Could inbred cases identified in GWAS data succeed in detecting rare recessive variants where affected sib-pairs have failed?

Human Heredity

Volumn 74, Issue 3-4, 2012, Pages 142-152

  Génin, Emmanuelle ^a,b,c   Sahbatou, Mourad ^d   Gazal, Steven ^a,b   Babron, Marie Claude ^a,b   Perdry, Hervé ^e,f   Leutenegger, Anne Louise ^a,b  

^a INSERM   (France)

^b UNIVERSITÉ PARIS DIDEROT   (France)

^c French Blood Agency   (France)

^d FONDATION JEAN DAUSSET CEPH   (France)

^e UNIVERSITÉ PARIS SACLAY   (France)

^f Universite Paris Sud   (France)

Author keywords

Association; Genome wide association studies; Inbreeding; Linkage; Rare recessive variants

Indexed keywords

ARTICLE; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC LINKAGE; HOMOZYGOSITY; HUMAN; MAJOR CLINICAL STUDY; MENDELIAN RANDOMIZATION ANALYSIS; QUANTITATIVE ANALYSIS; RECESSIVE INHERITANCE; THEORY;

EID: 84876500302     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000346790     Document Type: Article

References (41)

1. Manolio TA, Collins FS, Cox NJ, et al: Finding the missing heritability of complex diseases. Nature 2009; 461: 747-753.
2. Bodmer W, Bonilla C: Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008; 40: 695-701.
3. Zhu X, Feng T, Li Y, Lu Q, Elston RC: Detecting rare variants for complex traits using family and unrelated data. Genet Epidemiol 2010; 34: 171-187.
4. Feng T, Zhu X: Genome-wide searching of rare genetic variants in WTCCC data. Hum Genet 2010; 128: 269-280.
5. Browning SR, Thompson EA: Detecting rare variant associations by identity-by-descent mapping in case-control studies. Genetics 2012; 190: 1521-1531.
6. Houwen RH, Baharloo S, Blankenship K, Raeymaekers P, Juyn J, Sandkuijl LA, Freimer NB: Genome screening by searching for shared segments: mapping a gene for benign recurrent intrahepatic cholestasis. Nat Genet 1994; 8: 380-386.
7. Bourgain C, Genin E, Holopainen P, Mustalahti K, Maki M, Partanen J, Clerget-Darpoux F: Use of closely related affected individuals for the genetic study of complex diseases in founder populations. Am J Hum Genet 2001; 68: 154-159.
8. Browning BL, Browning SR: A fast, powerful method for detecting identity by descent. Am J Hum Genet 2011; 88: 173-182.
9. Wilkie AO: The molecular basis of genetic dominance. J Med Genet 1994; 31: 89-98.
10. Jimenez-Sanchez G, Childs B, Valle D: Human disease genes. Nature 2001; 409: 853-855.
11. Furney SJ, Alba MM, Lopez-Bigas N: Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics 2006; 7: 165.
12. Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, Kosiol C, Bustamante CD, Teshima KM, Przeworski M: Natural selection on genes that underlie human disease susceptibility. Curr Biol 2008; 18: 883-889.
13. Lettre G, Lange C, Hirschhorn JN: Genetic model testing and statistical power in population- based association studies of quantitative traits. Genet Epidemiol 2007; 31: 358-362.
14. Lander ES, Botstein D: Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science 1987; 236: 1567-1570.
15. Genin E, Todorov AA: Homozygosity Mapping: Encyclopedia of Life Science. Chichester, John Wiley and Sons Ltd., 2007.
16. Leutenegger AL, Labalme A, Genin E, Toutain A, Steichen E, Clerget-Darpoux F, Edery P: 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.
17. Leutenegger AL, Prum B, Genin E, Verny C, Lemainque A, Clerget-Darpoux F, Thompson EA: Estimation of the inbreeding coefficient through use of genomic data. Am J Hum Genet 2003; 73: 516-523.
18. Morton NE: Sequential tests for the detection of linkage. Am J Hum Genet 1955; 7: 277-318.
19. Edery P, Marcaillou C, Sahbatou M, et al: Association of TALS developmental disorder with defect in minor splicing component U4atac snRNA. Science 2011; 332: 240-243.
20. Gibbs JR, Singleton A: Application of genome- wide single nucleotide polymorphism typing: simple association and beyond. PLoS Genetics 2006; 2:e150.
21. Howrigan DP, Simonson MA, Keller MC: Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms. BMC Genomics 2011; 12: 460.
22. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R, Malhotra AK: Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA 2007; 104: 19942-19947.
23. Wang S, Haynes C, Barany F, Ott J: Genomewide autozygosity mapping in human populations. Genet Epidemiol 2009; 33: 172-180.
24. Zhang L, Yang W, Ying D, Cherny SS, Hildebrandt F, Sham PC, Lau YL: Homozygosity mapping on a single patient: identification of homozygous regions of recent common ancestry by using population data. Hum Mutat 2011; 32: 345-353.
25. Leutenegger AL, Sahbatou M, Gazal S, Cann H, Genin E: Consanguinity around the world: ehat do the genomic data of the HGDP-CEPH diversity panel tell us? Eur J Hum Genet 2011; 19: 583-587.
26. Xing C, Morris N, Xing G: Distribution of model-based multipoint heterogeneity lod scores. Genet Epidemiol 2010; 34: 912-916.
27. Genin E, Clerget-Darpoux F: Consanguinity and the sib-pair method: an approach using identity by descent between and within individuals. Am J Hum Genet 1996; 59: 1149-1162.
28. Lander E, Kruglyak L: Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 1995; 11: 241-247.
29. Risch N: Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs. Am J Hum Genet 1990; 46: 242-253.
30. Poznik GD, Adamska K, Xu X, Krolewski AS, Rogus JJ: A novel framework for sib pair linkage analysis. Am J Hum Genet 2006; 78: 222-230.
31. WTCCC: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007; 447: 661-678.
32. 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.
33. Willer CJ, Speliotes EK, Loos RJ, et al: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat Genet 2009; 41: 25-34.
34. Yang TL, Guo Y, Zhang LS, Tian Q, Yan H, Papasian CJ, Recker RR, Deng HW: Runs of homozygosity identify a recessive locus 12q21.31 for human adult height. J Clin Endocrinol Metab 2010; 95: 3777-3782.
35. Casey JP, Magalhaes T, Conroy JM, et al: A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Hum Genet 2011; 131: 565-579.
36. Hosking FJ, Papaemmanuil E, Sheridan E, et al: Genome-wide homozygosity signatures and childhood acute lymphoblastic leukemia risk. Blood 2010; 115: 4472-4477.
37. Kuningas M, McQuillan R, Wilson JF, Hofman A, van Duijn CM, Uitterlinden AG, Tiemeier H: Runs of homozygosity do not influence survival to old age. PloS One 2011; 6:e22580.
38. Sims R, Dwyer S, Harold D, et al: No evidence that extended tracts of homozygosity are associated with Alzheimer's disease. Am J Med Genet B Neuropsychiatr Genet 2011; 156B: 764-771.
39. Chahrour MH, Yu TW, Lim ET, et al: Wholeexome sequencing and homozygosity analysis implicate depolarization-regulated neuronal genes in autism. PLoS Genetics 2012; 8:e1002635.
40. Simon-Sanchez J, Kilarski LL, Nalls MA, et al: Cooperative genome-wide analysis shows increased homozygosity in early onset Parkinson's disease. PloS One 2012; 7:e28787.
41. Marenne G, Rodriguez-Santiago B, Closas MG, et al: Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Hum Mutat 2011; 32: 240-248.