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For: Ha C, Kim JW, Jang JH. Performance Evaluation of SpliceAI for the Prediction of Splicing of NF1 Variants. Genes (Basel) 2021;12:1308. [PMID: 34573290 PMCID: PMC8472818 DOI: 10.3390/genes12091308] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022]  Open
Number Cited by Other Article(s)
1
Keefer-Jacques E, Valente N, Jacko AM, Matwijec G, Reese A, Tekriwal A, Loomes KM, Spinner NB, Gilbert MA. Investigation of cryptic JAG1 splice variants as a cause of Alagille syndrome and performance evaluation of splice predictor tools. HGG ADVANCES 2024;5:100351. [PMID: 39244638 PMCID: PMC11440345 DOI: 10.1016/j.xhgg.2024.100351] [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: 07/02/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/09/2024]  Open
2
Donelson CJH, Ghiringhelli Borsa N, Taylor AO, Smith RJH, Zhang Y. Functional evaluation of rare variants in complement factor I using a minigene assay. Front Immunol 2024;15:1446081. [PMID: 39238643 PMCID: PMC11374653 DOI: 10.3389/fimmu.2024.1446081] [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: 06/09/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024]  Open
3
Wen D, Hunjan M, Bardhan A, Harper N, Ogboli M, Ozoemena L, Liu L, Fine JD, Chapple I, Balacco DL, Heagerty A. Genotype-Phenotype Correlation in Junctional Epidermolysis Bullosa: Signposts to Severity. J Invest Dermatol 2024;144:1334-1343.e14. [PMID: 38157931 DOI: 10.1016/j.jid.2023.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/10/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024]
4
Lord J, Oquendo CJ, Wai HA, Douglas AGL, Bunyan DJ, Wang Y, Hu Z, Zeng Z, Danis D, Katsonis P, Williams A, Lichtarge O, Chang Y, Bagnall RD, Mount SM, Matthiasardottir B, Lin C, Hansen TVO, Leman R, Martins A, Houdayer C, Krieger S, Bakolitsa C, Peng Y, Kamandula A, Radivojac P, Baralle D. Predicting the impact of rare variants on RNA splicing in CAGI6. Hum Genet 2024:10.1007/s00439-023-02624-3. [PMID: 38170232 DOI: 10.1007/s00439-023-02624-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/18/2023] [Indexed: 01/05/2024]
5
Smith C, Kitzman JO. Benchmarking splice variant prediction algorithms using massively parallel splicing assays. Genome Biol 2023;24:294. [PMID: 38129864 PMCID: PMC10734170 DOI: 10.1186/s13059-023-03144-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]  Open
6
Fraire CR, Mallinger PR, Hatton JN, Kim J, Dickens DS, Argenta PA, Milanovich S, Hartshorne T, Carey DJ, Haley JS, Urban G, Lee J, Hill DA, Stewart DR, Schultz KAP, Chen KS. Intronic Germline DICER1 Variants in Patients With Sertoli-Leydig Cell Tumor. JCO Precis Oncol 2023;7:e2300189. [PMID: 37883719 PMCID: PMC10860953 DOI: 10.1200/po.23.00189] [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: 04/21/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 10/28/2023]  Open
7
Foreman J, Perrett D, Mazaika E, Hunt SE, Ware JS, Firth HV. DECIPHER: Improving Genetic Diagnosis Through Dynamic Integration of Genomic and Clinical Data. Annu Rev Genomics Hum Genet 2023;24:151-176. [PMID: 37285546 PMCID: PMC7615097 DOI: 10.1146/annurev-genom-102822-100509] [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] [Indexed: 06/09/2023]
8
Walker LC, Hoya MDL, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet 2023;110:1046-1067. [PMID: 37352859 PMCID: PMC10357475 DOI: 10.1016/j.ajhg.2023.06.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023]  Open
9
Smith C, Kitzman JO. Benchmarking splice variant prediction algorithms using massively parallel splicing assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539398. [PMID: 37205456 PMCID: PMC10187268 DOI: 10.1101/2023.05.04.539398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
10
Walker LC, de la Hoya M, Wiggins GA, Lindy A, Vincent LM, Parsons M, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.24.23286431. [PMID: 36865205 PMCID: PMC9980257 DOI: 10.1101/2023.02.24.23286431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
11
Systematic analysis of CNGA3 splice variants identifies different mechanisms of aberrant splicing. Sci Rep 2023;13:2896. [PMID: 36801918 PMCID: PMC9938885 DOI: 10.1038/s41598-023-29452-9] [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: 07/29/2022] [Accepted: 02/06/2023] [Indexed: 02/20/2023]  Open
12
de Sainte Agathe JM, Filser M, Isidor B, Besnard T, Gueguen P, Perrin A, Van Goethem C, Verebi C, Masingue M, Rendu J, Cossée M, Bergougnoux A, Frobert L, Buratti J, Lejeune É, Le Guern É, Pasquier F, Clot F, Kalatzis V, Roux AF, Cogné B, Baux D. SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation. Hum Genomics 2023;17:7. [PMID: 36765386 PMCID: PMC9912651 DOI: 10.1186/s40246-023-00451-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023]  Open
13
Alenezi WM, Fierheller CT, Serruya C, Revil T, Oros KK, Subramanian DN, Bruce J, Spiegelman D, Pugh T, Campbell IG, Mes-Masson AM, Provencher D, Foulkes WD, Haffaf ZE, Rouleau G, Bouchard L, Greenwood CMT, Ragoussis J, Tonin PN. Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases. Front Oncol 2023;13:1111191. [PMID: 36969007 PMCID: PMC10030840 DOI: 10.3389/fonc.2023.1111191] [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: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023]  Open
14
Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene. Clin Exp Nephrol 2023;27:218-226. [PMID: 36371577 PMCID: PMC9950164 DOI: 10.1007/s10157-022-02294-x] [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: 07/27/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
15
Barbosa P, Savisaar R, Carmo-Fonseca M, Fonseca A. Computational prediction of human deep intronic variation. Gigascience 2022;12:giad085. [PMID: 37878682 PMCID: PMC10599398 DOI: 10.1093/gigascience/giad085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023]  Open
16
Suga A, Yoshitake K, Minematsu N, Tsunoda K, Fujinami K, Miyake Y, Kuniyoshi K, Hayashi T, Mizobuchi K, Ueno S, Terasaki H, Kominami T, Nao-I N, Mawatari G, Mizota A, Shinoda K, Kondo M, Kato K, Sekiryu T, Nakamura M, Kusuhara S, Yamamoto H, Yamamoto S, Mochizuki K, Kondo H, Matsushita I, Kameya S, Fukuchi T, Hatase T, Horiguchi M, Shimada Y, Tanikawa A, Yamamoto S, Miura G, Ito N, Murakami A, Fujimaki T, Hotta Y, Tanaka K, Iwata T. Genetic characterization of 1210 Japanese pedigrees with inherited retinal diseases by whole-exome sequencing. Hum Mutat 2022;43:2251-2264. [PMID: 36284460 DOI: 10.1002/humu.24492] [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: 07/19/2022] [Revised: 09/18/2022] [Accepted: 10/21/2022] [Indexed: 01/25/2023]
17
Comparison of In Silico Tools for Splice-Altering Variant Prediction Using Established Spliceogenic Variants: An End-User’s Point of View. Int J Genomics 2022;2022:5265686. [PMID: 36275637 PMCID: PMC9584665 DOI: 10.1155/2022/5265686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022]  Open
18
Artemaki PI, Kontos CK. Alternative Splicing in Human Physiology and Disease. Genes (Basel) 2022;13:1820. [PMID: 36292705 PMCID: PMC9601896 DOI: 10.3390/genes13101820] [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: 09/11/2022] [Accepted: 09/20/2022] [Indexed: 08/30/2023]  Open
19
Bueno‐Martínez E, Sanoguera‐Miralles L, Valenzuela‐Palomo A, Esteban‐Sánchez A, Lorca V, Llinares‐Burguet I, Allen J, García‐Álvarez A, Pérez‐Segura P, Durán M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco‐Sampedro EA. Minigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants. J Pathol 2022;258:83-101. [PMID: 35716007 PMCID: PMC9541484 DOI: 10.1002/path.5979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 12/29/2022]
20
Restivo C, Le Bras M, Deguigne P, Le Glatin L, Guerry C, Férec C, Le Maréchal C, Beloeil R, Fichou Y. The novel c.634+ 4A >G splicing variant in RHCE results in weak C and e antigen expression in a pregnant woman originated from Japan. Transfusion 2022;62:758-763. [DOI: 10.1111/trf.16811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 11/28/2022]
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