Multiple correspondence discriminant analysis: An application to detect stratification in copy number variation

Statistics in Medicine

Volumn 29, Issue 30, 2010, Pages 3284-3293

  Caceres, Alejandro ^a,b   Basagana, Xavier ^a,b,c   Gonzalez, Juan R ^a,b,c  

^a CENTRE FOR RESEARCH IN ENVIRONMENTAL EPIDEMIOLOGY CREAL   (Spain)

^b INST MUNIC D INVESTIGACIO MEDICA   (Spain)

^c Barcelona Biomedical Research Park   (Spain)

Author keywords

CNV association studies; Copy number variants; Multiple correspondence analysis; Variable selection

Indexed keywords

ARTICLE; COPY NUMBER VARIATION; CORRELATION ANALYSIS; CORRESPONDENCE ANALYSIS; DISCRIMINANT ANALYSIS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; HAPLOTYPE MAP; PREDICTION; SIMULATION;

COMPUTER SIMULATION; CONTINENTAL POPULATION GROUPS; DATA INTERPRETATION, STATISTICAL; DISCRIMINANT ANALYSIS; DNA COPY NUMBER VARIATIONS; GENETIC ASSOCIATION STUDIES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77955512136     PISSN: 02776715     EISSN: 10970258     Source Type: Journal    
DOI: 10.1002/sim.3890     Document Type: Article

References (13)

1. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 2006; 38:904-909. DOI: 10.1038/ng1847.
2. Heath SC, Gut IG, Brennan P, McKay JD, Bencko V, Fabianova E, Foretova L, Georges M, Janout V, Kabesch M, Krokan HE, Elvestad MB, Lissowska J, Mates D, Rudnai P, Skorpen F, Schreiber S, Soria JM, Syvanen AC, Meneton P, Hercberg S, Galan P, Szeszenia-Dabrowska N, Zaridze D, Genin E, Cardon LR, Lathrop M. Investigation of the fine structure of European populations with applications to disease association studies. European Journal of Human Genetics 2008; 16:1413-1429. DOI: 10.1038/ejhg.2008.210.
3. Price AL, Butler J, Patterson N, Capelli C, Pascali VL, Scarnicci F, Ruiz-Linares A, Groop L, Saetta AA, Korkolopoulou P, Seligsohn U, Waliszewska A, Schirmer C, Ardlie K, Ramos A, Nemesh J, Arbeitman L, Goldstein DB, Reich D, Hirschhorn JN. Discerning the ancestry of European Americans in genetic association studies. PLoS Genetics 2008; 4:e236. DOI: 10.1371/journal.pgen.0030236.
4. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nature Reviews Genetics 2006; 7:85-97. DOI: 10.1038/nrg1767.
5. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. Global variation in copy number in the human genome. Nature 2006; 444:444-454. DOI: 10.1038/nature05329.
6. Winchester L, Yau C, Ragoussis J. Comparing CNV detection methods for SNP arrays. Briefings in Functional Genomics and Proteomics 2009; 8:353-366. DOI: 10.1093/bfgp/elp017.
7. Pique-Regi R, Ortega A, Asgharzadeh S. Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA. Bioinformatics 2009; 25:1223-1230. DOI: 10.1093/bioinformatics/btp119.
8. Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004; 5:557-572. DOI: 10.1093/biostatistics/kxh008.
9. Conrad D, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews T, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm C, Kristiansson K, Macarthur D, Macdonald J, Onyiah I, Pang A, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Tyler-Smith C, Carter N, Lee C, Scherer S, Hurles M. Origins and functional impact of copy number variation in the human genome. Nature 2009; DOI: 10.1038/nature08516.
10. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PIW, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genetics 2008; 40:1166-1174. DOI: 10.1038/ng.238.
11. Greenacre MJ. Theory and Applications of Correspondence Analysis. Academic Press: London, 1984.
12. Van de Wiel MA, Van Wieringen WN. CGHregions: dimension reduction for array CGH data with minimal information loss. Cancer Informatics 2007; 2:55-63.
13. Teo YY, Small KS, Kwiatkowski DP. Methodological challenges of genome-wide association analysis in Africa. Nature Reviews Genetics 2010; 11:149-160. DOI: 10.1038/nrg2731.