Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data.

ABSTRACT:

Background

Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task.

Results

We introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy adopts many robust statistical techniques such as kernel smoothing of coverage differentiation information to discern signals from noise and combines ideas from time-series analysis and the signal-processing field to derive a range of estimates for the period in a histogram of coverage differentiation information. Statis

SUBMITTER: Fan X 

PROVIDER: S-EPMC7811225 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature