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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France; 4Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France ↵5 These authors contributed equally to this work. Corresponding author: dgresham@nyu.eduAbstractCopy number variants (CNVs), duplications and deletions of genomic...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
...(Quinlan and Hall 2010), enforcing the necessary parameters. In broad terms, window-based association signals were mapped to their respective structural variants and then intersected with the corresponding annotation files.lncRNAWe proposed the independent joint distribution of all copy number lncRNA...
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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
..., Wang Z, Rodriguez-Santiago B, Hutchinson A, Deng X, Liu C, Horner MJ, et al. 2012. Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet 44: 651–658. doi:10.1038/ng.2270 ↵Klopocki E, Mundlos S. 2011. Copy-number variations, noncoding sequences, and human phenotypes. Annu Rev...
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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
..., Ontario M5S 1A8, Canada Corresponding author: lars.feuk@igp.uu.seAbstractRare or de novo structural variation, primarily in the form of copy number variants, is detected in 5%–10% of autism spectrum disorder (ASD) families. While complex structural variants involving duplications can generally be detected...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...aberrations in cell-cycle control. In non-small-cell lung cancer (NSCLC), instability occurs early in tumor growth, resulting in pronounced intratumor heterogeneity, including changes in gene copy number, and whole- doubling (WGD) in ∼75% of tumors. Gene duplication, genetic drift, and selection mediate...
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Method: Polishing copy number variant calls on exome sequencing data via deep learning
- Furkan Özden,
- Can Alkan,
- and A. Ercüment Çiçek
Genome Res. June 2022 32: 1170-1182; Published in Advance June 13, 2022, doi:10.1101/gr.274845.120
...@cs.bilkent.edu.trAbstractAccurate and efficient detection of copy number variants (CNVs) is of critical importance owing to their significant association with complex genetic diseases. Although algorithms that use whole- sequencing (WGS) data provide stable results with mostly valid statistical assumptions, copy number detection on whole...
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Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
- Fei Qin,
- Guoshuai Cai,
- Christopher I. Amos,
- and Feifei Xiao
Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
...K, Porubsky D, van der Wekken AJ, Timens W, et al. 2017. Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small-cell lung cancer patient. Ann Oncol 28: 1668–1670. doi:10.1093/annonc/mdx182 ↵Fischer K, Pflugfelder GO...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...-GS SV callset and found Watershed-SV outperforms the WGS-only baseline models in prioritizing coding and noncoding variants. When applied to the UDN patient data set, Watershed-SV further provided additional disease-relevant SV candidates compared to CADD-SV and provided direct insights into the gene...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
...alterations.These observations highlight the need for comprehensive cytogenomic analysis beyond the detection of numerical or large copy number changes. Optical mapping (OGM) is a cytogenomic technique that has the ability to detect several classes of structural variants (SVs) including triploidy, aneuploidy...
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Method: A machine-learning approach for accurate detection of copy number variants from exome sequencing
- Vijay Kumar Pounraja,
- Gopal Jayakar,
- Matthew Jensen,
- Neil Kelkar,
- and Santhosh Girirajan
Genome Res. July 2019 29: 1134-1143; Published in Advance June 6, 2019, doi:10.1101/gr.245928.118
...Corresponding author: sxg47@psu.eduAbstractCopy number variants (CNVs) are a major cause of several genetic disorders, making their detection an essential component of genetic analysis pipelines. Current methods for detecting CNVs from exome-sequencing data are limited by high false-positive rates and low...

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