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For: van den Akker J, Mishne G, Zimmer AD, Zhou AY. A machine learning model to determine the accuracy of variant calls in capture-based next generation sequencing. BMC Genomics 2018;19:263. [PMID: 29665779 PMCID: PMC5904977 DOI: 10.1186/s12864-018-4659-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/10/2018] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Isago H, Watanabe K, Satoh Y, Kurano M. Correlation between variant call accuracy and quality parameters in comprehensive cancer genomic profiling tests. Pract Lab Med 2024;39:e00369. [PMID: 38404524 PMCID: PMC10884978 DOI: 10.1016/j.plabm.2024.e00369] [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: 11/28/2023] [Revised: 02/04/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]  Open
2
Choon YW, Choon YF, Nasarudin NA, Al Jasmi F, Remli MA, Alkayali MH, Mohamad MS. Artificial intelligence and database for NGS-based diagnosis in rare disease. Front Genet 2024;14:1258083. [PMID: 38371307 PMCID: PMC10870236 DOI: 10.3389/fgene.2023.1258083] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/24/2023] [Indexed: 02/20/2024]  Open
3
Eren KK, Çınar E, Karakurt HU, Özgür A. Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics. Bioinformatics 2023;39:btad694. [PMID: 38019945 PMCID: PMC10692869 DOI: 10.1093/bioinformatics/btad694] [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: 05/12/2023] [Revised: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]  Open
4
Choate LA, Koleilat A, Harris K, Vidal-Folch N, Guenzel A, Newman J, Peterson BJ, Peterson SE, Rice CS, Train LJ, Hasadsri L, Marcou CA, Moyer AM, Baudhuin LM. Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing. Clin Chem 2023;69:1155-1162. [PMID: 37566393 DOI: 10.1093/clinchem/hvad110] [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: 03/16/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
5
Crooks KR, Farwell Hagman KD, Mandelker D, Santani A, Schmidt RJ, Temple-Smolkin RL, Lincoln SE. Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors. J Mol Diagn 2023;25:411-427. [PMID: 37207865 DOI: 10.1016/j.jmoldx.2023.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/27/2023] [Accepted: 03/30/2023] [Indexed: 05/21/2023]  Open
6
Cechova M, Miga KH. Satellite DNAs and human sex chromosome variation. Semin Cell Dev Biol 2022;128:15-25. [PMID: 35644878 PMCID: PMC9233459 DOI: 10.1016/j.semcdb.2022.04.022] [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: 03/15/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
7
Wagner U, Wong C, Camenisch U, Zimmermann K, Rechsteiner M, Valtcheva N, Theocharides A, Widmer CC, Manz MG, Moch H, Wild PJ, Balabanov S. Comprehensive Validation of Diagnostic Next-Generation Sequencing Panels for Acute Myeloid Leukemia Patients. J Mol Diagn 2022;24:935-954. [PMID: 35718092 DOI: 10.1016/j.jmoldx.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/11/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022]  Open
8
Watson CM, Crinnion LA, Simmonds J, Camm N, Adlard J, Bonthron DT. Long-read nanopore sequencing enables accurate confirmation of a recurrent PMS2 insertion-deletion variant located in a region of complex genomic architecture. Cancer Genet 2021;256-257:122-126. [PMID: 34116445 DOI: 10.1016/j.cancergen.2021.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/08/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
9
Prasad A, Bhargava H, Gupta A, Shukla N, Rajagopal S, Gupta S, Sharma A, Valadi J, Nigam V, Suravajhala P. Next Generation Sequencing. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
10
Adedokun B, Zheng Y, Ndom P, Gakwaya A, Makumbi T, Zhou AY, Yoshimatsu TF, Rodriguez A, Madduri RK, Foster IT, Sallam A, Olopade OI, Huo D. Prevalence of Inherited Mutations in Breast Cancer Predisposition Genes among Women in Uganda and Cameroon. Cancer Epidemiol Biomarkers Prev 2019;29:359-367. [PMID: 31871109 DOI: 10.1158/1055-9965.epi-19-0506] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/23/2019] [Accepted: 12/09/2019] [Indexed: 11/16/2022]  Open
11
Methods for Identifying Patients with Tropomyosin Receptor Kinase (TRK) Fusion Cancer. Pathol Oncol Res 2019;26:1385-1399. [PMID: 31256325 PMCID: PMC7297824 DOI: 10.1007/s12253-019-00685-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/11/2019] [Indexed: 11/01/2022]
12
Martinez-Martin N, Magnus D. Privacy and ethical challenges in next-generation sequencing. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019;4:95-104. [PMID: 32775691 PMCID: PMC7413244 DOI: 10.1080/23808993.2019.1599685] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/22/2019] [Indexed: 02/04/2023]
13
Muzzey D, Kash S, Johnson JI, Melroy LM, Kaleta P, Pierce KA, Ready K, Kang HP, Haas KR. Software-Assisted Manual Review of Clinical Next-Generation Sequencing Data. J Mol Diagn 2019;21:296-306. [DOI: 10.1016/j.jmoldx.2018.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/24/2018] [Accepted: 10/24/2018] [Indexed: 12/13/2022]  Open
14
Lincoln SE, Truty R, Lin CF, Zook JM, Paul J, Ramey VH, Salit M, Rehm HL, Nussbaum RL, Lebo MS. A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing. J Mol Diagn 2019;21:318-329. [PMID: 30610921 PMCID: PMC6629256 DOI: 10.1016/j.jmoldx.2018.10.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 12/17/2022]  Open
15
Parikh RB, Gdowski A, Patt DA, Hertler A, Mermel C, Bekelman JE. Using Big Data and Predictive Analytics to Determine Patient Risk in Oncology. Am Soc Clin Oncol Educ Book 2019;39:e53-e58. [PMID: 31099672 DOI: 10.1200/edbk_238891] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
16
Evaluation for Genetic Disorders in the Absence of a Clinical Indication for Testing. J Mol Diagn 2019;21:3-12. [DOI: 10.1016/j.jmoldx.2018.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/29/2018] [Accepted: 09/17/2018] [Indexed: 01/01/2023]  Open
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