Journal ArticleDOI
Applications of computational algorithm tools to identify functional SNPs
C. George Priya Doss,C. Sudandiradoss,R. Rajasekaran,Parikshit Choudhury,Priyanka Sinha,Pragnya Hota,Udit Prakash Batra,Sethumadhavan Rao +7 more
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TLDR
This work analyzed the SNPs that can alter the expression and function of transcriptional factor TP53 as a pipeline and proposed modeled structure for the mutant proteins and compared them with the native protein.Abstract:
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variations in humans Understanding the functions of SNPs can greatly help to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases The method to identify functional SNPs from a pool, containing both functional and neutral SNPs is challenging by experimental protocols To explore possible relationships between genetic mutation and phenotypic variation, different computational algorithm tools like Sorting Intolerant from Tolerant, Polymorphism Phenotyping, UTRscan, FASTSNP, and PupaSuite were used for prioritization of high-risk SNPs in coding region (exonic nonsynonymous SNPs) and noncoding regions (intronic and exonic 5' and 3'-untranslated region (UTR) SNPs) In this work, we have analyzed the SNPs that can alter the expression and function of transcriptional factor TP53 as a pipeline and for providing a guide to experimental work We identified the possible mutations and proposed modeled structure for the mutant proteins and compared them with the native protein These nsSNPs play a critical role in cancer association studies aiming to explain the disparity in cancer treatment responses as well as to improve the effectiveness of the cancer treatments Our results endorse the study with in vivo experimental protocolsread more
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Advances in translational bioinformatics: computational approaches for the hunting of disease genes
TL;DR: This review highlights the latest advances in the field of translational bioinformatics, focusing on the advances of computational techniques to search for and classify disease genes.
Journal ArticleDOI
Single nucleotide polymorphisms of Toll-like receptor 4 decrease the risk of development of hepatocellular carcinoma.
Shi Minmin,Xu Xiaoqian,Chen Hao,Chen Hao,Shen Baiyong,Shen Baiyong,Deng Xiaxing,Deng Xiaxing,Xie Junjie,Zhan Xi,Zhao Jianquan,Jiang Songyao +11 more
TL;DR: It is suggested that the risk of hepatocellular carcinoma was associated with TLR4 sequence variation, and single nucleotide polymorphisms ofTLR4 may play an important protective role in the development of liver cancer.
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Toll-Like Receptor (TLR2 and TLR4) Polymorphisms and Chronic Obstructive Pulmonary Disease
Simona E. Budulac,H. Marike Boezen,Pieter S. Hiemstra,Thérèse S. Lapperre,Judith M. Vonk,Wim Timens,Dirkje S. Postma +6 more
TL;DR: This is the first longitudinal study showing that tagging SNPs in TLR2 and TLR4 are associated with the level and decline of lung function as well as with inflammatory cell numbers in induced sputum in COPD patients, suggesting a role in the severity and progression of COPD.
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A Comprehensive In Silico Analysis of the Functional and Structural Impact of SNPs in the IGF1R Gene
TL;DR: A comprehensive analysis of the functional and structural impact of all known SNPs in this gene using publicly available computational prediction tools shows that a mutation from arginine to cysteine at position 1216 on the surface of the protein caused the greatest impact on stability.
Journal ArticleDOI
Genetic variations in TERT-CLPTM1L locus are associated with risk of lung cancer in Chinese population.
Rong Zhong,Li Liu,Li Zou,Yaowu Zhu,Wei Chen,Beibei Zhu,Na Shen,Rui Rui,Lu Long,Juntao Ke,Xuzai Lu,Ti Zhang,Yu Zhang,Zhenling Wang,Lifeng Liu,Yu Sun,Liming Cheng,Xiaoping Miao +17 more
TL;DR: Findings indicated that the function‐validated and potentially functional variations in TERT‐CLPTM1L locus, modified by smoking, may play a substantial role in the susceptibility to lung cancer.
References
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Journal ArticleDOI
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
TL;DR: The SNPeffect database, based on the Ensembl human databases, has been remodeled to better fit an automatically updatable structure and holds the molecular phenotype of 74 567 nsSNPs in 23 426 proteins.
Journal ArticleDOI
Meta-analysis of the p53 mutation database for mutant p53 biological activity reveals a methodologic bias in mutation detection.
Thierry Soussi,Bernard Asselain,Dalil Hamroun,Shunsuke Kato,Chikashi Ishioka,Mireille Claustres,Christophe Béroud +6 more
TL;DR: This analysis reveals that some reports of infrequent mutations are associated with almost normal activities of p53 proteins, showing the importance of accurate functional analysis before inferring any genetic variation.
Book
Single nucleotide polymorphisms : methods and protocols
TL;DR: This work presents a meta-anatomy of SNP Genotyping, a probabilistic approach to estimating the number of SNP bases in DNA using a single sample, and some of the techniques used to achieve this result.
Journal ArticleDOI
Mapping SNPs to protein sequence and structure data
A. Cavallo,Andrew J. Martin +1 more
TL;DR: The initial aim is to create a completely automatically maintained database of SAAPs mapped to individual residues in the Protein Data Bank (PDB) updated as new mutations or structures become available.
Journal ArticleDOI
Genetic variation in TP53 and risk of breast cancer in a population-based case–control study
Brian L. Sprague,Amy Trentham-Dietz,Montserrat Garcia-Closas,Polly A. Newcomb,Polly A. Newcomb,Linda Titus-Ernstoff,John M. Hampton,Stephen J. Chanock,Jonathan L. Haines,Kathleen M. Egan +9 more
TL;DR: Results indicate that common variation in the TP53 gene could modify the risk of invasive breast cancer, and the overall association with breast cancer risk was assessed using a global score test.