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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...with this sequencing depth makes this approach cost-effective and scalable for clonal tracking, integrity screenings, and cancer alterations studies, with the addition of joint profiling of RT and gene regulation. For Repli-seq analysis in PARTAGE, we took advantage of our optimized Repli-seq workflow, which reduced...
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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
...CNAs occurred randomly in lymphocytesWe further analyzed CNA profile similarities between cells to try to capture clonal amplification signatures. Dimension-reduction analysis of single-cell copy number profiles produced a few clusters based on large-CNA patterns (Fig. 2A; Supplemental Fig. S5A...
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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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Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
- Ryan O'Hara,
- Enzo Tedone,
- Andrew Ludlow,
- Ejun Huang,
- Beatrice Arosio,
- Daniela Mari,
- and Jerry W. Shay
Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
...are needed.Therefore, we next investigated whether ddMDM was sensitive enough to reliably measure mtDNA copy number in single cells. Starting with a clonal population, single H1299 human lung cancer cells were plated in 1-µL aliquots onto glass slides and visually confirmed for the presence of exactly one...
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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
..., Sei E, Shi X, Wang Y, Tsai P-C, Casasent A, Waters J, Zhang H, et al. 2016. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat Genet 48: 1119–1130. doi:10.1038/ng.3641 ↵Gerlinger M, Rowan AJ, Horswell S, Math M, Larkin J, Endesfelder D, Gronroos E, Martinez P...
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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
....marques@upf.eduAbstractExtreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive -wide...
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Research: Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
- Jing Xia,
- Aarthi Venkat,
- Rachel E. Bainbridge,
- Michael L. Reese,
- Karine G. Le Roch,
- Ferhat Ay,
- and Jon P. Boyle
Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
...RH88 using Nanopore reads revises the T. gondii karyotypeThe majority of the T. gondii isolates collected from North America and Europe belong to three predominant clonal lineages, types I, II, and III (Sibley and Ajioka 2008), and RH strain is a representative strain of the type I lineage (Pfefferkorn...
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Research: Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease
- Stephanie Y. Yang,
- Christina A. Castellani,
- Ryan J. Longchamps,
- Vamsee K. Pillalamarri,
- Brian O'Rourke,
- Eliseo Guallar,
- and Dan E. Arking
Genome Res. March 2021 31: 349-358; Published in Advance January 13, 2021, doi:10.1101/gr.269381.120
...A, Kamal A, Bakhiet M. 2018. Peripheral blood mitochondrial DNA copy number as a novel potential biomarker for diabetic nephropathy in type 2 diabetes patients. Exp Ther Med 16: 1483–1492. doi:10.3892/etm.2018.6319 ↵Aran D, Hu Z, Butte AJ. 2017. xCell: digitally portraying the tissue cellular...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
..., an insignificant difference (ART cohort as baseline, IRR = 1.14, 95% CI: 0.41–3.19, P = 0.796) (Supplemental Table S5). Approximately half of these SV calls localize to a cluster of C2H2 KRAB zinc finger proteins on distal Chromosome 4 (145.3 Mb), a locus recently shown to be highly copy number variable in house...
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Corrigendum: Corrigendum: 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. March 2024 34: 514; doi:10.1101/gr.279293.124
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