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Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic

Ching-Yu Shih1, Amrita Chattopadhyay1, Chien-Hui Wu2,3

  • 1Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan.

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Summary
This summary is machine-generated.

This study introduces TransAT, an R package for genetic variant annotation. TransAT provides SNP ID, genomic positions, and allele frequencies for transcripts, aiding personalized medicine and drug treatment decisions.

Keywords:
Allele frequencyR packageTransATTranscript annotationVariant annotation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Pharmacogenomics

Background:

  • Genetic variations, like single nucleotide polymorphisms (SNPs), influence RNA and protein production.
  • Identifying pathogenic variants requires analyzing SNP frequencies in patient populations.
  • Existing annotation tools lack the ability to use transcript IDs for variant retrieval.

Purpose of the Study:

  • To develop a novel R package for transcript annotation.
  • To enable users to obtain SNP ID, genomic position, and allele frequencies from transcript IDs.
  • To facilitate personalized medicine by providing crucial genetic information.

Main Methods:

  • Developed the R package 'transcript annotation tool' (TransAT).
  • Integrated data extraction and collection for SNP and allele frequency information.
  • Ensured easy data retrieval and downloadability via simple command lines.

Main Results:

  • TransAT successfully provides SNP ID and genomic positions for user-provided transcript IDs.
  • The tool offers allele frequencies for SNPs from global populations.
  • All data is presented in an easily downloadable format.

Conclusions:

  • TransAT is a novel tool for seamless genetic annotation of transcripts.
  • The tool aids physicians in making individualized drug treatment decisions.
  • Allele frequencies highlight the impact of ethnicity on patient pathogenicity.