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Using bioinformatics to predict the functional impact of SNVs

M. S. Cline, R. Karchin
2010 Bioinformatics  
Here, we describe the essential components of bionformatics tools that predict functional SNVs.  ...  Results: Bioinformatics tools have great potential to identify functional SNVs, but the black box nature of many tools can be a pitfall for researchers.  ...  ACKNOWLEDGEMENT We thank Laurence Meyer for insightful discussions and critical review of the manuscript.  ... 
doi:10.1093/bioinformatics/btq695 pmid:21159622 pmcid:PMC3105482 fatcat:ammdqhjj2re4dgpxyu6agn2bmm

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini
2015 Briefings in Bioinformatics  
Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various Khader Shameer, PhD, obtained his MSc  ...  Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions.  ...  The Mayo Clinic Bioinformatics Core provided infrastructure and analytical support to K.R.K. R.S. would like to thank National Centre for Biological Sciences (TIFR) for infrastructural support.  ... 
doi:10.1093/bib/bbv084 pmid:26494363 pmcid:PMC6078163 fatcat:xeldhpluhjajnnatu44secmb3u

Impact of genetic variation on three dimensional structure and function of proteins

Roshni Bhattacharya, Peter W. Rose, Stephen K. Burley, Andreas Prlić, Yang Zhang
2017 PLoS ONE  
Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease.  ...  , some in the context of large assemblies.  ...  Acknowledgments We thank Hagen Tilgner, Lilia Iakoucheva, and Roser Corominas for useful discussions, Sajani Swamy for feedback on the manuscript.  ... 
doi:10.1371/journal.pone.0171355 pmid:28296894 pmcid:PMC5351996 fatcat:fu6vzdo4hjdrliuimow2h56xe4

Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein–protein interfaces: Fig. 1

Miguel Vázquez, Alfonso Valencia, Tirso Pons
2015 Bioinformatics  
We illustrate the usefulness of Structure-PPi with the interpretation of 1 027 122 non-synonymous SNVs from COSMIC and the 1000G Project that provides a collection of 172 700 SNVs mapped onto the protein  ...  Current tools that annotate mutations fall short on several aspects, including the ability to use protein structure information or the interpretation of mutations in protein complexes.  ...  Acknowledgement The authors thank all members of the Structural Computational Biology group for useful feedback.  ... 
doi:10.1093/bioinformatics/btv142 pmid:25765346 pmcid:PMC4495296 fatcat:4azjty3eijgobe3kxvym3x5xfq

Comparative Panel Sequencing of DNA Variants in cf-, ev- and tumorDNA for Pancreatic Ductal Adenocarcinoma Patients

Mareike Waldenmaier, Lucas Schulte, Jonathan Schönfelder, Axel Fürstberger, Johann M. Kraus, Nora Daiss, Tanja Seibold, Mareen Morawe, Thomas J. Ettrich, Hans A. Kestler, Christoph Kahlert, Thomas Seufferlein (+1 others)
2022 Cancers  
Stringent bioinformatic processing revealed a significant advantage of evDNA with respect to cfDNA concerning detection performance for SNVs and a numerical increase for indels.  ...  A combination of ev- and cfDNA was clearly superior for SNV detection, as compared to either single analyte, thus potentially improving actionable variant prediction upon further optimization.  ...  The authors would like to thank Ralf Marienfeld from the Department of Pathology (Ulm University) for providing samples and for helpful insights on bioinformatic processing of sequencing data.  ... 
doi:10.3390/cancers14041074 pmid:35205822 pmcid:PMC8870073 fatcat:4l6q7tzem5djpm2ehvsn2jztma

Bioinformatics for personal genome interpretation

E. Capriotti, N. L. Nehrt, M. G. Kann, Y. Bromberg
2012 Briefings in Bioinformatics  
This information has enabled researchers to develop bioinformatics tools to analyze the rapidly increasing amount of newly extracted variation data and to predict the effect of uncharacterized variants  ...  In this work, we review the most important developments in the fieldçthe databases and bioinformatics tools that will be of utmost importance in our concerted effort to interpret the human variome.  ...  The mention of commercial products herein is not to be construed as either an actual or implied endorsement of such products by the Department of Health and Human Services.  ... 
doi:10.1093/bib/bbr070 pmid:22247263 pmcid:PMC3404395 fatcat:zdu5z4bbtncerp7cyw6mjrf3d4

seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data

Erik Fasterius, Cristina Al-Khalili Szigyarto
2018 F1000Research  
Its ease of use, installation, complete data-to-conclusions functionality and the inherent flexibility of the R programming language make seqCAT a powerful tool for variant analyses compared to already  ...  A publicly available dataset of liver cancer-derived organoids is analysed herein using the seqCAT package, demonstrating that the organoids are genetically stable.  ...  Acknowledgements We would like to acknowledge support from Science for Life Laboratory (SciLifeLab), the National Genomics Infrastructure (NGI) and Uppmax for providing assistance in computational infrastructure  ... 
doi:10.12688/f1000research.16083.1 fatcat:6yyebvg7pjb4dd27khdvrh4qlu

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

Abel Gonzalez-Perez, Jordi Deu-Pons, Nuria Lopez-Bigas
2012 Genome Medicine  
Our new method, transformed Functional Impact score for Cancer (transFIC), improves the assessment of the functional impact of tumor nsSNVs by taking into account the baseline tolerance of genes to functional  ...  One important step in this task is to assess the functional impact of tumor somatic mutations.  ...  We acknowledge funding from the Spanish Ministry of Science and Technology (grant number SAF2009-06954) and the Spanish National Institute of Bioinformatics (INB).  ... 
doi:10.1186/gm390 pmid:23181723 pmcid:PMC4064314 fatcat:2cbveb2kgvdntnhallvanjvu7y

Exome Sequencing Identified NRG3 as a Novel Susceptible Gene of Hirschsprung's Disease in a Chinese Population

Jun Yang, Shengyu Duan, Rong Zhong, Jieyun Yin, Jiarui Pu, Juntao Ke, Xuzai Lu, Li Zou, Hongmei Zhang, Zhidong Zhu, Depeng Wang, Huasheng Xiao (+5 others)
2013 Molecular Neurobiology  
Although the genetic defect of enteric nervous system (ENS) was identified to play a critical role in the progress of HSCR, the systemic genetic dissection of HSCR still needs to be clarified.  ...  After the initial quality filtering (coverage≥5X and SNP quality score≥40) of the raw data, we identified 13,948 and 13,856 single nucleotide variants (SNVs), respectively.  ...  The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1007/s12035-012-8392-4 pmid:23315268 fatcat:xm54nigtsneh3lf72y5nsuj5ka

Double hits in schizophrenia

Jacob A S Vorstman, Loes M Olde Loohuis, René S Kahn, Roel A Ophoff, Behrooz Z Alizadeh, Agna A Bartels-Velthuis, Nico J van Beveren, Richard Bruggeman, Wiepke Cahn, Lieuwe de Haan, Philippe Delespaul, Carin J Meijer (+16 others)
2018 Human Molecular Genetics  
We provide early evidence that deletions co-occurring with a functional variant may be relevant, albeit of modest impact, for the genetic etiology of schizophrenia.  ...  The Authors have declared that there are no conflicts of interest in relation to the subject of this study.  ...  Acknowledgements We are grateful for the generosity of time and effort by the patients, their families and healthy subjects.  ... 
doi:10.1093/hmg/ddy175 pmid:29767709 fatcat:oaxtmbszwbc7va7tghc4z6wa7y

Novel sequencing technologies and bioinformatic tools for deciphering the non-coding genome

Jana Marie Schwarz, Richard Lüpken, Dominik Seelow, Birte Kehr
2021 Medizinische Genetik  
bioinformatic tools for the prediction of effects variants may have in the non-coding part of the genome.  ...  This is primarily due to a substantially increased identification rate of disease mutations in the coding sequence, primarily SNVs and indels.  ...  Improving the prediction of the functional impact of the DNA variants is subject of future research.  ... 
doi:10.1515/medgen-2021-2072 fatcat:dec3cgwpzbhjxn6ult6yrz7vny

Prediction of driver variants in the cancer genome via machine learning methodologies

Mark F Rogers, Tom R Gaunt, Colin Campbell
2020 Briefings in Bioinformatics  
Sequencing technologies have led to the identification of many variants in the human genome which could act as disease-drivers.  ...  As a consequence, a variety of bioinformatics tools have been proposed for predicting which variants may drive disease, and which may be causatively neutral.  ...  Funding The Integrative Epidemiology Unit is supported by the Medical Research Council (MC_UU_00011/) and the University of Bristol, and we also acknowledge funding from the Cancer Research UK Integrative  ... 
doi:10.1093/bib/bbaa250 pmid:33094325 pmcid:PMC8293831 fatcat:6j5rda4mifa7rn7jdivsh4wkkm

MORFEE: a new tool for detecting and annotating single nucleotide variants creating premature ATG codons from VCF files [article]

Dylan Aissi, Omar Soukarieh, Carole Proust, Beatrice Jaspard-Vinassa, Pierre Fautrad, Manal Ibrahim-Kosta, Felipe Leal-Valentim, Maguelonne Roux, Delphine Bacq-Daian, Robert Olaso, Jean-Francois Deleuze, Pierre-Emmanuel Morange (+1 others)
2020 bioRxiv   pre-print
We here describe MORFEE, a new bioinformatics tool that detects, annotates and predicts, from a standard VCF file, the creation of uORF by any 5'UTR variants on uORF creation.  ...  MORFEE was applied to two genomic resources and identified candidate functional variants that could explain statistical association signals observed in the context of Genome Wide Association Studies or  ...  Funding This work was supported by the GENMED Laboratory of Excellence on Medical Genomics [ANR-10-LABX-0013 to OS]. D.A was partially financially supported by a ANR-18-PERM-0004 grant.  ... 
doi:10.1101/2020.03.29.012054 fatcat:rfpernksovb2fmkw2wnxdtj34i

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures

Noushin Niknafs, Dewey Kim, RyangGuk Kim, Mark Diekhans, Michael Ryan, Peter D. Stenson, David N. Cooper, Rachel Karchin
2013 Human Genetics  
The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure  ...  Multiple SNVs may be mapped onto each structure, enabling 3D visualization of SNV clusters and their relationship to functionally annotated positions.  ...  Acknowledgments We used the Broad Institute Firehose standardization run from 7 July, 2012, which may be foundhere in the TCGA Data Coordination Center: http://gdac.broadinstitute.org/runs/stddata__2012  ... 
doi:10.1007/s00439-013-1325-0 pmid:23793516 pmcid:PMC3797853 fatcat:l4f552uhzfaqflhigwtl32m5ou

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

G. De Baets, J. Van Durme, J. Reumers, S. Maurer-Stroh, P. Vanhee, J. Dopazo, J. Schymkowitz, F. Rousseau
2011 Nucleic Acids Research  
The SNPeffect database (http://snpeffect.switchlab.org) uses sequenceand structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins.  ...  Linking structural effects of non-synonymous SNVs to functional outcomes is a major issue in structural bioinformatics.  ...  Coding non-synonymous SNVs can affect protein structure and function to various degrees (12, 13) .  ... 
doi:10.1093/nar/gkr996 pmid:22075996 pmcid:PMC3245173 fatcat:fsc43yiupvad3gmuuni4ezhjyu
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