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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...). Although short-read sequencing produced nearly eight times more aligned reads, long-read sequencing identified 2.3 times as many SNPs, demonstrating that the greater number of informative positions in long-read data enhances allelic assignment accuracy and gene-specific ASE reproducibility (rho = 0...
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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
...predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can systematically miss or misrepresent certain types of alterations, especially structural variants, complex rearrangements, and alterations within repetitive regions. Long-read...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...out using tools like Modkit and Jasmine for PacBio or the basecaller Dorado for ONT (see Table 1). Fiber-seq (Stergachis et al. 2020), which requires prior handling of methyltransferases to alter the sample, allows the detection of open chromatin to provide additional insights. Long-read sequencing...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...of HCC. Long-read RNA sequencing reveals that some HBV-induced SVs impact cancer-associated genes, with TRAs being capable of inducing the formation of fusion genes. These findings enhance our understanding of somatic SVs in HCC and their role in early tumorigenesis.As the most prevalent form of primary...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...alternative transcript starts (TSSs) and ends (PASs), leading to different isoforms expressed from the same gene with variable cellular consequences. (B) Representative example of long-read RNA sequencing reads for CDC42 in K562 cells. To aid visualization, 280 randomly sampled reads from each sequencing...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...-cell methodsThe first long-read sequencing platform to be commercialized was the single-molecule real-time (SMRT) sequencing method from Pacific Biosciences (PacBio), where a zero-mode waveguide confines the fluorescent signal generated as DNA polymerase synthesizes a new strand while using the original strand...
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Method: CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
- Kaiyuan Zhu,
- Matthew G. Jones,
- Jens Luebeck,
- Xinxin Bu,
- Hyerim Yi,
- King L. Hung,
- Ivy Tsz-Lo Wong,
- Shu Zhang,
- Paul S. Mischel,
- Howard Y. Chang,
- and Vineet Bafna
Genome Res. September 2024 34: 1344-1354; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
...); instead, it reports a smaller cycle of a size of ∼90 kbp containing the breakpoint by itself. Furthermore, subwalk constraints owing to long reads linked truncated PVT1 and MYC on a single molecule. Correspondingly, CoRAL reconstructions of cycles in COLO320-DM (mono), COLO320-DM (Hung et al. 2021...
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Method: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil
- Mădălina Giurgiu,
- Nadine Wittstruck,
- Elias Rodriguez-Fos,
- Rocío Chamorro González,
- Lotte Brückner,
- Annabell Krienelke-Szymansky,
- Konstantin Helmsauer,
- Anne Hartebrodt,
- Philipp Euskirchen,
- Richard P. Koche,
- Kerstin Haase,
- Knut Reinert,
- and Anton G. Henssen
Genome Res. September 2024 34: 1355-1364; Published in Advance August 7, 2024, doi:10.1101/gr.279123.124
...with LASSO regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de novo assembly and alignment-based methods in simulated long-read sequencing data for both simple and complex ec...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...revealed by single-molecule sequencingThe high conservation of the gene structures led us to analyze the evolution of transcript expression in primates. We focused on the set of orthologous transcript models in the five s, and quantified transcript expression levels using high-depth RNA-seq data from 15...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...understanding of the evolutionary history and structural variation within these important chromosomes across large pan data sets such as the HPRC (Liao et al. 2023).To simplify sequencing requirements, Verkko2 now supports multiple long-read data types, in addition to HiFi, for initial construction of the LA...
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