High-throughput amplicon-based copy number detection of 11 genes in formalin-fixed paraffin-embedded ovarian tumour samples by MLPA-seq

O Kondrashova; CJ Love; S Lunke; AL Hsu; D Bowtell; G Chenevix-Trench; A Green; P Webb; A DeFazio; D Gertig; N Traficante; S Fereday; S Moore; J Hung; K Harrap; T Sadkowsky; N Pandeya; M Malt; A Mellon; R Robertson; T Vanden Bergh; M Jones; P Mackenzie; J Maidens; K Nattress; YE Chiew; A Stenlake; H Sullivan; B Alexander; P Ashover; S Brown; T Corrish; L Green; L Jackman; K Ferguson; K Martin; A Martyn; B Ranieri; J White; V Jayde; P Mamers; L Bowes; L Galletta; D Giles; J Hendley; K Alsop; T Schmidt; H Shirley; C Ball; C Young; S Viduka; H Tran; S Bilic; L Glavinas; J Brooks; R Stuart-Harris; F Kirsten; J Rutovitz; P Clingan; A Glasgow; A Proietto; S Braye; G Otton; J Shannon; T Bonaventura; J Stewart; S Begbie; M Friedlander; D Bell; S Baron-Hay; A Ferrier; G Gard; D Nevell; N Pavlakis; S Valmadre; B Young; C Camaris; R Crouch; L Edwards; N Hacker; D Marsden; G Robertson; P Beale; J Beith; J Carter; C Dalrymple; R Houghton; P Russell; M Links; J Grygiel; J Hill; A Brand; K Byth; R Jaworski; P Harnett; R Sharma; G Wain; B Ward; D Papadimos; A Crandon

Journal article

High-throughput amplicon-based copy number detection of 11 genes in formalin-fixed paraffin-embedded ovarian tumour samples by MLPA-seq

O Kondrashova, CJ Love, S Lunke, AL Hsu, D Bowtell, G Chenevix-Trench, A Green, P Webb, A DeFazio, D Gertig, N Traficante, S Fereday, S Moore, J Hung, K Harrap, T Sadkowsky, N Pandeya, M Malt, A Mellon, R Robertson Show all

Plos One | PUBLIC LIBRARY SCIENCE | Published : 2015

DOI: 10.1371/journal.pone.0143006

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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 ..

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University of Melbourne Researchers

Sebastian Lunke Author

David Bowtell Author

Julie Fereday Author

Kathryn Alsop Author

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Funding Acknowledgements

The AOCS was supported by the U.S. Army Medical Research and Materiel Command under DAMD17-01-1-0729, The Cancer Council Tasmania and The Cancer Foundation of Western Australia and the National Health and Medical Research Council of Australia (NHMRC, ID400413), the Peter MacCallum Cancer Foundation and Ovarian Cancer Australia (OCA). This work was supported by research grants from the Victorian Comprehensive Cancer Centre, the Victorian Cancer Agency (TRP13088), and the National Health and Medical Research Council (APP1034301) with infrastructure support for sequencing from the University of Melbourne and Therapeutic Innovation Australia. The Victorian Cancer Biobank is supported by the Victorian Government. GT is part supported by the Herman Trust.