Reconstructing cancer karyotypes from short read data: the half empty and half full glass.

ABSTRACT:

Background

During cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions.The result is a highly complex, patient-specific cancer karyotype. Using high-throughput technologies of deep sequencing and microarrays it is possible to interrogate a cancer genome and produce chromosomal copy number profiles and a list of breakpoints ("jumps") relative to the normal genome. This information is very detailed but local, and does not give the overall picture of the cancer genome. One of the basic challenges in cancer genome research is to use such information to infer the cancer karyotype. We present here an algorithmic approach, based on graph theory and integer l

SUBMITTER: Eitan R 

PROVIDER: S-EPMC5688766 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature