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For: Muller E, Goardon N, Brault B, Rousselin A, Paimparay G, Legros A, Fouillet R, Bruet O, Tranchant A, Domin F, San C, Quesnelle C, Frebourg T, Ricou A, Krieger S, Vaur D, Castera L. OutLyzer: software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Oncotarget 2018;7:79485-79493. [PMID: 27825131 PMCID: PMC5346729 DOI: 10.18632/oncotarget.13103] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023]  Open
Number Cited by Other Article(s)
1
Chen H, Yu F, Lu D, Huang S, Liu S, Zhang B, Shu K, Pu D. Enhanced Error Suppression for Accurate Detection of Low-Frequency Variants. Electrophoresis 2025;46:65-75. [PMID: 39679747 DOI: 10.1002/elps.202400202] [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: 09/11/2024] [Revised: 10/21/2024] [Accepted: 11/15/2024] [Indexed: 12/17/2024]
2
Gilbert A, Tudor M, Delaunay A, Leman R, Levilly J, Atkinson A, Castéra L, Dinischiotu A, Savu DI, Valable S, Chevalier F. Radiosensitizing Effect of PARP Inhibition on Chondrosarcoma and Chondrocyte Cells Is Dependent on Radiation LET. Biomolecules 2024;14:1071. [PMID: 39334838 PMCID: PMC11429578 DOI: 10.3390/biom14091071] [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: 07/12/2024] [Revised: 08/14/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024]  Open
3
Xiang X, Lu B, Song D, Li J, Shu K, Pu D. Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data. Sci Rep 2023;13:20444. [PMID: 37993475 PMCID: PMC10665316 DOI: 10.1038/s41598-023-47135-3] [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: 08/11/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]  Open
4
Leman R, Muller E, Legros A, Goardon N, Chentli I, Atkinson A, Tranchant A, Castera L, Krieger S, Ricou A, Boulouard F, Joly F, Boucly R, Dumont A, Basset N, Coulet F, Chevalier LM, Rouleau E, Leitner K, González-Martin A, Gargiulo P, Lück HJ, Genestie C, Ray-Coquard I, Pujade-Lauraine E, Vaur D. Validation of the Clinical Use of GIScar, an Academic-developed Genomic Instability Score Predicting Sensitivity to Maintenance Olaparib for Ovarian Cancer. Clin Cancer Res 2023;29:4419-4429. [PMID: 37756555 PMCID: PMC10618649 DOI: 10.1158/1078-0432.ccr-23-0898] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/12/2023] [Accepted: 08/15/2023] [Indexed: 09/29/2023]
5
Steiert TA, Parra G, Gut M, Arnold N, Trotta JR, Tonda R, Moussy A, Gerber Z, Abuja P, Zatloukal K, Röcken C, Folseraas T, Grimsrud M, Vogel A, Goeppert B, Roessler S, Hinz S, Schafmayer C, Rosenstiel P, Deleuze JF, Gut I, Franke A, Forster M. A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Res 2023;51:7143-7162. [PMID: 37351572 PMCID: PMC10415133 DOI: 10.1093/nar/gkad519] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023]  Open
6
Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. Nat Med 2022;28:1662-1671. [PMID: 35953718 PMCID: PMC9388377 DOI: 10.1038/s41591-022-01927-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
7
Dodani DD, Nguyen MH, Morin RD, Marra MA, Corbett RD. Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data. Front Genet 2022;13:834764. [PMID: 35571031 PMCID: PMC9092826 DOI: 10.3389/fgene.2022.834764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022]  Open
8
Sater V, Viailly PJ, Lecroq T, Prieur-Gaston É, Bohers É, Viennot M, Ruminy P, Dauchel H, Vera P, Jardin F. UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data. Methods Mol Biol 2022;2493:235-245. [PMID: 35751818 DOI: 10.1007/978-1-0716-2293-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
9
Woerner AE, Mandape S, King JL, Muenzler M, Crysup B, Budowle B. Reducing noise and stutter in short tandem repeat loci with unique molecular identifiers. Forensic Sci Int Genet 2020;51:102459. [PMID: 33429137 DOI: 10.1016/j.fsigen.2020.102459] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022]
10
Sater V, Viailly PJ, Lecroq T, Prieur-Gaston É, Bohers É, Viennot M, Ruminy P, Dauchel H, Vera P, Jardin F. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries. Bioinformatics 2020;36:2718-2724. [PMID: 31985795 DOI: 10.1093/bioinformatics/btaa053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/18/2019] [Accepted: 01/20/2020] [Indexed: 01/03/2023]  Open
11
Sater V, Viailly PJ, Lecroq T, Ruminy P, Bérard C, Prieur-Gaston É, Jardin F. UMI-Gen: A UMI-based read simulator for variant calling evaluation in paired-end sequencing NGS libraries. Comput Struct Biotechnol J 2020;18:2270-2280. [PMID: 32952940 PMCID: PMC7484502 DOI: 10.1016/j.csbj.2020.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 11/02/2022]  Open
12
Butz H, Nyírő G, Kurucz PA, Likó I, Patócs A. Molecular genetic diagnostics of hypogonadotropic hypogonadism: from panel design towards result interpretation in clinical practice. Hum Genet 2020;140:113-134. [PMID: 32222824 PMCID: PMC7864839 DOI: 10.1007/s00439-020-02148-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022]
13
Friedlaender A, Nouspikel T, Christinat Y, Ho L, McKee T, Addeo A. Tissue-Plasma TMB Comparison and Plasma TMB Monitoring in Patients With Metastatic Non-small Cell Lung Cancer Receiving Immune Checkpoint Inhibitors. Front Oncol 2020;10:142. [PMID: 32117779 PMCID: PMC7028749 DOI: 10.3389/fonc.2020.00142] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022]  Open
14
Sensitization of chondrosarcoma cells with PARP inhibitor and high-LET radiation. J Bone Oncol 2019;17:100246. [PMID: 31312595 PMCID: PMC6609837 DOI: 10.1016/j.jbo.2019.100246] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/04/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]  Open
15
Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019;17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023]  Open
16
What Does This Mutation Mean? The Tools and Pitfalls of Variant Interpretation in Lymphoid Malignancies. Int J Mol Sci 2018;19:ijms19041251. [PMID: 29677173 PMCID: PMC5979354 DOI: 10.3390/ijms19041251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 01/21/2023]  Open
17
Lesueur P, Chevalier F, El-Habr EA, Junier MP, Chneiweiss H, Castera L, Müller E, Stefan D, Saintigny Y. Radiosensitization Effect of Talazoparib, a Parp Inhibitor, on Glioblastoma Stem Cells Exposed to Low and High Linear Energy Transfer Radiation. Sci Rep 2018;8:3664. [PMID: 29483558 PMCID: PMC5826933 DOI: 10.1038/s41598-018-22022-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/15/2018] [Indexed: 11/09/2022]  Open
18
Xu C. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Comput Struct Biotechnol J 2018;16:15-24. [PMID: 29552334 PMCID: PMC5852328 DOI: 10.1016/j.csbj.2018.01.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/20/2018] [Accepted: 01/28/2018] [Indexed: 02/06/2023]  Open
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