Literature DB >> 30240882

A review study: Computational techniques for expecting the impact of non-synonymous single nucleotide variants in human diseases.

Marwa S Hassan1, A A Shaalan2, M I Dessouky3, Abdelaziz E Abdelnaiem2, Mahmoud ElHefnawi4.   

Abstract

Non-Synonymous Single-Nucleotide Variants (nsSNVs) and mutations can create a diversity effect on proteins as changing genotype and phenotype, which interrupts its stability. The alterations in the protein stability may cause diseases like cancer. Discovering of nsSNVs and mutations can be a useful tool for diagnosing the disease at a beginning stage. Many studies introduced the various predicting singular and consensus tools that based on different Machine Learning Techniques (MLTs) using diverse datasets. Therefore, we introduce the current comprehensive review of the most popular and recent unique tools that predict pathogenic variations and Meta-tool that merge some of them for enhancing their predictive power. Also, we scanned the several types computational techniques in the state-of-the-art and methods for predicting the effect both of coding and noncoding variants. We then displayed, the protein stability predictors. We offer the details of the most common benchmark database for variations including the main predictive features used by the different methods. Finally, we address the most common fundamental criteria for performance assessment of predictive tools. This review is targeted at bioinformaticians attentive in the characterization of regulatory variants, geneticists, molecular biologists attentive in understanding more about the nature and effective role of such variants from a functional point of views, and clinicians who may hope to learn about variants in human associated with a specific disease and find out what to do next to uncover how they impact on the underlying mechanisms.
Copyright © 2018 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Coding and noncoding variants; Genotype; Machine learning techniques (MLTs); Meta-tool; Non-synonymous single nucleotide variants; Pathogenic; Phenotype; Predictive power; Protein stability

Mesh:

Year:  2018        PMID: 30240882     DOI: 10.1016/j.gene.2018.09.028

Source DB:  PubMed          Journal:  Gene        ISSN: 0378-1119            Impact factor:   3.688


  12 in total

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3.  Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.

Authors:  Fang Ge; Ying Zhang; Jian Xu; Arif Muhammad; Jiangning Song; Dong-Jun Yu
Journal:  Brief Bioinform       Date:  2022-01-17       Impact factor: 11.622

4.  A comparison on predicting functional impact of genomic variants.

Authors:  Dong Wang; Jie Li; Yadong Wang; Edwin Wang
Journal:  NAR Genom Bioinform       Date:  2022-01-14

5.  PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions.

Authors:  Ning Zhang; Yuting Chen; Feiyang Zhao; Qing Yang; Franco L Simonetti; Minghui Li
Journal:  PLoS Comput Biol       Date:  2018-12-11       Impact factor: 4.475

6.  High-Throughput Genetic Testing in ALS: The Challenging Path of Variant Classification Considering the ACMG Guidelines.

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7.  SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability.

Authors:  Gen Li; Shailesh Kumar Panday; Emil Alexov
Journal:  Int J Mol Sci       Date:  2021-01-09       Impact factor: 5.923

8.  Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants.

Authors:  Yannick Mahlich; Maximillian Miller; Zishuo Zeng; Yana Bromberg
Journal:  Front Mol Biosci       Date:  2021-03-18

9.  MutTMPredictor: Robust and accurate cascade XGBoost classifier for prediction of mutations in transmembrane proteins.

Authors:  Fang Ge; Yi-Heng Zhu; Jian Xu; Arif Muhammad; Jiangning Song; Dong-Jun Yu
Journal:  Comput Struct Biotechnol J       Date:  2021-11-19       Impact factor: 7.271

10.  Predicting the most deleterious missense nsSNPs of the protein isoforms of the human HLA-G gene and in silico evaluation of their structural and functional consequences.

Authors:  Elaheh Emadi; Fatemeh Akhoundi; Seyed Mehdi Kalantar; Modjtaba Emadi-Baygi
Journal:  BMC Genet       Date:  2020-08-31       Impact factor: 2.797

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