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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.
Lunke, S.
Hsu, A.
Australian Ovarian Cancer Study (AOCS) Group
Waring, P.
Taylor, G.
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
Editor: Galli, A.
Statement of
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
Ovarian Neoplasms
Receptor, erbB-2
Cyclin E
Oncogene Proteins
BRCA1 Protein
BRCA2 Protein
Paraffin Embedding
Tissue Fixation
Sensitivity and Specificity
Reproducibility of Results
Gene Dosage
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
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