Journal article
qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles
S Song, K Nones, D Miller, I Harliwong, KS Kassahn, M Pinese, M Pajic, AJ Gill, AL Johns, M Anderson, O Holmes, C Leonard, D Taylor, S Wood, Q Xu, F Newell, MJ Cowley, J Wu, P Wilson, L Fink Show all
Plos One | Published : 2012
Abstract
Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects the sensitivity of mutation detection, copy number analysis, cancer gene expression and methylation profiling. Tumour cellularity is traditionally estimated by pathological review of sectioned specimens; however this method is both subjective and prone to error due to heterogeneity within lesions and cellularity differences between the sample viewed during pathological review and tissue used for research purposes. In this paper we describe a statistical model to estimate tumour cellularity from SNP array profiles of paired tumour and normal samples using shifts in SNP allele frequency at regions of lo..
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Grants
Awarded by National Health and Medical Research Council
Funding Acknowledgements
This research has been supported by the National Health and Medical Research Council of Australia (NHMRC; 631701, 535903, 427601); the Australian Government: Department of Innovation, Industry, Science and Research; the Australian Cancer Research Foundation; the Queensland Government (National and International Research Alliances Program); the University of Queensland; the Cancer Council New South Wales (NSW): (SRP06-01); the Cancer Institute NSW: (06/ECF/1-24; 09/CDF/2-40; 07/CDF/1-03; 10/CRF/1-01, 08/RSA/1-15, 07/CDF/1-28, 10/CDF/2-26,10/FRL/2-03, 06/RSA/1-05, 09/RIG/1-02, 10/TPG/1-04, 11/REG/1-10, 11/CDF/3-26); the Garvan Institute of Medical Research; the Avner Nahmani Pancreatic Cancer Research Foundation; the R.T. Hall Trust; the Petre Foundation; the Gastroenterological Society of Australia; the American Association for Cancer Research Landon Foundation INNOVATOR Award; the Royal Australasian College of Surgeons; the Royal Australasian College of Physicians; and the Royal College of Pathologists of Australasia. SG is a recipient of a NHMRC Principal Research Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.