Large scale analysis of positional effects of single-base mismatches on microarray gene expression data

BackgroundAffymetrix GeneChips utilize 25-mer oligonucleotides probes linked to a silica surface to detect targets in solution. Mismatches due to single nucleotide polymorphisms (SNPs) can affect the hybridization between probes and targets. Previous research has indicated that binding between probes and targets strongly depends on the positions of these mismatches. However, there has been substantial variability in the effect of mismatch type across studies.MethodsBy taking advantage of naturally occurring mismatches between rhesus macaque transcripts and human probes from the Affymetrix U133 Plus 2 GeneChip, we collected the largest 25-mer probes dataset with single-base mismatches at each of the 25 positions on the probe ever used in this type of analysis.ResultsA mismatch at the center of a probe led to a greater loss in signal intensity than a mismatch at the ends of the probe, regardless of the mismatch type. There was a slight asymmetry between the ends of a probe: effects of mismatches at the 3' end of a probe were greater than those at the 5' end. A cross study comparison of the effect of mismatch types revealed that results were not in good agreement among different reports. However, if the mismatch types were consolidated to purine or pyrimidine mismatches, cross study conclusions could be generated.ConclusionThe comprehensive assessment of the effects of single-base mismatches on microarrays provided in this report can be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms.

[1]  Toralf Kirsten,et al.  Interactions in Oligonucleotide Hybrid Duplexes on Microarrays , 2004 .

[2]  Linda Cardle,et al.  Single-feature polymorphism discovery in the barley transcriptome , 2005, Genome Biology.

[3]  Rafael A. Irizarry,et al.  A Model-Based Background Adjustment for Oligonucleotide Expression Arrays , 2004 .

[4]  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.

[5]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Jin Xu,et al.  Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit , 2005, Bioinform..

[7]  J. Schelter,et al.  Designing siRNA That Distinguish between Genes That Differ by a Single Nucleotide , 2006, PLoS genetics.

[8]  D. Tautz,et al.  Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted , 2006, Nucleic Acids Research.

[9]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[10]  Modeling of microarray data with zippering , 2004, q-bio/0406039.

[11]  K. Aldape,et al.  A model of molecular interactions on short oligonucleotide microarrays , 2003, Nature Biotechnology.

[12]  N. Sugimoto,et al.  Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes. , 2000, Biochemistry.

[13]  Robert Gentleman,et al.  matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements , 2004, Bioinform..

[14]  A. Ott,et al.  Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: Comparison of single base mismatches and base bulges , 2008, BMC biotechnology.

[15]  E. Spindel,et al.  Intercenter reliability and validity of the rhesus macaque GeneChip , 2007, BMC Genomics.

[16]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[17]  Hans Binder,et al.  Thermodynamics of competitive surface adsorption on DNA microarrays , 2006 .

[18]  H. Auer,et al.  Expression Profiling Using Affymetrix GeneChip Microarrays. , 2009, Methods in molecular biology.

[19]  Lei Zhang,et al.  Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations , 2005, Nucleic acids research.

[20]  Erdogan Gulari,et al.  On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes , 2006, Nucleic acids research.