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dc.contributor.authorWilmott, James S-
dc.contributor.authorField, Matthew A-
dc.contributor.authorJohansson, Peter A-
dc.contributor.authorKakavand, Hojabr-
dc.contributor.authorShang, Ping-
dc.contributor.authorDe Paoli-Iseppi, Ricardo-
dc.contributor.authorVilain, Ricardo E-
dc.contributor.authorPupo, Gulietta M-
dc.contributor.authorTembe, Varsha-
dc.contributor.authorJakrot, Valerie-
dc.contributor.authorShang, Catherine A-
dc.contributor.authorCebon, Jonathan S-
dc.contributor.authorShackleton, Mark-
dc.contributor.authorFitzgerald, Anna-
dc.contributor.authorThompson, John F-
dc.contributor.authorHayward, Nicholas K-
dc.contributor.authorMann, Graham J-
dc.contributor.authorScolyer, Richard A-
dc.identifier.citationPathology 2015; 47(7): 683-693en_US
dc.descriptionErratum in: Erratum: Wilmott JS, Field MA, Johansson PA, et al. Tumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomes. Pathology 2015; 47: 683-93. Pathology 2016; 48(1): 104en_US
dc.description.abstractWhole genome sequencing (WGS) of cancer patients' tumours offers the most comprehensive method of identifying both novel and known clinically-actionable genomic targets. However, the practicalities of performing WGS on clinical samples are poorly defined.This study was designed to test sample preparation, sequencing specifications and bioinformatic algorithms for their effect on accuracy and cost-efficiency in a large WGS analysis of human melanoma samples.WGS was performed on melanoma cell lines (n = 15) and melanoma fresh frozen tumours (n = 222). The appropriate level of coverage and the optimal mutation detection algorithm for the project pipeline were determined.An incremental increase in sequencing coverage from 36X to 132X in melanoma tissue samples and 30X to 103X for cell lines only resulted in a small increase (1-2%) in the number of mutations detected, and the quality scores of the additional mutations indicated a low probability that the mutations were real. The results suggest that 60X coverage for melanoma tissue and 40X for melanoma cell lines empower the detection of 98-99% of informative single nucleotide variants (SNVs), a sensitivity level at which clinical decision making or landscape research projects can be carried out with a high degree of confidence in the results. Likewise the bioinformatic mutation analysis methodology strongly influenced the number and quality of SNVs detected. Detecting mutations in the blood genomes separate to the tumour genomes generated 41% more SNVs than if the blood and melanoma tissue genomes were analysed simultaneously. Therefore, simultaneous analysis should be employed on matched melanoma tissue and blood genomes to reduce errors in mutation detection.This study provided valuable insights into the accuracy of SNV with WGS at various coverage levels in human clinical cancer specimens. Additionally, we investigated the accuracy of the publicly available mutation detection algorithms to detect cancer specific SNVs which will aid researchers and clinicians in study design and implementation of WGS for the identification of somatic mutations in other cancers.en_US
dc.subjectDNA Mutational Analysisen_US
dc.subjectDNA, Neoplasmen_US
dc.subjectSpecimen Handlingen_US
dc.titleTumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomesen_US
dc.typeJournal Articleen_US
dc.identifier.affiliationAustin Health, Heidelberg, Victoria, Australiaen_US
dc.identifier.affiliationMelanoma Institute Australia, North Sydney, NSW, Australiaen_US
dc.identifier.affiliationSydney Medical School, The University of Sydney, Camperdown, NSW, Australiaen_US
dc.identifier.affiliationImmunogenomics Laboratory, Australian National University, Canberra, ACT, Australiaen_US
dc.identifier.affiliationOncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australiaen_US
dc.identifier.affiliationCentre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australiaen_US
dc.identifier.affiliationBioplatforms Australia, Macquarie University, North Ryde, NSW, Australiaen_US
dc.identifier.affiliationLudwig Institute for Cancer Research, Olivia Newton-John Cancer and Wellness Centre, Austin Health, Heidelberg, Victoria, Australiaen_US
dc.identifier.affiliationThe Cancer Development and Treatment Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australiaen_US
dc.identifier.affiliationDepartments of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australiaen_US
dc.identifier.affiliationTissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australiaen_US
dc.type.austinJournal Articleen_US
item.fulltextNo Fulltext-
item.openairetypeJournal Article- Newton-John Cancer Research Institute-
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