Challenges in the identification and use of rare disease-associated predisposition variants

Current Opinion in Genetics and Development

Volumn 20, Issue 3, 2010, Pages 277-281

  Carvajal Carmona, Luis G ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSIDAD DEL TOLIMA   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; EFFECT SIZE; EPIGENETICS; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENOTYPE ENVIRONMENT INTERACTION; GERM LINE; HERITABILITY; HUMAN; LINKAGE ANALYSIS; MATHEMATICAL MODEL; MISSENSE MUTATION; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; RARE DISEASE; REVIEW; RISK ASSESSMENT; ALLELE; GENETICS; MUTATION; PROCEDURES;

ALLELES; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MUTATION; RARE DISEASES;

EID: 77953614624     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2010.05.005     Document Type: Review

References (41)

1. Fisher R. The correlation between relatives on the supposition of Mendelian inheritance. Philos Trans R Soc Edinb 1918, 52:34.
2. Reich D.E., Lander E.S. On the allelic spectrum of human disease. Trends Genet 2001, 17:502-510.
3. Pritchard J.K. Are rare variants responsible for susceptibility to complex diseases?. Am J Hum Genet 2001, 69:124-137.
4. Bodmer W., Bonilla C. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008, 40:695-701.
5. Schork N.J., Murray S.S., Frazer K.A., Topol E.J. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev 2009, 19:212-219.
6. Klein R.J., Zeiss C., Chew E.Y., Tsai J.Y., Sackler R.S., Haynes C., Henning A.K., SanGiovanni J.P., Mane S.M., Mayne S.T., et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005, 308:385-389.
7. Consortium W.T.C.C. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447:661-678.
8. Hirschhorn J.N. Genomewide association studies-illuminating biologic pathways. N Engl J Med 2009, 360:1699-1701.
9. Broderick P., Carvajal-Carmona L., Pittman A.M., Webb E., Howarth K., Rowan A., Lubbe S., Spain S., Sullivan K., Fielding S., et al. A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. Nat Genet 2007, 39:1315-1317.
10. Houlston R.S., Webb E., Broderick P., Pittman A.M., Di Bernardo M.C., Lubbe S., Chandler I., Vijayakrishnan J., Sullivan K., Penegar S., et al. Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat Genet 2008, 40:1426-1435.
11. Jaeger E., Webb E., Howarth K., Carvajal-Carmona L., Rowan A., Broderick P., Walther A., Spain S., Pittman A., Kemp Z., et al. Common genetic variants at the CRAC1 (HMPS) locus on chromosome 15q13.3 influence colorectal cancer risk. Nat Genet 2008, 40:26-28.
12. Pittman A.M., Webb E., Carvajal-Carmona L., Howarth K., Di Bernardo M.C., Broderick P., Spain S., Walther A., Price A., Sullivan K., et al. Refinement of the basis and impact of common 11q23.1 variation to the risk of developing colorectal cancer. Hum Mol Genet 2008, 17:3720-3727.
13. Tenesa A., Farrington S.M., Prendergast J.G., Porteous M.E., Walker M., Haq N., Barnetson R.A., Theodoratou E., Cetnarskyj R., Cartwright N., et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet 2008, 40:631-637.
14. Tomlinson I., Webb E., Carvajal-Carmona L., Broderick P., Kemp Z., Spain S., Penegar S., Chandler I., Gorman M., Wood W., et al. A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet 2007, 39:984-988.
15. Tomlinson I.P., Webb E., Carvajal-Carmona L., Broderick P., Howarth K., Pittman A.M., Spain S., Lubbe S., Walther A., Sullivan K., et al. A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet 2008, 40:623-630.
16. Van Limbergen J., Wilson D.C., Satsangi J. The genetics of Crohn's disease. Annu Rev Genom Hum Genet 2009, 10:89-116.
17. DeWan A., Bracken M.B., Hoh J. Two genetic pathways for age-related macular degeneration. Curr Opin Genet Dev 2007, 17:228-233.
18. Goldstein D.B. Common genetic variation and human traits. N Engl J Med 2009, 360:1696-1698.
19. Alleyne R., Devlin K. Genetic 'magic bullet' cures have proven a 'false dawn'. The Daily Telegraph 2009.
20. McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P., Hirschhorn J.N. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 2008, 9:356-369.
21. Renwick A., Thompson D., Seal S., Kelly P., Chagtai T., Ahmed M., North B., Jayatilake H., Barfoot R., Spanova K., et al. ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nat Genet 2006, 38:873-875.
22. Seal S., Thompson D., Renwick A., Elliott A., Kelly P., Barfoot R., Chagtai T., Jayatilake H., Ahmed M., Spanova K., et al. Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nat Genet 2006, 38:1239-1241.
23. Rahman N., Seal S., Thompson D., Kelly P., Renwick A., Elliott A., Reid S., Spanova K., Barfoot R., Chagtai T., et al. PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nat Genet 2007, 39:165-167.
24. Erkko H., Dowty J.G., Nikkila J., Syrjakoski K., Mannermaa A., Pylkas K., Southey M.C., Holli K., Kallioniemi A., Jukkola-Vuorinen A., et al. Penetrance analysis of the PALB2 c.1592delT founder mutation. Clin Cancer Res 2008, 14:4667-4671.
25. Easton D.F., Deffenbaugh A.M., Pruss D., Frye C., Wenstrup R.J., Allen-Brady K., Tavtigian S.V., Monteiro A.N., Iversen E.S., Couch F.J., et al. A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Am J Hum Genet 2007, 81:873-883.
26. Hofstra R.M., Spurdle A.B., Eccles D., Foulkes W.D., de Wind N., Hoogerbrugge N., Hogervorst F.B. Tumor characteristics as an analytic tool for classifying genetic variants of uncertain clinical significance. Hum Mutat 2008, 29:1292-1303.
27. Meindl A., Hellebrand H., Wiek C., Erven V., Wappenschmidt B., Niederacher D., Freund M., Lichtner P., Hartmann L., Schaal H., et al. Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nat Genet 2010, 42:410-414.
28. Levitus M., Waisfisz Q., Godthelp B.C., de Vries Y., Hussain S., Wiegant W.W., Elghalbzouri-Maghrani E., Steltenpool J., Rooimans M.A., Pals G., et al. The DNA helicase BRIP1 is defective in Fanconi anemia complementation group. J Nat Genet 2005, 37:934-935.
29. Levran O., Attwooll C., Henry R.T., Milton K.L., Neveling K., Rio P., Batish S.D., Kalb R., Velleuer E., Barral S., et al. The BRCA1-interacting helicase BRIP1 is deficient in Fanconi anemia. Nat Genet 2005, 37:931-933.
30. Bridge W.L., Vandenberg C.J., Franklin R.J., Hiom K. The BRIP1 helicase functions independently of BRCA1 in the Fanconi anemia pathway for DNA crosslink repair. Nat Genet 2005, 37:953-957.
31. Reid S., Schindler D., Hanenberg H., Barker K., Hanks S., Kalb R., Neveling K., Kelly P., Seal S., Freund M., et al. Biallelic mutations in PALB2 cause Fanconi anemia subtype FA-N and predispose to childhood cancer. Nat Genet 2007, 39:162-164.
32. Vaz F., Hanenberg H., Schuster B., Barker K., Wiek C., Erven V., Neveling K., Endt D., Kesterton I., Autore F., et al. Mutation of the RAD51C gene in a Fanconi anemia-like disorder. Nat Genet 2010, 42:406-409.
33. Howlett N.G., Taniguchi T., Olson S., Cox B., Waisfisz Q., De Die-Smulders C., Persky N., Grompe M., Joenje H., Pals G., et al. Biallelic inactivation of BRCA2 in Fanconi anemia. Science 2002, 297:606-609.
34. Manolio T.A., Collins F.S., Cox N.J., Goldstein D.B., Hindorff L.A., Hunter D.J., McCarthy M.I., Ramos E.M., Cardon L.R., Chakravarti A., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
35. Consortium W.T.C.C. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 2010, 464:713-720.
36. Gudbjartsson D.F., Walters G.B., Thorleifsson G., Stefansson H., Halldorsson B.V., Zusmanovich P., Sulem P., Thorlacius S., Gylfason A., Steinberg S., et al. Many sequence variants affecting diversity of adult human height. Nat Genet 2008, 40:609-615.
37. Lettre G., Jackson A.U., Gieger C., Schumacher F.R., Berndt S.I., Sanna S., Eyheramendy S., Voight B.F., Butler J.L., Guiducci C., et al. Identification of ten loci associated with height highlights new biological pathways in human growth. Nat Genet 2008, 40:584-591.
38. Sanna S., Jackson A.U., Nagaraja R., Willer C.J., Chen W.M., Bonnycastle L.L., Shen H., Timpson N., Lettre G., Usala G., et al. Common variants in the GDF5-UQCC region are associated with variation in human height. Nat Genet 2008, 40:198-203.
39. Weedon M.N., Lango H., Lindgren C.M., Wallace C., Evans D.M., Mangino M., Freathy R.M., Perry J.R., Stevens S., Hall A.S., et al. Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet 2008, 40:575-583.
40. Weedon M.N., Lettre G., Freathy R.M., Lindgren C.M., Voight B.F., Perry J.R., Elliott K.S., Hackett R., Guiducci C., Shields B., et al. A common variant of HMGA2 is associated with adult and childhood height in the general population. Nat Genet 2007, 39:1245-1250.
41. Gudmundsson J., Sulem P., Gudbjartsson D.F., Jonasson J.G., Sigurdsson A., Bergthorsson J.T., He H., Blondal T., Geller F., Jakobsdottir M., et al. Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. Nat Genet 2009, 41:460-464.