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@ARTICLE{Daenekas:287227,
author = {B. Daenekas and E. Pérez and F. Boniolo and S. Stefan and
S. Benfatto and M. Sill$^*$ and D. Sturm$^*$ and D. T. W.
Jones$^*$ and D. Capper$^*$ and M. Zapatka$^*$ and V.
Hovestadt},
title = {{C}onumee 2.0: {E}nhanced copy-number variation analysis
from {DNA} methylation arrays for humans and mice.},
journal = {Bioinformatics},
volume = {40},
number = {2},
issn = {0266-7061},
address = {Oxford},
publisher = {Oxford Univ. Press},
reportid = {DKFZ-2024-00176},
pages = {btae029},
year = {2024},
note = {2024 Feb 1;40(2):btae029},
abstract = {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.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 batch effects. Segmentation results were
validated in a lung squamous cell carcinoma dataset from
TCGA (n = 367 samples) by comparison to segmentations
derived from genotyping arrays (Pearson's correlation
coefficient of 0.91). We further introduce a segmented block
bootstrapping approach to detect focal alternations that
achieved $60.9\%$ sensitivity and $98.6\%$ specificity for
deletions affecting CDKN2A/B $(60.0\%$ and $96.9\%$ for RB1,
respectively) in a low-grade glioma cohort from TCGA (n =
239 samples). Finally, our tool provides functionality to
detect and summarize CNVs across large sample
cohorts.Conumee 2.0 is available under open-source license
at: https://github.com/hovestadtlab/conumee2.Supplementary
data are available at Bioinformatics online.},
cin = {B062 / HD01 / B360 / BE01 / B060},
ddc = {570},
cid = {I:(DE-He78)B062-20160331 / I:(DE-He78)HD01-20160331 /
I:(DE-He78)B360-20160331 / I:(DE-He78)BE01-20160331 /
I:(DE-He78)B060-20160331},
pnm = {312 - Funktionelle und strukturelle Genomforschung
(POF4-312)},
pid = {G:(DE-HGF)POF4-312},
typ = {PUB:(DE-HGF)16},
pubmed = {pmid:38244574},
doi = {10.1093/bioinformatics/btae029},
url = {https://inrepo02.dkfz.de/record/287227},
}