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Statistics and Informatics in Molecular Cancer Research$
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Carsten Wiuf and Claus L. Andersen

Print publication date: 2009

Print ISBN-13: 9780199532872

Published to Oxford Scholarship Online: September 2009

DOI: 10.1093/acprof:oso/9780199532872.001.0001

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PRINTED FROM OXFORD SCHOLARSHIP ONLINE (oxford.universitypressscholarship.com). (c) Copyright Oxford University Press, 2021. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in OSO for personal use. date: 17 September 2021

Analysis of DNA methylation in cancer

Analysis of DNA methylation in cancer

(p.102) 5 Analysis of DNA methylation in cancer
Statistics and Informatics in Molecular Cancer Research

Fabian Model

Jörn Lewin

Catherine Lofton-Day

Gunter Weiss

Oxford University Press

This chapter gives an overview of algorithms and statistical methods used for measuring and analyzing DNA methylation in cancer research. It starts with a short introduction into the biology of DNA methylation and its role in cancer. This is followed by an overview of measurement technologies and a detailed description of data pre-processing algorithms for normalization and calibration of direct bisulphite DNA sequencing and DNA methylation microarray measurements. The second part of the chapter explores some typical examples of DNA methylation data analysis in cancer research and diagnostics: the classification of tumour tissue samples, the detection of cancer in plasma samples, and the tissue based prediction of tumour recurrence.

Keywords:   DNA methylation, bisulphite sequencing, methylation odds, tissue classification, feature selection, marker panel, logistic regression, survival analysis

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