Fine-scale genetic mapping using independent component analysis

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 5, Issue 3, 2008, Pages 448-460

  Dawy, Zaher ^a   Sarkis, Michel ^b   Hagenauer, Joachim ^b   Mueller, Jakob C ^b  

^a AMERICAN UNIVERSITY OF BEIRUT   (Lebanon)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Association mapping; Complex diseases; Independent component analysis (ICA); Linkage disequilibrium; Principal component analysis (PCA); Single nucleotide polymorphisms (SNPs)

Indexed keywords

BIOLOGICAL SYSTEMS; CHLORINE COMPOUNDS; CONFORMAL MAPPING; MIXING; NUCLEIC ACIDS; ORGANIC ACIDS;

ASSOCIATION MAPPING; CLINICAL DATA; COMPLEX DISEASES; COMPLEX TRAITS; DNA POLYMORPHISMS; GENETIC MAPPING; INDEPENDENT COMPONENT ANALYSIS (ICA); INDEPENDENT COMPONENTS; LINEAR MIXING; LINKAGE DISEQUILIBRIUM; PRINCIPAL COMPONENT ANALYSIS (PCA); SAMPLE SIZES; SIMULATION STUDIES; SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS);

INDEPENDENT COMPONENT ANALYSIS;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHROMOSOME MAP; DNA SEQUENCE; GENE LINKAGE DISEQUILIBRIUM; GENETIC PREDISPOSITION; GENETICS; HUMAN; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS; SCHIZOPHRENIA; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; CHROMOSOME MAPPING; DATA INTERPRETATION, STATISTICAL; GENETIC PREDISPOSITION TO DISEASE; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; SCHIZOPHRENIA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 49249103767     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.1072     Document Type: Conference Paper

References (33)

1. H. Cordell and D. Clayton, "A Unified Stepwise Regression Procedure for Evaluating the Relative Effects of Polymorphisms within a Gene Using Case/Control or Family Data: Application to HLA in Type 1 Diabetes," Am. J. Human Genetics, vol. 70, no. 1, pp. 124-141, Jan. 2002.
2. R. Zee, J. Hoh, S. Cheng, R. Reynolds, M. Grow, A. Silbergleit, K. Walker, L. Steiner, G. Zangenberg, A. Fernandez-Ortiz, C. Macaya, E. Pintor, A. Fernandez-Cruz, J. Ott, and K. Lindpaintner, "Multi-Locus Interactions Predict Risk for Post-PTCA Restenosis: An Approach to the Genetic Analysis of Common Complex Disease," The Pharmacogenomics J., vol. 2, pp. 197-201, 2002.
3. J.C. Mueller, J. Fuchs, A. Hofer, A. Zimprich, P. Lichtner, T. Illig, D. Berg, U. Wuellner, T. Meitinger, and T. Gasser, "Multiple Regions of α-Synuelein Are Associated with Parkinson's Disease," Annals of Neurology, vol. 57, pp. 535-541, Apr. 2005.
4. L.R. Cardon and J.I. Bell, "Association Study Designs for Complex Diseases," Nature Rev. Genetics, vol. 2, pp. 91-99, 2001.
5. J. Hoh and J. Ott, "Mathematical Multi-Locus Approaches to Localizing Complex Human Trait Genes," Nature Rev. Genetics, vol. 4, pp. 701-709, 2003.
6. D.J. Balding, M. Bishop, and C. Cannings, Handbook of Statistical Genetics. John Wiley & Sons, 2001.
7. M.S. McPeek and A. Strahs, "Assessment of Linkage Disequilibrium by the Decay of Haplotype Sharing, with Application to Fine-Scale Genetic Mapping," Am. J. Human Genetics, vol. 65, pp. 858-875, 1999.
8. A.P. Morris, J.C. Whittaker, and D.J. Balding, "Bayesian Fine-Scale Mapping of Disease Loci by Hidden Markov Models," Am. J. Human Genetics, vol. 67, pp. 155-169, 2000.
9. Z. Dawy, B. Goebel, J. Hagenauer, C. Andreoli, T. Meitinger, and J. Mueller, "Gene Mapping and Marker Clustering Using Shannon's Mutual Information," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 1, pp. 47-56, Jan.-Mar. 2006.
10. D. Zaykin, P. Westfall, S. Young, M. Karnoub, M. Wagner, and M. Ehm, "Testing Association of Statistically Inferred Haplotypes with Discrete and Continuous Traits in Samples of Unrelated Individuals," Human Heredity, vol. 53, no. 2, pp. 79-91, May 2002.
11. J. Hoh, A. Wille, and J. Ott, "Trimming, Weighting, and Grouping SNPs in Human Case-Control Association Studies," Genome Research, vol. 11, pp. 2115-2119, 2001.
12. D.J. Schaid, C.M. Rowland, D.E. Tines, R.M. Jacobson, and G.A. Poland, "Score Tests for Association between Traits and Haplotypes When Linkage Phase Is Ambiguous," Am. J. Human Genetics, vol. 70, pp. 425-434, 2002.
13. M.R. Nelson, S.L.R. Kardia, R.E. Ferrell, and C.F. Sing, "A Combinatorial Partitioning Method to Identify Multilocus Genotype Partitions that Predict Quantitative Trait Variation," Genome Research, vol. 11, pp. 458-470, Mar. 2001.
14. C. Kooperberg and I. Ruczinski, "Identifying Interacting SNPs Using Monte Carlo Logic Regression," Genetic Epidemiology, vol. 28, pp. 157-170, Feb. 2005.
15. O. Alter, P. Brown, and D. Botstein, "Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Data Sets of Two Different Organisms," Proc. Nat'l Academy of Sciences, vol. 100, no. 6, pp. 3351-3356, Mar. 2003.
16. B.D. Home and N.J. Camp, "Principal Component Analysis for Selection of Optimal SNP-Sets That Capture Intragenic Genetic Variation," Genetic Epidemiology, vol. 26, pp. 11-21, Jan. 2004.
17. W. Liebermeister, "Linear Modes of Gene Expression Determined by Independent Component Analysis," Bioinformatics, vol. 18, no. 1, pp. 51-60, Feb. 2002.
18. A. Hyvaerinen, J. Karhunen, and E. Oja, Independent Component Analysis. Wiley, 2001.
19. P. Comon, "Independent Component Analysis: A New Concept," Elsevier Signal Processing, vol. 36, no. 3, pp. 287-314, Apr. 1994.
20. O. Troyanskaya, M. Cantor, G. Sherlock, P. Brown, T. Hastie, R. Tibshirani, D. Botstein, and R.B. Altman, "Missing Value Estimation Methods for DNA Microarrays," Bioinformatics, vol. 17, no. 6, pp. 520-525, June 2001.
21. L. Liu, D. Hawkins, S. Gosh, and S. Young, "Robust Singular Value Decomposition Analysis of Microarray Data," Proc. Nat'l Academy of Sciences, vol. 100, no. 23, pp. 13167-13172, Nov. 2003.
22. K. Gabriel and S. Zamir, "Lower Rank Approximation of Matrices by Least Squares with Any Choice of Weights," Technometrics, vol. 21, no. 4, pp. 489-498, Nov. 1979.
23. S. Oba, M. Sato, I. Takemasa, M. Monden, K. Matsubara, and S. Ishii, "A Bayesian Missing Value Estimation Method for Gene Expression Profile Data," Bioinformatics, vol. 19, no. 16, pp. 2088-2096, Nov. 2003.
24. H.F. Kaiser, "The Varimax Criterion for Analytic Rotation in Factor Analysis," Psychometrika, vol. 23, pp. 187-200, 1958.
25. M. Sarkis, Z. Dawy, F. Obermeier, and K. Diepold, "Automatic Model-Order Selection for PCA," Proc. IEEE Int'l Conf. Image Processing (ICIP '06), Oct. 2006.
26. A. Machado, J. Gee, and M. Campos, "Visual Data Mining for Modeling Prior Distributions in Morphometry," IEEE Signal Processing Magazine, vol. 21, no. 3, pp. 20-27, May 2004.
27. G.A. Churchill and R.W. Doerge, "Empirical Threshold Values for Quantitative Trait Mapping," Genetics, vol. 138, no. 3, pp. 963-971, Nov. 1994.
28. R. Hudson, "Generating Samples under a Wright-Fisher Neutral Model of Genetic Variation," Bioinformatics, vol. 18, pp. 337-338, Feb. 2002.
29. M. Nothnagel, "Simulation of LD Block-Structured SNP Haplotype Data and Its Use for the Analysis of Case-Control Data by Supervised Learning Methods," Am. J. Human Genetics, vol. 71, no. A2363, Oct. 2002.
30. D. Collett, Modelling Binary Data, second ed. Chapman and Hall/CRC Press, 2002.
31. S. Shwartz, M. Zibulevsky, and Y.Y. Schechner, "ICA Using Kernel Entropy Estimation with NlogN Complexity," Proc. Fifth Int'l Conf. Independent Component Analysis (ICA '04), Sept. 2004.
32. A. Hyvaerinen, "Fast and Robust Fixed-Point Algorithms for Independent Component Analysis," IEEE Trans. Neural Networks, vol. 10, no. 3, pp. 626-634, May 1999.
33. J.M. Akey, K. Zhang, M. Xiong, P. Doris, and L. Jin, "The Effect that Genotyping Errors Have on the Robustness of Common Linkage-Disequilibrium Measures," Am. J. Human Genetics, vol. 68, pp. 1447-1456, 2001.