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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. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...joint profiling of copy number variation (CNV), RT, and gene expression from the same sample, providing a more accurate integrated view of the complex relationships between RT and gene regulation.Human cells duplicate their by the firing of thousands of origins that are activated in clusters following...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...resources, supervision, and funding. K.B.S. performed bioinformatic analysis. K.B.S. and A.S.M. performed initial data curation and formal analysis, and M.E., A.L., J.E. C.M.B.C., C.M.G., and E.S.L. helped with clinical and genomic interpretations of results. M.E. did wet-laboratory experiments. K.B.S., A...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...methods require considerable manual expertise and have a low resolution of 3–10 Mbp (Shaffer and Bejjani 2004). They can be combined with CMA or whole-exome sequencing to improve resolution for detecting copy number (CN) changes. These high-resolution methods (CMA, panel sequencing) do not easily detect...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...coverage requirements, sensitivity, and specificity in other imprinted regions and for mosaic alterations for clinical applications.EpimutationsIn genomic diagnostics, it is crucial to determine if variants occur in cis (same chromosome) or in trans (opposite chromosomes). This is particularly valuable...
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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
...is a significant predictor of large-scale deletion and inversion frequency induced by CRISPR-Cas9 in K562 cells. This finding has implications for understanding SVs in the human and for the future application of CRISPR-Cas9 in gene editing and the modeling of rare SVs.Structural variations (SVs) encompass...
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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
...Mol Genet 26: 860–872. doi:10.1093/hmg/ddx002 ↵Uddin M, Thiruvahindrapuram B, Walker S, Wang Z, Hu P, Lamoureux S, Wei J, MacDonald JF, Pellecchia G, Lu C, et al. 2015. A high-resolution copy-number variation resource for clinical and population genetics. Genet Med 17: 747–752. doi:10.1038/gim.2014...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45 Gothenburg, Sweden Corresponding authors: jesper.eisfeldt@scilifelab.se, anna.lindstrand@ki.seAbstractChromosomal inversions (INVs) are particularly challenging to detect due to their copy-number neutral state and association...
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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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Resource: Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
- Tatiana Maroilley,
- Stephane Flibotte,
- Francesca Jean,
- Victoria Rodrigues Alves Barbosa,
- Andrew Galbraith,
- Afiya Razia Chida,
- Filip Cotra,
- Xiao Li,
- Larisa Oncea,
- Mark Edgley,
- Don Moerman,
- and Maja Tarailo-Graovac
Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122
...a comprehensive resource of complex genomic variations in C. elegans and highlights the power of srWGS to study the complexity of s by applying tailored analyses.Balancer chromosomes typically contain chromosomal rearrangements that cover a large portion of s in model organisms (Edgley et al. 2006). They permit...
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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
...from at least one caller. Our study underscores the limitations of current approaches for CNV identification and provides an effective method that yields high-quality CNVs for application in clinical diagnostics.Copy number variants (CNVs) are a major source for genomic variation, evolution...

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