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Research: Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations
- Maitri Y. Shah,
- Manuela Ferracin,
- Valentina Pileczki,
- Baoqing Chen,
- Roxana Redis,
- Linda Fabris,
- Xinna Zhang,
- Cristina Ivan,
- Masayoshi Shimizu,
- Cristian Rodriguez-Aguayo,
- Mihnea Dragomir,
- Katrien Van Roosbroeck,
- Maria Ines Almeida,
- Maria Ciccone,
- Daniela Nedelcu,
- Maria Angelica Cortez,
- Taghi Manshouri,
- Steliana Calin,
- Muharrem Muftuoglu,
- Pinaki P. Banerjee,
- Mustafa H. Badiwi,
- Jan Parker-Thornburg,
- Asha Multani,
- James William Welsh,
- Marcos Roberto Estecio,
- Hui Ling,
- Ciprian Tomuleasa,
- Delia Dima,
- Hui Yang,
- Hector Alvarez,
- M. James You,
- Milan Radovich,
- Elizabeth Shpall,
- Muller Fabbri,
- Katy Rezvani,
- Leonard Girnita,
- Ioana Berindan-Neagoe,
- Anirban Maitra,
- Srdan Verstovsek,
- Riccardo Fodde,
- Carlos Bueso-Ramos,
- Mihai Gagea,
- Guillermo Garcia Manero,
- and George A. Calin
Genome Res. April 2018 28: 432-447; Published in Advance March 22, 2018, doi:10.1101/gr.225128.117
...of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA; 9Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA; 10Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA; 11Department of Stem Cell...
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Research: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
- Kasper D. Rasmussen,
- Ivan Berest,
- Sandra Keβler,
- Koutarou Nishimura,
- Lucía Simón-Carrasco,
- George S. Vassiliou,
- Marianne T. Pedersen,
- Jesper Christensen,
- Judith B. Zaugg,
- and Kristian Helin
Genome Res. April 2019 29: 564-575; Published in Advance February 22, 2019, doi:10.1101/gr.239277.118
...to chromatin remain poorly understood (for review, see Rasmussen and Helin 2016).Loss-of-function mutations of TET2 have been found in patients with a wide range of hematological diseases, including acute myeloid leukemia (AML) (Scourzic et al. 2015). More recently, high frequencies of TET2 mutations have also...
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Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
...(SVs), defined as insertions, deletions, and rearrangements larger than 50 base pairs (bp), represent an important subset of somatic driver events in tumors (Aganezov et al. 2020; Espejo Valle-Inclan et al. 2022). Examples include the amplification of oncogenes (e.g., ERBB2) (Nattestad et al. 2018...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
..., stomach, and metastatic prostate cancer (Pritchard et al. 2016; Li et al. 2022; Momozawa et al. 2022). It has therefore become best practice in oncology to test for inherited damaging variants in these genes and to profile tumors for somatic mutations in the same genes (Gradishar et al. 2024).Nonetheless...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...for melanoma drug resistance (Emert et al. 2021), cancer cell origin and stem cell hierarchies in rhabdomyosarcoma (Wei et al. 2022), clonal dynamics and drug resistance in chronic leukemia lymphoma (CLL) (Gutierrez et al. 2021), clonal behavior in patient-derived xenografts of metastatic triple...
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Research: Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
- Aneta Mikulasova,
- Daniel Kent,
- Marco Trevisan-Herraz,
- Nefeli Karataraki,
- Kent T.M. Fung,
- Cody Ashby,
- Agata Cieslak,
- Shmuel Yaccoby,
- Frits van Rhee,
- Maurizio Zangari,
- Sharmilan Thanendrarajan,
- Carolina Schinke,
- Gareth J. Morgan,
- Vahid Asnafi,
- Salvatore Spicuglia,
- Chris A. Brackley,
- Anne E. Corcoran,
- Sophie Hambleton,
- Brian A. Walker,
- Daniel Rico,
- and Lisa J. Russell
Genome Res. July 2022 32: 1343-1354; Published in Advance December 21, 2021, doi:10.1101/gr.276042.121
...cells, (GC) germinal center, (CLL) chronic lymphocytic leukemia, (MCL) mantle cell lymphoma, (DLBCL) diffuse large B cell lymphoma, (BL) Burkitt lymphoma, and (MM) multiple myeloma.Epigenomic cartography of the human CCND1 geneThe proto-oncogene CCND1 is one of the most common IGH translocation partner...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...to these preexisting genomic elements, a modern human retrovirus, human T cell leukemia 19 virus type 1 (HTLV-1), encodes an ectopic CTCF binding site (Satou et al. 2016). This ectopic insertion results 20 in characteristic CTCF epigenetic insulator activity and induces novel genomic loops which alter the expression...
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Resource: Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
- Michael N. Edmonson,
- Aman N. Patel,
- Dale J. Hedges,
- Zhaoming Wang,
- Evadnie Rampersaud,
- Chimene A. Kesserwan,
- Xin Zhou,
- Yanling Liu,
- Scott Newman,
- Michael C. Rusch,
- Clay L. McLeod,
- Mark R. Wilkinson,
- Stephen V. Rice,
- Thierry Soussi,
- J. Paul Taylor,
- Michael Benatar,
- Jared B. Becksfort,
- Kim E. Nichols,
- Leslie L. Robison,
- James R. Downing,
- and Jinghui Zhang
Genome Res. September 2019 29: 1555-1565; Published in Advance August 22, 2019, doi:10.1101/gr.250357.119
...susceptibility to B-ALL, which corresponds to somatic mutations detected in pediatric B-ALL and lymphoma (Shah et al. 2013). A similar profile was observed in the example WES data from an ALL patient presented in Figure 1B: MedalCeremony assigned a single gold medal—a novel ETV6 nonsense variant within the ETS...
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Research: In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors
- Arnoud Boot,
- Mi Ni Huang,
- Alvin W.T. Ng,
- Szu-Chi Ho,
- Jing Quan Lim,
- Yoshiiku Kawakami,
- Kazuaki Chayama,
- Bin Tean Teh,
- Hidewaki Nakagawa,
- and Steven G. Rozen
Genome Res. May 2018 28: 654-665; Published in Advance April 9, 2018, doi:10.1101/gr.230219.117
...insertion and deletion mutations (indels), copy number alterations, and structural variants in the cisplatin-exposed MCF-10A and HepG2 clones. We identified 4208 indels in the cisplatin-exposed clones. The indels were unremarkable, consisting primarily of single-nucleotide insertions or deletions (∼78...
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Method: A virome-wide clonal integration analysis platform for discovering cancer viral etiology
- Xun Chen,
- Jason Kost,
- Arvis Sulovari,
- Nathalie Wong,
- Winnie S. Liang,
- Jian Cao,
- and Dawei Li
Genome Res. May 2019 29: 819-830; Published in Advance March 14, 2019, doi:10.1101/gr.242529.118
.... Oncoviral profiles can be obtained from cancer sequencing data; however, widespread viral sequence contamination and noncausal viruses complicate the process of identifying genuine oncoviruses. Here, we propose a novel strategy to address these challenges by performing virome-wide screening of early...

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