On Single-Array Genotype Calling Algorithms

This paper describes issues in using single-array algorithms for calling genotypes for Affymetrix arrays, and introduces a computationally efficient procedure that is designed to be used as a complement to the multi-arrays algorithms. The new tool is based on ideas from a previously introduced algorithm [9] with modifications that improve accuracy. These modifications are also necessary for handling the data from the new arrays which have a modified design with no perfect-matches. The main gain in accuracy is obtained from the partitioning of the probes in homogeneous clusters based on measures of efficiency of probe hybridization that are calculated from the probe sequence composition, and based on measures of probe performance that are calculated using a small training dataset.

[1]  A. Buhot,et al.  Sensitivity, specificity, and the hybridization isotherms of DNA chips. , 2003, Biophysical journal.

[2]  G. T. Barkema,et al.  Effective affinities in microarray data , 2006, q-bio/0605007.

[3]  BRLMM-P : a Genotype Calling Method for the SNP 5 . 0 Array , 2007 .

[4]  Jing Huang,et al.  Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays , 2005, Bioinform..

[5]  Alexander C. Cambon,et al.  Analysis of probe level patterns in Affymetrix microarray data , 2007, BMC Bioinformatics.

[6]  N. Sugimoto,et al.  Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. , 1996, Nucleic acids research.

[7]  Jean Yee Hwa Yang,et al.  A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays , 2007, Bioinform..

[8]  Chunlei Wu,et al.  Free energy of DNA duplex formation on short oligonucleotide microarrays , 2006, Nucleic acids research.

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

[10]  S. P. Fodor,et al.  Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays , 2004, Nature Methods.

[11]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Felix Naef,et al.  Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[13]  Xiaolin Wu,et al.  GEL: a novel genotype calling algorithm using empirical likelihood , 2006, Bioinform..

[14]  Simon C. Potter,et al.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls , 2007, Nature.