Genome Wide Association Study to predict severe asthma exacerbations in children using random forests classifiers

BMC Medical Genetics

Volumn 12, Issue , 2011, Pages

  Xu, Mousheng ^a,b   Tantisira, Kelan G ^a   Wu, Ann ^a   Litonjua, Augusto A ^a   Chu, Jen Hwa ^a   Himes, Blanca E ^a   Damask, Amy ^c   Weiss, Scott T ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b BOSTON UNIVERSITY   (United States)

^c NOVARTIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BUDESONIDE; NEDOCROMIL; PLACEBO;

AGE DISTRIBUTION; ALGORITHM; AREA UNDER THE CURVE; ARTICLE; ASTHMA; CHILD; CHILDHOOD DISEASE; CLASSIFIER; CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; DISEASE EXACERBATION; DISEASE SEVERITY; DOUBLE BLIND PROCEDURE; EMERGENCY WARD; ENVIRONMENTAL FACTOR; FEMALE; FORCED EXPIRATORY VOLUME; FOREST DYNAMICS; GENETIC ASSOCIATION; GENETIC TRAIT; GENOTYPE; HEREDITY; HOSPITALIZATION; HUMAN; MAJOR CLINICAL STUDY; MALE; MULTICENTER STUDY; PHENOTYPE; PREDICTION; PREDICTIVE VALUE; PRESCHOOL CHILD; RANDOM FORESTS CLASSIFIER; RANDOMIZED CONTROLLED TRIAL; RISK FACTOR; SCHOOL CHILD; SCORING SYSTEM; SEX RATIO; SINGLE NUCLEOTIDE POLYMORPHISM; TREATMENT OUTCOME; ARTIFICIAL INTELLIGENCE; GENETICS;

ALGORITHMS; AREA UNDER CURVE; ARTIFICIAL INTELLIGENCE; ASTHMA; CHILD; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PREDICTIVE VALUE OF TESTS;

EID: 79959682373     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-12-90     Document Type: Article

References (39)

1. Bodmer W, Bonilla C. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008, 40(6):695-701. 10.1038/ng.f.136, 2527050, 18509313.
2. Haga SB, Khoury MJ, Burke W. Genomic profiling to promote a healthy lifestyle: not ready for prime time. Nat Genet 2003, 34(4):347-350. 10.1038/ng0803-347, 12923535.
3. Katsanis SH, Javitt G, Hudson K. Public health. A case study of personalized medicine. Science 2008, 320(5872):53-54. 10.1126/science.1156604, 18388277.
4. Tate SK, Goldstein DB. Will tomorrow's medicines work for everyone?. Nat Genet 2004, 36(11 Suppl):S34-42.
5. Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, Mangino M, Freathy RM, Perry JR, Stevens S, Hall AS, Samani NJ, Shields B, Prokopenko I, Farrall M, Dominiczak A, , Johnson T, Bergmann S, Beckmann JS, Vollenweider P, Waterworth DM, Mooser V, Palmer CN, Morris AD, Ouwehand WH, Zhao JH, Li S, Loos RJ, et al. Diabetes Genetics Initiative, Wellcome Trust Case Control Consortium, Cambridge GEM Consortium Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet 2008, 40(5):575-583. 10.1038/ng.121, 2681221, 18391952, Diabetes Genetics Initiative, Wellcome Trust Case Control Consortium, Cambridge GEM Consortium.
6. Breiman L. Random Forests. Machine Learning 2001, 45:5-32.
7. Banfield RE, Hall LO, Bowyer KW, Kegelmeyer WP. A comparison of decision tree ensemble creation techniques. IEEE Trans Pattern Anal Mach Intell 2007, 29(1):173-180.
8. Berce V, Repnik K, Potocnik U. Association of CCR5-delta32 mutation with reduced risk of nonatopic asthma in Slovenian children. J Asthma 2008, 45(9):780-784. 10.1080/02770900802386024, 18972295.
9. Fuhlbrigge AL, Weiss ST, Kuntz KM, Paltiel AD. Forced expiratory volume in 1 second percentage improves the classification of severity among children with asthma. Pediatrics 2006, 118(2):e347-355. 10.1542/peds.2005-2962, 16864642.
10. Hersh CP, Raby BA, Soto-Quiros ME, Murphy AJ, Avila L, Lasky-Su J, Sylvia JS, Klanderman BJ, Lange C, Weiss ST, Celedón JC. Comprehensive testing of positionally cloned asthma genes in two populations. Am J Respir Crit Care Med 2007, 176(9):849-857. 10.1164/rccm.200704-592OC, 2048676, 17702965.
11. Moffatt MF. Genes in asthma: new genes and new ways. Curr Opin Allergy Clin Immunol 2008, 8(5):411-417. 10.1097/ACI.0b013e32830f1dc1, 18769193.
12. Movahedi M, Mahdaviani SA, Rezaei N, Moradi B, Dorkhosh S, Amirzargar AA. IL-10, TGF-beta, IL-2, IL-12, and IFN-gamma cytokine gene polymorphisms in asthma. J Asthma 2008, 45(9):790-794. 10.1080/02770900802207261, 18972297.
13. Ho SM. Environmental epigenetics of asthma: an update. J Allergy Clin Immunol 2010, 126(3):453-465. 10.1016/j.jaci.2010.07.030, 20816181.
14. Gelfand EW. Pediatric asthma: a different disease. Proc Am Thorac Soc 2009, 6(3):278-282. 10.1513/pats.200808-090RM, 2677403, 19387030.
15. Eder W, Ege MJ, von Mutius E. The asthma epidemic. N Engl J Med 2006, 355(21):2226-2235. 10.1056/NEJMra054308, 17124020.
16. Cookson W. The alliance of genes and environment in asthma and allergy. Nature 1999, 402(6760 Suppl):B5-11.
17. Mannino DM, Homa DM, Akinbami LJ, Moorman JE, Gwynn C, Redd SC. Surveillance for asthma-United States, 1980-1999. MMWR Surveill Summ 2002, 51(1):1-13.
18. Krishnan V, Diette GB, Rand CS, Bilderback AL, Merriman B, Hansel NN, Krishnan JA. Mortality in patients hospitalized for asthma exacerbations in the United States. Am J Respir Crit Care Med 2006, 174(6):633-638. 10.1164/rccm.200601-007OC, 2648055, 16778163.
19. Razi CH, Turktas I, Bakirtas A. Comparison of single 2000-microg dose treatment vs. sequential repeated-dose 500-microg treatments with nebulized budesonide in acute asthma exacerbations. Ann Allergy Asthma Immunol 2008, 100(4):370-376. 10.1016/S1081-1206(10)60601-1, 18450124.
20. Walsh-Kelly CM, Kelly KJ, Drendel AL, Grabowski L, Kuhn EM. Emergency department revisits for pediatric acute asthma exacerbations: association of factors identified in an emergency department asthma tracking system. Pediatr Emerg Care 2008, 24(8):505-510. 10.1097/PEC.0b013e318180fdcb, 18645538.
21. Arnold DH, Gebretsadik T, Minton PA, Higgins S, Hartert TV. Assessment of severity measures for acute asthma outcomes: a first step in developing an asthma clinical prediction rule. Am J Emerg Med 2008, 26(4):473-479. 10.1016/j.ajem.2007.05.026, 18410819.
22. Kunkov S, Pinedo V, Silver EJ, Crain EF. Predicting the need for hospitalization in acute childhood asthma using end-tidal capnography. Pediatr Emerg Care 2005, 21(9):574-577. 10.1097/01.pec.0000177197.83655.d8, 16160659.
23. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81(3):559-575. 10.1086/519795, 1950838, 17701901.
24. Lasko TA, Bhagwat JG, Zou KH, Ohno-Machado L. The use of receiver operating characteristic curves in biomedical informatics. J Biomed Inform 2005, 38(5):404-415. 10.1016/j.jbi.2005.02.008, 16198999.
25. Swets JA. Signal detection theory and ROC analysis in psychology and diagnostics: Collected papers. 1995,
26. DeLong ER, DeLong DM, Clarke-Pearson DL. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 1988, 44(3):837-845. 10.2307/2531595, 3203132.
27. Weiss ST, Raby BA, Rogers A. Asthma genetics and genomics 2009. Curr Opin Genet Dev 2009, 19(3):279-282. 10.1016/j.gde.2009.05.001, 19481925.
28. Talmud PJ, Hingorani AD, Cooper JA, Marmot MG, Brunner EJ, Kumari M, Kivimaki M, Humphries SE. Utility of genetic and non-genetic risk factors in prediction of type 2 diabetes: Whitehall II prospective cohort study. BMJ 2010, 340:b4838. 10.1136/bmj.b4838, 2806945, 20075150.
29. Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science 2008, 322(5903):881-888. 10.1126/science.1156409, 2694957, 18988837.
30. Gail MH. Discriminatory accuracy from single-nucleotide polymorphisms in models to predict breast cancer risk. J Natl Cancer Inst 2008, 100(14):1037-1041. 10.1093/jnci/djn180, 2528005, 18612136.
31. Gail MH, Brinton LA, Byar DP, Corle DK, Green SB, Schairer C, Mulvihill JJ. Projecting individualized probabilities of developing breast cancer for white females who are being examined annually. J Natl Cancer Inst 1989, 81(24):1879-1886. 10.1093/jnci/81.24.1879, 2593165.
32. Rosner B, Colditz GA, Iglehart JD, Hankinson SE. Risk prediction models with incomplete data with application to prediction of estrogen receptor-positive breast cancer: prospective data from the Nurses' Health Study. Breast Cancer Res 2008, 10(4):R55. 10.1186/bcr2110, 2575548, 18598349.
33. Alvarez GG, Schulzer M, Jung D, Fitzgerald JM. A systematic review of risk factors associated with near-fatal and fatal asthma. Can Respir J 2005, 12(5):265-270.
34. Li D, German D, Lulla S, Thomas RG, Wilson SR. Prospective study of hospitalization for asthma. A preliminary risk factor model. Am J Respir Crit Care Med 1995, 151(3 Pt 1):647-655.
35. Swern AS, Tozzi CA, Knorr B, Bisgaard H. Predicting an asthma exacerbation in children 2 to 5 years of age. Ann Allergy Asthma Immunol 2008, 101(6):626-630. 10.1016/S1081-1206(10)60226-8, 19119707.
36. Wasilewski Y, Clark NM, Evans D, Levison MJ, Levin B, Mellins RB. Factors associated with emergency department visits by children with asthma: implications for health education. Am J Public Health 1996, 86(10):1410-1415. 10.2105/AJPH.86.10.1410, 1380652, 8876510.
37. Miller MK, Lee JH, Miller DP, Wenzel SE. Recent asthma exacerbations: a key predictor of future exacerbations. Respir Med 2007, 101(3):481-489. 10.1016/j.rmed.2006.07.005, 16914299.
38. Bouzigon E, Corda E, Aschard H, Dizier MH, Boland A, Bousquet J, Chateigner N, Gormand F, Just J, Le Moual N, Scheinmann P, Siroux V, Vervloet D, Zelenika D, Pin I, Kauffmann F, Lathrop M, Demenais F. Effect of 17q21 variants and smoking exposure in early-onset asthma. N Engl J Med 2008, 359(19):1985-1994. 10.1056/NEJMoa0806604, 18923164.
39. Liang PH, Shyur SD, Huang LH, Wen DC, Chiang YC, Lin MT, Yang HC. Risk factors and characteristics of early-onset asthma in Taiwanese children. J Microbiol Immunol Infect 2006, 39(5):414-421.