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Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data.

Alessandro Romanel1

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

Methods in Molecular Biology (Clifton, N.J.)
|November 1, 2018
PubMed
Summary

Allele-specific expression in cancer is poorly understood. This study presents a fast, reliable pipeline using next-generation sequencing to analyze allele-specific expression in tumors.

Keywords:
Allele-specific featuresGenome analysisNext-generation sequencingParallel computationSNPsTranscriptome analysis

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Area of Science:

  • Genomics
  • Cancer Biology
  • Bioinformatics

Background:

  • Allele-specific expression (ASE) occurs when gene transcription differs between alleles.
  • Understanding ASE in cancer is crucial but remains limited.
  • Previous research has focused on detection and characterization, but cancer-specific ASE landscapes are underexplored.

Purpose of the Study:

  • To develop and present a rapid and dependable analysis pipeline for studying allele-specific expression in cancer.
  • To enable a comprehensive analysis of ASE using next-generation sequencing (NGS) data in the context of cancer.

Main Methods:

  • The pipeline employs a gene-level analysis strategy.
  • It leverages paired germline DNA and tumor RNA sequencing data.
  • The approach is designed to utilize parallel computation for efficiency.

Main Results:

  • A fast and reliable analysis pipeline for allele-specific expression in cancer has been established.
  • The pipeline facilitates the study of ASE using NGS data.
  • The methodology is scalable and benefits from parallel processing.

Conclusions:

  • The developed pipeline offers a robust method for investigating allele-specific expression in cancer.
  • This tool can advance our understanding of the role of ASE in tumorigenesis.
  • The pipeline provides a valuable resource for cancer genomics research.