Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/98104
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Type: | Journal article |
Title: | High-throughput amplicon-based copy number detection of 11 genes in formalin-fixed paraffin-embedded ovarian tumour samples by MLPA-seq |
Author: | Kondrashova, O. Love, C.J. Lunke, S. Hsu, A.L. Australian Ovarian Cancer Study (AOCS) Group, Waring, P.M. Taylor, G.R. Bowtell, D. Chenevix-Trench, G. Green, A. Webb, P. DeFazio, A. Gertig, D. Traficante, N. Fereday, S. Moore, S. Hung, J. Harrap, K. Sadkowsky, T. Pandeya, N. et al. |
Citation: | PLoS One, 2015; 10(11):e0143006-1-e0143006-14 |
Publisher: | Public Library of Science |
Issue Date: | 2015 |
ISSN: | 1932-6203 1932-6203 |
Editor: | Galli, A. |
Statement of Responsibility: | Olga Kondrashova, Clare J. Love, Sebastian Lunke, Arthur L. Hsu, Australian Ovarian Cancer Study, AOCS, Group, Paul M. Waring, Graham R. Taylor |
Abstract: | Whilst next generation sequencing can report point mutations in fixed tissue tumour samples reliably, the accurate determination of copy number is more challenging. The conventional Multiplex Ligation-dependent Probe Amplification (MLPA) assay is an effective tool for measurement of gene dosage, but is restricted to around 50 targets due to size resolution of the MLPA probes. By switching from a size-resolved format, to a sequence-resolved format we developed a scalable, high-throughput, quantitative assay. MLPA-seq is capable of detecting deletions, duplications, and amplifications in as little as 5ng of genomic DNA, including from formalin-fixed paraffin-embedded (FFPE) tumour samples. We show that this method can detect BRCA1, BRCA2, ERBB2 and CCNE1 copy number changes in DNA extracted from snap-frozen and FFPE tumour tissue, with 100% sensitivity and >99.5% specificity. |
Keywords: | Australian Ovarian Cancer Study (AOCS) Group Humans Ovarian Neoplasms Formaldehyde Receptor, erbB-2 Cyclin E Oncogene Proteins BRCA1 Protein BRCA2 Protein Paraffin Embedding Tissue Fixation Sensitivity and Specificity Reproducibility of Results Gene Dosage Female Genes, Neoplasm DNA Copy Number Variations Limit of Detection High-Throughput Nucleotide Sequencing Multiplex Polymerase Chain Reaction |
Description: | The Clinical and Scientific Collaborators of the AOCS group include Martin Oehler. |
Rights: | © 2015 Kondrashova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
DOI: | 10.1371/journal.pone.0143006 |
Grant ID: | http://purl.org/au-research/grants/nhmrc/400413 http://purl.org/au-research/grants/nhmrc/1034301 |
Published version: | http://dx.doi.org/10.1371/journal.pone.0143006 |
Appears in Collections: | Aurora harvest 3 Medicine publications |
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hdl_98104.pdf | Published version | 1.29 MB | Adobe PDF | View/Open |
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