Bayesian Classification Algorithms for Automated Allele Assignment

The application of Bayesian analysis to the classification of discretized BeadChip™ signal intensities generated in the context of multiplex allele analysis is described in this chapter. This analysis enables reliable allele assignment for polymorphic genes, notably those encoding the human leukocyte antigens and the variants of RhCE and RhD antigens.

[1]  James Robinson,et al.  IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex , 2003, Nucleic Acids Res..

[2]  Terence P. Speed,et al.  Genome analysis A genotype calling algorithm for affymetrix SNP arrays , 2005 .

[3]  John V Pearson,et al.  SNiPer: Improved SNP genotype calling for Affymetrix 10K GeneChip microarray data , 2005, BMC Genomics.

[4]  Harriet Noreen,et al.  Common and well-documented HLA alleles: report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics. , 2007, Human immunology.

[5]  K. Gunderson,et al.  High-throughput SNP genotyping on universal bead arrays. , 2005, Mutation research.

[6]  M. Seul,et al.  Determination of 24 minor red blood cell antigens for more than 2000 blood donors by high‐throughput DNA analysis , 2007, Transfusion.

[7]  K. Cao,et al.  Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. , 2001, Human immunology.

[8]  Nasser M. Nasrabadi,et al.  Pattern Recognition and Machine Learning , 2006, Technometrics.

[9]  Norman Abramson,et al.  Information theory and coding , 1963 .

[10]  Ruben H. Zamar,et al.  Dynamic variable selection in SNP genotype autocalling from APEX microarray data , 2006, BMC Bioinformatics.

[11]  Geoffrey I. Webb,et al.  On Why Discretization Works for Naive-Bayes Classifiers , 2003, Australian Conference on Artificial Intelligence.

[12]  R. J. Beynon Computing in the biological sciences--a survey , 1985, Comput. Appl. Biosci..

[13]  Bor-Sen Chen,et al.  On the attenuation and amplification of molecular noise in genetic regulatory networks , 2006, BMC Bioinformatics.

[14]  Chun-Nan Hsu,et al.  Why Discretization Works for Naive Bayesian Classifiers , 2000, ICML.

[15]  Pedro M. Domingos,et al.  On the Optimality of the Simple Bayesian Classifier under Zero-One Loss , 1997, Machine Learning.

[16]  Steven G E Marsh,et al.  The IMGT/HLA database. , 2007, Methods in molecular biology.

[17]  Lipo Wang,et al.  Effective selection of informative SNPs and classification on the HapMap genotype data , 2007, BMC Bioinformatics.

[18]  Eleni Giannoulatou,et al.  GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population , 2008, Bioinform..

[19]  David G. Stork,et al.  Pattern Classification , 1973 .