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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: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...-associated bubble upstream of the KIT gene. (A) Bandage plots showing the paths traversed for the three observed alleles (two for white-headed breeds and one for color-headed) through the pan. Unless stated otherwise, n = 1 for the breed. The gray arrow paths indicate the segmental duplication regions, whereas...
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
..., and VEGFA, as well as potentially novel oncogenes such as GRHL2, IRF2BP2, and CREB3L1. In particular, we identify a duplication hotspot on Chromosome 10p15 harboring a cluster of enhancers, which skips over two genes, through a long-range chromatin interaction, to activate an oncogenic isoform of the NET1...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian s Anguo Liu1,2,7, Nini Wang1,3,7, Guoxiang Xie1,2,7, Yang Li1,2, Xixi Yan1,2, Xinmei Li1,2, Zhenliang Zhu2,4,5, Zhuohui Li1,2, Jing Yang2,4,5, Fanxin Meng1, Mingle Dou1,2, Weihuang Chen1, Nange...
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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
...a more accurate integrated view of the complex relationships between RT and gene regulation. [Supplemental material is available for this article.] Human cells duplicate their by the firing of thousands of origins that are activated in clusters following a precise temporal order (Rivera-Mulia and Gilbert...
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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
...correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human s sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...enriched in neurodegenerative disease pathways, including PD, ALS, and Huntington’s disease (Supplemental Fig. S5G), whereas downregulated DEGs were enriched in cell adhesion molecules pathways (Supplemental Fig. S5H). To explore the dynamics of gene expression changes with age, we performed clustering...
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
...@gs.washington.eduAbstractDespite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...introduce new elements, such as exogenous proteins, activating mutations, plasmids, artificial chromosomes, or knock-in modifications. Conversely, loss-of-function approaches remove specific factors using mutations, siRNA silencing, or gene-editing techniques. These modifications can be applied to either...
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Method: Detection and analysis of ancient segmental duplications in mammalian genomes
- Lianrong Pu,
- Yu Lin,
- and Pavel A. Pevzner
Genome Res. June 2018 28: 901-909; Published in Advance May 7, 2018, doi:10.1101/gr.228718.117
..., San Diego, California 92093, USA; 3Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia Corresponding author: ppevzner@cs.ucsd.eduAbstractAlthough segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes...

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