Genetic prediction of common diseases: Still no help for the clinical diabetologist!

Nutrition, Metabolism and Cardiovascular Diseases

Volumn 22, Issue 11, 2012, Pages 929-936

  Prudente, S ^a   Dallapiccola, B ^b   Pellegrini, F ^a,c   Doria, A ^d,e,f   Trischitta, V ^a,g  

^a CASA SOLLIEVO DELLA SOFFERENZA HOSPITAL   (Italy)

^b BAMBINO GESÙ CHILDREN S HOSPITAL   (Italy)

^c Santa Maria Imbaro   (Italy)

^d JOSLIN DIABETES CENTER   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^g SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Common multifactorial diseases; Direct to consumer testing; Diseases prediction models; Ethical, legal and social issues; Genetic counseling; Genome wide association studies; Next generation sequencing

Indexed keywords

BIOLOGICAL MODEL; CORONARY ARTERY DISEASE; GENE FREQUENCY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC COUNSELING; GENETIC MARKER; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; HUMAN; METHODOLOGY; NON INSULIN DEPENDENT DIABETES MELLITUS; OBESITY; REVIEW; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM;

CORONARY ARTERY DISEASE; DIABETES MELLITUS, TYPE 2; GENE FREQUENCY; GENETIC COUNSELING; GENETIC LOCI; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC; OBESITY; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS;

EID: 84868342964     PISSN: 09394753     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.numecd.2012.04.010     Document Type: Review

References (66)

1. Maher B. Personal genomes: the case of the missing heritability. Nature 2008, 456:18-21.
2. Manolio T.A., Collins F.S., Cox N.J., Goldstein D.B., Hindorff L.A., Hunter D.J., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
3. McCarthy MI. Genomics, type 2 diabetes, and obesity. N Engl J Med; 363:2339-2350.
4. Newman B., Selby J.V., King M.C., Slemenda C., Fabsitz R., Friedman G.D. Concordance for type 2 (non-insulin-dependent) diabetes mellitus in male twins. Diabetologia 1987, 30:763-768.
5. Weijnen C.F., Rich S.S., Meigs J.B., Krolewski A.S., Warram J.H. Risk of diabetes in siblings of index cases with type 2 diabetes: implications for genetic studies. Diabet Med 2002, 19:41-50.
6. Almgren P., Lehtovirta M., Isomaa B., Sarelin L., Taskinen M.R., Lyssenko V., et al. Heritability and familiality of type 2 diabetes and related quantitative traits in the Botnia study. Diabetologia 2011, 54:2811-2819.
7. Cauchi S., Meyre D., Durand E., Proenca C., Marre M., Hadjadj S., et al. Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value. PLoS One 2008, 3:e2031.
8. Pisabarro R.E., Sanguinetti C., Stoll M., Prendez D. High incidence of type 2 diabetes in peroxisome proliferator-activated receptor gamma2 Pro12Ala carriers exposed to a high chronic intake of trans fatty acids and saturated fatty acids. Diabetes Care 2004, 27:2251-2252.
9. Fisher E., Boeing H., Fritsche A., Doering F., Joost H.G., Schulze M.B. Whole-grain consumption and transcription factor-7-like 2 (TCF7L2) rs7903146: gene-diet interaction in modulating type 2 diabetes risk. Br J Nutr 2009, 101:478-481.
10. Morini E., Prudente S., Succurro E., Chandalia M., Zhang Y.Y., Mammarella S., et al. IRS1 G972R polymorphism and type 2 diabetes: a paradigm for the difficult ascertainment of the contribution to disease susceptibility of 'low-frequency-low-risk' variants. Diabetologia 2009, 52:1852-1857.
11. Prudente S., Morini E., Trischitta V. Insulin signaling regulating genes: effect on T2DM and cardiovascular risk. Nat Rev Endocrinol 2009, 5:682-693.
12. de Miguel-Yanes J.M., Shrader P., Pencina M.J., Fox C.S., Manning A.K., Grant R.W., et al. Genetic risk reclassification for type 2 diabetes by age below or above 50 years using 40 type 2 diabetes risk single nucleotide polymorphisms. Diabetes Care 2011, 34:121-125.
13. Giacco R., Della Pepa G., Luongo D., Riccardi G. Whole grain intake in relation to body weight: from epidemiological evidence to clinical trials. Nutr Metab Cardiovasc Dis 2011, 21:901-908.
14. Lyssenko V., Jonsson A., Almgren P., Pulizzi N., Isomaa B., Tuomi T., et al. Clinical risk factors, DNA variants, and the development of type 2 diabetes. N Engl J Med 2008, 359:2220-2232.
15. Meigs J.B., Shrader P., Sullivan L.M., McAteer J.B., Fox C.S., Dupuis J., et al. Genotype score in addition to common risk factors for prediction of type 2 diabetes. N Engl J Med 2008, 359:2208-2219.
16. Vaxillaire M., Veslot J., Dina C., Proenca C., Cauchi S., Charpentier G., et al. Impact of common type 2 diabetes risk polymorphisms in the DESIR prospective study. Diabetes 2008, 57:244-254.
17. van Hoek M., Dehghan A., Witteman J.C., van Duijn C.M., Uitterlinden A.G., Oostra B.A., et al. Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study. Diabetes 2008, 57:3122-3128.
18. Talmud P.J., Hingorani A.D., Cooper J.A., Marmot M.G., Brunner E.J., Kumari M., et al. Utility of genetic and non-genetic risk factors in prediction of type 2 diabetes: Whitehall II prospective cohort study. BMJ 2010, 340:b4838.
19. Lange L.A., Bowden D.W., Langefeld C.D., Wagenknecht L.E., Carr J.J., Rich S.S., et al. Heritability of carotid artery intima-medial thickness in type 2 diabetes. Stroke 2002, 33:1876-1881.
20. Marenberg M.E., Risch N., Berkman L.F., Floderus B., de Faire U. Genetic susceptibility to death from coronary heart disease in a study of twins. N Engl J Med 1994, 330:1041-1046.
21. Wagenknecht L.E., Bowden D.W., Carr J.J., Langefeld C.D., Freedman B.I., Rich S.S. Familial aggregation of coronary artery calcium in families with type 2 diabetes. Diabetes 2001, 50:861-866.
22. Rivellese A.A., Piatti P.M. Consensus on: screening and therapy of coronary heart disease in diabetic patients. Nutr Metab Cardiovasc Dis 2011, 21:757-764.
23. Samani N.J., Erdmann J., Hall A.S., Hengstenberg C., Mangino M., Mayer B., et al. Genomewide association analysis of coronary artery disease. N Engl J Med 2007, 357:443-453.
24. McPherson R., Pertsemlidis A., Kavaslar N., Stewart A., Roberts R., Cox D.R., et al. A common allele on chromosome 9 associated with coronary heart disease. Science 2007, 316:1488-1491.
25. Erdmann J., Grosshennig A., Braund P.S., Konig I.R., Hengstenberg C., Hall A.S., et al. New susceptibility locus for coronary artery disease on chromosome 3q22.3. Nat Genet 2009, 41:280-282.
26. Tregouet D.A., Konig I.R., Erdmann J., Munteanu A., Braund P.S., Hall A.S., et al. Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat Genet 2009, 41:283-285.
27. Schunkert H., Konig I.R., Kathiresan S., Reilly M.P., Assimes T.L., Holm H., et al. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet 2011, 43:333-338.
28. Coronary artery disease (C4D) genetics consortium: a genome-wide association study in Europeans and south Asians identifies five new loci for coronary artery disease. Nat Genet 2011, 43:339-344.
29. Qi L., Parast L., Cai T., Powers C., Gervino E.V., Hauser T.H., et al. Genetic susceptibility to coronary heart disease in type 2 diabetes 3 independent studies. J Am Coll Cardiol 2011, 58:2675-2682.
30. Stern M.P. Diabetes and cardiovascular disease. The "common soil" hypothesis. Diabetes 1995, 44:369-374.
31. Pfister R., Barnes D., Luben R.N., Khaw K.T., Wareham N.J., Langenberg C. Individual and cumulative effect of type 2 diabetes genetic susceptibility variants on risk of coronary heart disease. Diabetologia 2011, 54:2283-2287.
32. Pizzuti A., Frittitta L., Argiolas A., Baratta R., Goldfine I.D., Bozzali M., et al. A polymorphism (K121Q) of the human glycoprotein PC-1 gene coding region is strongly associated with insulin resistance. Diabetes 1999, 48:1881-1884.
33. Hribal M.L., Federici M., Porzio O., Lauro D., Borboni P., Accili D., et al. The Gly-->Arg972 amino acid polymorphism in insulin receptor substrate-1 affects glucose metabolism in skeletal muscle cells. J Clin Endocrinol Metab 2000, 85:2004-2013.
34. Prudente S., Hribal M.L., Flex E., Turchi F., Morini E., De Cosmo S., et al. The functional Q84R polymorphism of mammalian Tribbles homolog TRB3 is associated with insulin resistance and related cardiovascular risk in Caucasians from Italy. Diabetes 2005, 54:2807-2811.
35. Lappalainen T., Kolehmainen M., Schwab U.S., Tolppanen A.M., Stancakova A., Lindstrom J., et al. Association of the FTO gene variant (rs9939609) with cardiovascular disease in men with abnormal glucose metabolism-the Finnish diabetes prevention study. Nutr Metab Cardiovasc Dis 2011, 21:691-698.
36. Ripatti S., Tikkanen E., Orho-Melander M., Havulinna A.S., Silander K., Sharma A., et al. A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses. Lancet 2010, 376:1393-1400.
37. Thomas D. Gene-environment-wide association studies: emerging approaches. Nat Rev Genet 2010, 11:259-272.
38. Mukherjee B., Ahn J., Gruber S.B., Chatterjee N. Testing gene-environment interaction in large-scale case-control association studies: possible choices and comparisons. Am J Epidemiol 2012, 175:177-190.
39. Cornelis M.C., Tchetgen E.J., Liang L., Qi L., Chatterjee N., Hu F.B., et al. Gene-environment interactions in genome-wide association studies: a comparative study of tests applied to empirical studies of type 2 diabetes. Am J Epidemiol 2012, 175:191-202.
40. Thomas D.C., Lewinger J.P., Murcray C.E., Gauderman W.J. Invited commentary: GE-Whiz! Ratcheting gene-environment studies up to the whole genome and the whole exposome. Am J Epidemiol 2012, 175:203-207. discussion 208-209.
41. Mukherjee B.A.J., Gruber S.B., Chatterjee N. Response to invited commentary: Mukherjee et al. respond to "GE-Whiz! ratcheting up gene-environment studies". Am J Epidemiol 2012, 175:208-209.
42. Cook N.R. Use and misuse of the receiver operating characteristic curve in risk prediction. Circulation 2007, 115:928-935.
43. Pencina M.J., D'Agostino R.B., D'Agostino R.B., Vasan R.S. Evaluating the added predictive ability of a new marker: from area under the ROC curve to reclassification and beyond. Stat Med 2008, 27:157-172. discussion 207-212.
44. Bacci S., Rizza S., Prudente S., Spoto B., Powers C., Facciorusso A., et al. The ENPP1 Q121 variant predicts major cardiovascular events in high-risk individuals: evidence for interaction with obesity in diabetic patients. Diabetes 2011, 60:1000-1007.
45. Pencina M.J., D'Agostino R.B., Steyerberg E.W. Extensions of net reclassification improvement calculations to measure usefulness of new biomarkers. Stat Med 2011, 30:11-21.
46. Cook N.R., Paynter N.P. Comments on 'extensions of net reclassification improvement calculations to measure usefulness of new biomarkers' by M.J. Pencina, R.B. D'Agostino, Sr. and E.W. Steyerberg. Stat Med 2012, 31:93-95.
47. Janssens A.C., Ioannidis J.P., van Duijn C.M., Little J., Khoury M.J. Strengthening the reporting of genetic risk prediction studies: the GRIPS statement. Eur J Clin Invest 2011, 41:1004-1009.
48. Reich D.E., Lander E.S. On the allelic spectrum of human disease. Trends Genet 2001, 17:502-510.
49. 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.
50. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945.
51. Metzker M.L. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46.
52. 1000 genomes project consortium: a map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
53. Bick D., Dimmock D. Whole exome and whole genome sequencing. Curr Opin Pediatr 2011, 23:594-600.
54. Cirulli E.T., Goldstein D.B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 2010, 11:415-425.
55. Janssens A.C., Gwinn M., Bradley L.A., Oostra B.A., van Duijn C.M., Khoury M.J. A critical appraisal of the scientific basis of commercial genomic profiles used to assess health risks and personalize health interventions. Am J Hum Genet 2008, 82:593-599.
56. European society of human genetics: statement of the ESHG on direct-to-consumer genetic testing for health-related purposes. Eur J Hum Genet 2010, 18:1271-1273.
57. Grant R.W., Hivert M., Pandiscio J.C., Florez J.C., Nathan D.M., Meigs J.B. The clinical application of genetic testing in type 2 diabetes: a patient and physician survey. Diabetologia 2009, 52:2299-2305.
58. Ransohoff D.F., Khoury M.J. Personal genomics: information can be harmful. Eur J Clin Invest 2010, 40:64-68.
59. Ormond K.E., Wheeler M.T., Hudgins L., Klein T.E., Butte A.J., Altman R.B., et al. Challenges in the clinical application of whole-genome sequencing. Lancet 2010, 375:1749-1751.
60. Skirton H., Lewis C., Kent A., Coviello D.A. Genetic education and the challenge of genomic medicine: development of core competences to support preparation of health professionals in Europe. Eur J Hum Genet 2010, 18:972-977.
61. Janssens A.C., van Duijn C.M. Genome-based prediction of common diseases: advances and prospects. Hum Mol Genet 2008, 17:R166-R173.
62. Cornelis M.C., Qi L., Zhang C., Kraft P., Manson J., Cai T., et al. Joint effects of common genetic variants on the risk for type 2 diabetes in U.S. men and women of European ancestry. Ann Intern Med 2009, 150:541-550.
63. Timpson N.J., Lindgren C.M., Weedon M.N., Randall J., Ouwehand W.H., Strachan D.P., et al. Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data. Diabetes 2009, 58:505-510.
64. Doria A., Wojcik J., Xu R., Gervino E.V., Hauser T.H., Johnstone M.T., et al. Interaction between poor glycemic control and 9p21 locus on risk of coronary artery disease in type 2 diabetes. J Am Med Assoc 2008, 300:2389-2397.
65. Kathiresan S., Voight B.F., Purcell S., Musunuru K., Ardissino D., Mannucci P.M., et al. Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet 2009, 41:334-341.
66. Helgadottir A., Thorleifsson G., Manolescu A., Gretarsdottir S., Blondal T., Jonasdottir A., et al. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 2007, 316:1491-1493.