Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice
Broad Institute · Dana-Farber Cancer Institute · +6 more institutions
Abstract
MOTIVATION: Copy-number variations (CNVs) are common genetic alterations in cancer and their detection may impact tumor classification and therapeutic decisions. However, detection of clinically relevant large and focal CNVs remains challenging when sample material or resources are limited. This has motivated us to create a software tool to infer CNVs from DNA methylation arrays which are often generated as part of clinical routines and in research settings. RESULTS: We present our R package, conumee 2.0, that combines tangent normalization, an adjustable genomic binning heuristic, and weighted circular binary segmentation to utilize DNA methylation arrays for CNV analysis and mitigate technical biases and…
Citation impact
- FWCI
- 36.46
- Percentile
- 100%
- References
- 38
Authors
11- BDBjarne DaenekasCorresponding
Broad Institute, Dana-Farber Cancer Institute, Charité - Universitätsmedizin Berlin
- EPEilís Pérez
Charité - Universitätsmedizin Berlin
- FBFabio Boniolo
Broad Institute, Dana-Farber Cancer Institute
- SŞSabina Ştefan
Broad Institute, Dana-Farber Cancer Institute
- SBSalvatore Benfatto
Broad Institute, Dana-Farber Cancer Institute
Topics & keywords
- Copy-number variation
- DNA methylation
- CDKN2A
- Computer science
- Copy number analysis
- Computational biology
- Biology
- Genotyping