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Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays.

ABSTRACT: BACKGROUND:High-density oligonucleotide arrays (HDONAs) are a powerful tool for assessing differential mRNA expression levels. To establish the statistical significance of an observed change in expression, one must take into account the noise introduced by the enzymatic and hybridization steps, called type I noise. We undertake an empirical characterization of the experimental repeatability of results by carrying out statistical analysis of a large number of duplicate HDONA experiments. RESULTS:We assign scoring functions for expression ratios and associated quality measures. Both the perfect-match (PM) probes and the differentials between PM and single-mismatch (MM) probes are considered as raw intensities. We then calculate the log-ratio of the noise structure using robust estimates of their intensity-dependent variance. The noise structure in the log-ratios follows a local log-normal distribution in both the PM and PM-MM cases. Significance relative to the type I noise can therefore be quantified reliably using the local standard deviation (SD). We discuss the intensity dependence of the SD and show that ratio scores greater than 1.25 are significant in the mid- to high-intensity range. CONCLUSIONS:The noise inherent in HDONAs is characteristically dependent on intensity and can be well described in terms of local normalization of log-ratio distributions. Therefore, robust estimates of the local SD of these distributions provide a simple and powerful way to assess significance (relative to type I noise) in differential gene expression, and will be helpful in practice for improving the reliability of predictions from hybridization experiments.

SUBMITTER: Naef F

PROVIDER: S-EPMC115253 | biostudies-literature | 2002

REPOSITORIES: biostudies-literature

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Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays.

Naef Felix F Hacker Coleen R CR Patil Nila N Magnasco Marcelo M

Genome biology 20020322 4

<h4>Background</h4>High-density oligonucleotide arrays (HDONAs) are a powerful tool for assessing differential mRNA expression levels. To establish the statistical significance of an observed change in expression, one must take into account the noise introduced by the enzymatic and hybridization steps, called type I noise. We undertake an empirical characterization of the experimental repeatability of results by carrying out statistical analysis of a large number of duplicate HDONA experiments.< ...[more]

PMID: 11983059

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Project description:Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous microarray-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs). Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA), to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM) and mismatch (MM) probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH) without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number estimations using a single array provides additional insight into the structure of genomic alterations. With mean and median inter-SNP euchromatin distances of 244 kilobases (kb) and 119 kb, respectively, this method affords a resolution that is not easily achievable with non-oligonucleotide-based experimental approaches.

Dataset Information

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays.

Publications

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays.

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