METHODS AND APPARATUS FOR ANALYZING AND QUANTIFYING DNA ALTERATIONS IN CANCER

摘要

Methods and apparatus for inferring purity and ploidy from a sample of cells (e.g., a sample comprising cancer and normal cells) are described. Copy number per cell of interest (e.g., cancer cell) is determined by optimizing purity and ploidy for the sample based, at least in part, on relative copy number profile information. One or more likelihood fit scores are determined for each of a plurality of candidate solutions generated by the methods described herein. A solution is selected based, at least in part on the likelihood fit score(s) and the copy number per cancer cell is determined in accordance with the selected solution.

主权项

1. A method of determining a copy number per cancer cell in a sample of cells, the method comprising:
receiving a relative copy number profile for DNA segments extracted from the sample; determining based, at least in part, on the relative copy number profile, a set of candidate solutions by estimating purity and ploidy from first information about somatic copy number alterations in the sample; determining a likelihood fit score for each of the solutions in the set of candidate solutions, wherein the likelihood fit score is determined based, at least in part, on the first information about somatic copy number alterations in the sample and second information, wherein the second information comprises information about one or more mutations detected in the sample and/or information about karyotype copy profile characteristics of a particular disease; selecting a solution from the set of candidate solutions based, at least in part, on the likelihood fit score associated with each candidate solution; and determining the copy number per cancer cell in accordance with the selected solution.