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Toolbox for mobile-element insertion detection on cancer genomes.

Wan-Ping Lee1, Jiantao Wu2, Gabor T Marth3

  • 1Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at Seven Bridges Genomics, Cambridge, MA, USA.

Cancer Informatics
|May 2, 2015
PubMed
Summary

TANGRAM, a tool for detecting mobile-element insertions (MEIs), now supports various mapping tools for broader genomic analysis. This advancement aids in identifying disease-causing genomic changes, particularly in cancer research.

Keywords:
ALUmobile-element insertionstructural variation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Mobile elements comprise over 45% of the human genome.
  • Active mobile elements like ALU, LINE1, and SVA can cause diseases, including cancer.
  • Accurate detection of mobile-element insertions (MEIs) is crucial for understanding genomic instability and disease.

Purpose of the Study:

  • To enhance the TANGRAM software package for mobile-element insertion (MEI) detection.
  • To expand TANGRAM's compatibility with various mainstream short-read mappers.
  • To demonstrate TANGRAM's utility in cancer genome analysis.

Main Methods:

  • Developed TANGRAM, a software package for MEI detection in next-generation sequencing data.
  • Integrated a new feature allowing TANGRAM to process alignments from any mainstream short-read mapper.
  • Applied TANGRAM to the TCGA mutation calling benchmark 4 dataset for cancer genome analysis.

Main Results:

  • TANGRAM now offers broader compatibility, accepting alignments from diverse short-read mappers.
  • The enhanced TANGRAM demonstrated its effectiveness in analyzing cancer genomes.
  • TANGRAM is confirmed to be a fast, accurate, and user-friendly tool for MEI detection.

Conclusions:

  • The updated TANGRAM significantly increases accessibility for genomic users.
  • TANGRAM is a valuable tool for mobile-element insertion detection, especially in cancer research.
  • TANGRAM is available as an open-source package for the scientific community.