Bioinformatics Seminars

Current Bioinformatics Seminar

24 October 2017

Computational methods for the analysis of molecular phenotypes in cancer

Sepideh Foroutan
WEHI Bioinformatics

Metastasis is the main cause of cancer-related death and so it is very important to detect metastasis at very early stages. Likewise, understanding the mechanisms underlying metastasis can be improved by directly studying metastatic cells. However, current imaging technologies are usually unable to detect micro-metastasis, and biopsy of overt metastasis is invasive and only possible in some tissues. Therefore liquid biopsies, such as the measurement of circulating tumour cells (CTCs) and circulating tumour DNAs in blood, provide a non-invasive approach to monitor tumour progression and therapy response.
In this talk, I will first introduce singscore, a single-sample scoring method that scores individual samples based on their concordance with defined molecular phenotypes. This scoring approach produces the stable and readily interpretable scores compared to other commonly used scoring methods, and is suitable for use in data sets with small number of samples (often the case in clinical and pre-clinical context). I will then show the applications of this method in molecular phenotyping and sample stratification in the second part of my talk, where I discuss breast cancer CTC markers. I will explain the current approaches being used for isolating CTCs, assess the suitability of established CTC markers, and finish my talk by introducing novel genes as potential markers for CTCs, including those distinguishing epithelial and mesenchymal sub-populations.

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