A comparison of oligonucleotide and cDNA-based microarray systems

Mah, Nancy; Thelin, Anders; Lu, Tim; Nikolaus, Susanna; Kühbacher, Tanja; Gürbüz, Yeşim; Eickhoff, Holger; Klöppel, G.; Lehrach, Hans; Mellgård, Björn; Costello, Christine; Schreiber, Stefan

doi:10.1152/physiolgenomics.00080.2003

Cited by 112 publications

(76 citation statements)

References 23 publications

(24 reference statements)

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“…Indeed, the IFM signature is based on a custom cDNA-based gene expression platform, rather than the Affymetrix GeneChips, which have become common for MM GEP studies. 32 The cDNA platforms have been reported to be difficult to compare with the Affymetrix oligonucleotide platform. 12 Although the MILLENNIUM signature was generated using Affymetrix GeneChips, the use of an earlier version of this platform may have contributed to the limited performance of this signature.…”

Section: Discussionmentioning

confidence: 99%

A gene expression signature for high-risk multiple myeloma

et al. 2012

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There is a strong need to better predict the survival of patients with newly diagnosed multiple myeloma (MM). As gene expression profiles (GEPs) reflect the biology of MM in individual patients, we built a prognostic signature based on GEPs. GEPs obtained from newly diagnosed MM patients included in the HOVON65/GMMG-HD4 trial (n ¼ 290) were used as training data. Using this set, a prognostic signature of 92 genes (EMC-92-gene signature) was generated by supervised principal component analysis combined with simulated annealing. Performance of the EMC-92-gene signature was confirmed in independent validation sets of newly diagnosed (total therapy (TT)2, n ¼ 351; TT3, n ¼ 142; MRC-IX, n ¼ 247) and relapsed patients (APEX, n ¼ 264). In all the sets, patients defined as high-risk by the EMC-92-gene signature show a clearly reduced overall survival (OS) with a hazard ratio (HR) of 3.40 (95% confidence interval (CI): 2.19-5.29) for the TT2 study, 5.23 (95% CI: 2.46-11.13) for the TT3 study, 2.38 (95% CI: 1.65-3.43) for the MRC-IX study and 3.01 (95% CI: 2.06-4.39) for the APEX study (Po0.0001 in all studies). In multivariate analyses this signature was proven to be independent of the currently used prognostic factors. The EMC-92-gene signature is better or comparable to previously published signatures. This signature contributes to risk assessment in clinical trials and could provide a tool for treatment choices in high-risk MM patients.

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Section: Discussionmentioning

confidence: 99%

A gene expression signature for high-risk multiple myeloma

et al. 2012

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“…Biopsies were taken endoscopically from a defined area of the colon and immediately snap-frozen in liquid nitrogen. Total RNA was extracted and processed as previously described (Mah et al 2004) and quality controlled using an Agilent Bioanalyzer according to the manufacturer's guidelines. DNA was extracted from biopsies using the QIAamp Tissue DNA preparation kit (Qiagen).…”

Section: Biopsy Processing and Sample Preparationmentioning

confidence: 99%

A functional methylome map of ulcerative colitis

et al. 2012

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The etiology of inflammatory bowel diseases is only partially explained by the current genetic risk map. It is hypothesized that environmental factors modulate the epigenetic landscape and thus contribute to disease susceptibility, manifestation, and progression. To test this, we analyzed DNA methylation (DNAm), a fundamental mechanism of epigenetic long-term modulation of gene expression. We report a three-layer epigenome-wide association study (EWAS) using intestinal biopsies from 10 monozygotic twin pairs (n = 20 individuals) discordant for manifestation of ulcerative colitis (UC). Genome-wide expression scans were generated using Affymetrix UG 133 Plus 2.0 arrays (layer 1). Genome-wide DNAm scans were carried out using Illumina 27k Infinium Bead Arrays to identify methylation variable positions (MVPs, layer 2), and MeDIP-chip on Nimblegen custom 385k Tiling Arrays to identify differentially methylated regions (DMRs, layer 3). Identified MVPs and DMRs were validated in two independent patient populations by quantitative real-time PCR and bisulfite-pyrosequencing (n = 185). The EWAS identified 61 disease-associated loci harboring differential DNAm in cis of a differentially expressed transcript. All constitute novel candidate risk loci for UC not previously identified by GWAS. Among them are several that have been functionally implicated in inflammatory processes, e.g., complement factor CFI, the serine protease inhibitor SPINK4, and the adhesion molecule THY1 (also known as CD90). Our study design excludes nondisease inflammation as a cause of the identified changes in DNAm. This study represents the first replicated EWAS of UC integrated with transcriptional signatures in the affected tissue and demonstrates the power of EWAS to uncover unexplained disease risk and molecular events of disease manifestation.

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“…In addition, labelling, hybridisation and processing of Affymetrix GeneChip arrays is highly automated, thereby producing very reproducible results, whereas cDNA arrays are less automated and therefore likely to be less reproducible. In addition, GeneChips have been shown to be more specific and have a greater dynamic range than cDNA arrays (Mah et al, 2004;Woo et al, 2004) and there are numerous publically available data sets for human GeneChips that could be directly compared with experiments performed using this technique. This method will allow transcriptome analysis of developmental and metabolic processes, as well as disease responses, in sheep and possibly other species for which specific microarrays are not available.…”

Section: Discussionmentioning

confidence: 99%

Use of the Affymetrix Human GeneChip array and genomic DNA hybridisation probe selection to study ovine transcriptomes

Graham

May

Daniel

et al. 2011

Animal

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Affymetrix GeneChip microarrays are a powerful tool to study global gene expression profiles and have been used on many species. However, no sheep-specific Affymetrix GeneChip is currently available and the bovine array is fairly limited in its coverage and annotation. Previously, a probe-selection method based on hybridisation of genomic DNA (gDNA) was developed, which enables GeneChips to be used for species that they were not designed for. This approach can greatly increase the number of potential annotated genes that can be studied beyond that which is currently available, particularly for species that do not have comprehensively characterised genomes. In this study, we demonstrate that gDNA-based probe selection on the Affymetrix Human U133+2 GeneChip array can be used to study gene expression profiles in sheep tissues. More than 20 000 transcripts were detected in triplicate ovine skeletal muscle and liver samples, which is more than would be possible using the commercially available sheep-specific microarray. The majority of the top 15 differentially expressed genes for each tissue were known to either be expressed in a tissue-specific manner or relate to specific functions of that tissue. Gene ontology analysis of the differentially expressed genes revealed the expected differences in gene expression profiles between the two tissues. Besides demonstrating that the probe selection method can be used to study the ovine transcriptome, the benefits of this approach are that it can greatly increase the number of annotated and novel genes that can be studied beyond those currently possible using ovine- or bovine-specific microarrays. This same method also has the potential to allow the study of other species where species-specific microarrays are not available or whose genomes have not been comprehensively characterised.

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A comparison of oligonucleotide and cDNA-based microarray systems

Cited by 112 publications

References 23 publications

A gene expression signature for high-risk multiple myeloma

A gene expression signature for high-risk multiple myeloma

A functional methylome map of ulcerative colitis

Use of the Affymetrix Human GeneChip array and genomic DNA hybridisation probe selection to study ovine transcriptomes

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