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Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
2007
PLoS Computational Biology
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Citation: Karchin R, Monteiro ANA, Tavtigian SV, Carvalho MA, Sali A (2007) Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol 3(2): e26. ...
Here we describe a supervised learning approach to classification of BRCA1 UCVs. ...
The project has been supported by US National Institutes of Health grants F32 GM-072403-02, U01 GM-61390-04, R01 CA92309; the Sandler Family Supporting Foundation; an IBM SUR grant; and computer hardware ...
doi:10.1371/journal.pcbi.0030026
pmid:17305420
pmcid:PMC1797820
fatcat:p6ptmtdujrgmhmobd6s7yadbxu
Functional impact of missense variants in BRCA1 predicted by supervised learning
2005
PLoS Computational Biology
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Citation: Karchin R, Monteiro ANA, Tavtigian SV, Carvalho MA, Sali A (2007) Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol 3(2): e26. ...
Here we describe a supervised learning approach to classification of BRCA1 UCVs. ...
The project has been supported by US National Institutes of Health grants F32 GM-072403-02, U01 GM-61390-04, R01 CA92309; the Sandler Family Supporting Foundation; an IBM SUR grant; and computer hardware ...
doi:10.1371/journal.pcbi.0030026.eor
fatcat:ttoi4iypgvgf5gd4fue53i5ufa
Prediction of the functional impact of missense variants in BRCA1 and BRCA2 with BRCA-ML
[article]
2019
bioRxiv
pre-print
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In silico predictions of missense variants is an important consideration when interpreting variants of uncertain significance (VUS) in the BRCA1 and BRCA2 genes. ...
We trained and evaluated hundreds of machine learning algorithms based on results from validated functional assays to better predict missense variants in these genes as damaging or neutral. ...
Many in silico prediction models are derived from supervised learning methods using variants in many different genes across the genome. ...
doi:10.1101/792754
fatcat:unvown5h6bglbdjg2hpx5pfvga
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1
2009
Mutation research
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We analyzed the variants using a functional assay based on the transcription activation property of BRCA1 combined with supervised learning computational models. ...
The purpose of the present study was to functionally evaluate seven unclassified variants of BRCA1 including a genomic deletion that leads to the in-frame loss of exons 16/17 (Δ exons 16/17) in the mRNA ...
Structural analysis Prediction of the impact of amino acid changes in the BRCT domains was obtained by previously described bioinformatics supervised learning computation models [18, [25] [26] [27] . ...
doi:10.1016/j.mrfmmm.2008.09.017
pmid:18992264
pmcid:PMC2682550
fatcat:xosspn4uwvekzowg5bidt7rjjm
Predicting Pathogenicity of Missense Variants with Weakly Supervised Regression
[article]
2019
bioRxiv
pre-print
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On the platform enabled by CAGI (Critical Assessment of Genome Interpretation), we develop a novel "weakly supervised" regression (WSR) model that not only predicts precise clinical significance (probability ...
WSR model interpretation and protein structural interpretation reach consensus in corroborating the most probable molecular mechanisms by which some pathogenic BRCA1 variants confer clinical significance ...
approach the task with supervised learning, we collected missense variants data similarly classified using the five-tier clinical significance system and publicly available in the ClinVar database (Landrum ...
doi:10.1101/545913
fatcat:b3hcztp4nragxevj2ceh6mgssu
Analysis of BRCA gene missense mutations
2015
Journal of Biomedical Engineering and Informatics
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The interpretation of VUSs has been challenging due to the discordance of prediction results and their classification in different locus-specific databases (LSDBs). ...
With the significant progress in sequencing technologies over the last 10 years, a concomitant increase in the detection of variants of uncertain significance (VUSs) has been reported with an increasing ...
This tool compiles and displays all the functional data for all documented variants in the BRCA1 gene, which allows direct comparisons between functional data and strengthens the classification system ...
doi:10.5430/jbei.v2n1p91
fatcat:e5ouxxyv6jfstgsf63iyrzy3dm
Predicting functional effect of missense variants using graph attention neural networks
[article]
2021
bioRxiv
pre-print
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Finally, the model supports transfer learning to optimize gain- and loss-of-function predictions in sodium and calcium channels. ...
Evaluated by deep mutational scan data, gMVP outperforms published methods in identifying damaging variants in TP53, PTEN, BRCA1, and MSH2. ...
Acknowledgements This work was supported by NIH grants R01GM120609, R03HL147197, and U01HG008680. We thank Dr. Xiao Fan, Yige Zhao, Guojie Zhong, Dr. Mohammed AlQuraishi, and Dr. ...
doi:10.1101/2021.04.22.441037
fatcat:k6ritpllxbbm7llhyr7ossd64e
Clinical Classification ofBRCA1DNA Missense Variants: H1686Q Is a Novel Pathogenic Mutation Occurring in the Ontogenetically Invariant THV Motif of the N-Terminal BRCT Domain
2008
Journal of Clinical Oncology
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Karchin R, Monteiro AN, Tavtigian SV, et al: Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol 3:e26 2007
20. ...
Analysis of the impact of the H1686Q substitution on BRCAI protein function performed by the PolyPhen software (http://genetics.bwh.harvard .edu/pph/) predicted that the mutation is probably damaging with ...
doi:10.1200/jco.2008.18.2089
pmid:18757339
fatcat:7rnlw52oizc5bfaggtnjne7g6y
In Reply
2008
Journal of Clinical Oncology
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Karchin R, Monteiro AN, Tavtigian SV, et al: Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol 3:e26 2007
20. ...
Glover JN, Williams RS, Lee MS: Interacti phosphoproteins: Tangled up in two nd 3. Karchin R, Monteiro AN, Tavtigian SV, tior 5 variants in BRCA1 predicted by supervised learning. ...
doi:10.1200/jco.2008.18.2667
fatcat:nopqb4lcmrdvlfuxwycbp2vjza
Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios
2008
Cancer Informatics
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We present a computational method that produces a probabilistic likelihood ratio predictive of whether a missense variant impairs protein function. ...
Bioinformatics approaches for predicting the impact of these variants have not yet found their footing in clinical practice because 1) interpreting the medical relevance of predictive scores is difficult ...
The content is solely the responsibility of the authors and does not necessarily represent the offi cial view of the NCRR or the National Institutes of Health. ...
pmid:19043619
pmcid:PMC2587343
fatcat:slvl7vcvbrf47itel4e6kwj42a
In silico analysis of missense substitutions using sequence-alignment based methods
2008
Human Mutation
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In this paper, we review and/or make suggestions with respect to 1) the rationale for using in silico methods to help predict the consequences of missense variants, 2) important aspects of creating PMSAs ...
) of the gene of interest for almost any missense sequence variant, and 2) for many variants, structural features of wild type and variant proteins. ...
Acknowledgments This work was supported by grants from the National Institutes of Health (CA 96536, MSG) and the Lake Champlain Cancer Research Organization (MSG). ...
doi:10.1002/humu.20892
pmid:18951440
pmcid:PMC3431198
fatcat:3lta2476pbcofmgfhamdnpf37q
Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics
2017
Human Genomics
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Contemporary variant effect prediction tools are unlikely to be as accurate at the general prediction of functional impacts on proteins as reported prior. ...
Genetic variant effect prediction algorithms are used extensively in clinical genomics and research to determine the likely consequences of amino acid substitutions on protein function. ...
Acknowledgements This work was supported by Melbourne Bioinformatics through Resource Allocation VR0002. ...
doi:10.1186/s40246-017-0104-8
pmid:28511696
pmcid:PMC5433009
fatcat:2fyw2qxmdjdcljt2tiji7eczoq
Characterization of Synonymous BRCA1:c.132C>T as a Pathogenic Variant
2022
Frontiers in Oncology
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By analyzing variants recorded in the BRCA Exchange database, we found synonymous changes at the ends of exons could potentially influence splicing; meanwhile, current in silico tools could not predict ...
Collectively, we classified BRCA1:c.132C>T (p.Cys44=) as a pathogenic variant, as evidenced by functional studies, RNA analysis, and the patients' family histories. ...
Most VUSs in BRCA1/2 are missense variants, which have uncertain influences on the function of the protein product and the cancer risk of the carrier in question. ...
doi:10.3389/fonc.2021.812656
pmid:35087763
pmcid:PMC8789006
fatcat:zmaplxqsrberbpo6aevqa5wz24
Literature Review of BARD1 as a Cancer Predisposing Gene with a Focus on Breast and Ovarian Cancers
2020
Genes
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Soon after the discovery of BRCA1 and BRCA2 over 20 years ago, it became apparent that not all hereditary breast and/or ovarian cancer syndrome families were explained by germline variants in these cancer ...
biological assays of BARD1 variants to assess their effect on protein function; and (iii) association studies of BARD1 variants in family-based and case-control study groups to assess cancer risk. ...
The authors acknowledge the National Comprehensive Cancer Network guidelines for information regarding clinical management of carriers of variants in cancer predisposing genes. ...
doi:10.3390/genes11080856
pmid:32726901
fatcat:euxfw6xw35fp5bsrftjgk5r33m
Using deep mutational scanning data to benchmark computational phenotype predictors and identify pathogenic missense mutations
[article]
2019
bioRxiv
pre-print
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We also evaluate the ability of DMS measurements and computational phenotype predictors to discriminate between pathogenic and benign missense variants. ...
AbstractIn order to deal with the huge number of novel protein-coding variants being identified by genome and exome sequencing studies, many computational phenotype predictors have been developed. ...
BL is supported by the MRC Precision Medicine Doctoral Training Programme. ...
doi:10.1101/855957
fatcat:e32bscszb5czdmajtgfm3yl5my
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