How to characterize DNA samples

Abstract

A method for characterizing DNA samples obtained from tumors, comprising: (a) obtaining a tumor copy number profile for each sample; (b) quantifying a set of copy number features in the copy number profile; and (c) determining exposure to one or more signatures of chromosomal instability based on the quantified features. The copy number features are metrics that characterize copy number events in the copy number profile. The set of features does not include absolute copy numbers of segments in the copy number profile. The signature of chromosomal instability is obtained by quantifying a set of copy number features in multiple tumor samples and identifying one or more mutation signatures that may result in the copy number profile of multiple tumor samples. Methods for characterizing the type of chromosomal instability present in a sample, providing a prognosis, identifying a drug target, or identifying a therapy for a subject are also described.

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