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Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization.

Forreryd, Andy LU ; Johansson, Henrik LU ; Albrekt, Ann-Sofie LU and Lindstedt, Malin LU (2014) In BMC Genomics 15.
Abstract
Allergic contact dermatitis (ACD) develops upon exposure to certain chemical compounds termed skin sensitizers. To reduce the occurrence of skin sensitizers, chemicals are regularly screened for their capacity to induce sensitization. The recently developed Genomic Allergen Rapid Detection (GARD) assay is an in vitro alternative to animal testing for identification of skin sensitizers, classifying chemicals by evaluating transcriptional levels of a genomic biomarker signature. During assay development and biomarker identification, genome-wide expression analysis was applied using microarrays covering approximately 30,000 transcripts. However, the microarray platform suffers from drawbacks in terms of low sample throughput, high cost per... (More)
Allergic contact dermatitis (ACD) develops upon exposure to certain chemical compounds termed skin sensitizers. To reduce the occurrence of skin sensitizers, chemicals are regularly screened for their capacity to induce sensitization. The recently developed Genomic Allergen Rapid Detection (GARD) assay is an in vitro alternative to animal testing for identification of skin sensitizers, classifying chemicals by evaluating transcriptional levels of a genomic biomarker signature. During assay development and biomarker identification, genome-wide expression analysis was applied using microarrays covering approximately 30,000 transcripts. However, the microarray platform suffers from drawbacks in terms of low sample throughput, high cost per sample and time consuming protocols and is a limiting factor for adaption of GARD into a routine assay for screening of potential sensitizers. With the purpose to simplify assay procedures, improve technical parameters and increase sample throughput, we assessed the performance of three high throughput gene expression platforms - nCounter®, BioMark HD™ and OpenArray® - and correlated their performance metrics against our previously generated microarray data. We measured the levels of 30 transcripts from the GARD biomarker signature across 48 samples. Detection sensitivity, reproducibility, correlations and overall structure of gene expression measurements were compared across platforms. (Less)
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author
organization
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Contribution to journal
publication status
published
subject
keywords
Genomic biomarker signature, GARD, Microarrays, nCounter (R), BioMark HD, (TM), OpenArray (R)
in
BMC Genomics
volume
15
publisher
BioMed Central
external identifiers
  • pmid:24886304
  • wos:000336677700002
  • scopus:84901437249
ISSN
1471-2164
DOI
10.1186/1471-2164-15-379
language
English
LU publication?
yes
id
f3e405bc-8bf6-41d7-8492-35800f324de3 (old id 4529503)
date added to LUP
2014-07-16 13:10:33
date last changed
2017-08-13 03:52:31
@article{f3e405bc-8bf6-41d7-8492-35800f324de3,
  abstract     = {Allergic contact dermatitis (ACD) develops upon exposure to certain chemical compounds termed skin sensitizers. To reduce the occurrence of skin sensitizers, chemicals are regularly screened for their capacity to induce sensitization. The recently developed Genomic Allergen Rapid Detection (GARD) assay is an in vitro alternative to animal testing for identification of skin sensitizers, classifying chemicals by evaluating transcriptional levels of a genomic biomarker signature. During assay development and biomarker identification, genome-wide expression analysis was applied using microarrays covering approximately 30,000 transcripts. However, the microarray platform suffers from drawbacks in terms of low sample throughput, high cost per sample and time consuming protocols and is a limiting factor for adaption of GARD into a routine assay for screening of potential sensitizers. With the purpose to simplify assay procedures, improve technical parameters and increase sample throughput, we assessed the performance of three high throughput gene expression platforms - nCounter®, BioMark HD™ and OpenArray® - and correlated their performance metrics against our previously generated microarray data. We measured the levels of 30 transcripts from the GARD biomarker signature across 48 samples. Detection sensitivity, reproducibility, correlations and overall structure of gene expression measurements were compared across platforms.},
  articleno    = {379},
  author       = {Forreryd, Andy and Johansson, Henrik and Albrekt, Ann-Sofie and Lindstedt, Malin},
  issn         = {1471-2164},
  keyword      = {Genomic biomarker signature,GARD,Microarrays,nCounter (R),BioMark HD,(TM),OpenArray (R)},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Genomics},
  title        = {Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization.},
  url          = {http://dx.doi.org/10.1186/1471-2164-15-379},
  volume       = {15},
  year         = {2014},
}