Accounting for uncertainty when assessing association between copy number and disease: A latent class model

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  González, Juan R ^a,b,c   Subirana, Isaac ^b,c   Escaramís, Geòrgia ^b,d   Peraza, Solymar ^b,d   Cáceres, Alejandro ^a,c   Estivill, Xavier ^b,d   Armengol, Lluís ^d  

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

^b CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

^c INST MUNIC D INVESTIGACIO MEDICA   (Spain)

^d CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CASE-CONTROL STUDY; COPY NUMBER VARIATIONS; DISEASE RISKS; LATENT CLASS MODEL; PROBE SIGNALS; REAL DATA SETS; REGULATORY ELEMENTS; SIMULATION STUDIES;

DISEASE CONTROL;

UNCERTAINTY ANALYSIS;

ARTICLE; COMPUTER SIMULATION; COPY NUMBER VARIATION; DISEASE COURSE; GENE DOSAGE; GENETIC DISORDER; GENETIC VARIABILITY; PATHOGENESIS; PHENOTYPE; REGULATORY SEQUENCE; STATISTICAL ANALYSIS; ALGORITHM; COMPARATIVE GENOMIC HYBRIDIZATION; GENETIC PREDISPOSITION; HUMAN; METHODOLOGY; STATISTICAL MODEL;

ALGORITHMS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER SIMULATION; DISEASE PROGRESSION; GENE DOSAGE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, STATISTICAL;

EID: 67650556405     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-172     Document Type: Article

References (32)

1. Locke DP Sharp AJ McCarroll SA McGrath SD Newman TL Cheng Z Schwartz S Albertson DG Pinkel D Altshuler DM Eichler EE Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome Am J Hum Genet 2006, 79(2):275-90. 1559496 16826518 10.1086/505653
2. 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 Grata-cos 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 Armengol L Conrad DF Es-tivill 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(7118):444-54. 2669898 17122850 10.1038/nature05329
3. Wong KK deLeeuw RJ Dosanjh NS Kimm LR Cheng Z Horsman DE MacAulay C Ng RT Brown CJ Eichler EE Lam WL A comprehensive analysis of common copy-number variations in the human genome Am J Hum Genet 2007, 80:91-104. 1785303 17160897 10.1086/510560
4. Feuk L Carson AR Scherer SW Structural variation in the human genome Nat Rev Genet 2006, 7(2):85-97. 10.1038/nrg1767 16418744
5. Stranger BE Forrest MS Dunning M Ingle CE Beazley C Thorne N Redon R Bird CP de Grassi A Lee C Tyler-Smith C Carter N Scherer SW Tavare S Deloukas P Hurles ME Dermitzakis ET Relative impact of nucleotide and copy number variation on gene expression phenotypes Science 2007, 315(5813):848-53. 2665772 17289997 10.1126/science.1136678
6. Gonzalez E Kulkarni H Bolivar H Mangano A Sanchez R Catano G Nibbs RJ Freedman BI Quinones MP Bamshad MJ Murthy KK Rovin BH Bradley W Clark RA Anderson SA O'Connell RJ Agan BK Ahuja SS Bologna R Sen L Dolan MJ Ahuja SK The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility Science 2005, 307(5714):1434-40. 10.1126/ science.1101160 15637236
7. Rovelet-Lecrux A Hannequin D Raux G Le Meur N Laquerriere A Vital A Dumanchin C Feuillette S Brice A Vercelletto M Dubas F Frebourg T Campion D APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy Nat Genet 2006, 38:24-6. 10.1038/ng1718 16369530
8. Le Marechal C Masson E Chen JM Morel F Ruszniewski P Levy P Ferec C Hereditary pancreatitis caused by triplication of the trypsinogen locus Nat Genet 2006, 38(12):1372-4. 10.1038/ng1904 17072318
9. Schouten JP McElgunn CJ Waaijer R Zwijnenburg D Diepvens F G P Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification Nucleic Acids Res 2002, 30(12):e57. 117299 12060695 10.1093/nar/gnf056
10. González J Carrasco J Armengol L Villatoro S Jover L Yasui Y Estivill X Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA) BMC Bioinformatics 2008, 9:261. 2492880 18522760 10.1186/ 1471-2105-9-261
11. Engert S Wappenschmidt B Betz B Kast K Kutsche M Hellebrand H Goecke T Kiechle M Niederacher D Schmutzler R Meindl A MLPA screening in the BRCA1 gene from 1,506 German hereditary breast cancer cases: Novel deletions, frequent involvement of exon 17, and occurrence in single early-onset cases Hum Genet 2008, 29(7):948-58.
12. Hansen T Jonson L Albrechtsen A Andersen M Ejlertsen B Nielsen F Large BRCA1 and BRCA2 genomic rearrangements in Danish high risk breast-ovarian cancer families Breast Cancer Res Treat 2008.
13. Aitman T Dong R Vyse T Norsworthy P Johnson M Smith J Mangion J Roberton-Lowe C Marshall A Petretto M Hodges E Bhangal G Patel S Sheehan-Rooney K Duda M Cook P Evans D Domin J Flint J Boyle J Pusey C Cook H Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans Nature 2006, 439(7078):851-5. 10.1038/nature04489 16482158
14. Fellermann K Stange D Schaeffeler E Schmalzl H Wehkamp J Bevins C Reinisch W Teml A Schwab M Lichter P Radlwimmer B Stange E A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon Am J Hum Genet 2006, 79(3):439-48. 1559531 16909382 10.1086/505915
15. Ionita-Laza I Rogers AJ Lange C Raby BA Lee C Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis Genomics 2009, 93:22-26. 10.1016/j.ygeno.2008.08.012 18822366
16. Fraley C Raftery AE How many clusters? Which clustering method? Answers via model-based cluster analysis The Computer Journal 1998, 41:578-588. 10.1093/comjnl/41.8.578
17. Picard F Robin S Lebarbier E Daudin JJ A segmentation/clustering model for the analysis of array CGH data Biometrics 2007, 63(3):758-766. 10.1111/j.1541-0420.2006.00729.x 17825008
18. Wiel van de MA Kim KI Vosse SJ van Wieringen WN Wilting SM Ylstra B CGHcall: Calling aberrations for array CGH tumor profiles Bioinformatics 2007, 23(7):892-894. 10.1093/bioinformatics/btm030 17267432
19. Leisch F A general framework for finite mixture models and latent class regression in R Journal of Statistical Software 2004, 11(8):1-18.
20. Du J Combined Algorithms for Fitting Finite Mixture Distributions PhD thesis McMaster University, Ontario, Canada; 2002.
21. Bashir S Duffy S The correction of risk estimates for measuremente error Ann Epidem 1993, 7:156-164.
22. Davidov O Faraggi D Reiser B Misclassification in logistic regression with discrete covariates Biometrical Journal 2003, 5:541-553. 10.1002/ bimj.200390031
23. Greenland S Basic methods for sensitivity analysis of biases Int J Epi 1996, 25:1107-1115. 10.1093/ije/25.6.1107-a
24. Spiegelman D Rosner B Logan R Estimation and inference for logistic regression with covariate missclassification and measurement error, in main study/validation study designs J Am Stat Assoc 2000, 95:51-61. 10.2307/2669522
25. CREAL's web-page http://www.creal.cat/jrgonzalez/software.htm
26. Wiel van de M van Wieringen W CGHregions: Dimension reduction for array CGH data with minimal information loss Cancer Informatics 2007, 2:55-63.
27. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing J Roy Statist Soc Ser B 1995, 57:289-300.
28. Sarkar S False discovery and false nondiscovery rates in single-step multiple testing procedures The Annals of Statistics 2006, 34:394-415. 10.1214/009053605000000778
29. Neve RM Chin K Fridlyand J Yeh J Baehner FL Fevr T Clark L Bayani N Coppe JP Tong F Speed T Spellman PT DeVries S Lapuk A Wang NJ Kuo WL Stilwell JL Pinkel D Albertson DG Waldman FM McCormick F Dickson RB Johnson MD Lippman M Ethier S Gazdar A Gray JW A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes Cancer Cell 2006, 10(6):515-527. 10.1016/j.ccr.2006.10.008 17157791
30. Bioconductor's web-page http://www.bioconductor.org/
31. M Neve et al in Gray Lab at LBL Neve2006: Expression and CGH data on breast cancer cell lines. [R package version 0.1.6]
32. van Wieringen WN Wiel van de MA Nonparametric testing for DNA copy number induced differential mRNA gene expression Biometrics 2009, 65:19-29. 10.1111/j.1541-0420.2008.01052.x 18479479