Harbin: a quantitation PCR analysis tool

Bester, R., Pepler, P. T. , Aldrich, D. J. and Maree, H. J. (2017) Harbin: a quantitation PCR analysis tool. Biotechnology Letters, 39(1), pp. 171-178. (doi: 10.1007/s10529-016-2221-1) (PMID:27695982)

Abstract

Objectives: To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments. Results: Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets. Conclusions: The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required.

• Item Type: Articles
• Keywords: Bootstrap; Concentration ratios; Genetic variants; GLRaV-3; Harbin; Location-scale-shape problem; Quantile-based scoring; RT-qPCR.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Pepler, Dr Theo
• Authors: Bester, R., Pepler, P. T., Aldrich, D. J., and Maree, H. J.
• Subjects: Q Science > QH Natural history > QH426 Genetics
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Biotechnology Letters
• Publisher: Springer
• ISSN: 0141-5492
• ISSN (Online): 1573-6776
• Published Online: 01 October 2016
• Copyright Holders: Copyright © 2016 Springer Science+Business Media Dordrech
• First Published: First published in Biotechnology Letters 39(1):171-178
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher