Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases

SNP markers are becoming central for studying genetic determinants of complex diseases. Large SNP data collected in such studies call for the development of specialized analysis tools. We present methods for selecting sets of SNPs that can be associated to sample properties in case/control studies. We also describe how scoring and selection can be statistically tested. This is done at the single locus as well as at the set level.

[1]  Josef Kittler,et al.  Floating search methods in feature selection , 1994, Pattern Recognit. Lett..

[2]  R. S. Spielman,et al.  A genome–wide search for human non–insulin–dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2 , 1996, Nature Genetics.

[3]  Thomas M. Cover,et al.  Elements of Information Theory , 2005 .

[4]  N. Risch,et al.  Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs. , 1990, American journal of human genetics.

[5]  N Risch,et al.  The Future of Genetic Studies of Complex Human Diseases , 1996, Science.

[6]  J. Mesirov,et al.  Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. , 1999, Science.

[7]  Richard O. Duda,et al.  Pattern classification and scene analysis , 1974, A Wiley-Interscience publication.

[8]  Nancy J. Cox,et al.  Loci on chromosomes 2 (NIDDM1) and 15 interact to increase susceptibility to diabetes in Mexican Americans , 1999, Nature Genetics.

[9]  J. Ott,et al.  Trimming, weighting, and grouping SNPs in human case-control association studies. , 2001, Genome research.

[10]  Nir Friedman,et al.  Class discovery in gene expression data , 2001, RECOMB.

[11]  Todd,et al.  Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning , 2002, Nature Medicine.

[12]  J. Sudbø,et al.  Gene-expression profiles in hereditary breast cancer. , 2001, The New England journal of medicine.

[13]  Tom H. Lindner,et al.  Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus , 2000, Nature Genetics.

[14]  Nir Friedman,et al.  Tissue classification with gene expression profiles , 2000, RECOMB '00.

[15]  E. Dougherty,et al.  Gene-expression profiles in hereditary breast cancer. , 2001, The New England journal of medicine.

[16]  David W. Aha,et al.  A Comparative Evaluation of Sequential Feature Selection Algorithms , 1995, AISTATS.

[17]  N. Sampas,et al.  Molecular classification of cutaneous malignant melanoma by gene expression profiling , 2000, Nature.