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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
...OMKar automates karyotyping using optical maps to identify constitutional abnormalities Siavash Raeisi Dehkordi1,2,5, Zhaoyang Jia1,5, Joey Estabrook2, Jen Hauenstein2, Neil Miller2, Naz Güleray-Lafci3, Jürgen Neesen3, Alex Hastie2, Alka Chaubey2, Andy Wing Chun Pang2, Paul Dremsek3 and Vineet...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...with bifid nose, a characteristic trait of Çatalburun dogs, implicating the gene's role in midline closure. Two additional LCORL variants, both associated with canine body size are also discovered: a frameshift that causes a premature stop in large breeds (>25 kg) and an intronic substitution found in small...
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Research: Extensive protein dosage compensation in aneuploid human cancers
- Klaske M. Schukken and
- Jason M. Sheltzer
Genome Res. July 2022 32: 1254-1270; Published in Advance June 14, 2022, doi:10.1101/gr.276378.121
...copy number changes influence the cancer proteome, we conducted an analysis of hundreds of human cancer cell lines and tumors with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins show dosage compensation and fail to change by the degree expected...
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Resource: Modeling molecular development of breast cancer in canine mammary tumors
- Kiley Graim,
- Dmitriy Gorenshteyn,
- David G. Robinson,
- Nicholas J. Carriero,
- James A. Cahill,
- Rumela Chakrabarti,
- Michael H. Goldschmidt,
- Amy C. Durham,
- Julien Funk,
- John D. Storey,
- Vessela N. Kristensen,
- Chandra L. Theesfeld,
- Karin U. Sorenmo,
- and Olga G. Troyanskaya
Genome Res. February 2021 31: 337-347; Published in Advance December 23, 2020, doi:10.1101/gr.256388.119
...; Rowell et al. 2011; Cekanova and Rathore 2014; Kol et al. 2015; Kristiansen et al. 2016). Canine simple carcinomas share especially strong similarities with human breast cancer in terms of both histological and genetic features (Liu et al. 2014). Additionally, BRCA and CMT share chromosomal abnormalities...
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Method: A general calculus of fitness landscapes finds genes under selection in cancers
- Teng-Kuei Hsu,
- Jennifer Asmussen,
- Amanda Koire,
- Byung-Kwon Choi,
- Mayur A. Gadhikar,
- Eunna Huh,
- Chih-Hsu Lin,
- Daniel M. Konecki,
- Young Won Kim,
- Curtis R. Pickering,
- Marek Kimmel,
- Lawrence A. Donehower,
- Mitchell J. Frederick,
- Jeffrey N. Myers,
- Panagiotis Katsonis,
- and Olivier Lichtarge
Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
...of cancer patients, should be associated with a large displacement in the fitness landscape. The average number of coding mutations per tumor can be as small as about eight in leukemia but is more often confoundingly large, such as about 1600 in colorectal cancers (Vogelstein et al. 2013). Among these...
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Research: Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
- Hyunchul Jung,
- Jung Kyoon Choi,
- and Eunjung Alice Lee
Genome Res. August 2018 28: 1136-1146; Published in Advance July 3, 2018, doi:10.1101/gr.231837.117
...-high phenotype, and nonsynonymous mutations in TP53 are marked with filled boxes. Higher somatic SNV counts, RNA editing level, and counts of genes with somatic copy number aberrations are marked in darker colors. The color scale was separately normalized for stomach-esophageal cancer and colorectal cancer...
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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: 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
...of unambiguous copy number losses or gains (Supplemental Fig. S1D,E; Supplemental Notes). Most of the quality filtering of single-cell sequencing data was done with combinatorial criteria, including mean absolute deviation of pairwise difference, degree of ploidy abnormality, and degree of fragmentation...
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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
...and CNA detection performance of FLCNA, benchmarking it against existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. Application of FLCNA to a scDNA-seq data set of breast cancer revealed different genomic variation patterns in neoadjuvant...
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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
...and abnormal (e.g., infected or cancerous) cells in the body and thus represent a valuable model to study the physiological function of the adaptive immune system. Previous studies have shown a progressive decline of mtDNA copy number in resting PBMCs during aging (Kim et al. 2013; Mengel-From et al. 2014...
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