Journal Article

DZNE-2026-00918

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png CNV-Finder: streamlining copy number variation discovery.

Kuznetsov, N. ; Daida, K. ; Makarious, M. B. ; Al-Mubarak, B. ; Atterling Brolin, K. ; Malik, L. ; Kouam, C. ; Baker, B. ; Real, R. ; Step, K. ; Lange, L. M. ; Wu, L. ; Ostrozovicova, M. ; Andersh, K. M. ; Kung, P.-J. ; Mecheri, Y. ; Tay, Y.-W. ; Soundous Malek, B. ; Al Tassan, N. ; Periñan, M. T. ; Hong, S. ; Koretsky, M. J. ; Sargeant, L. ; Levine, K. ; Blauwendraat, C. ; Billingsley, K. J. ; Bandres-Ciga, S. ; Leonard, H. L.DZNE* ; Bardien, S. ; Morris, H. R. ; Singleton, A. B. ; Nalls, M. A. ; Vitale, D.

2026
Oxford University Press Oxford

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Please use a persistent id in citations: doi:10.1093/bioadv/vbag205

Abstract: Copy Number Variations (CNVs) play pivotal roles in complex disease etiology, often requiring large sample sizes to analyze disease associations. While genotyping arrays offer a cost-effective approach for CNV detection using Log R Ratio (LRR) and B Allele Frequency (BAF) signals, existing independent array-based callers suffer from high false positive rates and noise susceptibility, burdening manual validation.We present CNV-Finder, a deep learning pipeline employing Long Short-Term Memory (LSTM) networks for large-scale CNV identification within user-defined genomic regions. Trained on expert-annotated samples from the Global Parkinson's Genetics Program across four neurodegenerative disease-associated genes (PRKN, LINGO2, MAPT, SNCA), CNV-Finder integrates human feedback to iteratively improve performance. In benchmarking across 105 936 samples spanning 11 ancestries and nearly 150 cohorts, the model achieved 91% and 89% visual confirmation rates for PRKN deletions and duplications at high-confidence thresholds. In two validation cohorts, CNV-Finder nominated 83% fewer candidates than a popular Hidden Markov Model-based caller while maintaining higher confirmation rates. Validation through MLPA, short-read, and long-read sequencing demonstrated robust performance, generalizing to diverse signatures including homozygous deletions and SNCA triplications absent from training. Our findings highlight human expertise's value in complex loci like 17q21.31.CNV-Finder is freely available at https://github.com/nvk23/CNV-Finder.

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Contributing Institute(s):

1. Parkinson Genetics (AG Gasser)

Research Program(s):

1. 353 - Clinical and Health Care Research (POF4-353) (POF4-353)

Appears in the scientific report 2026

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Database coverage:
; ; ; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; DOAJ Seal ; Emerging Sources Citation Index ; Fees ; PubMed Central ; SCOPUS ; Web of Science Core Collection

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