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ASEQ: fast allele-specific studies from next-generation sequencing data.

Alessandro Romanel1, Sara Lago2, Davide Prandi3

  • 1Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy. romanel@science.unitn.it.

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Summary

We developed ASEQ, a new tool for allele-specific expression (ASE) analysis from next-generation sequencing (NGS) data. ASEQ efficiently identifies genetic variations in large datasets, aiding in disease research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Next-generation sequencing (NGS) enables quantitative assessment of biological phenomena like mosaicism and allele-specific expression (ASE).
  • Genome-wide investigations across large datasets face computational challenges.
  • Initiatives like the 1,000 Genomes Project and TCGA generate vast amounts of genomic data.

Purpose of the Study:

  • To introduce ASEQ, a novel computational tool for gene-level allele-specific expression (ASE) analysis.
  • To enable ASE analysis from paired genomic and transcriptomic NGS data without parental genome information.
  • To provide a user-friendly tool with a fast computational engine for large-scale genomic studies.

Main Methods:

  • ASEQ analyzes gene-level allele-specific expression (ASE) using paired genomic and transcriptomic NGS data.
  • The tool does not require paternal and maternal genome data for analysis.
  • ASEQ incorporates a fast computational engine and offers various user-friendly modes.

Main Results:

  • ASEQ demonstrated effective performance on 20 individuals from the 1,000 Genomes Project, highlighting its power in detecting imprinted genes.
  • High concordance was observed when comparing ASEQ's allele-specific expression (ASE) calls with existing tools like AlleleSeq and MBASED.
  • Analysis of a prostate cancer dataset revealed a higher fraction of ASE genes in cancer compared to healthy individuals, with ASEQ identifying allele-specific events in disease-implicated genes.

Conclusions:

  • ASEQ provides a rapid and reliable method for screening large NGS datasets to identify allele-specific features.
  • The tool is easily integrated into existing NGS pipelines.
  • ASEQ is compatible with various computing systems, including multi-CPU, multi-core, and cluster environments.