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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
...or disabling tumor suppressors and contributing to cancer. While most cancer-relevant fusion genes are found at low levels of recurrence in surveys of diverse tumor types, certain fusions represent hallmark drivers of cancer found at high levels of recurrence, such as BCR::ABL1 in chronic myelogenous leukemia...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...measured by PCR-based approaches. These relationships strongly suggest that the chimeric mtRNAs are transcriptional products of the mtDNA deletion events.Many aspects of the chimeric mtRNAs strengthen what is known about mtDNA deletion mutations from DNA-based assays such as Southern blot (Corral...
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Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...DRS and PCS to study clear cell renal cell carcinoma (ccRCC), focusing on new transcript and gene discovery. Twelve primary ccRCC archival tumors, six from patients who went on to relapse, were analyzed. Results were validated in an independent cohort of 20 patients by qRT-PCR and compared to DRS...
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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
.... 2014). Epitypes 5 and 6 were enriched in a variety of chromosomal rearrangements generating fusions involving KMT2A (previously known as MLL) on 11q23. Multiple KMT2A fusion partners have been described in acute leukemias (Winters and Bernt 2017), and we observed common AML fusion partners in both...
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Research: Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia
- Susanna Teppo,
- Saara Laukkanen,
- Thomas Liuksiala,
- Jessica Nordlund,
- Mikko Oittinen,
- Kaisa Teittinen,
- Toni Grönroos,
- Pascal St-Onge,
- Daniel Sinnett,
- Ann-Christine Syvänen,
- Matti Nykter,
- Keijo Viiri,
- Merja Heinäniemi,
- and Olli Lohi
Genome Res. November 2016 26: 1468-1477; Published in Advance September 12, 2016, doi:10.1101/gr.193649.115
...-regulation, respectively. E/R-mediated changes were predominantly repressive (for genes, see Supplemental Table S5). ETV6-RUNX1 down-regulates eRNA and target gene loci Genome Research 1469 www..org as measured by RT-qPCR showed considerable concordance with primary transcription in GRO-seq (Supplemental Table S1...
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Research: Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia
- Tyrone Ryba,
- Dana Battaglia,
- Bill H. Chang,
- James W. Shirley,
- Quinton Buckley,
- Benjamin D. Pope,
- Meenakshi Devidas,
- Brian J. Druker,
- and David M. Gilbert
Genome Res. October 2012 22: 1833-1844; Published in Advance May 24, 2012, doi:10.1101/gr.138511.112
...with similar replication timing are not expected to produce abrupt shifts. This is consistent with results in patient 10-668, in which a Philadelphia chromosome translocation t(9;22)(q34;q11) fuses two regions that are normally late replicating, and remain late after translocation (data not shown). Figure 2...
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Method: High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics
- Maurizio Pellegrino,
- Adam Sciambi,
- Sebastian Treusch,
- Robert Durruthy-Durruthy,
- Kaustubh Gokhale,
- Jose Jacob,
- Tina X. Chen,
- Jennifer A. Geis,
- William Oldham,
- Jairo Matthews,
- Hagop Kantarjian,
- P. Andrew Futreal,
- Keyur Patel,
- Keith W. Jones,
- Koichi Takahashi,
- and Dennis J. Eastburn
Genome Res. September 2018 28: 1345-1352; Published in Advance August 7, 2018, doi:10.1101/gr.232272.117
...M Tris at pH 8.0, 0.5% IGEPAL, proteinase K 1.0 mg/mL) to prevent premature lysing of cells (Eastburn et al. 2013). The resultant emulsions were then incubated for 16–20 h at 37°C prior to heat inactivation of the protease.Droplet PCR reactions consisted of 1× platinum multiplex PCR master mix (Thermo...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...@iisermohali.ac.inAbstractIsoform diversity is known to enhance a gene's functional repertoire by producing protein variants with distinct functional implications. Despite numerous studies on transcriptome diversifying processes (alternative splicing/transcription), understanding their extent and correlated impact on proteome diversity...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...Fusion, fission, and scrambling of the bilaterian in Bryozoa Thomas D. Lewin1, Isabel Jiah-Yih Liao1, Mu-En Chen1, John D.D. Bishop2, Peter W.H. Holland3 and Yi-Jyun Luo1 1Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; 2Marine Biological Association, Plymouth PL1 2PB, United...
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Research: Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP
- Maoxiang Qian,
- Hui Zhang,
- Shirley Kow-Yin Kham,
- Shuguang Liu,
- Chuang Jiang,
- Xujie Zhao,
- Yi Lu,
- Charnise Goodings,
- Ting-Nien Lin,
- Ranran Zhang,
- Takaya Moriyama,
- Zhaohong Yin,
- Zhenhua Li,
- Thuan Chong Quah,
- Hany Ariffin,
- Ah Moy Tan,
- Shuhong Shen,
- Deepa Bhojwani,
- Shaoyan Hu,
- Suning Chen,
- Huyong Zheng,
- Ching-Hon Pui,
- Allen Eng-Juh Yeoh,
- and Jun J. Yang
Genome Res. February 2017 27: 185-195; Published in Advance November 30, 2016, doi:10.1101/gr.209163.116
...with BCR-ABL1, ETV6-RUNX1, TCF3-PBX1, TCF3-HLF, or MLL [also called KMT2A] rearrangements), we observed comparable frequencies of EP300-ZNF384 (2.0%, n = 12) and CREBBPZNF384 fusions (1.8%, n = 11) as detected by RT-PCR and Sanger sequencing. Our subsequent functional studies primarily focused on EP300-ZNF...

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