Consanguinity around the world: What do the genomic data of the HGDP-CEPH diversity panel tell us?

European Journal of Human Genetics

Volumn 19, Issue 5, 2011, Pages 583-587

  Leutenegger, Anne Louise ^a,b   Sahbatou, Mourad ^c   Gazal, Steven ^a,b,d   Cann, Howard ^c   Génin, Emmanuelle ^a,b  

^a INSERM   (France)

^b UNIVERSITÉ PARIS DIDEROT   (France)

^c FONDATION JEAN DAUSSET CEPH   (France)

^d UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

Genome based IBD; HGDP; Homozygosity by descent; Inbreeding; Linkage disequilibrium; Mating type inference

Indexed keywords

ARTICLE; CONSANGUINEOUS MARRIAGE; CONSANGUINITY; GENE FREQUENCY; GENE MAPPING; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HOMOZYGOSITY; HUMAN; INBREEDING; MOLECULAR GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

CONSANGUINITY; FEMALE; HUMAN GENOME PROJECT; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MARRIAGE; MODELS, GENETIC; PEDIGREE;

EID: 79955772284     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2010.205     Document Type: Article

References (29)

1. Bittles AH, Black ML: Evolution in health and medicine sackler colloquium: Consanguinity, human evolution, and complex diseases. Proc Natl Acad Sci USA 2009; 107 (Suppl 1): 1779-1786.
2. Leutenegger AL, Prum B, Genin E et al: Estimation of the inbreeding coefficient through use of genomic data. Am J Hum Genet 2003; 73: 516-523. (Pubitemid 37076266)
3. Carothers AD, Rudan I, Kolcic I et al: Estimating human inbreeding coefficients: Comparison of genealogical and marker heterozygosity approaches. Ann Hum Genet 2006; 70: 666-676. (Pubitemid 44173375)
4. Purcell S, Neale B, Todd-Brown K et al: PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575. (Pubitemid 47330214)
5. Leutenegger AL, Labalme A, Genin E et al: Using genomic inbreeding coefficient estimates for homozygosity mapping of rare recessive traits: Application to Taybi-Linder syndrome. Am J Hum Genet 2006; 79: 62-66. (Pubitemid 43927377)
6. Wang S, Haynes C, Barany F, Ott J: Genome-wide autozygosity mapping in human populations. Genet Epidemiol 2009; 33: 172-180.
7. Curtis D, Vine AE, Knight J: Study of regions of extended homozygosity provides a powerful method to explore haplotype structure of human populations. Ann Hum Genet 2008; 72: 261-278. (Pubitemid 351228465)
8. McQuillan R, Leutenegger AL, Abdel-Rahman R et al: Runs of homozygosity in European populations. Am J Hum Genet 2008; 83: 359-372.
9. Polasek O, Hayward C, Bellenguez C et al: Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data. BMC Genomics 2010; 11: 139.
10. Bellenguez C, Ober C, Bourgain C: Linkage analysis with dense SNP maps in isolated populations. Hum Hered 2009; 68: 87-97.
11. Cann HM, de Toma C, Cazes L et al: A human genome diversity cell line panel. Science 2002; 296: 261-262. (Pubitemid 34303653)
12. Li JZ, Absher DM, Tang H et al: Worldwide human relationships inferred from genomewide patterns of variation. Science 2008; 319: 1100-1104. (Pubitemid 351300793)
13. Rosenberg NA: Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet 2006; 70: 841-847. (Pubitemid 44530648)
14. Kong A, Gudbjartsson DF, Sainz J et al: A high-resolution recombination map of the human genome. Nat Genet 2002; 31: 241-247.
15. Jakobsson M, Scholz SW, Scheet P et al: Genotype, haplotype and copy-number variation in worldwide human populations. Nature 2008; 451: 998-1003. (Pubitemid 351301742)
16. Itsara A, Cooper GM, Baker C et al: Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 2009; 84: 148-161.
17. Akaike H: A new look at the statistical identification model. IEEE Trans Automat Contr 1974; 19: 716-723.
18. Wright S: Coefficient of inbreeding and relationship. Am Nat 1922; 56: 330-338.
19. Rosenberg NA: DISTRUCT: A program for the graphical display of population structure. Mol Ecol Notes 2004; 4: 137-138. (Pubitemid 38261335)
20. Scott-Emuakpor AB: The mutation load in an African population. I. An analysis of consanguineous marriages in Nigeria. Am J Hum Genet 1974; 26: 674-682.
21. Calafell F, Shuster A, Speed WC, Kidd JR, Black FL, Kidd KK: Genealogy reconstruction from short tandem repeat genotypes in an Amazonian population. Am J Phys Anthropol 1999; 108: 137-146 (http://info.med.yale.edu/genetics/kkidd/ 302.pdf). (Pubitemid 29062087)
22. Kidd JR, Pakstis AJ, Kidd KK: Global Levels of DNA Variation. Proceedings from The Fourth International Symposium on Human Identification 1993 (http://info.med. yale.edu/genetics/kkidd/302.pdf).
23. Wang S, Lewis CM, Jakobsson M et al: Genetic variation and population structure in native Americans. PLoS Genet 2007; 3: E185.
24. Browning SR: Estimation of pairwise identity by descent from dense genetic marker data in a population sample of haplotypes. Genetics 2008; 178: 2123-2132.
25. Thompson EA: Analysis of data on related individuals through inference of identity by descent. Seattle: Department of Statistics, University of Washington, Technical Report 539 2008.
26. Browning SR, Browning BL: High-resolution detection of identity by descent in unrelated individuals. Am J Hum Genet 2010; 86: 526-539.
27. Epstein MP, Duren WL, Boehnke M: Improved inference of relationship for pairs of individuals. Am J Hum Genet 2000; 67: 1219-1231.
28. Sieberts SK, Wijsman EM, Thompson EA: Relationship inference from trios of individuals, in the presence of typing error. Am J Hum Genet 2002; 70: 170-180. (Pubitemid 34031706)
29. Sun L, Wilder K, McPeek MS: Enhanced pedigree error detection. Hum Hered 2002; 54: 99-110. (Pubitemid 36091883)