A comparison of principal component analysis and factor analysis strategies for uncovering pleiotropic factors

Genetic Epidemiology

Volumn 33, Issue 4, 2009, Pages 325-331

  Wang, Xiaojing ^a   Kammerer, Candace M ^a   Anderson, Stewart ^b   Lu, Jiang ^b   Feingold, Eleanor ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Factor analysis; Multivariate analysis; PCA; Quantitative traits

Indexed keywords

ARTICLE; CONTROLLED STUDY; ENVIRONMENTAL FACTOR; FACTORIAL ANALYSIS; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC TRAIT; HEREDITY; INTERMETHOD COMPARISON; LINKAGE ANALYSIS; MATHEMATICAL COMPUTING; PHENOTYPE; PLEIOTROPY; PRINCIPAL COMPONENT ANALYSIS; PROBABILITY; SIMULATION;

DATABASES, GENETIC; DISEASE; ENVIRONMENT; EPIDEMIOLOGIC METHODS; FACTOR ANALYSIS, STATISTICAL; FEMALE; HUMANS; MALE; MODELS, GENETIC; MODELS, STATISTICAL; MULTIVARIATE ANALYSIS; PHENOTYPE; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE TRAIT, HERITABLE;

EID: 66249116670     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20384     Document Type: Article

References (24)

1. Aldridge K, Kane AA, Marsh JL, Panchal J, Boyadjiev SA, Yan P, Govier D, Ahmad W, Richtsmeier JT. 2005. Brain morphology in nonsyndromic unicoronal craniosynostosis. Anat Rec A Discov Mol Cell Evol Biol 285:690-698.
2. Austin MA, Edwards KL, McNeely MJ, Chandler WL, Leonetti DL, Talmud PJ, Humphries SE, Fujimoto WY. 2004. Heritability of multivariate factors of the metabolic syndrome in nondiabetic Japanese americans. Diabetes 53:1166-1169.
3. Chase K, Carrier DR, Adler FR, Jarvik T, Ostrander EA, Lorentzen TD, Lark KG. 2002. Genetic basis for systems of skeletal quantitative traits: principal component analysis of the canid skeleton. Proc Nat Acad Sci USA 99:9930-9935.
4. Deng FY, Lei SF, Li MX, Jiang C, Dvornyk V, Deng HW. 2006. Genetic determination and correlation of body mass index and bone mineral density at the spine and hip in Chinese Han ethnicity. Osteoporos Int 17:119-124.
5. Devoto M, Spotila LD, Stabley DL, Wharton GN, Rydbeck H, Korkko J, Kosich R, Prockop D, Tenenhouse A, Sol-Church K. 2005. Univariate and bivariate variance component linkage analysis of a whole-genome scan for loci contributing to bone mineral density. Eur J Hum Genet 13:781-788.
6. Guo Y, Zhao LJ, Shen H, Guo Y, Deng HW. 2005. Genetic and environmental correlations between age at menarche and bone mineral density at different skeletal sites. Calcif Tissue Int 77:356-360.
7. Hakulinen MA, Day JS, Toyras J, Weinans H, Jurvelin JS. 2006. Ultrasonic characterization of human trabecular bone microstructure. Phys Med Biol 51:1633-1648.
8. Hegele RA. 1997. Candidate genes, small effects, and the prediction of atherosclerosis. Crit Rev Clin Lab Sci 34:343-367.
9. Holberg CJ, Halonen M, Solomon S, Graves PE, Baldini M, Erickson RP, Martinez FD. 2001. Factor analysis of asthma and atopy traits shows 2 major components, one of which is linked to markers on chromosome 5q. J Allergy Clin Immunol 108:772-780.
10. Karasik D, Cupples LA, Hannan MT, Kiel DP. 2004. Genome screen for a combined bone phenotype using principal component analysis: the Framingham study. Bone 34:547-556.
11. Klein RF, Turner RJ, Skinner LD, Vartanian KA, Serang M, Carlos AS, Shea M, Belknap JK, Orwoll ES. 2002. Mapping quantitative trait loci that influence femoral cross-sectional area in mice. J Bone Miner Res 17:1752-1760.
12. Lee WT, Cheung AY, Lau J, Lee SK, Qin L, Cheng JC. 2004. Bone densitometry: which skeletal sites are best predicted by bone mass determinants? J Bone Miner Metab 22:447-455.
13. Li X, Masinde G, Gu W, Wergedal J, Mohan S, Baylink DJ. 2002. Genetic dissection of femur breaking strength in a large population (MRL/MpJ x SJL/J) of F2 Mice: single QTL effects, epistasis, and pleiotropy. Genomics 79:734-740.
14. Li X, Quinones MJ, Wang D, Bulnes-Enriquez I, Jimenez X, De La Rosa R, Aurea GL, Taylor KD, Hsueh WA, Rotter JI, et al. 2006. Genetic effects on obesity assessed by bivariate genome scan: the Mexican-American coronary artery disease study. Obesity 14:1192-1200.
15. Lin HF, Boden-Albala B, Juo SH, Park N, Rundek T, Sacco RL. 2005. Heritabilities of the metabolic syndrome and its components in the Northern Manhattan Family Study. Diabetologia 48:2006-2012.
16. Livshits G, Deng HW, Nguyen TV, Yakovenko K, Recker RR, Eisman JA. 2004. Genetics of bone mineral density: evidence for a major pleiotropic effect from an intercontinental study. J Bone Miner Res 19:914-923.
17. Martin LJ, Cianflone K, Zakarian R, Nagrani G, Almasy L, Rainwater DL, Cole S, Hixson JE, MacCluer JW, Blangero J, et al. 2004. Bivariate linkage between acylation-stimulating protein and BMI and high-density lipoproteins. Obes Res 12:669-678.
18. Masinde GL, Wergedal J, Davidson H, Mohan S, Li R, Li X, Baylink DJ. 2003. Quantitative trait loci for periosteal circumference (PC): identification of single loci and epistatic effects in F2 MRL/SJL mice. Bone 32:554-560.
19. Mitchell BD, Kammerer CM, Mahaney MC, Blangero J, Comuzzie AG, Atwood LD, Haffner SM, Stern MP, MacCluer JW. 1996. Genetic analysis of the IRS. Pleiotropic effects of genes influencing insulin levels on lipoprotein and obesity measures. Arterioscler Thromb Vasc Biol 16:281-288.
20. Musani SK, Huang-Ge Z, Hsu H-C, Yi N-J, Gorman BS, Allison DB. 2006. Principal component analysis of quantitative trait loci for immune response to adenovirus in mice. Hereditas 143:189-197.
21. Peacock M, Koller DL, Hui S, Johnston CC, Foroud T, Econs MJ. 2004. Peak bone mineral density at the hip is linked to chromosomes 14q and 15q. Osteoporos Int 15:489-496.
22. R-Development-Core-Team. 2007. R: A language and environment for statistical computing. Vienna, Austria.
23. Wang X, Kammerer CM, Wheeler VW, Patrick AL, Bunker CH, Zmuda JM. 2007a. Genetic and environmental determinants of volumetric and areal BMD in multi-generational families of African ancestry: the Tobago Family Health Study. J Bone Miner Res 22:527-536.
24. Wang X, Kammerer CM, Wheeler VW, Patrick AL, Bunker CH, Zmuda JM. 2007b. Pleiotropy and heterogeneity in the expression of bone strength-related phenotypes in extended pedigrees. J Bone Miner Res 22:1766-1772.