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

Fenghai Duan, Mark A Pauley, Eliot R. Spindel, Li Zhang, Robert B Norgren

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Background. Affymetrix 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. Methods. By 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. Results. A 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. Conclusion. The 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.

Original languageEnglish (US)
Article number2
JournalBioData Mining
Volume3
Issue number1
DOIs
StatePublished - Apr 30 2010

Fingerprint

Oligonucleotide Probes
Microarrays
Gene Expression Data
Microarray Data
Macaca mulatta
Gene expression
Silicon Dioxide
Single Nucleotide Polymorphism
Probe
Gene Expression
Research
Microarray
Target
purine
Datasets
pyrimidine
Single nucleotide Polymorphism
Oligonucleotides
Polymorphism
Nucleotides

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Large scale analysis of positional effects of single-base mismatches on microarray gene expression data. / Duan, Fenghai; Pauley, Mark A; Spindel, Eliot R.; Zhang, Li; Norgren, Robert B.

In: BioData Mining, Vol. 3, No. 1, 2, 30.04.2010.

Research output: Contribution to journalArticle

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