The browser you are using is not supported by this website. All versions of Internet Explorer are no longer supported, either by us or Microsoft (read more here: https://www.microsoft.com/en-us/microsoft-365/windows/end-of-ie-support).

Please use a modern browser to fully experience our website, such as the newest versions of Edge, Chrome, Firefox or Safari etc.

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

På svenska

Author

Summary, in English

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.

Publishing year

2014

Language

English

Publication/Series

BMC Genomics

Volume

15

Document type

Journal article

Publisher

BioMed Central (BMC)

Topic

  • Genetics

Keywords

  • Genomic biomarker signature
  • GARD
  • Microarrays
  • nCounter (R)
  • BioMark HD
  • (TM)
  • OpenArray (R)

Status

Published

ISBN/ISSN/Other

  • ISSN: 1471-2164