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Petukhova L, Shimomura Y, Wajid M, Gorroochurn P, Hodge SE, Christiano AM. The effect of inbreeding on the distribution of compound heterozygotes: a lesson from Lipase H mutations in autosomal recessive woolly hair/hypotrichosis. Hum Hered 2009; 68:117-30. [PMID: 19365138 DOI: 10.1159/000212504] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 12/15/2008] [Indexed: 01/03/2023] Open
Abstract
Autozygosity mapping in consanguineous families has proven to be a powerful method for identifying recessive disease genes. Using this technique with whole genome SNP data generated from low density mapping arrays, we previously identified two genes that underlie autosomal recessive woolly hair (ARWH/hypotrichosis; OMIM278150), specifically P2RY5 and Lipase H (LIPH). In the current study, we sought to identify a novel disease locus for ARWH/hypotrichosis by analyzing two large consanguineous families from Pakistan who had initially been excluded for mutations at either of these disease loci by haplotype analysis with microsatellite markers. A genome-wide analysis of 10 members from each of the two families failed to identify significant regions of autozygosity or linkage. Upon genotyping an additional 10 family members in one of the families, parametric linkage analysis identified a region on chromosome 3q27 with evidence for linkage (Z = 2.5). Surprisingly, this region contains the LIPH gene. Microsatellite markers located within the LIPH gene were used for haplotype analysis and demonstrated that not one, but two haplotypes were segregating with the phenotype in each of these families. DNA sequencing identified two distinct LIPH mutations (280_369dup90 and 659_660delTA). Each affected individual (n = 38) was either homozygous for one mutation (n = 7 and 16 respectively), or compound heterozygous (n = 15). A review of the literature identified several reports of compound heterozygotes in consanguineous families. Prompted by this finding, we derived the probability that a patient affected with a recessive disease is carrying two mutations at the disease locus. We suggest that the validity of the IBD assumption may be challenged in large consanguineous families.
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Affiliation(s)
- Lynn Petukhova
- Department of Dermatology, School of Public Health, Columbia University, New York, N.Y. 10032, USA
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52
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Lyons EJ, Frodsham AJ, Zhang L, Hill AVS, Amos W. Consanguinity and susceptibility to infectious diseases in humans. Biol Lett 2009; 5:574-6. [PMID: 19324620 PMCID: PMC2684220 DOI: 10.1098/rsbl.2009.0133] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Studies of animal populations suggest that low genetic heterozygosity is an important risk factor for infection by a diverse range of pathogens, but relatively little research has looked to see whether similar patterns exist in humans. We have used microsatellite genome screen data for tuberculosis (TB), hepatitis and leprosy to test the hypothesis that inbreeding depression increases risk of infection. Our results indicate that inbred individuals are more common among our infected cases for TB and hepatitis, but only in populations where consanguineous marriages are common. No effect was found either for leprosy, which is thought to be oligogenic, or for hepatitis in Italy where consanguineous marriages are rare. Our results suggest that consanguinity is an important risk factor in susceptibility to infectious diseases in humans.
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Affiliation(s)
- Emily J Lyons
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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53
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Nalls MA, Simon-Sanchez J, Gibbs JR, Paisan-Ruiz C, Bras JT, Tanaka T, Matarin M, Scholz S, Weitz C, Harris TB, Ferrucci L, Hardy J, Singleton AB. Measures of autozygosity in decline: globalization, urbanization, and its implications for medical genetics. PLoS Genet 2009; 5:e1000415. [PMID: 19282984 PMCID: PMC2652078 DOI: 10.1371/journal.pgen.1000415] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 02/10/2009] [Indexed: 11/18/2022] Open
Abstract
This research investigates the influence of demographic factors on human genetic sub-structure. In our discovery cohort, we show significant demographic trends for decreasing autozygosity associated with population variation in chronological age. Autozygosity, the genomic signature of consanguinity, is identifiable on a genome-wide level as extended tracts of homozygosity. We identified an average of 28.6 tracts of extended homozygosity greater than 1 Mb in length in a representative population of 809 unrelated North Americans of European descent ranging in chronological age from 19–99 years old. These homozygous tracts made up a population average of 42 Mb of the genome corresponding to 1.6% of the entire genome, with each homozygous tract an average of 1.5 Mb in length. Runs of homozygosity are steadily decreasing in size and frequency as time progresses (linear regression, p<0.05). We also calculated inbreeding coefficients and showed a significant trend for population-wide increasing heterozygosity outside of linkage disequilibrium. We successfully replicated these associations in a demographically similar cohort comprised of a subgroup of 477 Baltimore Longitudinal Study of Aging participants. We also constructed statistical models showing predicted declining rates of autozygosity spanning the 20th century. These predictive models suggest a 14.0% decrease in the frequency of these runs of homozygosity and a 24.3% decrease in the percent of the genome in runs of homozygosity, as well as a 30.5% decrease in excess homozygosity based on the linkage pruned inbreeding coefficients. The trend for decreasing autozygosity due to panmixia and larger effective population sizes will likely affect the frequency of rare recessive genetic diseases in the future. Autozygosity has declined, and it seems it will continue doing so. Population geneticists use genetic markers to quantify and compare levels of inbreeding in populations and identify disease-associated loci; epidemiologists utilize demographic factors to quantify disease risk modifiers. Our research group sought to investigate the intersection of these two disciplines and examine the way in which demographic trends associated with decreasing levels of inbreeding may influence genomic structure and how this may affect medical genetics research. By examining two age-heterogeneous populations of outbred North Americans, we were able to ascertain genetic changes occurring over the past century that have been likely brought about by recent increases in mobility, urbanization, and population admixture. Using multiple measures of the genomic manifestations of distant consanguinity, we showed significant trends towards decreasing levels of autozygosity and more marginal inbreeding coefficients as study participant birth years neared the chronological present day. We believe this finding is particularly important, as decreasing autozygosity and less homozygosity genome-wide may help to slightly reduce the burden of rare recessive diseases in the future.
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Affiliation(s)
- Michael A. Nalls
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
- Laboratory of Epidemiology, Demography and Biometry, Intramural Research Program, National Institute on Aging, Maryland, United States of America
| | - Javier Simon-Sanchez
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
- Unidad de Genética Molecular, Departamento de Genómica y Proteómica, Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, London, United Kingdom
| | - Coro Paisan-Ruiz
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, London, United Kingdom
| | - Jose Tomas Bras
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Toshiko Tanaka
- Longitudinal Studies Section, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Mar Matarin
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Sonja Scholz
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, London, United Kingdom
| | - Charles Weitz
- Department of Anthropology, Biological Anthropology Program, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography and Biometry, Intramural Research Program, National Institute on Aging, Maryland, United States of America
| | - Luigi Ferrucci
- Longitudinal Studies Section, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
| | - John Hardy
- Department of Molecular Neuroscience and Reta Lila Weston Laboratories, Institute of Neurology, London, United Kingdom
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, United States of America
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF. Runs of homozygosity in European populations. Am J Hum Genet 2008; 83:359-72. [PMID: 18760389 DOI: 10.1016/j.ajhg.2008.08.007] [Citation(s) in RCA: 756] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2008] [Revised: 08/12/2008] [Accepted: 08/13/2008] [Indexed: 12/28/2022] Open
Abstract
Estimating individual genome-wide autozygosity is important both in the identification of recessive disease variants via homozygosity mapping and in the investigation of the effects of genome-wide homozygosity on traits of biomedical importance. Approaches have tended to involve either single-point estimates or rather complex multipoint methods of inferring individual autozygosity, all on the basis of limited marker data. Now, with the availability of high-density genome scans, a multipoint, observational method of estimating individual autozygosity is possible. Using data from a 300,000 SNP panel in 2618 individuals from two isolated and two more-cosmopolitan populations of European origin, we explore the potential of estimating individual autozygosity from data on runs of homozygosity (ROHs). Termed F(roh), this is defined as the proportion of the autosomal genome in runs of homozygosity above a specified length. Mean F(roh) distinguishes clearly between subpopulations classified in terms of grandparental endogamy and population size. With the use of good pedigree data for one of the populations (Orkney), F(roh) was found to correlate strongly with the inbreeding coefficient estimated from pedigrees (r = 0.86). Using pedigrees to identify individuals with no shared maternal and paternal ancestors in five, and probably at least ten, generations, we show that ROHs measuring up to 4 Mb are common in demonstrably outbred individuals. Given the stochastic variation in ROH number, length, and location and the fact that ROHs are important whether ancient or recent in origin, approaches such as this will provide a more useful description of genomic autozygosity than has hitherto been possible.
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Affiliation(s)
- Ruth McQuillan
- Public Health Sciences, University of Edinburgh Medical School, Edinburgh EH8 9AG, UK
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55
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Álvarez I, Royo L, Gutiérrez J, Fernández I, Arranz J, Goyache F. Relationship between genealogical and microsatellite information characterizing losses of genetic variability: Empirical evidence from the rare Xalda sheep breed. Livest Sci 2008. [DOI: 10.1016/j.livsci.2007.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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56
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Quantifying the increase in average human heterozygosity due to urbanisation. Eur J Hum Genet 2008; 16:1097-102. [PMID: 18322453 DOI: 10.1038/ejhg.2008.48] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The human population is undergoing a major transition from a historical metapopulation structure of relatively isolated small communities to an outbred structure. This process is predicted to increase average individual genome-wide heterozygosity (h) and could have effects on health. We attempted to quantify this increase in mean h. We initially sampled 1001 examinees from a metapopulation of nine isolated villages on five Dalmatian islands (Croatia). Village populations had high levels of genetic differentiation, endogamy and consanguinity. We then selected 166 individuals with highly specific personal genetic histories to form six subsamples, which could be ranked a priori by their predicted level of outbreeding. The measure h was then estimated in the 166 examinees by genotyping 1184 STR/indel markers and using two different computation methods. Compared to the value of mean h in the least outbred sample, values of h in the remaining samples increased successively with predicted outbreeding by 0.023, 0.038, 0.058, 0.067 and 0.079 (P<0.0001), where these values are measured on the same scale as the inbreeding coefficient (but opposite sign). We have shown that urbanisation was associated with an average increase in h of up to 0.08-0.10 in this Croatian metapopulation, regardless of the method used. Similar levels of differentiation have been described in many populations. Therefore, changes in the level of heterozygosity across the genome of this magnitude may be common during isolate break-up in humans and could have significant health effects through the established genetic mechanism of hybrid vigour/heterosis.
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57
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Becquet C, Patterson N, Stone AC, Przeworski M, Reich D. Genetic structure of chimpanzee populations. PLoS Genet 2007; 3:e66. [PMID: 17447846 PMCID: PMC1853122 DOI: 10.1371/journal.pgen.0030066] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 03/13/2007] [Indexed: 11/18/2022] Open
Abstract
Little is known about the history and population structure of our closest living relatives, the chimpanzees, in part because of an extremely poor fossil record. To address this, we report the largest genetic study of the chimpanzees to date, examining 310 microsatellites in 84 common chimpanzees and bonobos. We infer three common chimpanzee populations, which correspond to the previously defined labels of "western," "central," and "eastern," and find little evidence of gene flow between them. There is tentative evidence for structure within western chimpanzees, but we do not detect distinct additional populations. The data also provide historical insights, demonstrating that the western chimpanzee population diverged first, and that the eastern and central populations are more closely related in time.
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Affiliation(s)
- Celine Becquet
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
| | - Molly Przeworski
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - David Reich
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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58
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Campbell H, Carothers AD, Rudan I, Hayward C, Biloglav Z, Barac L, Pericic M, Janicijevic B, Smolej-Narancic N, Polasek O, Kolcic I, Weber JL, Hastie ND, Rudan P, Wright AF. Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits. Hum Mol Genet 2007; 16:233-41. [PMID: 17220173 DOI: 10.1093/hmg/ddl473] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The dramatic changes in human population structure over the last 200 years have resulted in significant levels of outbreeding, which, in turn, is predicted to lead to increased levels of individual genetic diversity (genome-wide heterozygosity, h). To investigate possible effects of these large demographic changes on global health, we studied the effect of h, measured as relative heterozygosity, h(R), on 15 disease-related traits in four groups of individuals with widely differing ancestral histories (ranging from outbred to inbred) from the Dalmatian islands in Croatia. Higher levels of h(R), estimated using 1184 STR/indel markers, were found in the outbred group (P < 0.0001) and were associated with lower blood pressure (BP) and total/LDL cholesterol (P = 0.01 and 0.01, respectively) after controlling for other factors, with BP showing a strong sex effect (males P > 0.5 and females P = 0.002). These findings, if replicated, suggest that h(R) be considered as a genetic risk factor in genetic epidemiological studies on common disease traits. They are consistent with the well-known effects of heterosis (hybrid vigour) described when outcrossing animals and plants. Outbreeding resulting from urbanization and migration from traditional population subgroups may be leading to increasing h(R) and may have beneficial effects on a range of traits associated with human health and disease. Other traits, such as age at menarche, IQ and lifespan, which have been changing during the decades of urbanization, may also have been influenced by demographic factors.
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Affiliation(s)
- Harry Campbell
- Department of Public Health Sciences, University of Edinburgh, Edinburgh, UK.
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