TY - JOUR
T1 - High-throughput amplicon-based copy number detection of 11 genes in formalin-fixed paraffin-embedded ovarian tumour samples by MLPA-seq
AU - Kondrashova, Olga
AU - Love, Clare J.
AU - Lunke, Sebastian
AU - Hsu, Arthur L.
AU - Australian Ovarian Cancer Study Group (AOCS)
AU - Ganju, V.
AU - Zeps, N.
AU - Waring, Paul M.
AU - Taylor, Graham R.
PY - 2015/11/16
Y1 - 2015/11/16
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/84957108905
U2 - 10.1371/journal.pone.0143006
DO - 10.1371/journal.pone.0143006
M3 - Article
C2 - 26569395
AN - SCOPUS:84957108905
SN - 1932-6203
VL - 10
JO - PLoS ONE
JF - PLoS ONE
IS - 11
M1 - e0143006
ER -