Principal-Component Analysis for Assessment of Population Stratification in Mitochondrial Medical Genetics

American Journal of Human Genetics

Volumn 86, Issue 6, 2010, Pages 904-917

  Biffi, Alessandro ^a,b   Anderson, Christopher D ^a,b   Nalls, Michael A ^c   Rahman, Rosanna ^a,b   Sonni, Akshata ^a,b   Cortellini, Lynelle ^a,b   Rost, Natalia S ^a,b   Matarin, Mar ^c,d   Hernandez, Dena G ^c,e   Plourde, Anna ^a,b   de Bakker, Paul I W ^b,f   Ross, Owen A ^g   Greenberg, Steven M ^a   Furie, Karen L ^a   Meschia, James F ^g   Singleton, Andrew B ^c   Saxena, Richa ^a,b   Rosand, Jonathan ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c NATIONAL INSTITUTE ON AGING   (United States)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e UNIVERSITY COLLEGE LONDON   (United Kingdom)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

^g MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; CONTROLLED STUDY; EUROPEAN AMERICAN; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC MARKER; GENOTYPE; HAPLOIDY; HUMAN; MAJOR CLINICAL STUDY; MITOCHONDRIAL GENETICS; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; RELIABILITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

DNA, MITOCHONDRIAL; EUROPE; GENE FREQUENCY; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION GROUPS; PRINCIPAL COMPONENT ANALYSIS;

EID: 77953123927     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2010.05.005     Document Type: Article

References (29)

1. Webb E., Broderick P., Chandler I., Lubbe S., Penegar S., Tomlinson I.P., and Houlston R.S. Comprehensive analysis of common mitochondrial DNA variants and colorectal cancer risk. Br. J. Cancer 99 (2008) 2088-2093
2. Saxena R., de Bakker P.I., Singer K., Mootha V., Burtt N., Hirschhorn J.N., Gaudet D., Isomaa B., Daly M.J., Groop L., et al. Comprehensive association testing of common mitochondrial DNA variation in metabolic disease. Am. J. Hum. Genet. 79 (2006) 54-61
3. Hudson G., Mowbray C., Elson J.L., Jacob A., Boggild M., Torroni A., and Chinnery P.F. Does mitochondrial DNA predispose to neuromyelitis optica (Devic's disease)?. Brain 131 (2008) e93
4. Poyton R.O., Ball K.A., and Castello P.R. Mitochondrial generation of free radicals and hypoxic signaling. Trends Endocrinol. Metab. 20 (2009) 332-340
5. Valko M., Leibfritz D., Moncol J., Cronin M.T., Mazur M., and Telser J. Free radicals and antioxidants in normal physiological functions and human disease. Int. J. Biochem. Cell Biol. 39 (2007) 44-84
6. Raule N., Sevini F., Santoro A., Altilia S., and Franceschi C. Association studies on human mitochondrial DNA: methodological aspects and results in the most common age-related diseases. Mitochondrion 7 (2007) 29-38
7. Ziegler A., König I.R., and Thompson J.R. Biostatistical aspects of genome-wide association studies. Biom. J. 50 (2008) 8-28
8. Tiwari H.K., Barnholtz-Sloan J., Wineinger N., Padilla M.A., Vaughan L.K., and Allison D.B. Review and evaluation of methods correcting for population stratification with a focus on underlying statistical principles. Hum. Hered. 66 (2008) 67-86
9. Pakendorf B., and Stoneking M. Mitochondrial DNA and human evolution. Annu. Rev. Genomics Hum. Genet. 6 (2005) 165-183
10. Hudson G., Carelli V., Spruijt L., Gerards M., Mowbray C., Achilli A., Pyle A., Elson J., Howell N., La Morgia C., et al. Clinical expression of Leber hereditary optic neuropathy is affected by the mitochondrial DNA-haplogroup background. Am. J. Hum. Genet. 81 (2007) 228-233
11. Yu X., Koczan D., Sulonen A.M., Akkad D.A., Kroner A., Comabella M., Costa G., Corongiu D., Goertsches R., Camina-Tato M., et al. mtDNA nt13708A variant increases the risk of multiple sclerosis. PLoS ONE 3 (2008) e1530
12. Novembre J., Johnson T., Bryc K., Kutalik Z., Boyko A.R., Auton A., Indap A., King K.S., Bergmann S., Nelson M.R., et al. Genes mirror geography within Europe. Nature 456 (2008) 98-101
13. HUGO Pan-Asian SNP Consortium. Mapping human genetic diversity in Asia. Science 326 (2009) 1541-1545
14. Kelly P.J., Shih V.E., Kistler J.P., Barron M., Lee H., Mandell R., and Furie K.L. Low vitamin B6 but not homocyst(e)ine is associated with increased risk of stroke and transient ischemic attack in the era of folic acid grain fortification. Stroke 34 (2003) e51-e54
15. Rosand J., Eckman M.H., Knudsen K.A., Singer D.E., and Greenberg S.M. The effect of warfarin and intensity of anticoagulation on outcome of intracerebral hemorrhage. Arch. Intern. Med. 164 (2004) 880-884
16. Meschia J.F., Brott T.G., Brown Jr. R.D., Crook R.J., Frankel M., Hardy J., Merino J.G., Rich S.S., Silliman S., Worrall B.B., et al. The Ischemic Stroke Genetics Study (ISGS). Protocol. BMC Neurol. 3 (2003) 4
17. Meschia J.F., Brown Jr. R.D., Brott T.G., Chukwudelunzu F.E., Hardy J., and Rich S.S. The Siblings With Ischemic Stroke Study (SWISS) protocol. BMC Med. Genet. 3 (2002) 1
18. Li J.Z., Absher D.M., Tang H., Southwick A.M., Casto A.M., Ramachandran S., Cann H.M., Barsh G.S., Feldman M., Cavalli-Sforza L.L., et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319 (2008) 1100-1104
19. Jakobsson M., Scholz S.W., Scheet P., Gibbs J.R., VanLiere J.M., Fung H.C., Szpiech Z.A., Degnan J.H., Wang K., Guerreiro R., et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451 (2008) 998-1003
20. Cann H.M., de Toma C., Cazes L., Legrand M.F., Morel V., Piouffre L., Bodmer J., Bodmer W.F., Bonne-Tamir B., Cambon-Thomsen A., et al. A human genome diversity cell line panel. Science 296 (2002) 261-262
21. McRae A.F., Byrne E.M., Zhao Z.Z., Montgomery G.W., and Visscher P.M. Power and SNP tagging in whole mitochondrial genome association studies. Genome Res. 18 (2008) 911-917
22. Price A.L., Butler J., Patterson N., Capelli C., Pascali V.L., Scarnicci F., Ruiz-Linares A., Groop L., Saetta A.A., Korkolopoulou P., et al. Discerning the ancestry of European Americans in genetic association studies. PLoS Genet. 4 (2008) e236
23. Patterson N., Price A.L., and Reich D. Population structure and eigenanalysis. PLoS Genet. 2 (2006) e190
24. Price A.L., Patterson N.J., Plenge R.M., Weinblatt M.E., Shadick N.A., and Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38 (2006) 904-909
25. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A., Bender D., Maller J., Sklar P., de Bakker P.I., Daly M.J., and Sham P.C. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81 (2007) 559-575
26. Price A.L., Weale M.E., Patterson N., Myers S.R., Need A.C., Shianna K.V., Ge D., Rotter J.I., Torres E., Taylor K.D., et al. Long-range LD can confound genome scans in admixed populations. Am. J. Hum. Genet. 83 (2008) 132-135 author reply 135-139
27. Ioannidis J.P. Interpretation of tests of heterogeneity and bias in meta-analysis. J. Eval. Clin. Pract. 14 (2008) 951-957
28. de Bakker P.I., Ferreira M.A., Jia X., Neale B.M., Raychaudhuri S., and Voight B.F. Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum. Mol. Genet. 17 R2 (2008) R122-R128
29. Ghezzi D., Marelli C., Achilli A., Goldwurm S., Pezzoli G., Barone P., Pellecchia M.T., Stanzione P., Brusa L., Bentivoglio A.R., et al. Mitochondrial DNA haplogroup K is associated with a lower risk of Parkinson's disease in Italians. Eur. J. Hum. Genet. 13 (2005) 748-752