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For: Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol 2019;20:213. [PMID: 31639029 PMCID: PMC6802306 DOI: 10.1186/s13059-019-1842-9] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/28/2019] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
1
Zhou K, Zhang M, Zhai D, Wang Z, Liu T, Xie Y, Shi Y, Shi H, Chen Q, Li X, Xu J, Cai Z, Zhang Y, Shao N, Lin Y. Genomic and transcriptomic profiling of inflammatory breast cancer reveals distinct molecular characteristics to non-inflammatory breast cancers. Breast Cancer Res Treat 2024:10.1007/s10549-024-07437-0. [PMID: 39030466 DOI: 10.1007/s10549-024-07437-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
2
Zhang H, Liu B, Cheng J, Li Z, Jia M, Li M, Zhao L, Wang L, Xi Y. Characterization and integrated analysis of extrachromosomal DNA amplification in hematological malignancies. Neoplasia 2024;56:101025. [PMID: 38996538 DOI: 10.1016/j.neo.2024.101025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
3
Mulet-Lazaro R, van Herk S, Nuetzel M, Sijs-Szabo A, Díaz N, Kelly K, Erpelinck-Verschueren C, Schwarzfischer-Pfeilschifter L, Stanewsky H, Ackermann U, Glatz D, Raithel J, Fischer A, Pohl S, Rijneveld A, Vaquerizas JM, Thiede C, Plass C, Wouters BJ, Delwel R, Rehli M, Gebhard C. Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia. Nat Commun 2024;15:5693. [PMID: 38972954 PMCID: PMC11228033 DOI: 10.1038/s41467-024-49811-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024]  Open
4
Kim SW, Kim N, Choi YJ, Lee ST, Choi JR, Shin S. Real-World Clinical Utility of Targeted RNA Sequencing in Leukemia Diagnosis and Management. Cancers (Basel) 2024;16:2467. [PMID: 39001529 PMCID: PMC11240350 DOI: 10.3390/cancers16132467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024]  Open
5
Xu H, Chen X, Sun Y, Hu X, Zhang X, Wang Y, Tang Q, Zhu Q, Song K, Chen H, Sheng X, Yao Y, Zhuang D, Chen L, Mao Y, Qin Z. Comprehensive molecular characterization of long-term glioblastoma survivors. Cancer Lett 2024;593:216938. [PMID: 38734160 DOI: 10.1016/j.canlet.2024.216938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
6
Mochizuki A, Shiraishi K, Honda T, Higashiyama RI, Sunami K, Matsuda M, Shimada Y, Miyazaki Y, Yoshida Y, Watanabe SI, Yatabe Y, Hamamoto R, Kohno T. Passive Smoking-Induced Mutagenesis as a Promoter of Lung Carcinogenesis. J Thorac Oncol 2024;19:984-994. [PMID: 38382595 DOI: 10.1016/j.jtho.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
7
Zheng D, Elnegiry AA, Luo C, Bendahou MA, Xie L, Bell D, Takahashi Y, Hanna E, Mias GI, Tsoi MF, Gu B. Brd4::Nutm1 fusion gene initiates NUT carcinoma in vivo. Life Sci Alliance 2024;7:e202402602. [PMID: 38724194 PMCID: PMC11082452 DOI: 10.26508/lsa.202402602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]  Open
8
Meijer DM, Ruano D, Briaire-de Bruijn IH, Wijers-Koster PM, van de Sande MAJ, Gelderblom H, Cleton-Jansen AM, de Miranda NFCC, Kuijjer ML, Bovée JVMG. The Variable Genomic Landscape During Osteosarcoma Progression: Insights From a Longitudinal WGS Analysis. Genes Chromosomes Cancer 2024;63:e23253. [PMID: 39023390 DOI: 10.1002/gcc.23253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]  Open
9
Masago K, Kuroda H, Sasaki E, Fujita Y, Fujita S, Horio Y, Endo M, Ishihara H, Hanai N, Matsushita H. Novel gene fusions in human oropharyngeal carcinoma. Cancer Genet 2024;286-287:29-34. [PMID: 38971117 DOI: 10.1016/j.cancergen.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/13/2024] [Accepted: 06/30/2024] [Indexed: 07/08/2024]
10
Tlemsani C, Heske CM, Elloumi F, Pongor L, Khandagale P, Varma S, Luna A, Meltzer PS, Khan J, Reinhold WC, Pommier Y. Sarcoma_CellminerCDB: A tool to interrogate the genomic and functional characteristics of a comprehensive collection of sarcoma cell lines. iScience 2024;27:109781. [PMID: 38868205 PMCID: PMC11167437 DOI: 10.1016/j.isci.2024.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 04/15/2024] [Indexed: 06/14/2024]  Open
11
Huang CY, Jiang N, Shen M, Lai GG, Tan AC, Jain A, Saw SP, Ang MK, Ng QS, Lim DW, Kanesvaran R, Tan EH, Tan WL, Ong BH, Chua KL, Anantham D, Takano AM, Lim KH, Tam WL, Sim NL, Skanderup AJ, Tan DS, Rozen SG. Oncogene-Driven Non-Small Cell Lung Cancers in Patients with a History of Smoking Lack Smoking-Induced Mutations. Cancer Res 2024;84:2009-2020. [PMID: 38587551 DOI: 10.1158/0008-5472.can-23-2551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/29/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
12
Suzuki K, Koyama D, Oka Y, Sato Y, Sekine R, Fukatsu M, Hayashi K, Takano M, Hashimoto Y, Ikezoe T. Myeloid sarcoma with plasmacytoid dendritic cell-like proliferation associated with IKZF1, ETV6 and DNMT3A mutations. Int J Hematol 2024:10.1007/s12185-024-03806-z. [PMID: 38861243 DOI: 10.1007/s12185-024-03806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
13
Hamdi Y, Boujemaa M, Ben Aissa-Haj J, Radouani F, Khyatti M, Mighri N, Hannachi M, Ghedira K, Souiai O, Hkimi C, Kammoun MS, Mejri N, Bouaziz H, Beloufa MA, Charoute H, Barakat A, Najjar I, Taniguchi H, Pietrosemoli N, Dellagi K, Abdelhak S, Boubaker MS, Chica C, Rouleau E. A regionally based precision medicine implementation initiative in North Africa:The PerMediNA consortium. Transl Oncol 2024;44:101940. [PMID: 38537326 DOI: 10.1016/j.tranon.2024.101940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/21/2024]  Open
14
Mariella E, Grasso G, Miotto M, Buzo K, Reilly NM, Andrei P, Vitiello PP, Crisafulli G, Arena S, Rospo G, Corti G, Lorenzato A, Cancelliere C, Barault L, Gionfriddo G, Linnebacher M, Russo M, Di Nicolantonio F, Bardelli A. Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer. Mol Oncol 2024;18:1460-1485. [PMID: 38468448 PMCID: PMC11161737 DOI: 10.1002/1878-0261.13622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024]  Open
15
Poscente M, Tolomeo D, Arshadi A, Agostini A, L'Abbate A, Solimando AG, Palumbo O, Carella M, Palumbo P, González T, Hernández-Rivas JM, Bassi L, Isidori R, Dell'Aquila M, Trapè G, Latagliata R, Pessina G, Natoni F, Storlazzi CT. Aggressive systemic mastocytosis with the co-occurrence of PRKG2::PDGFRB, KAT6A::NCOA2, and RXRA::NOTCH1 fusion transcripts and a heterozygous RUNX1 frameshift mutation. Cancer Genet 2024;284-285:5-11. [PMID: 38471404 DOI: 10.1016/j.cancergen.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/05/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
16
Lang F, Sorn P, Suchan M, Henrich A, Albrecht C, Köhl N, Beicht A, Riesgo-Ferreiro P, Holtsträter C, Schrörs B, Weber D, Löwer M, Sahin U, Ibn-Salem J. Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates. BIOINFORMATICS ADVANCES 2024;4:vbae080. [PMID: 38863673 PMCID: PMC11165244 DOI: 10.1093/bioadv/vbae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/26/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]
17
Hofvander J, Qiu A, Lee K, Bilenky M, Carles A, Cao Q, Moksa M, Steif J, Su E, Sotiriou A, Goytain A, Hill LA, Singer S, Andrulis IL, Wunder JS, Mertens F, Banito A, Jones KB, Underhill TM, Nielsen TO, Hirst M. Synovial Sarcoma Chromatin Dynamics Reveal a Continuum in SS18:SSX Reprograming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594262. [PMID: 38798672 PMCID: PMC11118320 DOI: 10.1101/2024.05.14.594262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
18
Park SJ, Ju S, Goh SH, Yoon BH, Park JL, Kim JH, Lee S, Lee SJ, Kwon Y, Lee W, Park KC, Lee GK, Park SY, Kim S, Kim SY, Han JY, Lee C. Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations. Cancer Res 2024;84:1491-1503. [PMID: 38607364 DOI: 10.1158/0008-5472.can-23-1551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/24/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024]
19
Priesterbach-Ackley LP, van Kuik J, Tops BBJ, Lasorella A, Iavarone A, van Hecke W, Robe PA, Wesseling P, de Leng WWJ. RT-PCR assay to detect FGFR3::TACC3 fusions in formalin-fixed, paraffin-embedded glioblastoma samples. Neurooncol Pract 2024;11:142-149. [PMID: 38496910 PMCID: PMC10940835 DOI: 10.1093/nop/npad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]  Open
20
Lee Y, Chowdhury T, Kim S, Yu HJ, Kim KM, Kang H, Kim MS, Kim JW, Kim YH, Ji SY, Hwang K, Han JH, Hwang J, Yoo SK, Lee KS, Choe G, Won JK, Park SH, Lee YK, Shin JH, Park CK, Kim CY, Kim JI. Central neurocytoma exhibits radial glial cell signatures with FGFR3 hypomethylation and overexpression. Exp Mol Med 2024;56:975-986. [PMID: 38609519 PMCID: PMC11059271 DOI: 10.1038/s12276-024-01204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 04/14/2024]  Open
21
Jiang YZ, Ma D, Jin X, Xiao Y, Yu Y, Shi J, Zhou YF, Fu T, Lin CJ, Dai LJ, Liu CL, Zhao S, Su GH, Hou W, Liu Y, Chen Q, Yang J, Zhang N, Zhang WJ, Liu W, Ge W, Yang WT, You C, Gu Y, Kaklamani V, Bertucci F, Verschraegen C, Daemen A, Shah NM, Wang T, Guo T, Shi L, Perou CM, Zheng Y, Huang W, Shao ZM. Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities. NATURE CANCER 2024;5:673-690. [PMID: 38347143 DOI: 10.1038/s43018-024-00725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/04/2024] [Indexed: 04/30/2024]
22
Acanda De La Rocha AM, Berlow NE, Fader M, Coats ER, Saghira C, Espinal PS, Galano J, Khatib Z, Abdella H, Maher OM, Vorontsova Y, Andrade-Feraud CM, Daccache A, Jacome A, Reis V, Holcomb B, Ghurani Y, Rimblas L, Guilarte TR, Hu N, Salyakina D, Azzam DJ. Feasibility of functional precision medicine for guiding treatment of relapsed or refractory pediatric cancers. Nat Med 2024;30:990-1000. [PMID: 38605166 PMCID: PMC11031400 DOI: 10.1038/s41591-024-02848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/31/2024] [Indexed: 04/13/2024]
23
Liu XD, Zhang Y, He HY. Targeted next-generation sequencing of 491 lung cancers in clinical practice: Implications for future detection strategy and targeted therapy. Heliyon 2024;10:e27591. [PMID: 38496837 PMCID: PMC10944278 DOI: 10.1016/j.heliyon.2024.e27591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024]  Open
24
Yuan X, Wang H, Sun Z, Zhou C, Chu SC, Bu J, Shen N. Anchored-fusion enables targeted fusion search in bulk and single-cell RNA sequencing data. CELL REPORTS METHODS 2024;4:100733. [PMID: 38503288 PMCID: PMC10985232 DOI: 10.1016/j.crmeth.2024.100733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/15/2024] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
25
Zakimi N, Nguyen MP, Raleigh DR. Gene transcript fusions are associated with clinical outcomes and molecular groups of meningiomas. Acta Neuropathol 2024;147:57. [PMID: 38509407 PMCID: PMC10954959 DOI: 10.1007/s00401-024-02708-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
26
Fiflis DN, Rey NA, Venugopal-Lavanya H, Sewell B, Mitchell-Dick A, Clements KN, Milo S, Benkert AR, Rosales A, Fergione S, Asokan A. Repurposing CRISPR-Cas13 systems for robust mRNA trans-splicing. Nat Commun 2024;15:2325. [PMID: 38485709 PMCID: PMC10940283 DOI: 10.1038/s41467-024-46172-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024]  Open
27
Budurlean L, Tukaramrao DB, Zhang L, Dovat S, Broach J. Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection. J Pers Med 2024;14:291. [PMID: 38541033 PMCID: PMC10971281 DOI: 10.3390/jpm14030291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024]  Open
28
Chen L, Zhang C, Xue R, Liu M, Bai J, Bao J, Wang Y, Jiang N, Li Z, Wang W, Wang R, Zheng B, Yang A, Hu J, Liu K, Shen S, Zhang Y, Bai M, Wang Y, Zhu Y, Yang S, Gao Q, Gu J, Gao D, Wang XW, Nakagawa H, Zhang N, Wu L, Rozen SG, Bai F, Wang H. Deep whole-genome analysis of 494 hepatocellular carcinomas. Nature 2024;627:586-593. [PMID: 38355797 DOI: 10.1038/s41586-024-07054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
29
Martin SB, Polubothu S, Bruzos AL, Kelly G, Horswell S, Sauvadet A, Bryant D, Zecchin D, Riachi M, Michailidis F, Sadri A, Muwanga-Nanyonjo N, Lopez-Balboa P, Knöpfel N, Bulstrode N, Pittman A, Yeh I, Kinsler VA. Mosaic BRAF Fusions Are a Recurrent Cause of Congenital Melanocytic Nevi Targetable by MAPK Pathway Inhibition. J Invest Dermatol 2024;144:593-600.e7. [PMID: 37716647 DOI: 10.1016/j.jid.2023.06.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 09/18/2023]
30
Xu SM, Cheng Y, Fisher H, Janitz M. Recent advances in the investigation of fusion RNAs and their role in molecular pathology of cancer. Int J Biochem Cell Biol 2024;168:106529. [PMID: 38246262 DOI: 10.1016/j.biocel.2024.106529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
31
Yeung MC, Dermawan JK, Liu AP, Lam AY, Antonescu CR, Shek TW. Spindle cell neoplasms with novel LTK fusion - Expanding the spectrum of kinase fusion-positive soft tissue tumors. Genes Chromosomes Cancer 2024;63:e23227. [PMID: 38517106 PMCID: PMC10963038 DOI: 10.1002/gcc.23227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/24/2024] [Indexed: 03/23/2024]  Open
32
Qin Q, Popic V, Yu H, White E, Khorgade A, Shin A, Wienand K, Dondi A, Beerenwinkel N, Vazquez F, Al’Khafaji AM, Haas BJ. CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581862. [PMID: 38464114 PMCID: PMC10925146 DOI: 10.1101/2024.02.24.581862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
33
Zhang W, Schmitz AA, Kallionpää RE, Perälä M, Pitkänen N, Tukiainen M, Alanne E, Jöhrens K, Schulze-Rath R, Farahmand B, Zong J. Neurotrophic-tyrosine receptor kinase gene fusion in papillary thyroid cancer: A clinicogenomic biobank and record linkage study from Finland. Oncotarget 2024;15:106-116. [PMID: 38329731 PMCID: PMC10852057 DOI: 10.18632/oncotarget.28555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/28/2023] [Indexed: 02/09/2024]  Open
34
Saba KH, Difilippo V, Kovac M, Cornmark L, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Bidgoli M, Jonson T, Sumathi VP, Brosjö O, Staaf J, Foijer F, Styring E, Nathrath M, Baumhoer D, Nord KH. Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway. J Pathol 2024;262:147-160. [PMID: 38010733 DOI: 10.1002/path.6219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 11/29/2023]
35
Bagger FO, Borgwardt L, Jespersen AS, Hansen AR, Bertelsen B, Kodama M, Nielsen FC. Whole genome sequencing in clinical practice. BMC Med Genomics 2024;17:39. [PMID: 38287327 PMCID: PMC10823711 DOI: 10.1186/s12920-024-01795-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/01/2024] [Indexed: 01/31/2024]  Open
36
Güllülü Ö, Mayer BE, Toplek FB. Linking Gene Fusions to Bone Marrow Failure and Malignant Transformation in Dyskeratosis Congenita. Int J Mol Sci 2024;25:1606. [PMID: 38338888 PMCID: PMC10855549 DOI: 10.3390/ijms25031606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]  Open
37
Balle CM, Kassentoft CG, van Heusden JI, Knudsen M, Raaby L, Gravholt CH. Rare Case of a Turner Syndrome Patient with Metastatic Dysgerminoma and No Y-Chromosomal Material with Pathogenic Variants Found in KIT and MTOR. Sex Dev 2024;17:203-210. [PMID: 38281483 DOI: 10.1159/000536236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]  Open
38
Kumar H, Luo R, Wen J, Yang C, Zhou X, Kim P. FusionNeoAntigen: a resource of fusion gene-specific neoantigens. Nucleic Acids Res 2024;52:D1276-D1288. [PMID: 37870454 PMCID: PMC10767944 DOI: 10.1093/nar/gkad922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]  Open
39
Itoh T, Omori Y, Seino M, Hirose K, Date F, Ono Y, Mizukami Y, Aoki S, Ishida M, Mizuma M, Morikawa T, Higuchi R, Honda G, Okamura Y, Kinoshita K, Unno M, Furukawa T. Gene Rearrangement and Expression of PRKACA and PRKACB Govern Morphobiology of Pancreatobiliary Oncocytic Neoplasms. Mod Pathol 2024;37:100358. [PMID: 37871652 DOI: 10.1016/j.modpat.2023.100358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/29/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023]
40
Koduru P, Chen W, Fuda F, Kaur G, Awan F, John S, Garcia R, Gagan J. RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024;17:2632010X241230262. [PMID: 38371338 PMCID: PMC10874141 DOI: 10.1177/2632010x241230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
41
Khan S, Baligar P, Tandon C, Nayyar J, Tandon S. Molecular heterogeneity in prostate cancer and the role of targeted therapy. Life Sci 2024;336:122270. [PMID: 37979833 DOI: 10.1016/j.lfs.2023.122270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
42
Difilippo V, Saba KH, Styring E, Magnusson L, Nilsson J, Nathrath M, Baumhoer D, Nord KH. Osteosarcomas With Few Chromosomal Alterations or Adult Onset Are Genetically Heterogeneous. J Transl Med 2024;104:100283. [PMID: 37931683 DOI: 10.1016/j.labinv.2023.100283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]  Open
43
Hafstað V, Häkkinen J, Larsson M, Staaf J, Vallon-Christersson J, Persson H. Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification. BMC Genomics 2023;24:783. [PMID: 38110872 PMCID: PMC10726539 DOI: 10.1186/s12864-023-09889-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/10/2023] [Indexed: 12/20/2023]  Open
44
Zhou BW, Wu QQ, Mauki DH, Wang X, Zhang SR, Yin TT, Chen FL, Li C, Liu YH, Wang GD, Zhang YP. Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility. iScience 2023;26:108431. [PMID: 38205119 PMCID: PMC10777377 DOI: 10.1016/j.isci.2023.108431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/24/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024]  Open
45
Zong L, Zhu Y, Jiang Y, Xia Y, Liu Q, Jiang S. A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples. BMC Genomics 2023;24:777. [PMID: 38102591 PMCID: PMC10722801 DOI: 10.1186/s12864-023-09886-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]  Open
46
Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023;14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]  Open
47
Pan J, Wei S, Qiu Q, Tong X, Shen Z, Zhu M, Hu X, Gong C. A novel chimeric RNA originating from BmCPV S4 and Bombyx mori HDAC11 transcripts regulates virus proliferation. PLoS Pathog 2023;19:e1011184. [PMID: 38048361 PMCID: PMC10721177 DOI: 10.1371/journal.ppat.1011184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 12/14/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023]  Open
48
Maslov AY, Vijg J. Somatic mutation burden in relation to aging and functional life span: implications for cellular reprogramming and rejuvenation. Curr Opin Genet Dev 2023;83:102132. [PMID: 37931583 PMCID: PMC10841402 DOI: 10.1016/j.gde.2023.102132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/02/2023] [Accepted: 10/07/2023] [Indexed: 11/08/2023]
49
Zhao J, Li S, Xu Y, Ahmad N, Kuang B, Feng M, Wei N, Yang X. The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis. J Adv Res 2023;54:1-13. [PMID: 36781019 DOI: 10.1016/j.jare.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/13/2023]  Open
50
He F, Bandyopadhyay AM, Klesse LJ, Rogojina A, Chun SH, Butler E, Hartshorne T, Holland T, Garcia D, Weldon K, Prado LNP, Langevin AM, Grimes AC, Sugalski A, Shah S, Assanasen C, Lai Z, Zou Y, Kurmashev D, Xu L, Xie Y, Chen Y, Wang X, Tomlinson GE, Skapek SX, Houghton PJ, Kurmasheva RT, Zheng S. Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer. Nat Commun 2023;14:7600. [PMID: 37990009 PMCID: PMC10663468 DOI: 10.1038/s41467-023-43373-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023]  Open
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