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For: García-García G, Baux D, Faugère V, Moclyn M, Koenig M, Claustres M, Roux AF. Assessment of the latest NGS enrichment capture methods in clinical context. Sci Rep 2016;6:20948. [PMID: 26864517 PMCID: PMC4750071 DOI: 10.1038/srep20948] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/13/2016] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Liu W, Jin KM, Zhang MH, Bao Q, Liu M, Xu D, Wang K, Xing BC. Recurrence Prediction by Circulating Tumor DNA in the Patient with Colorectal Liver Metastases After Hepatectomy: A Prospective Biomarker Study. Ann Surg Oncol 2023;30:4916-4926. [PMID: 37219651 DOI: 10.1245/s10434-023-13362-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/02/2023] [Indexed: 05/24/2023]
2
Zeineldin M, Camp P, Farrell D, Lehman K, Thacker T. Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture. Front Microbiol 2023;14:1141651. [PMID: 37275178 PMCID: PMC10232834 DOI: 10.3389/fmicb.2023.1141651] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023]  Open
3
La Polla R, Goumaidi A, Daniau M, Legras-Lachuer C, De Saint-Vis B. NGS method by library enrichment for rapid pestivirus purity testing in biologics. Vaccine 2023;41:855-861. [PMID: 36564275 DOI: 10.1016/j.vaccine.2022.12.040] [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: 03/04/2022] [Revised: 09/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
4
Steiert TA, Fuß J, Juzenas S, Wittig M, Hoeppner M, Vollstedt M, Varkalaite G, ElAbd H, Brockmann C, Görg S, Gassner C, Forster M, Franke A. High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing. NAR Genom Bioinform 2022;4:lqac051. [PMID: 35855323 PMCID: PMC9278042 DOI: 10.1093/nargab/lqac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/08/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]  Open
5
Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022;13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022]  Open
6
Belova V, Shmitko A, Pavlova A, Afasizhev R, Cheranev V, Tabanakova A, Ponikarovskaya N, Rebrikov D, Korostin D. Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing. BMC Genomics 2022;23:582. [PMID: 35962321 PMCID: PMC9375261 DOI: 10.1186/s12864-022-08825-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022]  Open
7
Belova V, Pavlova A, Afasizhev R, Moskalenko V, Korzhanova M, Krivoy A, Cheranev V, Nikashin B, Bulusheva I, Rebrikov D, Korostin D. System analysis of the sequencing quality of human whole exome samples on BGI NGS platform. Sci Rep 2022;12:609. [PMID: 35022470 PMCID: PMC8755732 DOI: 10.1038/s41598-021-04526-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/16/2021] [Indexed: 12/05/2022]  Open
8
Kim MJ, Lee S, Yun H, Cho SI, Kim B, Lee JS, Chae JH, Sun C, Park SS, Seong MW. Consistent count region-copy number variation (CCR-CNV): an expandable and robust tool for clinical diagnosis of copy number variation at the exon level using next-generation sequencing data. Genet Med 2021;24:663-672. [PMID: 34906491 DOI: 10.1016/j.gim.2021.10.025] [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: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]  Open
9
Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021;2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
10
Remec ZI, Trebusak Podkrajsek K, Repic Lampret B, Kovac J, Groselj U, Tesovnik T, Battelino T, Debeljak M. Next-Generation Sequencing in Newborn Screening: A Review of Current State. Front Genet 2021;12:662254. [PMID: 34122514 PMCID: PMC8188483 DOI: 10.3389/fgene.2021.662254] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022]  Open
11
De Las Casas LE, Hicks DG. Pathologists at the Leading Edge of Optimizing the Tumor Tissue Journey for Diagnostic Accuracy and Molecular Testing. Am J Clin Pathol 2021;155:781-792. [PMID: 33582767 PMCID: PMC8130880 DOI: 10.1093/ajcp/aqaa212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
12
Taron UH, Paijmans JLA, Barlow A, Preick M, Iyengar A, Drăgușin V, Vasile Ș, Marciszak A, Roblíčková M, Hofreiter M. Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe. Genes (Basel) 2021;12:144. [PMID: 33499169 PMCID: PMC7911384 DOI: 10.3390/genes12020144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/11/2023]  Open
13
Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. Urine as a high-quality source of host genomic DNA from wild populations. Mol Ecol Resour 2021;21:170-182. [PMID: 32985084 PMCID: PMC7746602 DOI: 10.1111/1755-0998.13260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022]
14
Steele JL, Stevens RC, Cabrera OA, Bassill GJ, Cramer SM, Guzman F, Shuber AP. Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations. PLoS One 2020;15:e0243781. [PMID: 33362267 PMCID: PMC7757808 DOI: 10.1371/journal.pone.0243781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/25/2020] [Indexed: 01/10/2023]  Open
15
Mc Connell L, Gazdova J, Beck K, Srivastava S, Harewood L, Stewart JP, Hübschmann D, Stenzinger A, Glimm H, Heilig CE, Fröhling S, Gonzalez D. Detection of Structural Variants in Circulating Cell-Free DNA from Sarcoma Patients Using Next Generation Sequencing. Cancers (Basel) 2020;12:E3627. [PMID: 33287361 PMCID: PMC7761870 DOI: 10.3390/cancers12123627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022]  Open
16
Helpful Criteria When Implementing NGS Panels in Childhood Lymphoblastic Leukemia. J Pers Med 2020;10:jpm10040244. [PMID: 33255984 PMCID: PMC7711852 DOI: 10.3390/jpm10040244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 11/17/2022]  Open
17
Vaché C, Puechberty J, Faugère V, Darmaisin F, Liquori A, Baux D, Blanchet C, Garcia-Garcia G, Meunier I, Pellestor F, Koenig M, Roux AF. A 4.6 Mb Inversion Leading to PCDH15-LINC00844 and BICC1-PCDH15 Fusion Transcripts as a New Pathogenic Mechanism Implicated in Usher Syndrome Type 1. Front Genet 2020;11:623. [PMID: 32714370 PMCID: PMC7343966 DOI: 10.3389/fgene.2020.00623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/22/2020] [Indexed: 01/17/2023]  Open
18
Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length. Sci Rep 2020;10:9424. [PMID: 32523024 PMCID: PMC7287100 DOI: 10.1038/s41598-020-66331-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/23/2020] [Indexed: 12/16/2022]  Open
19
Borges MG, Rocha CS, Carvalho BS, Lopes-Cendes I. Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis. Genet Mol Biol 2020;43:e20190270. [PMID: 32343762 PMCID: PMC7198014 DOI: 10.1590/1678-4685-gmb-2019-0270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/16/2020] [Indexed: 11/24/2022]  Open
20
de Haan A, Eijgelsheim M, Vogt L, Knoers NVAM, de Borst MH. Diagnostic Yield of Next-Generation Sequencing in Patients With Chronic Kidney Disease of Unknown Etiology. Front Genet 2019;10:1264. [PMID: 31921302 PMCID: PMC6923268 DOI: 10.3389/fgene.2019.01264] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022]  Open
21
Debode F, Hulin J, Charloteaux B, Coppieters W, Hanikenne M, Karim L, Berben G. Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies. Sci Rep 2019;9:15595. [PMID: 31666537 PMCID: PMC6821802 DOI: 10.1038/s41598-019-51668-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/20/2019] [Indexed: 12/12/2022]  Open
22
Caspar SM, Dubacher N, Kopps AM, Meienberg J, Henggeler C, Matyas G. Clinical sequencing: From raw data to diagnosis with lifetime value. Clin Genet 2019;93:508-519. [PMID: 29206278 DOI: 10.1111/cge.13190] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022]
23
Mallampati S, Zalles S, Duose DY, Hu PC, Medeiros LJ, Wistuba II, Kopetz S, Luthra R. Development and Application of Duplex Sequencing Strategy for Cell-Free DNA-Based Longitudinal Monitoring of Stage IV Colorectal Cancer. J Mol Diagn 2019;21:994-1009. [PMID: 31401123 DOI: 10.1016/j.jmoldx.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/08/2019] [Accepted: 06/12/2019] [Indexed: 02/09/2023]  Open
24
Ascierto PA, Bifulco C, Palmieri G, Peters S, Sidiropoulos N. Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis. J Mol Diagn 2019;21:756-767. [PMID: 31251989 DOI: 10.1016/j.jmoldx.2019.05.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/23/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022]  Open
25
Mittempergher L, Delahaye LJMJ, Witteveen AT, Spangler JB, Hassenmahomed F, Mee S, Mahmoudi S, Chen J, Bao S, Snel MHJ, Leidelmeijer S, Besseling N, Bergstrom Lucas A, Pabón-Peña C, Linn SC, Dreezen C, Wehkamp D, Chan BY, Bernards R, van 't Veer LJ, Glas AM. MammaPrint and BluePrint Molecular Diagnostics Using Targeted RNA Next-Generation Sequencing Technology. J Mol Diagn 2019;21:808-823. [PMID: 31173928 DOI: 10.1016/j.jmoldx.2019.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/21/2019] [Accepted: 04/16/2019] [Indexed: 01/31/2023]  Open
26
Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet 2019;20:341-355. [PMID: 30918369 PMCID: PMC6858796 DOI: 10.1038/s41576-019-0113-7] [Citation(s) in RCA: 682] [Impact Index Per Article: 136.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
27
Hadfield J, Bénard A, Domman D, Thomson N. The Hidden Genomics of Chlamydia trachomatis. Curr Top Microbiol Immunol 2019;412:107-131. [PMID: 29071471 DOI: 10.1007/82_2017_39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
28
Mallampati S, Duose DY, Harmon MA, Mehrotra M, Kanagal-Shamanna R, Zalles S, Wistuba II, Sun X, Luthra R. Rational "Error Elimination" Approach to Evaluating Molecular Barcoded Next-Generation Sequencing Data Identifies Low-Frequency Mutations in Hematologic Malignancies. J Mol Diagn 2019;21:471-482. [PMID: 30794984 PMCID: PMC6521894 DOI: 10.1016/j.jmoldx.2019.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/31/2018] [Accepted: 01/18/2019] [Indexed: 12/18/2022]  Open
29
Stevens RC, Steele JL, Glover WR, Sanchez-Garcia JF, Simpson SD, O’Rourke D, Ramsdell JS, MacManes MD, Thomas WK, Shuber AP. A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment. PLoS One 2019;14:e0215441. [PMID: 30998719 PMCID: PMC6472885 DOI: 10.1371/journal.pone.0215441] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/03/2019] [Indexed: 01/08/2023]  Open
30
Understanding the basis of Ehlers-Danlos syndrome in the era of the next-generation sequencing. Arch Dermatol Res 2019;311:265-275. [PMID: 30826961 DOI: 10.1007/s00403-019-01894-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/26/2018] [Accepted: 02/12/2019] [Indexed: 01/08/2023]
31
Alonso CM, Llop M, Sargas C, Pedrola L, Panadero J, Hervás D, Cervera J, Such E, Ibáñez M, Ayala R, Martínez-López J, Onecha E, de Juan I, Palanca S, Martínez-Cuadrón D, Rodríguez-Veiga R, Boluda B, Montesinos P, Sanz G, Sanz MA, Barragán E. Clinical Utility of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia Diagnostics. J Mol Diagn 2019;21:228-240. [DOI: 10.1016/j.jmoldx.2018.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 09/06/2018] [Accepted: 09/20/2018] [Indexed: 10/27/2022]  Open
32
Richards SM, Hovhannisyan N, Gilliham M, Ingram J, Skadhauge B, Heiniger H, Llamas B, Mitchell KJ, Meachen J, Fincher GB, Austin JJ, Cooper A. Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes. PLoS One 2019;14:e0209499. [PMID: 30716066 PMCID: PMC6361428 DOI: 10.1371/journal.pone.0209499] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/06/2018] [Indexed: 11/23/2022]  Open
33
Chen W, Wang P. Molecular Analysis for Characterizing Transgenic Events. Methods Mol Biol 2019;1864:397-410. [PMID: 30415348 DOI: 10.1007/978-1-4939-8778-8_24] [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] [Indexed: 06/09/2023]
34
Pel J, Leung A, Choi WWY, Despotovic M, Ung WL, Shibahara G, Gelinas L, Marziali A. Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers. PLoS One 2018;13:e0208283. [PMID: 30517195 PMCID: PMC6281261 DOI: 10.1371/journal.pone.0208283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/14/2018] [Indexed: 11/18/2022]  Open
35
D'Amore A, Tessa A, Casali C, Dotti MT, Filla A, Silvestri G, Antenora A, Astrea G, Barghigiani M, Battini R, Battisti C, Bruno I, Cereda C, Dato C, Di Iorio G, Donadio V, Felicori M, Fini N, Fiorillo C, Gallone S, Gemignani F, Gigli GL, Graziano C, Guerrini R, Gurrieri F, Kariminejad A, Lieto M, Marques LourenḈo C, Malandrini A, Mandich P, Marcotulli C, Mari F, Massacesi L, Melone MAB, Mignarri A, Milone R, Musumeci O, Pegoraro E, Perna A, Petrucci A, Pini A, Pochiero F, Pons MR, Ricca I, Rossi S, Seri M, Stanzial F, Tinelli F, Toscano A, Valente M, Federico A, Rubegni A, Santorelli FM. Next Generation Molecular Diagnosis of Hereditary Spastic Paraplegias: An Italian Cross-Sectional Study. Front Neurol 2018;9:981. [PMID: 30564185 PMCID: PMC6289125 DOI: 10.3389/fneur.2018.00981] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022]  Open
36
Smielewska A, Emmott E, Ranellou K, Popay A, Goodfellow I, Jalal H. UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis. Wellcome Open Res 2018;3:118. [PMID: 30569021 PMCID: PMC6281019 DOI: 10.12688/wellcomeopenres.14730.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 01/01/2023]  Open
37
Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018;3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
38
Rosa-Rosa JM, Caniego-Casas T, Leskela S, Muñoz G, Del Castillo F, Garrido P, Palacios J. Modified SureSelectQXT Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples. Biol Proced Online 2018;20:19. [PMID: 30337841 PMCID: PMC6182866 DOI: 10.1186/s12575-018-0084-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022]  Open
39
Johnson B, Doak R, Allsup D, Astwood E, Evans G, Grimley C, James B, Myers B, Stokley S, Thachil J, Wilde J, Williams M, Makris M, Lowe GC, Wallis Y, Daly ME, Morgan NV. A comprehensive targeted next-generation sequencing panel for genetic diagnosis of patients with suspected inherited thrombocytopenia. Res Pract Thromb Haemost 2018;2:640-652. [PMID: 30349881 PMCID: PMC6178765 DOI: 10.1002/rth2.12151] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/20/2018] [Indexed: 01/10/2023]  Open
40
Smielewska A, Emmott E, Ranellou K, Popay A, Goodfellow I, Jalal H. UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis. Wellcome Open Res 2018;3:118. [PMID: 30569021 PMCID: PMC6281019 DOI: 10.12688/wellcomeopenres.14730.1] [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] [Accepted: 09/12/2018] [Indexed: 10/05/2023]  Open
41
Xiao Y, Nolting JM, Sheng ZM, Bristol T, Qi L, Bowman AS, Taubenberger JK. Design and validation of a universal influenza virus enrichment probe set and its utility in deep sequence analysis of primary cloacal swab surveillance samples of wild birds. Virology 2018;524:182-191. [PMID: 30212665 DOI: 10.1016/j.virol.2018.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 11/25/2022]
42
Zenagui R, Lacourt D, Pegeot H, Yauy K, Juntas Morales R, Theze C, Rivier F, Cances C, Sole G, Renard D, Walther-Louvier U, Ferrer-Monasterio X, Espil C, Arné-Bes MC, Cintas P, Uro-Coste E, Martin Negrier ML, Rigau V, Bieth E, Goizet C, Claustres M, Koenig M, Cossée M. A Reliable Targeted Next-Generation Sequencing Strategy for Diagnosis of Myopathies and Muscular Dystrophies, Especially for the Giant Titin and Nebulin Genes. J Mol Diagn 2018;20:533-549. [DOI: 10.1016/j.jmoldx.2018.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 01/05/2023]  Open
43
Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis. Methods Mol Biol 2018;1838:125-140. [PMID: 30128994 PMCID: PMC7121196 DOI: 10.1007/978-1-4939-8682-8_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Münz M, Mahamdallie S, Yost S, Rimmer A, Poyastro-Pearson E, Strydom A, Seal S, Ruark E, Rahman N. CoverView: a sequence quality evaluation tool for next generation sequencing data. Wellcome Open Res 2018;3:36. [PMID: 29881786 PMCID: PMC5964631 DOI: 10.12688/wellcomeopenres.14306.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 01/05/2023]  Open
45
Shinozuka H, Sudheesh S, Shinozuka M, Cogan NOI. Homology-based enzymatic DNA fragment assembly-based illumina sequencing library preparation. Biol Methods Protoc 2018;3:bpy001. [PMID: 32161795 PMCID: PMC6994068 DOI: 10.1093/biomethods/bpy001] [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: 10/12/2017] [Revised: 01/03/2018] [Accepted: 01/19/2018] [Indexed: 11/14/2022]  Open
46
Rubinsteyn A, Kodysh J, Hodes I, Mondet S, Aksoy BA, Finnigan JP, Bhardwaj N, Hammerbacher J. Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial. Front Immunol 2018;8:1807. [PMID: 29403468 PMCID: PMC5778604 DOI: 10.3389/fimmu.2017.01807] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]  Open
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A robust targeted sequencing approach for low input and variable quality DNA from clinical samples. NPJ Genom Med 2018;3:2. [PMID: 29354287 PMCID: PMC5768874 DOI: 10.1038/s41525-017-0041-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/27/2017] [Accepted: 12/05/2017] [Indexed: 02/07/2023]  Open
48
Łopacińska-Jørgensen JM, Pedersen JN, Bak M, Mehrjouy MM, Sørensen KT, Østergaard PF, Bilenberg B, Kristensen A, Taboryski RJ, Flyvbjerg H, Marie R, Tommerup N, Silahtaroglu A. Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing. Sci Rep 2017;7:17893. [PMID: 29263336 PMCID: PMC5738345 DOI: 10.1038/s41598-017-18091-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022]  Open
49
Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R. High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat Genet 2017;49:1731-1740. [PMID: 29106417 PMCID: PMC5709232 DOI: 10.1038/ng.3988] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022]
50
Baux D, Vaché C, Blanchet C, Willems M, Baudoin C, Moclyn M, Faugère V, Touraine R, Isidor B, Dupin-Deguine D, Nizon M, Vincent M, Mercier S, Calais C, García-García G, Azher Z, Lambert L, Perdomo-Trujillo Y, Giuliano F, Claustres M, Koenig M, Mondain M, Roux AF. Combined genetic approaches yield a 48% diagnostic rate in a large cohort of French hearing-impaired patients. Sci Rep 2017;7:16783. [PMID: 29196752 PMCID: PMC5711943 DOI: 10.1038/s41598-017-16846-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/17/2017] [Indexed: 11/22/2022]  Open
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