High-throughput deep learning variant effect prediction with Sequence UNET
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens (human)
SUBMITTER: Alistair S. Dunham
PROVIDER: S-BSST732 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description:High-quality and high-throughput prediction of enzyme commission (EC) numbers is essential for accurate understanding of enzyme functions, which have many implications in pathologies and industrial biotechnology. Several EC number prediction tools are currently available, but their prediction performance needs to be further improved to precisely and efficiently process an ever-increasing volume of protein sequence data. Here, we report DeepEC, a deep learning-based computational framework that predicts EC numbers for protein sequences with high precision and in a high-throughput manner. DeepEC takes a protein sequence as input and predicts EC numbers as output. DeepEC uses 3 convolutional neural networks (CNNs) as a major engine for the prediction of EC numbers, and also implements homology analysis for EC numbers that cannot be classified by the CNNs. Comparative analyses against 5 representative EC number prediction tools show that DeepEC allows the most precise prediction of EC numbers, and is the fastest and the lightest in terms of the disk space required. Furthermore, DeepEC is the most sensitive in detecting the effects of mutated domains/binding site residues of protein sequences. DeepEC can be used as an independent tool, and also as a third-party software component in combination with other computational platforms that examine metabolic reactions.
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Project description:Here, we present DeepBIO, the first-of-its-kind automated and interpretable deep-learning platform for high-throughput biological sequence functional analysis. DeepBIO is a one-stop-shop web service that enables researchers to develop new deep-learning architectures to answer any biological question. Specifically, given any biological sequence data, DeepBIO supports a total of 42 state-of-the-art deep-learning algorithms for model training, comparison, optimization and evaluation in a fully automated pipeline. DeepBIO provides a comprehensive result visualization analysis for predictive models covering several aspects, such as model interpretability, feature analysis and functional sequential region discovery. Additionally, DeepBIO supports nine base-level functional annotation tasks using deep-learning architectures, with comprehensive interpretations and graphical visualizations to validate the reliability of annotated sites. Empowered by high-performance computers, DeepBIO allows ultra-fast prediction with up to million-scale sequence data in a few hours, demonstrating its usability in real application scenarios. Case study results show that DeepBIO provides an accurate, robust and interpretable prediction, demonstrating the power of deep learning in biological sequence functional analysis. Overall, we expect DeepBIO to ensure the reproducibility of deep-learning biological sequence analysis, lessen the programming and hardware burden for biologists and provide meaningful functional insights at both the sequence level and base level from biological sequences alone. DeepBIO is publicly available at https://inner.wei-group.net/DeepBIO.
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Project description:Sequence-to-function models have broad applications in interpreting the molecular impact of genetic variation, yet have been criticized for poor performance in this task. Here we show that training models on functional genomic data with matched personal genomes improves their performance at variant effect prediction. Variant effect representations are retained even when fine tuning models to unseen cellular contexts and experimental readouts. Our results have implications for interpreting trait-associated genetic variation.
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Project description:Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation. However, this is extremely difficult because of the enormous scale of the noncoding mutation space. We developed a deep learning-based framework, ExPecto, that can accurately predict, ab initio from a DNA sequence, the tissue-specific transcriptional effects of mutations, including those that are rare or that have not been observed. We prioritized causal variants within disease- or trait-associated loci from all publicly available genome-wide association studies and experimentally validated predictions for four immune-related diseases. By exploiting the scalability of ExPecto, we characterized the regulatory mutation space for human RNA polymerase II-transcribed genes by in silico saturation mutagenesis and profiled > 140 million promoter-proximal mutations. This enables probing of evolutionary constraints on gene expression and ab initio prediction of mutation disease effects, making ExPecto an end-to-end computational framework for the in silico prediction of expression and disease risk.
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Project description:BackgroundSplicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond those occurring at donor and acceptor dinucleotides. To address this, various methods aim to predict variant effects on splicing. Recently, deep neural networks (DNNs) have been shown to achieve better results in predicting splice variants than other strategies.MethodsIt has been unclear how best to integrate such process-specific scores into genome-wide variant effect predictors. Here, we use a recently published experimental data set to compare several machine learning methods that score variant effects on splicing. We integrate the best of those approaches into general variant effect prediction models and observe the effect on classification of known pathogenic variants.ResultsWe integrate two specialized splicing scores into CADD (Combined Annotation Dependent Depletion; cadd.gs.washington.edu ), a widely used tool for genome-wide variant effect prediction that we previously developed to weight and integrate diverse collections of genomic annotations. With this new model, CADD-Splice, we show that inclusion of splicing DNN effect scores substantially improves predictions across multiple variant categories, without compromising overall performance.ConclusionsWhile splice effect scores show superior performance on splice variants, specialized predictors cannot compete with other variant scores in general variant interpretation, as the latter account for nonsense and missense effects that do not alter splicing. Although only shown here for splice scores, we believe that the applied approach will generalize to other specific molecular processes, providing a path for the further improvement of genome-wide variant effect prediction.
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Project description:Recent advancements in high-throughput sequencing technologies have significantly enhanced our ability to unravel the intricacies of gene regulatory processes. A critical challenge in this endeavor is the identification of variant effects, a key factor in comprehending the mechanisms underlying gene regulation. Non-coding variants, constituting over 90% of all variants, have garnered increasing attention in recent years. The exploration of gene variant impacts and regulatory mechanisms has spurred the development of various deep learning approaches, providing new insights into the global regulatory landscape through the analysis of extensive genetic data. Here, we provide a comprehensive overview of the development of the non-coding variants models based on bulk and single-cell sequencing data and their model-based interpretation and downstream tasks. This review delineates the popular sequencing technologies for epigenetic profiling and deep learning approaches for discerning the effects of non-coding variants. Additionally, we summarize the limitations of current approaches in variant effect prediction research and outline opportunities for improvement. We anticipate that our study will offer a practical and useful guide for the bioinformatic community to further advance the unraveling of genetic variant effects.
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Project description:BackgroundDiagnosis of mitral regurgitation (MR) requires careful evaluation by echocardiography with Doppler imaging. This study presents the development and validation of a fully automated deep learning pipeline for identifying apical 4-chamber view videos with color Doppler echocardiography and detecting clinically significant (moderate or severe) MR from transthoracic echocardiograms.MethodsA total of 58 614 transthoracic echocardiograms (2 587 538 videos) from Cedars-Sinai Medical Center were used to develop and test an automated pipeline to identify apical 4-chamber view videos with color Doppler across the mitral valve and then assess MR severity. The model was tested internally on a test set of 1800 studies (80 833 videos) from Cedars-Sinai Medical Center and externally evaluated in a geographically distinct cohort of 915 studies (46 890 videos) from Stanford Healthcare.ResultsIn the held-out Cedars-Sinai Medical Center test set, the view classifier demonstrated an area under the curve (AUC) of 0.998 (0.998-0.999) and correctly identified 3452 of 3539 echocardiography videos as having color Doppler information across the mitral valve (sensitivity of 0.975 [0.968-0.982] and specificity of 0.999 [0.999-0.999] compared with manually curated videos). In the external test cohort from Stanford Healthcare, the view classifier correctly identified 1051 of 1055 manually curated videos with color Doppler information across the mitral valve (sensitivity of 0.996 [0.990-1.000] and specificity of 0.999 [0.999-0.999]). In the Cedars-Sinai Medical Center test cohort, MR moderate or greater in severity was detected with an AUC of 0.916 (0.899-0.932) and severe MR was detected with an AUC of 0.934 (0.913-0.953). In the Stanford Healthcare test cohort, the model detected MR moderate or greater in severity with an AUC of 0.951 (0.924-0.973) and severe MR with an AUC of 0.969 (0.946-0.987).ConclusionsIn this study, a novel automated pipeline for identifying clinically significant MR from full transthoracic echocardiography studies demonstrated excellent performance across large numbers of studies and across multiple institutions. Such an approach has the potential for automated screening and surveillance of MR.
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Project description:In recent years, it has been seen that artificial intelligence (AI) starts to bring revolutionary changes to chemical synthesis. However, the lack of suitable ways of representing chemical reactions and the scarceness of reaction data has limited the wider application of AI to reaction prediction. Here, we introduce a novel reaction representation, GraphRXN, for reaction prediction. It utilizes a universal graph-based neural network framework to encode chemical reactions by directly taking two-dimension reaction structures as inputs. The GraphRXN model was evaluated by three publically available chemical reaction datasets and gave on-par or superior results compared with other baseline models. To further evaluate the effectiveness of GraphRXN, wet-lab experiments were carried out for the purpose of generating reaction data. GraphRXN model was then built on high-throughput experimentation data and a decent accuracy (R2 of 0.712) was obtained on our in-house data. This highlights that the GraphRXN model can be deployed in an integrated workflow which combines robotics and AI technologies for forward reaction prediction.
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