby SNPs over distances of 2-4 cM. We propose an empirical method for estimating standard errors and hence individual F-values, based on the variation between individual autosomes. This method could provide useful estimates of average F-values for groups of individuals in population-based studies of the effects of inbreeding/homozygosity on quantitative traits.
@article{
 title = {Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches.},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Consanguinity,Croatia,Genealogy and Heraldry,Genotype,Heterozygote,Homozygote,Humans,Microsatellite Repeats,Microsatellite Repeats: genetics,Polymorphism, Genetic,Polymorphism, Single Nucleotide,Scotland},
 pages = {666-76},
 volume = {70},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/16907711},
 month = {9},
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 abstract = {We have used genealogies and genomic polymorphisms to estimate individual inbreeding coefficients (F) in 50 subjects with an expected range (based on recent genealogies) of F from 0.0 to 0.0625. The estimates were based on two approaches, using genotypes respectively from 410 microsatellite markers (410-STR panel) and from 10,000 SNPs (10K-SNP panel). The latter was performed in a sub-sample of 15 individuals. We concluded that for both marker panels measures of inbreeding based on the excess of homozygosity over Hardy-Weinberg expectation were not closely correlated with 4-5 generation genealogical F-values. For the 10K-SNP panel we found two alternative measures which correlated more closely with F, based respectively on standard errors and on paired homozygosity of nearby SNPs over distances of 2-4 cM. We propose an empirical method for estimating standard errors and hence individual F-values, based on the variation between individual autosomes. This method could provide useful estimates of average F-values for groups of individuals in population-based studies of the effects of inbreeding/homozygosity on quantitative traits.},
 bibtype = {article},
 author = {Carothers, A D and Rudan, I and Kolcic, I and Polasek, O and Hayward, C and Wright, A F and Campbell, H and Teague, P and Hastie, N D and Weber, J L},
 journal = {Annals of human genetics},
 number = {Pt 5}
}
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