Robust foreground detection in somatic copy number data

Aditya Deshpande, Trent Walradt, Ya Hu, Amnon Koren, Marcin Imielinski
2019 biorxiv/medrxiv  
Sensitive detection of somatic copy number alterations (SCNA) in cancer genomes is confounded by "waviness" in read depth data. We present , a signal processing algorithm to optimize SCNA detection in whole genome (WGS) and targeted sequencing platforms through foreground detection and background subtraction of read depth data. Application of to WGS demonstrates that WGS waviness is driven by replication timing. Re-analysis of thousands of tumor profiles reveals that provides superior detection
more » ... superior detection of biologically relevant SCNAs relative to state-of-the-art algorithms. Applied to tumor dilutions, improves the sensitivity of relapse detection 10-fold relative to current standards. is available as an R package in the GitHub repository
doi:10.1101/847681 fatcat:acnpepo2mrhopgekvp6zgqdipe