Incremental value of rare genetic variants for the prediction of multifactorial diseases

Genome Medicine

Volumn 5, Issue 8, 2013, Pages

  Mihaescu, Raluca ^a   Pencina, Michael J ^b,c   Alonso, Alvaro ^d   Lunetta, Kathryn L ^b,e   Heckbert, Susan R ^f   Benjamin, Emelia J ^e,g,h   Janssens, A Cecile J W ^a,i  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b BOSTON UNIVERSITY   (United States)

^c HARVARD CLINICAL RESEARCH INSTITUTE   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

^e FRAMINGHAM HEART STUDY   (United States)

^f UNIVERSITY OF WASHINGTON   (United States)

^g BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h BOSTON UNIVERSITY SCHOOL OF PUBLIC HEALTH   (United States)

ⁱ EMORY UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONGESTIVE HEART FAILURE; CONTROLLED STUDY; DIASTOLIC BLOOD PRESSURE; FOLLOW UP; GENE FREQUENCY; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HEART ATRIUM FIBRILLATION; HEART INFARCTION; HUMAN; HYPERTENSION; MORBIDITY; POPULATION SIZE; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTOLIC BLOOD PRESSURE;

EID: 84884508338     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm480     Document Type: Article

References (41)

1. Jostins L, Barrett JC. Genetic risk prediction in complex disease. Hum Mol Genet 2011, 20:R182-188.
2. Makowsky R, Pajewski NM, Klimentidis YC, Vazquez AI, Duarte CW, Allison DB, de los Campos G. Beyond missing heritability: prediction of complex traits. PLoS Genet 2011, 7:e1002051.
3. Bodmer W, Bonilla C. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008, 40:695-701.
4. Gorlov IP, Gorlova OY, Frazier ML, Spitz MR, Amos CI. Evolutionary evidence of the effect of rare variants on disease etiology. Clin Genet 2011, 79:199-206.
5. Visscher PM, Goddard ME, Derks EM, Wray NR. Evidence-based psychiatric genetics, AKA the false dichotomy between common and rare variant hypotheses. Mol Psychiatry 2012, 17:474-485.
6. Wang K, Dickson SP, Stolle CA, Krantz ID, Goldstein DB, Hakonarson H. Interpretation of association signals and identification of causal variants from genome-wide association studies. Am J Hum Genet 2010, 86:730-742.
7. Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, Nie X, Wu H, Zhao M, Cao H, Zou J, Shan Y, Li S, Yang Q, Ni P, Tian G, Xu J, Liu X, Jiang T, Wu R, et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 2010, 329:75-78.
8. Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 2010, 86:832-838.
9. Ji W, Foo JN, O'Roak BJ, Zhao H, Larson MG, Simon DB, Newton-Cheh C, State MW, Levy D, Lifton RP. Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet 2008, 40:592-599.
10. Nejentsev S, Walker N, Riches D, Egholm M, Todd JA. Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 2009, 324:387-389.
11. Wei C, Lu Q. Collapsing ROC approach for risk prediction research on both common and rare variants. BMC Proceedings 2011, (Suppl 9):S42.
12. Wu C, Walsh KM, ATD, JH, ZW. Disease risk prediction with rare and common variants. BMC Proceedings 2011, (Suppl 9):S61.
13. Cook NR. Use and misuse of the receiver operating characteristic curve in risk prediction. Circulation 2007, 115:928-935.
14. 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.
15. Pepe MS, Feng Z, Huang Y, Longton G, Prentice R, Thompson IM, Zheng Y. Integrating the predictiveness of a marker with its performance as a classifier. Am J Epidemiol 2008, 167:362-368.
16. Pencina MJ, D'Agostino RB S, D'Agostino RB J, 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. discussion 207-112.
17. Alonso A, Krijthe BP, Aspelund T, Stepas KA, Pencina MJ, Moser CB, Sinner MF, Sotoodehnia N, Fontes JD, Janssens AC, Kronmal RA, Magnani JW, Witteman JC, Chamberlain AM, Lubitz SA, Schnabel RB, Agarwal SK, McManus DD, Ellinor PT, Larson MG, Burke GL, Launer LJ, Hofman A, Levy D, Gottdiener JS, Kaab S, Couper D, Harris TB, Soliman EZ, Stricker BH, et al. Simple risk model predicts incidence of atrial fibrillation in a racially and geographically diverse population: the CHARGE-AF Consortium. J Am Heart Assoc 2013, 2:e000102.
18. Wolowacz SE, Samuel M, Brennan VK, Jasso-Mosqueda JG, Van Gelder IC. The cost of illness of atrial fibrillation: a systematic review of the recent literature. Europace 2011, 13:1375-1385.
19. Benjamin EJ, Rice KM, Arking DE, Pfeufer A, van Noord C, Smith AV, Schnabel RB, Bis JC, Boerwinkle E, Sinner MF, Dehghan A, Lubitz SA, D'Agostino RB, Lumley T, Ehret GB, Heeringa J, Aspelund T, Newton-Cheh C, Larson MG, Marciante KD, Soliman EZ, Rivadeneira F, Wang TJ, Eiriksdottir G, Levy D, Psaty BM, Li M, Chamberlain AM, Hofman A, Vasan RS, et al. Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry. Nat Genet 2009, 41:879-881.
20. Gudbjartsson DF, Arnar DO, Helgadottir A, Gretarsdottir S, Holm H, Sigurdsson A, Jonasdottir A, Baker A, Thorleifsson G, Kristjansson K, Palsson A, Blondal T, Sulem P, Backman VM, Hardarson GA, Palsdottir E, Helgason A, Sigurjonsdottir R, Sverrisson JT, Kostulas K, Ng MC, Baum L, So WY, Wong KS, Chan JC, Furie KL, Greenberg SM, Sale M, Kelly P, MacRae CA, et al. Variants conferring risk of atrial fibrillation on chromosome 4q25. Nature 2007, 448:353-357.
21. Ellinor PT, Lunetta KL, Glazer NL, Pfeufer A, Alonso A, Chung MK, Sinner MF, de Bakker PI, Mueller M, Lubitz SA, Fox E, Darbar D, Smith NL, Smith JD, Schnabel RB, Soliman EZ, Rice KM, Van Wagoner DR, Beckmann BM, van Noord C, Wang K, Ehret GB, Rotter JI, Hazen SL, Steinbeck G, Smith AV, Launer LJ, Harris TB, Makino S, Nelis M, et al. Common variants in KCNN3 are associated with lone atrial fibrillation. Nat Genet 2010, 42:240-244.
22. Ellinor PT, Lunetta KL, Albert CM, Glazer NL, Ritchie MD, Smith AV, Arking DE, Muller-Nurasyid M, Krijthe BP, Lubitz SA, Bis JC, Chung MK, Dorr M, Ozaki K, Roberts JD, Smith JG, Pfeufer A, Sinner MF, Lohman K, Ding J, Smith NL, Smith JD, Rienstra M, Rice KM, Van Wagoner DR, Magnani JW, Wakili R, Clauss S, Rotter JI, Steinbeck G, et al. Meta-analysis identifies six new susceptibility loci for atrial fibrillation. Nat Genet 2012, 44:670-675.
23. O'Donnell CJ, Nabel EG. Genomics of cardiovascular disease. N Engl J Med 2011, 365:2098-2109.
24. Parvez B, Darbar D. The "missing" link in atrial fibrillation heritability. J Electrocardiol 2011, 44:641-644.
25. Janssens AC, Aulchenko YS, Elefante S, Borsboom GJ, Steyerberg EW, van Duijn CM. Predictive testing for complex diseases using multiple genes: fact or fiction?. Genet Med 2006, 8:395-400.
26. Oexle K. A remark on rare variants. J Hum Genet 2010, 55:219-226.
27. Ionita-Laza I, Ottman R. Study designs for identification of rare disease variants in complex diseases: the utility of family-based designs. Genetics 2011, 189:1061-1068.
28. Pawitan Y, Seng KC, Magnusson PK. How many genetic variants remain to be discovered?. PLoS One 2009, 4:e7969.
29. Tsai CT, Lai LP, Hwang JJ, Lin JL, Chiang FT. Molecular genetics of atrial fibrillation. J Am Coll Cardiol 2008, 52:241-250.
30. Schnabel RB, Sullivan LM, Levy D, Pencina MJ, Massaro JM, D'Agostino RB, Newton-Cheh C, Yamamoto JF, Magnani JW, Tadros TM, Kannel WB, Wang TJ, Ellinor PT, Wolf PA, Vasan RS, Benjamin EJ. Development of a risk score for atrial fibrillation (Framingham Heart Study): a community-based cohort study. Lancet 2009, 373:739-745.
31. Chamberlain AM, Agarwal SK, Folsom AR, Soliman EZ, Chambless LE, Crow R, Ambrose M, Alonso A. A clinical risk score for atrial fibrillation in a biracial prospective cohort (from the Atherosclerosis Risk in Communities [ARIC] study). Am J Cardiol 2011, 107:85-91.
32. Schnabel RB, Larson MG, Yamamoto JF, Sullivan LM, Pencina MJ, Meigs JB, Tofler GH, Selhub J, Jacques PF, Wolf PA, Magnani JW, Ellinor PT, Wang TJ, Levy D, Vasan RS, Benjamin EJ. Relations of biomarkers of distinct pathophysiological pathways and atrial fibrillation incidence in the community. Circulation 2010, 121:200-207.
33. Smith JG, Newton-Cheh C, Almgren P, Struck J, Morgenthaler NG, Bergmann A, Platonov PG, Hedblad B, Engstrom G, Wang TJ, Melander O. Assessment of conventional cardiovascular risk factors and multiple biomarkers for the prediction of incident heart failure and atrial fibrillation. J Am Coll Cardiol 2010, 56:1712-1719.
34. The Atherosclerosis Risk in Communities (ARIC) Study: design and objectives. The ARIC investigators. Am J Epidemiol 1989, 129:687-702.
35. Fried LP, Borhani NO, Enright P, Furberg CD, Gardin JM, Kronmal RA, Kuller LH, Manolio TA, Mittelmark MB, Newman A, O'Leary DH, Psaty B, Rautaharju P, Tracy RP, Weiler PG. The Cardiovascular Health Study: design and rationale. Ann Epidemiol 1991, 1:263-276.
36. Feinleib M, Kannel WB, Garrison RJ, McNamara PM, Castelli WP. The Framingham Offspring Study. Design and preliminary data. Prev Med 1975, 4:518-525.
37. Pencina MJ, D'Agostino RB, Steyerberg EW. Extensions of net reclassification improvement calculations to measure usefulness of new biomarkers. Stat Med 2011, 30:11-21.
38. Vienna: R Foundation for Statistical Computing. R Development Core Team R: a language and environment for statistical computing. Version 2.8.0, Vienna: R Foundation for Statistical Computing. R Development Core Team., http://www.R-project.org
39. Guey LT, Kravic J, Melander O, Burtt NP, Laramie JM, Lyssenko V, Jonsson A, Lindholm E, Tuomi T, Isomaa B, Nilsson P, Almgren P, Kathiresan S, Groop L, Seymour AB, Altshuler D, Voight BF. Power in the phenotypic extremes: a simulation study of power in discovery and replication of rare variants. Genet Epidemiol 2011, Feb 9. doi: 10.1002/gepi.20572.
40. Wolf PA, Mitchell JB, Baker CS, Kannel WB, D'Agostino RB. Impact of atrial fibrillation on mortality, stroke, and medical costs. Arch Intern Med 1998, 158:229-234.
41. Fox CS, Parise H, D'Agostino RB S, Lloyd-Jones DM, Vasan RS, Wang TJ, Levy D, Wolf PA, Benjamin EJ. Parental atrial fibrillation as a risk factor for atrial fibrillation in offspring. JAMA 2004, 291:2851-2855.