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Daenekas B, Pérez E, Boniolo F, Stefan S, Benfatto S, Sill M, Sturm D, Jones DTW, Capper D, Zapatka M, Hovestadt V. Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice. Bioinformatics 2024; 40:btae029. [PMID: 38244574 PMCID: PMC10868300 DOI: 10.1093/bioinformatics/btae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
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 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. AVAILABILITY AND IMPLEMENTATION Conumee 2.0 is available under open-source license at: https://github.com/hovestadtlab/conumee2.
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Affiliation(s)
- Bjarne Daenekas
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Eilís Pérez
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Fabio Boniolo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Sabina Stefan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Salvatore Benfatto
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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