Dataset Information

P²T²: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants.

ABSTRACT:

Motivation

Genomic data are prevalent, leading to frequent encounters with uninterpreted variants or mutations with unknown mechanisms of effect. Researchers must manually aggregate data from multiple sources and across related proteins, mentally translating effects between the genome and proteome, to attempt to understand mechanisms.

Materials and methods

P²T² presents diverse data and annotation types in a unified protein-centric view, facilitating the interpretation of coding variants and hypothesis generation. Information from primary sequence, domain, motif, and structural levels are presented and also organized into the first Paralog Annotation Analysis across the human proteome.

Results

Our tool assists research efforts to interpret genomic variation by aggregating diverse, relevant, and proteome-wide information into a unified interactive web-based interface. Additionally, we provide a REST API enabling automated data queries, or repurposing data for other studies.

Conclusion

The unified protein-centric interface presented in P²T² will help researchers interpret novel variants identified through next-generation sequencing. Code and server link available at github.com/GenomicInterpretation/p2t2.

SUBMITTER: DeVoe E

PROVIDER: S-EPMC8346652 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Publications

P<sup>2</sup>T<sup>2</sup>: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants.

DeVoe Elias E Oliver Gavin R GR Zenka Roman R Blackburn Patrick R PR Cousin Margot A MA Boczek Nicole J NJ Kocher Jean-Pierre A JA Urrutia Raul R Klee Eric W EW Zimmermann Michael T MT

JAMIA open 20210701 3

<h4>Motivation</h4>Genomic data are prevalent, leading to frequent encounters with uninterpreted variants or mutations with unknown mechanisms of effect. Researchers must manually aggregate data from multiple sources and across related proteins, mentally translating effects between the genome and proteome, to attempt to understand mechanisms.<h4>Materials and methods</h4>P<sup>2</sup>T<sup>2</sup> presents diverse data and annotation types in a unified protein-centric view, facilitating the inte ...[more]

PMID: 34377961

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Project description:BackgroundAn individual's genetics play a role in how RNA transcripts are generated from DNA and consequently in their translation into protein. Transcriptional and translational profiling of patients furnishes the information that a specific marker is present; however, it fails to provide evidence whether the marker correlates with response to a therapeutic agent. A comparative analysis of the frequency of genetic variants, such as single nucleotide polymorphisms (SNPs), in diseased and general populations can identify pathogenic variants in individual patients. This is in part because SNPs have considerable effects on protein function and gene expression when they occur in coding regions and regulatory sequences, respectively. Therefore, a tool that can help users to obtain the allele frequency for a corresponding transcript is the need of the day. Several annotation tools such as SNPnexus and VariED are publicly available; however, none of them can use transcript IDs as input and provide the corresponding genomic positions of variants.ResultsIn this study, we developed an R package, called transcript annotation tool (TransAT), that provides (i) SNP ID and genomic position for a user-provided transcript ID from patients, and (ii) allele frequencies for the SNPs from publicly available global populations. All data elements are extracted, collected, and displayed in an easily downloadable format in two simple command lines. TransAT is available on Windows/Linux/MacOS and is operative for R version 4.0.4 or later. It is available at https://github.com/ShihChingYu/TransAT and can be downloaded and installed using devtools::install_github("ShihChingYu/TransAT", force=T) on the R execution page. Thereafter, all functions can be executed by loading the package into R with library(TransAT).ConclusionsTransAT is a novel tool that seamlessly provides genetic annotations for queried transcripts. Such easily obtainable information would be greatly advantageous for physicians, assisting them to make individualized decisions about specific drug treatments. Moreover, allele frequencies from user-chosen global ethnic populations will highlight the importance of ethnicity and its effect on patient pathogenicity.

Dataset Information

P²T²: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants.

Motivation

Materials and methods

Results

Conclusion

Publications

P<sup>2</sup>T<sup>2</sup>: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants.

Motivation

Materials and methods

Results

Conclusion

Publications

P<sup>2</sup>T<sup>2</sup>: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

P²T²: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants.