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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
...pancancer nonsynonymous single-nucleotide variants (SNVs) to generate a comprehensive set of mutation clusters on protein domain structures and then labeled clusters within 5 Å (5 Å = 5 × 10−10 m) of a functional site as “tunable sites.” These tunable sites were used to identify FIEs in lung tumors...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...and explore the cross-tissue communication beyond HPG axis. The results further enrich the duck regulatory variant resource, deepen our understanding of the genetic regulation of egg production, and broaden our insight into the systemic regulation of reproductive traits in poultry...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...peak (average signal across all lines), coordinates of the peak summit is indicated. (Below) Allelic imbalance (y-axis) for all variants in 2.5 kb radius around peak summit. Significant variants are shown in blue. Top significant variants with the same haplotype (0|1) are highlighted with gray box...
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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
...correlation coefficient of rare variant frequency and gene mutation probability across gene groups. Genes were grouped according to their mutation probabilities. The x-axis shows the number of groups used to calculate correlation coefficients. The number of groups decreases as group sizes get larger. Two...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...12504, USA Corresponding author: selmecki@umn.eduAbstractThe human fungal pathogen Candida albicans poses a significant burden on global health, causing high rates of mortality and antifungal drug resistance. C. albicans is a heterozygous diploid organism that reproduces asexually. Structural variants...
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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
.... Corresponding authors: smontgom@stanford.edu, mschatz@cs.jhu.edu, wheelerm@stanford.edu, ajbattle@jhu.eduAbstractRare structural variants (SVs)—insertions, deletions, and complex rearrangements—can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed...
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Review: A systematic review on the biochemical threshold of mitochondrial genetic variants
- Karan K. Smith,
- Jesse D. Moreira,
- Callum R. Wilson,
- June O. Padera,
- Ashlee N. Lamason,
- Liying Xue,
- Deepa M. Gopal,
- David B. Flynn,
- and Jessica L. Fetterman
Genome Res. March 2024 34: 341-365; Published in Advance April 16, 2024, doi:10.1101/gr.278200.123
...Corresponding author: jefetter@bu.eduAbstractMitochondrial DNA (mtDNA) variants cause a range of diseases from severe pediatric syndromes to aging-related conditions. The percentage of mtDNA copies carrying a pathogenic variant, variant allele frequency (VAF), must reach a threshold before a biochemical defect...
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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
...Resolving complex duplication variants in autism spectrum disorder using long-read sequencing Jesper Eisfeldt1,2, Edward J. Higginbotham3,4, Felix Lenner5, Jennifer Howe3,4, Bridget A. Fernandez6,7, Anna Lindstrand1,2, Stephen W. Scherer3,4,8 and Lars Feuk5 1Department of Molecular Medicine...
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Research: Long-read sequencing for non-small-cell lung cancer genomes
- Yoshitaka Sakamoto,
- Liu Xu,
- Masahide Seki,
- Toshiyuki T. Yokoyama,
- Masahiro Kasahara,
- Yukie Kashima,
- Akihiro Ohashi,
- Yoko Shimada,
- Noriko Motoi,
- Katsuya Tsuchihara,
- Susumu S. Kobayashi,
- Takashi Kohno,
- Yuichi Shiraishi,
- Ayako Suzuki,
- and Yutaka Suzuki
Genome Res. September 2020 30: 1243-1257; Published in Advance September 4, 2020, doi:10.1101/gr.261941.120
...Long-read sequencing for non-small-cell lung cancer s Yoshitaka Sakamoto1, Liu Xu1, Masahide Seki1, Toshiyuki T. Yokoyama1, Masahiro Kasahara1, Yukie Kashima2,3, Akihiro Ohashi3, Yoko Shimada4, Noriko Motoi5, Katsuya Tsuchihara2, Susumu S. Kobayashi3, Takashi Kohno4, Yuichi Shiraishi6, Ayako Suzuki...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
....05; the vertical line corresponds to a normalized activity score of 1 (wild-type). For visualization purposes, the y-axis is clipped to 10−15; 13 variants are hidden with activity scores greater than wild-type and P-values up to 10−26. (D) Quantized DMS activity scores for each variant, coloring low- and high...
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