EVENT : C3BI Seminars – Large audience
Performance evaluation of DNA copy number segmentation methods
Speaker : Pierre Neuvial, CNRS researcher from Laboratoire de Mathématiques et Modélisation d’Evry (LaMME) – Équipe Statistique & Génome – Université d’Evry Val d’Essonne Time : 02:00 pm Starting Date : 03/12/2015
Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris
A number of bioinformatic or biostatistical methods are available for segmenting DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these methods is generally assessed using unrealistic simulation studies, or based on small real data analyses.
In order to make an objective and reproducible performance assessment, we have designed and implemented a resampling-based framework to generate realistic DNA copy number profiles of cancer samples with known truth. In this talk, I will describe this framework and its application to a comparison study between methods for segmenting DNA copy number profiles from SNP microarrays.
This study indicates that no single method is uniformly better than all others. It also helps identifying pros and cons of the compared methods as a function of biologically informative parameters, such as the fraction of tumor cells in the sample and the proportion of heterozygous markers.
Reference: M. Pierre-Jean, G. Rigaill and P. Neuvial Performance evaluation of DNA copy number segmentation methods. Briefings in Bioinformatics (2015) http://bib.oxfordjournals.org/content/16/4/600
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