Platform influence on DNA microarray data in postmortem brain research
In addition to the substantial biological diversity among humans, our limited ability to reliably measure expression changes of small magnitude significantly reduces our capacity to obtain convergent sets of transcriptome data in postmortem brain. In particular, differences in the structure and sens...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2005-04-01
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| Series: | Neurobiology of Disease |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0969996104002657 |
| _version_ | 1818734849187381248 |
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| author | Deborah Hollingshead David A. Lewis Károly Mirnics |
| author_facet | Deborah Hollingshead David A. Lewis Károly Mirnics |
| author_sort | Deborah Hollingshead |
| collection | DOAJ |
| description | In addition to the substantial biological diversity among humans, our limited ability to reliably measure expression changes of small magnitude significantly reduces our capacity to obtain convergent sets of transcriptome data in postmortem brain. In particular, differences in the structure and sensitivity/reproducibility of microarray platforms, and in the variety of tools used to analyze microarray data, strongly influence experimental outcome. In order to better understand the sensitivity, dynamic range, and reproducibility of three common DNA microarray platforms, we compared two human postmortem samples on cDNA microarrays with dual-fluorescence, oligonucleotide GeneChips® (Affymetrix), and single-color gel matrix deposited CodeLink® oligonucleotide arrays. All three microarray platforms reported a good dynamic range and high correlation in replicate experiments, but they failed to consistently identify the same genes as differentially expressed between the same samples. Given their reproducibility and proven accuracy, different microarray platforms appear to be measuring different things by nature of their design and function. This needs to be taken into account when comparing data across studies. |
| first_indexed | 2024-12-18T00:11:54Z |
| format | Article |
| id | doaj.art-712598f1bb3448e1b05507fb641b4db2 |
| institution | Directory Open Access Journal |
| issn | 1095-953X |
| language | English |
| last_indexed | 2024-12-18T00:11:54Z |
| publishDate | 2005-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Neurobiology of Disease |
| spelling | doaj.art-712598f1bb3448e1b05507fb641b4db22022-12-21T21:27:39ZengElsevierNeurobiology of Disease1095-953X2005-04-01183649655Platform influence on DNA microarray data in postmortem brain researchDeborah Hollingshead0David A. Lewis1Károly Mirnics2Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA 15261, USA; Corresponding authors. Deborah Hollingshead is to be contacted at Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA 15261. Károly Mirnics, Department of Psychiatry, University of Pittsburgh, School of Medicine, W1655 Biomedical Science, Pittsburgh, PA 15261. Fax: +1 412 624 9410.Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15261, USADepartment of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Corresponding authors. Deborah Hollingshead is to be contacted at Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA 15261. Károly Mirnics, Department of Psychiatry, University of Pittsburgh, School of Medicine, W1655 Biomedical Science, Pittsburgh, PA 15261. Fax: +1 412 624 9410.In addition to the substantial biological diversity among humans, our limited ability to reliably measure expression changes of small magnitude significantly reduces our capacity to obtain convergent sets of transcriptome data in postmortem brain. In particular, differences in the structure and sensitivity/reproducibility of microarray platforms, and in the variety of tools used to analyze microarray data, strongly influence experimental outcome. In order to better understand the sensitivity, dynamic range, and reproducibility of three common DNA microarray platforms, we compared two human postmortem samples on cDNA microarrays with dual-fluorescence, oligonucleotide GeneChips® (Affymetrix), and single-color gel matrix deposited CodeLink® oligonucleotide arrays. All three microarray platforms reported a good dynamic range and high correlation in replicate experiments, but they failed to consistently identify the same genes as differentially expressed between the same samples. Given their reproducibility and proven accuracy, different microarray platforms appear to be measuring different things by nature of their design and function. This needs to be taken into account when comparing data across studies.http://www.sciencedirect.com/science/article/pii/S0969996104002657DNA microarrayPlatform comparisonGeneChipCodeLinkcDNA arrayHybridization |
| spellingShingle | Deborah Hollingshead David A. Lewis Károly Mirnics Platform influence on DNA microarray data in postmortem brain research Neurobiology of Disease DNA microarray Platform comparison GeneChip CodeLink cDNA array Hybridization |
| title | Platform influence on DNA microarray data in postmortem brain research |
| title_full | Platform influence on DNA microarray data in postmortem brain research |
| title_fullStr | Platform influence on DNA microarray data in postmortem brain research |
| title_full_unstemmed | Platform influence on DNA microarray data in postmortem brain research |
| title_short | Platform influence on DNA microarray data in postmortem brain research |
| title_sort | platform influence on dna microarray data in postmortem brain research |
| topic | DNA microarray Platform comparison GeneChip CodeLink cDNA array Hybridization |
| url | http://www.sciencedirect.com/science/article/pii/S0969996104002657 |
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