Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing.
- Publisher:
- OXFORD UNIV PRESS INC
- Publication Type:
- Journal Article
- Citation:
- G3 (Bethesda), 2024, 14, (2), pp. jkad264
- Issue Date:
- 2024-02-07
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Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing.pdf | Published version | 614.1 kB | Adobe PDF |
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Full metadata record
Field | Value | Language |
---|---|---|
dc.contributor.author | Cotter, DJ | |
dc.contributor.author | Severson, AL | |
dc.contributor.author | Kang, JTL | |
dc.contributor.author | Godrej, HN | |
dc.contributor.author | Carmi, S | |
dc.contributor.author | Rosenberg, NA | |
dc.contributor.editor | Ralph, P | |
dc.date.accessioned | 2024-08-06T03:08:54Z | |
dc.date.available | 2023-11-08 | |
dc.date.available | 2024-08-06T03:08:54Z | |
dc.date.issued | 2024-02-07 | |
dc.identifier.citation | G3 (Bethesda), 2024, 14, (2), pp. jkad264 | |
dc.identifier.issn | 2160-1836 | |
dc.identifier.issn | 2160-1836 | |
dc.identifier.uri | http://hdl.handle.net/10453/180086 | |
dc.description.abstract | Runs of homozygosity (ROH) and identity-by-descent (IBD) sharing can be studied in diploid coalescent models by noting that ROH and IBD-sharing at a genomic site are predicted to be inversely related to coalescence times-which in turn can be mathematically obtained in terms of parameters describing consanguinity rates. Comparing autosomal and X-chromosomal coalescent models, we consider ROH and IBD-sharing in relation to consanguinity that proceeds via multiple forms of first-cousin mating. We predict that across populations with different levels of consanguinity, (1) in a manner that is qualitatively parallel to the increase of autosomal IBD-sharing with autosomal ROH, X-chromosomal IBD-sharing increases with X-chromosomal ROH, owing to the dependence of both quantities on consanguinity levels; (2) even in the absence of consanguinity, X-chromosomal ROH and IBD-sharing levels exceed corresponding values for the autosomes, owing to the smaller population size and lower coalescence time for the X chromosome than for autosomes; (3) with matrilateral consanguinity, the relative increase in ROH and IBD-sharing on the X chromosome compared to the autosomes is greater than in the absence of consanguinity. Examining genome-wide SNPs in human populations for which consanguinity levels have been estimated, we find that autosomal and X-chromosomal ROH and IBD-sharing levels generally accord with the predictions. We find that each 1% increase in autosomal ROH is associated with an increase of 2.1% in X-chromosomal ROH, and each 1% increase in autosomal IBD-sharing is associated with an increase of 1.6% in X-chromosomal IBD-sharing. For each calculation, particularly for ROH, the estimate is reasonably close to the increase of 2% predicted by the population-size difference between autosomes and X chromosomes. The results support the utility of coalescent models for understanding patterns of genomic sharing and their dependence on sex-biased processes. | |
dc.format | ||
dc.language | eng | |
dc.publisher | OXFORD UNIV PRESS INC | |
dc.relation.ispartof | G3 (Bethesda) | |
dc.relation.isbasedon | 10.1093/g3journal/jkad264 | |
dc.rights | info:eu-repo/semantics/restrictedAccess | |
dc.subject | 0604 Genetics | |
dc.subject.classification | 3101 Biochemistry and cell biology | |
dc.subject.classification | 3105 Genetics | |
dc.subject.classification | 4905 Statistics | |
dc.subject.mesh | Humans | |
dc.subject.mesh | Consanguinity | |
dc.subject.mesh | Homozygote | |
dc.subject.mesh | Genome | |
dc.subject.mesh | Genomics | |
dc.subject.mesh | X Chromosome | |
dc.subject.mesh | Polymorphism, Single Nucleotide | |
dc.subject.mesh | Inbreeding | |
dc.subject.mesh | X Chromosome | |
dc.subject.mesh | Humans | |
dc.subject.mesh | Inbreeding | |
dc.subject.mesh | Genomics | |
dc.subject.mesh | Consanguinity | |
dc.subject.mesh | Homozygote | |
dc.subject.mesh | Polymorphism, Single Nucleotide | |
dc.subject.mesh | Genome | |
dc.subject.mesh | Humans | |
dc.subject.mesh | Consanguinity | |
dc.subject.mesh | Homozygote | |
dc.subject.mesh | Genome | |
dc.subject.mesh | Genomics | |
dc.subject.mesh | X Chromosome | |
dc.subject.mesh | Polymorphism, Single Nucleotide | |
dc.subject.mesh | Inbreeding | |
dc.title | Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. | |
dc.type | Journal Article | |
utslib.citation.volume | 14 | |
utslib.location.activity | England | |
utslib.for | 0604 Genetics | |
pubs.organisational-group | University of Technology Sydney | |
pubs.organisational-group | University of Technology Sydney/Faculty of Science | |
pubs.organisational-group | University of Technology Sydney/Strength - C3 - Climate Change Cluster | |
pubs.organisational-group | University of Technology Sydney/All Manual Groups | |
pubs.organisational-group | University of Technology Sydney/All Manual Groups/Climate Change Cluster Research Strength (C3) | |
utslib.copyright.status | recently_added | * |
dc.date.updated | 2024-08-06T03:08:52Z | |
pubs.issue | 2 | |
pubs.publication-status | Published | |
pubs.volume | 14 | |
utslib.citation.issue | 2 |
Abstract:
Runs of homozygosity (ROH) and identity-by-descent (IBD) sharing can be studied in diploid coalescent models by noting that ROH and IBD-sharing at a genomic site are predicted to be inversely related to coalescence times-which in turn can be mathematically obtained in terms of parameters describing consanguinity rates. Comparing autosomal and X-chromosomal coalescent models, we consider ROH and IBD-sharing in relation to consanguinity that proceeds via multiple forms of first-cousin mating. We predict that across populations with different levels of consanguinity, (1) in a manner that is qualitatively parallel to the increase of autosomal IBD-sharing with autosomal ROH, X-chromosomal IBD-sharing increases with X-chromosomal ROH, owing to the dependence of both quantities on consanguinity levels; (2) even in the absence of consanguinity, X-chromosomal ROH and IBD-sharing levels exceed corresponding values for the autosomes, owing to the smaller population size and lower coalescence time for the X chromosome than for autosomes; (3) with matrilateral consanguinity, the relative increase in ROH and IBD-sharing on the X chromosome compared to the autosomes is greater than in the absence of consanguinity. Examining genome-wide SNPs in human populations for which consanguinity levels have been estimated, we find that autosomal and X-chromosomal ROH and IBD-sharing levels generally accord with the predictions. We find that each 1% increase in autosomal ROH is associated with an increase of 2.1% in X-chromosomal ROH, and each 1% increase in autosomal IBD-sharing is associated with an increase of 1.6% in X-chromosomal IBD-sharing. For each calculation, particularly for ROH, the estimate is reasonably close to the increase of 2% predicted by the population-size difference between autosomes and X chromosomes. The results support the utility of coalescent models for understanding patterns of genomic sharing and their dependence on sex-biased processes.
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