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MutFormer: A context-dependent transformer-based model to predict pathogenic missense mutations [article]

Theodore Jiang, Kai Wang, Li Fang
2022 arXiv   pre-print
In this study, we introduce MutFormer, a transformer-based model for the prediction of pathogenic missense mutations, using reference and mutated amino acid sequences from the human genome as the features  ...  We next tested different fine-tuning methods for pathogenicity prediction, and determined that utilizing paired-protein sequences (concatenation of the wildtype and mutated protein sequence) yields the  ...  We would also like to acknowledge the TPU Research Cloud (TRC) program by Google, which provided us with TPUs for the duration of the project.  ... 
arXiv:2110.14746v2 fatcat:gnc5eub4gvhsnil55x3dd4jyzy

A forkhead-domain gene is mutated in a severe speech and language disorder

Cecilia S. L. Lai, Simon E. Fisher, Jane A. Hurst, Faraneh Vargha-Khadem, Anthony P. Monaco
2001 Nature  
Acknowledgements We are deeply indebted to the KE family whose continued cooperation has made this research possible. We also thank CS and family for agreeing to participate in this study. We  ...  The carboxy-terminal portion of the predicted protein sequence encoded by this gene (Fig. 2c) .  ...  We screened the newly de®ned coding regions (exons 1, 3b and 8± 17) of FOXP2 for mutations in the KE family.  ... 
doi:10.1038/35097076 pmid:11586359 fatcat:7ofwlgy6wngv3g7dxd46q5bip4

High-throughput screening

2001 Nature  
Acknowledgements We are deeply indebted to the KE family whose continued cooperation has made this research possible. We also thank CS and family for agreeing to participate in this study. We  ...  The carboxy-terminal portion of the predicted protein sequence encoded by this gene (Fig. 2c) .  ...  We screened the newly de®ned coding regions (exons 1, 3b and 8± 17) of FOXP2 for mutations in the KE family.  ... 
doi:10.1038/35097167 fatcat:7nmfs45corcgtgrbipack7f46m

A pathogenic PSEN2 p.His169Asn mutation associated with early-onset Alzheimer's disease

Vo Van Giau, Jung-Min Pyun, Eva Bagyinszky, Seong Soo A An, SangYun Kim
2018 Clinical Interventions in Aging  
The pathogenic nature of missense mutation and its 3D protein structure prediction were performed by in silico prediction programs.  ...  Genetic tests were performed in the patient to evaluate possible mutations using next-generation sequencing (NGS).  ...  The Ontology program, ClueGO, for the interaction prediction of the variant carrier proteins, could also help to understand the potential roles of PSEN2 in 2 major processes: amyloid-associated mechanisms  ... 
doi:10.2147/cia.s170374 pmid:30104866 pmcid:PMC6074827 fatcat:yl46p43b5vhv3lcw3te3ydsdka

Predicting the Disease Risk of Protein Mutation Sequences With Pre-training Model

Kuan Li, Yue Zhong, Xuan Lin, Zhe Quan
2020 Frontiers in Genetics  
The concatenation of two learned representations are then sent to the classifier to predict the missense mutations of protein sequences.  ...  In this paper, we propose a hybrid framework, called BertVS, that predicts the disease risk for the missense mutation of proteins.  ...  BERT Pre-training Model As a well-known language model, BERT has shown stateof-the-art performance in most natural language processing tasks (Devlin et al., 2018) .  ... 
doi:10.3389/fgene.2020.605620 pmid:33408741 pmcid:PMC7780924 fatcat:piymsy5m6zedpk3nsu7kwm4hlu

Conservation analysis and pathogenicity prediction of mutant genes of ectodysplasin a

Fangqi He, Hongfeng Wang, Xiaoyu Zhang, Qingping Gao, Feng Guo, Chang Chen
2018 BMC Medical Genetics  
SIFT and PolyPhen-2, the online gene function prediction software, were utilized to predict the pathogenicity of point mutation of c.878 T > G.  ...  In addition, the results of the pathogenicity prediction of point mutation of c.878 T > G by SIFT (P = 0.00) and PolyPhen-2 (S = 0.997) demonstrated that the mutation site had considerable pathogenicity  ...  Funding The present study was supported by the Natural Science Foundation of Hunan Province (grant numbers 2017JJ2377); the Hunan Provincial Science and Technology Department of China (grant numbers 2015JC3038  ... 
doi:10.1186/s12881-018-0726-2 fatcat:7yu2coun6rg4zhvvbgq5j2w56y

Role of CNTNAP2 in autism manifestation outlines the regulation of signaling between neurons at the synapse

Swati Agarwala, Nallur B. Ramachandra
2021 Egyptian Journal of Medical Human Genetics  
Secondary physical interactors of CNTNAP2 through CNTN2 proteins were mutated in the samples, further intensifying the severity.  ...  This sample cohort was used to identify causal mutations in autism-specific genes to create a mutational landscape focusing on the CNTNAP2 gene.  ...  Acknowledgements We thank the subjects and their families for participating in this study; the University of Mysore for their help and encouragement; the Department of Studies in Genetics and Genomics,  ... 
doi:10.1186/s43042-021-00138-z fatcat:imlqhhqabrcwhlhbhdxul7jmiq

A Novel Potentially Pathogenic Rare Variant in the DNAJC7 Gene Identified in Amyotrophic Lateral Sclerosis Patients From Mainland China

Mengli Wang, Zhen Liu, Yanchun Yuan, Jie Ni, Wanzhen Li, Yiting Hu, Pan Liu, Xiaorong Hou, Ling Huang, Bin Jiao, Lu Shen, Hong Jiang (+2 others)
2020 Frontiers in Genetics  
Variants in the DNAJC7 gene have been shown to be novel causes of amyotrophic lateral sclerosis (ALS). However, the contributions of DNAJC7 mutations in Asian ALS patients remain unclear.  ...  Our results expand the pathogenic variant spectrum of DNAJC7 and indicate that variants in the DNAJC7 gene may also contribute to ALS in the Chinese population.  ...  Data Bank (PDB) ID code] was used as the template.  ... 
doi:10.3389/fgene.2020.00821 pmid:33193563 pmcid:PMC7476650 fatcat:hcnujyqtvnehveywcaasoa4n5y

Deep Learning Architecture Optimization with Metaheuristic Algorithms for Predicting BRCA1/BRCA2 Pathogenicity NGS Analysis

Eric Pellegrino, Theo Brunet, Christel Pissier, Clara Camilla, Norman Abbou, Nathalie Beaufils, Isabelle Nanni-Metellus, Philippe Métellus, L'Houcine Ouafik
2022 BioMedInformatics  
and BRCA2 pathogenicity; Results, we will compare the results obtained by the two algorithms.  ...  They are involved in a considerable number of biological processes. To help the biologist in tumor classification, we developed a deep learning algorithm.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biomedinformatics2020016 fatcat:gcd5xrinjvaxdeh5ay2jwwopgy

C9ORF72 repeat expansions and other FTD gene mutations in a clinical AD patient series from Mayo Clinic

Aleksandra Wojtas, Kristin A Heggeli, Nicole Finch, Matt Baker, Mariely Dejesus-Hernandez, Steven G Younkin, Dennis W Dickson, Neill R Graff-Radford, Rosa Rademakers
2012 American Journal of Neurodegenerative Disease  
Pathogenic mutations of the amyloid precursor protein (APP) and presenilins 1 and 2 (PSEN1, PSEN2) genes have been linked to familial early-onset forms of AD; however, more recently mutations in the common  ...  found to carry expanded GGGGCC repeats in the non-coding region of C9ORF72.  ...  Acknowledgements This work was funded by the US National Institutes of Health (grants P50 AG016574, R01 AG026251, R01 AG18023 and R01 NS065782), the ALS Therapy Alliance, the Robert and Clarice Smith and  ... 
pmid:23383383 pmcid:PMC3560455 fatcat:v5ghdug5jvctxmvtq4bdtk6a44

New approaches to establish genetic causality

Elizabeth M. McNally, Alfred L. George
2015 Trends in cardiovascular medicine  
A survey of general approaches used for functional annotation of variants will also be presented.  ...  Whether one is seeking to discover the molecular basis for a disease in a research setting or trying to interpret results from a clinical genetic test, predicting the phenotypic effect of genetic variation  ...  Although the presence of pathogenic variants was highly meaningful for predicting disease in a given family, the rare nature of these genetic variants made their use across the population highly limited  ... 
doi:10.1016/j.tcm.2015.02.013 pmid:25864169 pmcid:PMC4560679 fatcat:by7xnhvvpbbpfh6etuxxscd4c4

Exploring dementia and neuronal ceroid lipofuscinosis genes in 100 FTD-like patients from 6 towns and rural villages on the Adriatic Sea cost of Apulia

Celeste Sassi, Rosa Capozzo, Monia Hammer, Chiara Zecca, Monica Federoff, Cornelis Blauwendraat, Nick Bernstein, Jinhui Ding, J. Raphael Gibbs, Timothy Price, Andrew Singleton, Giancarlo Logroscino
2021 Scientific Reports  
Although fully penetrant mutations in several genes have been identified and can explain the pathogenic mechanisms underlying a great portion of the Mendelian forms of the disease, still a significant  ...  We identified a nonsense mutation in SORL1 VPS domain (p.R744X), in 2 siblings displaying AD with severe language problems and primary progressive aphasia and a near splice-site mutation in CLCN6 (p.S116P  ...  Acknowledgements This work was supported in part by the Intramural Research Programs of the National Institute on Aging and the National Institutes of Neurological Disorders and Stroke, within the National  ... 
doi:10.1038/s41598-021-85494-x pmid:33737586 fatcat:2shyp32bejdibc7frywcijzkvy

Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry

Maria Anisimova
2015 BMC Evolutionary Biology  
Pharma and biotech industries can successfully use this potential, and should take the initiative to enhance their research and development with state of the art bioinformatics approaches.  ...  Results: Natural selection drives function conservation and adaptation to emerging pathogens or new environments; selection plays key role in immune and resistance systems.  ...  Acknowledgements This article was motivated by the mini-symposium "Life in numbers: the use of modeling and simulation in life sciences" which took place on the 5th of June 2014 at the Zürich University  ... 
doi:10.1186/s12862-015-0352-y pmid:25928234 pmcid:PMC4422139 fatcat:b3hgofdtojbbnhxfdytx2uqene

Genetic analyses of early-onset Alzheimer's disease using next generation sequencing

Vo Van Giau, Eva Bagyinszky, Young Soon Yang, Young Chul Youn, Seong Soo A. An, Sang Yun Kim
2019 Scientific Reports  
Many mutations in the amyloid precursor protein (APP) and presenilin 1 and 2 (PSEN1 and PSEN2) have been reported as the pathogenic causes of early-onset AD (EOAD), which accounts for up to 5% of all AD  ...  Main limitation of this study was the absence of functional assessment for possibly and probably pathogenic variants.  ...  SIFT uses different protein databases, such as SWISS-PROT, SWISS-PROT/TrEMBL, or protein databases of NCBI to calculate the possibility of the pathogenic nature of mutations by comparing mutant and normal  ... 
doi:10.1038/s41598-019-44848-2 pmid:31182772 pmcid:PMC6557896 fatcat:fkfnl5ffanbtphqchsen6z6llm

A novel phylogenetic analysis combined with a machine learning approach predicts human mitochondrial variant pathogenicity [article]

Bala Ani Akpinar, Paul O. Carlson, Cory D. Dunn
2020 bioRxiv   pre-print
Next, we use machine learning to predict the pathogenicity of thousands of so-far-uncharacterized human alleles catalogued in the clinic.  ...  However, the utility of multiple sequence alignments in pathogenicity prediction can be restricted by factors including sample set bias, alignment errors, and sequencing errors.  ...  First, we tested how the compared methods would fare against the training set that was used to build our own prediction model for variants in protein-coding genes.  ... 
doi:10.1101/2020.01.10.902239 fatcat:pcduneapozbczhokfi4fh7fks4
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