Table of Contents Author Guidelines
Advances in Bioinformatics
Volume 2016, Article ID 5614058, 10 pages
http://dx.doi.org/10.1155/2016/5614058
Research Article

Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions

Diagnostic Genetics, LabPLUS, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand

Received 25 January 2016; Revised 28 April 2016; Accepted 4 May 2016

Academic Editor: Eitan Rubin

Copyright © 2016 Rongying Tang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citations to this Article [19 citations]

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  • Jenny Lord, Giuseppe Gallone, Patrick J. Short, Jeremy F. McRae, Holly Ironfield, Elizabeth H. Wynn, Sebastian S. Gerety, Liu He, Bronwyn Kerr, Diana S. Johnson, Emma McCann, Esther Kinning, Frances Flinter, I. Karen Temple, Jill Clayton-Smith, Meriel McEntagart, Sally Ann Lynch, Shelagh Joss, Sofia Douzgou, Tabib Dabir, Virginia Clowes, Vivienne P. M. McConnell, Wayne Lam, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Jeffrey C. Barrett, and Matthew E. Hurles. View at Publisher · View at Google Scholar
  • Anasua Sarkar, Yang Yang, and Mauno Vihinen. View at Publisher · View at Google Scholar
  • Cristian G. Zimbru, Nicoleta Andreescu, Adela Chirita-Emandi, Antonius Stanciu, Ioan Silea, Mihai D. Niculescu, and Maria Puiu, “Splice site pattern analysis and identification of similar sequences in the deep intron areas of human chromosome 21,” 2017 E-Health and Bioengineering Conference (EHB), pp. 145–148, . View at Publisher · View at Google Scholar
  • Ivone U S Leong, Philippa A Dryland, Debra O Prosser, Stella W-S Lai, Mandy Graham, Martin Stiles, Jackie Crawford, Jonathan R Skinner, and Donald R Love, “Splice Site Variants in the KCNQ1 and SCN5A Genes: Transcript Analysis as a Tool in Supporting Pathogenicity.,” Journal of clinical medicine research, vol. 9, no. 8, pp. 709–718, 2017. View at Publisher · View at Google Scholar
  • Zachry T. Soens, Justin Branch, Shijing Wu, Zhisheng Yuan, Yumei Li, Hui Li, Keqing Wang, Mingchu Xu, Lavan Rajan, Fabiana L. Motta, Renata T. Simões, Irma Lopez-Solache, Radwan Ajlan, David G. Birch, Peiquan Zhao, Fernanda B. Porto, Juliana Sallum, Robert K. Koenekoop, Ruifang Sui, and Rui Chen, “Leveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance,” Human Mutation, 2017. View at Publisher · View at Google Scholar
  • Tatsuro Yamaguchi, Tomokazu Wakatsuki, Mari Kikuchi, Shin-Ichiro Horiguchi, and Kiwamu Akagi, “The silent mutation MLH1 c.543C>T resulting in aberrant splicing can cause Lynch syndrome: A case report,” Japanese Journal of Clinical Oncology, vol. 47, no. 6, pp. 576–580, 2017. View at Publisher · View at Google Scholar
  • Wen-Bin Zou, Hao Wu, Arnaud Boulling, David N. Cooper, Zhao-Shen Li, Zhuan Liao, Jian-Min Chen, and Claude Férec, “In silico prioritization and further functional characterization of SPINK1 intronic variants,” Human Genomics, vol. 11, no. 1, 2017. View at Publisher · View at Google Scholar
  • David K. Brown, and Özlem Tastan Bishop, “Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis,” Global Heart, 2017. View at Publisher · View at Google Scholar
  • Stéphanie S. Cornelis, Nathalie M. Bax, Jana Zernant, Rando Allikmets, Lars G. Fritsche, Johan T. den Dunnen, Muhammad Ajmal, Carel B. Hoyng, and Frans P. M. Cremers, “ In Silico Functional Meta-Analysis of 5,962 ABCA4 Variants in 3,928 Retinal Dystrophy Cases ,” Human Mutation, 2017. View at Publisher · View at Google Scholar
  • Alejandro Moles-Fernández, Laura Duran-Lozano, Gemma Montalban, Sandra Bonache, Irene López-Perolio, Mireia Menéndez, Marta Santamariña, Raquel Behar, Ana Blanco, Estela Carrasco, Adrià López-Fernández, Neda Stjepanovic, Judith Balmaña, Gabriel Capellá, Marta Pineda, Ana Vega, Conxi Lázaro, Miguel de la Hoya, Orland Diez, and Sara Gutiérrez-Enríquez, “Computational Tools for Splicing Defect Prediction in Breast/Ovarian Cancer Genes: How Efficient Are They at Predicting RNA Alterations?,” Frontiers in Genetics, vol. 9, 2018. View at Publisher · View at Google Scholar
  • Raphaël Leman, Pascaline Gaildrat, Gérald L Gac, Chandran Ka, Yann Fichou, Marie-Pierre Audrezet, Virginie Caux-Moncoutier, Sandrine M Caputo, Nadia Boutry-Kryza, Mélanie Léone, Sylvie Mazoyer, Françoise Bonnet-Dorion, Nicolas Sevenet, Marine Guillaud-Bataille, Etienne Rouleau, Brigitte Bressac-de Paillerets, Barbara Wappenschmidt, Maria Rossing, Danielle Muller, Violaine Bourdon, Françoise Revillon, Michael T Parsons, Antoine Rousselin, Grégoire Davy, Gaia Castelain, Laurent Castéra, Joanna Sokolowska, Florence Coulet, Capucine Delnatte, Claude Férec, Amanda B Spurdle, Alexandra Martins, Sophie Krieger, and Claude Houdayer, “Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort,” Nucleic Acids Research, 2018. View at Publisher · View at Google Scholar
  • Karen S. Raraigh, Sangwoo T. Han, Emily Davis, Taylor A. Evans, Matthew J. Pellicore, Allison F. McCague, Anya T. Joynt, Zhongzhou Lu, Melis Atalar, Neeraj Sharma, Molly B. Sheridan, Patrick R. Sosnay, and Garry R. Cutting, “Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity,” The American Journal of Human Genetics, 2018. View at Publisher · View at Google Scholar
  • Nizamettin Aydin, and Elham Pashaei, “Markovian encoding models in human splice site recognition using SVM,” Computational Biology and Chemistry, vol. 73, pp. 159–170, 2018. View at Publisher · View at Google Scholar
  • Cinthia Amiñoso, María Gordillo-Marañón, Jaime Hernández, and Jesús Solera, “Reevaluating the pathogenicity of the mutation c.1194 +5 G>A in GAA gene by functional analysis of RNA,” Neuromuscular Disorders, 2018. View at Publisher · View at Google Scholar
  • Jenny Lord, Giuseppe Gallone, Patrick J. Short, Jeremy F. McRae, Holly Ironfield, Elizabeth H. Wynn, Sebastian S. Gerety, Liu He, Bronwyn Kerr, Diana S. Johnson, Emma McCann, Esther Kinning, Frances Flinter, I. Karen Temple, Jill Clayton-Smith, Meriel McEntagart, Sally Ann Lynch, Shelagh Joss, Sofia Douzgou, Tabib Dabir, Virginia Clowes, Vivienne P.M. McConnell, Wayne Lam, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Jeffrey C. Barrett, and Matthew E. Hurles, “Pathogenicity and selective constraint on variation near splice sites,” Genome Research, vol. 29, no. 2, pp. 159–170, 2018. View at Publisher · View at Google Scholar
  • Annelot Baert, Eva Machackova, Ilse Coene, Carol Cremin, Kristin Turner, Cheryl Portigal-Todd, Marie Jill Asrat, Jennifer Nuk, Allison Mindlin, Sean Young, Andree MacMillan, Tom Van Maerken, Martin Trbusek, Wendy McKinnon, Marie E. Wood, William D. Foulkes, Marta Santamariña, Miguel de la Hoya, Lenka Foretova, Bruce Poppe, Anne Vral, Toon Rosseel, Kim De Leeneer, Ana Vega, and Kathleen B. M. Claes, “ Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2 allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11 ,” Human Mutation, 2018. View at Publisher · View at Google Scholar
  • Shi-Yi Chen, Cao Li, Xianbo Jia, and Song-Jia Lai, “Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes,” International Journal of Molecular Sciences, vol. 20, no. 15, pp. 3834, 2019. View at Publisher · View at Google Scholar
  • Upendra K. Katneni, Aaron Liss, David Holcomb, Nobuko H. Katagiri, Ryan Hunt, Haim Bar, Amra Ismail, Anton A. Komar, and Chava Kimchi-Sarfaty, “ Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants ,” Molecular Genetics & Genomic Medicine, pp. e840, 2019. View at Publisher · View at Google Scholar
  • Sanne K. Verbakel, Zeinab Fadaie, B. Jeroen Klevering, Maria M. van Genderen, Ilse Feenstra, Frans P. M. Cremers, Carel B. Hoyng, and Susanne Roosing, “ The identification of a RNA splice variant in TULP1 in two siblings with early‐onset photoreceptor dystrophy ,” Molecular Genetics & Genomic Medicine, pp. e660, 2019. View at Publisher · View at Google Scholar