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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...) to identify putative CREs that have evolved from TE-derived sequences. We then combine these TE-CRE annotations with analyses of the temporal dynamics of TE activity, analyses of gene coexpression, and massive parallel reporter assays. Our results support a link between WGD and TE-CRE evolution and support...
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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
...and mutations using data sets from tumor sequencing projects, such as The Cancer Genome Atlas (TCGA) (Hutter and Zenklusen 2018; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020). These tools employ a variety of approaches, including analysis of mutations using gene sequences, protein...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...and onco-exaptation events in the PAAD organoid cohortTo examine the products of TE activation, we utilized TEprof2 (Shah et al. 2023) to analyze TE-derived transcripts, specifically fusion transcripts between TE sequences and known genes, which we referred to as TE-chimeric transcripts. These transcripts...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...and consistent across all replicates. LongGF, while having high accuracy for the detection of fusions with simulated data, was found least effective here with each replicate missing 4/16 control fusions, and reporting either CCDC6::RET or NCOA4::RET fusions but not both together in any single replicate. TMPRSS2...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...), and the development of microarrays first (Schena et al. 1995) and high-throughput sequencing later (Margulies et al. 2005) boosted our capacity to analyze transcriptomes. Nowadays, the most common technique to analyze gene expression is RNA sequencing (RNA-seq). This technique consists of first isolating RNA from...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...Evidence for selfing in a vertebrate from whole- sequencing Astrid Böhne1, Zeynep Oğuzhan1, Ioannis Chrysostomakis1, Simon Vitt2, Denis Meuthen2,3, Sebastian Martin1, Sandra Kukowka1 and Timo Thünken2 1Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...LRTS analysis revealed a wide variety of transcripts, with more than two-thirds unannotated, or even more than 3000 transcripts from novel genes. This highlighted the importance of long-read sequencing for comprehensive transcriptome profiling, particularly for detecting novel splice variants and ASEs...
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Method: INTEGRATE: gene fusion discovery using whole genome and transcriptome data
- Jin Zhang,
- Nicole M. White,
- Heather K. Schmidt,
- Robert S. Fulton,
- Chad Tomlinson,
- Wesley C. Warren,
- Richard K. Wilson,
- and Christopher A. Maher
Genome Res. January 2016 26: 108-118; Published in Advance November 10, 2015, doi:10.1101/gr.186114.114
...-specific (ETS) transcription factor family members in prostate cancer (Tomlins et al. 2007), MAST and NOTCH kinases in breast cancer (Robinson et al. 2011), and ALK, ROS1, and RET fusions in lung cancer (Takeuchi et al. 2012). To date, many groups have used whole- sequencing (WGS) to identify structural...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...offers guidance to design cost-effective experimental strategies that do not compromise on discovering novel biology.Over the last five years, long-read sequencing (LRS) technologies have transformed the landscape of genetic variant discovery in two fundamental ways. First, they have increased...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...-read sequencing is rapidly emerging as a transformative technology for cancer research by providing a comprehensive view across the , transcriptome, and epi, including the ability to detect alterations that previous technologies have overlooked. In this Perspective, we explore the current applications of long...
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