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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...limitations remain unsolved, limiting the potential of downstream analysis. First, variant detection remains challenging due to the sparsity and low coverage of scRNA-seq assays, especially in LR assays despite rapid progress in the field (Dondi et al. 2023; Joglekar et al. 2023; Marx 2023; Al'Khafaji et al...
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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
...mutations in different biological backgrounds and confirmed their predominant impact on 3′AS usage and IR.Computational prediction of protein function and stability of individual splicing isoformsFurther on, we used the LRTS information on full-length transcripts to predict the potential coding sequences...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
.... Louis, Missouri 63110, USA; 3Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA; 4McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA ↵5 Present address: Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...cell population, enabling a more rapid and robust immune response.Sequencing immune-gene transcripts of individuals within a population reveals allelic diversity and allows comparison between immune responses to pathogenic antagonists, cancer, and autoimmune diseases (Boyd et al. 2010; Rodriguez et al...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...). These results suggested that tumor cells with IPA of ERCC1 would have dysregulated DNA repair functions, which might contribute to HCC development.Finally, we validated these two candidates by performing a 3′ rapid amplification of cDNA ends (3′ RACE) experiment in the liver cancer cell line HepG2. As shown...
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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
...–631. doi:10.1101/gr.279352.124 ↵Peng H, Jabbari JS, Tian L, Wang C, You Y, Chua CC, Anstee NS, Amin N, Wei AH, Davidson NM, et al. 2025. Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes. Genome Res (this issue) 35: 942–955. doi:10...

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