Genome-based prediction of common diseases: Methodological considerations for future research

Genome Medicine

Volumn 1, Issue 2, 2009, Pages

  Janssens, A Cecile J W ^a   Van Duijn, Cornelia M ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

AREA UNDER THE CURVE; BODY MASS; CALIBRATION; GENETIC ANALYSIS; GENETIC PREDISPOSITION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE ENVIRONMENT INTERACTION; HYPERTRIGLYCERIDEMIA; ISCHEMIC HEART DISEASE; LIFESTYLE; MALIGNANT NEOPLASTIC DISEASE; MEDICAL PRACTICE; METHODOLOGY; NON INSULIN DEPENDENT DIABETES MELLITUS; PREDICTION; PRIORITY JOURNAL; PUBLIC HEALTH SERVICE; REVIEW; SYSTEMIC LUPUS ERYTHEMATOSUS;

EID: 68949191441     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm20     Document Type: Review

References (35)

1. Manolio TA, Brooks LD, Collins FS: A HapMap harvest of insights into the genetics of common disease. J Clin Invest 2008, 118:1590-1605.
2. Guttmacher AE, Collins FS: Realizing the promise of genomics in biomedical research. JAMA 2005, 294:1399-1402.
3. Brand A, Brand H, Schulte in den Bäumen T: The impact of genetics and genomics on public health. Eur J Hum Genet 2008, 16:5-13.
4. Pharoah PD, Antoniou AC, Easton DF, Ponder BA: Polygenes, risk prediction, and targeted prevention of breast cancer. N Engl J Med 2008, 358:2796-2803.
5. Janssens ACJW, Van Duijn CM: Genome-based prediction of common diseases: advances and prospects. Hum Mol Genet 2008, 17: R166-R173.
6. Janssens ACJW, Aulchenko YS, Elefante S, Borsboom GJJM, Steyerberg EW, Van Duijn CM: Predictive testing for complex diseases using multiple genes: fact or fiction? Genet Med 2006, 8:395-400.
7. Janssens ACJW, Gwinn M, Bradley LA, Oostra BA, Van Duijn CM, Khoury MJ: 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.
8. Khoury MJ, Gwinn M, Yoon PW, Dowling N, Moore CA, Bradley L: The continuum of translation research in genomic medicine: how can we accelerate the appropriate integration of human genome discoveries into health care and disease prevention? Genet Med 2007, 9:665-674.
9. Haga SB, Khoury MJ, Burke W: Genomic profiling to promote a healthy lifestyle: not ready for prime time. Nat Genet 2003, 34:347-350.
10. Cauchi S, Meyre D, Durand E, Proença C, Marre M, Hadjadj S, Choquet H, De Graeve F, Gaget S, Allegaert F, Delplanque J, Permutt MA, Wasson J, Blech I, Charpentier G, Balkau B, Vergnaud AC, Czernichow S, Patsch W, Chikri M, Glaser B, Sladek R, Froguel P: 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.
11. Lango H; UK Type 2 Diabetes Genetics Consortium, Palmer CN, Morris AD, Zeggini E, Hattersley AT, McCarthy MI, Frayling TM, Weedon MN: Assessing the combined impact of 18 common genetic variants of modest effect sizes on type 2 diabetes risk. Diabetes 2008, 57:3129-3135.
12. Wang J, Ban MR, Zou GY, Cao H, Lin T, Kennedy BA, Anand S, Yusuf S, Huff MW, Pollex RL, Hegele RA: Polygenic determinants of severe hypertriglyceridemia. Hum Mol Genet 2008, 17:2894-2899.
13. Maller J, George S, Purcell S, Fagerness J, Altshuler D, Daly MJ, Seddon JM: Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration. Nat Genet 2006, 38:1055-1059.
14. van Hoek M, Dehghan A, Witteman JCM, Van Duijn CM, Uitterlinden AG, Oostra BA, Hofman A, Sijbrands EJ, Janssens AC: Predicting type 2 diabetes based on polymorphisms from genome wide association studies: a population-based study. Diabetes 2008, 57:3122-3128.
15. Humphries SE, Cooper JA, Talmud PJ, Miller GJ: Candidate gene genotypes, along with conventional risk factor assessment, improve estimation of coronary heart disease risk in healthy UK men. Clin Chem 2007, 53:8-16.
16. Morrison AC, Bare LA, Chambless LE, Ellis SG, Malloy M, Kane JP, Pankow JS, Devlin JJ, Willerson JT, Boerwinkle E: Prediction of coronary heart disease risk using a genetic risk score: the Atherosclerosis Risk in Communities Study. Am J Epidemiol 2007, 166:28-35.
17. van der Net JB, Janssens ACJW, Defesche JC, Kastelein JJP, Sijbrands EJG, Steyerberg EW: Usefulness of genetic polymorphisms and conventional risk factors to predict coronary heart disease in patients with familial hypercholesterolemia. Am J Cardiol 2009, 103: 375-380.
18. Kathiresan S, Melander O, Anevski D, Guiducci C, Burtt NP, Roos C, Hirschhorn JN, Berglund G, Hedblad B, Groop L, Altshuler DM, Newton-Cheh C, Orho-Melander M: Polymorphisms associated with cholesterol and risk of cardiovascular events. N Engl J Med 2008, 358:1240-1249.
19. Weedon MN, McCarthy MI, Hitman G, Walker M, Groves CJ, Zeggini E, Rayner NW, Shields B, Owen KR, Hattersley AT, Frayling TM: Combining information from common type 2 diabetes risk polymorphisms improves disease prediction. PLOS Med 2006, 3:e374.
20. Zheng SL, Sun J, Wiklund F, Smith S, Stattin P, Li G, Adami HO, Hsu FC, Zhu Y, Bälter K, Kader AK, Turner AR, Liu W, Bleecker ER, Meyers DA, Duggan D, Carpten JD, Chang BL, Isaacs WB, Xu J, Grönberg H: Cumulative association of five genetic variants with prostate cancer. N Engl J Med 2008, 358:910-919.
21. Lyssenko V, Jonsson A, Almgren P, Pulizzi N, Isomaa B, Tuomi T, Berglund G, Altshuler D, Nilsson P, Groop L: Clinical risk factors, DNA variants, and the development of type 2 diabetes. N Engl J Med 2008, 359:2220-2232.
22. Meigs JB, Shrader P, Sullivan LM, McAteer JB, Fox CS, Dupuis J, Manning AK, Florez JC, Wilson PW, D'Agostino RB Sr, Cupples LA: Genotype score in addition to common risk factors for prediction of type 2 diabetes. N Engl J Med 2008, 359:2208-2219.
23. Weersma RK, Stokkers PC, van Bodegraven AA, van Hogezand RA, Verspaget HW, de Jong DJ, van der Woude CJ, Oldenburg B, Linskens R, van der Steege G, Festen EA, Hommes DW, Crusius JB, Wijmenga C, Nolte IM, Dijkstra G, Dutch Initiative on Crohn and Colitis (ICC).: Molecular prediction of disease risk and severity in a large Dutch Crohn's disease cohort. Gut 2009, 58:338-395.
24. Janssens ACJW, Moonesinghe R, Yang Q, Steyerberg EW, Van Duijn CM, Khoury MJ: The impact of genotype frequencies on the clinical validity of genomic profiling for predicting common chronic diseases. Genet Med 2007, 9:528-535.
25. Yeh CC, Sung FC, Tang R, Chang-Chieh CR, Hsieh LL: Association between polymorphisms of biotransformation and DNA-repair genes and risk of colorectal cancer in Taiwan. J Biomed Sci 2007, 14:183-193.
26. Podgoreanu MV, White WD, Morris RW, Mathew JP, Stafford-Smith M, Welsby IJ, Grocott HP, Milano CA, Newman MF, Schwinn DA; Perioperative Genetics and Safety Outcomes Study (PEGASUS) Investigative Team: Inflammatory gene polymorphisms and risk of postoperative myocardial infarction after cardiac surgery. Circulation 2006, 114:I275-I281.
27. Vaxillaire M, Veslot J, Dina C, Proença C, Cauchi S, Charpentier G, Tichet J, Fumeron F, Marre M, Meyre D, Balkau B, Froguel P; DESIR Study Group: Impact of common type 2 diabetes risk polymorphisms in the DESIR prospective study. Diabetes 2008, 57:244-254.
28. International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN), Harley JB, Alarcón-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, Moser KL, Tsao BP, Vyse TJ, Langefeld CD, Nath SK, Guthridge JM, Cobb BL, Mirel DB, Marion MC, Williams AH, Divers J, Wang W, Frank SG, Namjou B, Gabriel SB, Lee AT, Gregersen PK, Behrens TW, Taylor KE, Fernando M, Zidovetzki R, Gaffney PM, Edberg JC, Rioux JD, et al.: Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 2008, 40:204-210.
29. Janssens ACJW, Van Duijn CM: Five genetic variants associated with prostate cancer. N Engl J Med 2008, 358:2739.
30. Lyssenko V, Almgren P, Anevski D, Orho-Melander M, Sjogren M, Saloranta C, Tuomi T, Groop L; Botnia Study Group: Genetic prediction of future type 2 diabetes. PLOS Med 2005, 2:e345.
31. Cook NR: Use and misuse of the receiver operating characteristic curve in risk prediction. Circulation 2007, 115:928-935.
32. Pencina MJ, D'Agostino RB Sr, D'Agostino RB Jr, Vasan RS: 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.
33. Pepe MS, Janes HE: Gauging the performance of SNPs, biomarkers, and clinical factors for predicting risk of breast cancer. J Natl Cancer Inst 2008, 100:978-979.
34. Thorgeirsson TE, Geller F, Sulem P, Rafnar T, Wiste A, Magnusson KP, Manolescu A, Thorleifsson G, Stefansson H, Ingason A, Stacey SN, Bergthorsson JT, Thorlacius S, Gudmundsson J, Jonsson T, Jakobsdottir M, Saemundsdottir J, Olafsdottir O, Gudmundsson LJ, Bjornsdottir G, Kristjansson K, Skuladottir H, Isaksson HJ, Gudbjartsson T, Jones GT, Mueller T, Gottsäter A, Flex A, Aben KK, de Vegt F, et al.: A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature 2008, 452:638-642.
35. van der Net JB, van Etten J, Yazdanpanah M, Dallinga-Thie GM, Kastelein JJ, Defesche JC, Koopmans RP, Steyerberg EW, Sijbrands EJ: Gene-load score of the renin-angiotensin-aldosterone system is associated with coronary heart disease in familial hypercholesterolaemia. Eur Heart J 2008, 29:1370-1376.