CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications

Author:

Rapti Melivoia12,Zouaghi Yassine12,Meylan Jenny1,Ranza Emmanuelle3,Antonarakis Stylianos E34,Santoni Federico A132ORCID

Affiliation:

1. Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland

2. Univesity of Lausanne, Lausanne, Switzerland

3. Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland

4. University of Geneva Medical Faculty, Geneva, Switzerland

Abstract

AbstractCoverageMaster (CoM) is a copy number variation (CNV) calling algorithm based on depth-of-coverage maps designed to detect CNVs of any size in exome [whole exome sequencing (WES)] and genome [whole genome sequencing (WGS)] data. The core of the algorithm is the compression of sequencing coverage data in a multiscale Wavelet space and the analysis through an iterative Hidden Markov Model. CoM processes WES and WGS data at nucleotide scale resolution and accurately detects and visualizes full size range CNVs, including single or partial exon deletions and duplications. The results obtained with this approach support the possibility for coverage-based CNV callers to replace probe-based methods such as array comparative genomic hybridization and multiplex ligation-dependent probe amplification in the near future.

Funder

EU Framework Programme for Research and Innovation Action

Swiss National Science Foudation

Novartis Foundation

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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