The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
Extended tracts of homozygosity in outbred human populations
Open accessAbstract
Long tracts of consecutive homozygous single nucleotide polymorphisms (SNPs) can arise in the genome through a number of mechanisms. These include inbreeding in which an individual inherits chromosomal segments that are identical by descent from each parent. However, recombination and other processes break up chromosomal segments over generations. The longest tracts are therefore to be expected in populations with an appreciable degree of inbreeding. We examined the length, number and distribution of long tracts of homozygosity in the apparently outbred HapMap populations. We observed 1393 tracts exceeding 1 Mb in length among the 209 unrelated HapMap individuals. The longest was an uninterrupted run of 3922 homozygous SNPs spanning 17.9 Mb in a Japanese individual. We find that homozygous tracts are significantly more common in regions with high linkage disequilibrium and low recombination, and the location of tracts is similar across all populations. The Yoruba sample has the fewest long tracts per individual, consistent with a larger number of generations (and hence amount of recombination) since the founding of that population. Our results suggest that multiple-megabase-scale ancestral haplotypes persist in outbred human populations in broad genomic regions which have lower than average recombination rates. We observed three outlying individuals who have exceptionally long and numerous homozygous tracts that are not associated with recombination suppressed areas of the genome. We consider that this reflects a high level of relatedness in their ancestry which is too recent to have been influenced by the local recombination intensity. Possible alternative mechanisms and the implications of long homozygous tracts in the genome are discussed.
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Cites
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
High-resolution haplotype structure in the human genome
Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J., & Lander, E. S. (2001) · Nature Genetics · doi:10.1038/ng1001-229 · Cited by 1,717
Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene
Bersaglieri, T., Sabeti, P. C., Patterson, N., Vanderploeg, T., Schaffner, S. F., Drake, J. A., Rhodes, M., Reich, D. E., & Hirschhorn, J. N. (2004) · The American Journal of Human Genetics · doi:10.1086/421051 · Cited by 1,142
Jeffreys, A. J., Kauppi, L., & Neumann, R. (2001) · Nature Genetics · doi:10.1038/ng1001-217 · Cited by 835
Broman, K. W., & Weber, J. L. (1999) · The American Journal of Human Genetics · doi:10.1086/302661 · Cited by 356
A Combined Linkage-Physical Map of the Human Genome
Kong, X., Murphy, K., Raj, T., He, C., White, P. S., & Matise, T. C. (2004) · The American Journal of Human Genetics · doi:10.1086/426405 · Cited by 245
The first linkage disequilibrium (LD) maps: Delineation of hot and cold blocks by diplotype analysis
Maniatis, N., Collins, A., Xu, C.-F., McCarthy, L. C., Hewett, D. R., Tapper, W., Ennis, S., Ke, X., & Morton, N. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.042680999 · Cited by 182
Self-citationVega, F. M. D. L., Isaac, H., Collins, A., Scafe, C., Halldorsson, B. V., XiaoPing, S., Lippert, R. A., Wang, Y., Laig-Webster, M., Koehler, R. T., et al. (2005) · Genome Research · doi:10.1101/gr.3241705 · Cited by 120
Self-citationProperties of linkage disequilibrium (LD) maps
Zhang, W., Collins, A. R., Maniatis, N., Tapper, W., & Morton, N. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012672899 · Cited by 102
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Cited by
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
Runs of Homozygosity in European Populations
McQuillan, R., Leutenegger, A.-L., Abdel-Rahman, R., Franklin, C. S., Pericic, M., Barac-Lauc, L., Smolej-Narancic, N., Janicijevic, B., Polasek, O., Tenesa, A., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.08.007 · Cited by 1,369
Runs of homozygosity: windows into population history and trait architecture
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J. F. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.109 · Cited by 1,006
Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
Hoban, S., Kelley, J. L., Lotterhos, K. E., Antolin, M. F., Bradburd, G., Lowry, D. B., Poss, M. L., Reed, L. K., Storfer, A., & Whitlock, M. C. (2016) · The American Naturalist · doi:10.1086/688018 · Cited by 876
“A reference genome also allows for haplotype structure assessment and, in turn, analyses of signatures of selective sweeps (Maynard Smith and Haigh 1974; Gibson et al. 2006; Sabeti et al. 2007; see table 1).”
Crow, Y. J., Leitch, A., Hayward, B. E., Garner, A., Parmar, R., Griffith, E., Ali, M., Semple, C., Aicardi, J., Babul-Hirji, R., et al. (2006) · Nature Genetics · doi:10.1038/ng1842 · Cited by 675
Metadata
- Authors
- Gibson, J., Morton, N. E., & Collins, A.
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-25
- Volume
- 15
- Issue
- 5
- Pages
- 789-795
- ISSN
- 0964-6906 (ISSN-L)
- 1460-2083
- OpenAlex
- W2137073429
- Cited by
- 489
- References
- 13
- FWCI
- 12.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
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