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tHapMix: simulating tumour samples through haplotype mixtures.

Sergii Ivakhno1, Camilla Colombo1, Stephen Tanner2

  • 1Chesterford Research Park, Illumina Cambridge Ltd, Little Chesterford, CB10 1XL, UK.

Bioinformatics (Oxford, England)
|September 9, 2016
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Summary

We developed tHapMix, a scalable simulation framework for creating diverse tumor genomes. This tool aids in developing and testing variant calling tools for somatic genome analysis.

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Area of Science:

  • Genomics
  • Computational Biology

Background:

  • Somatic genome diversity arises from complex rearrangements and clonal evolution, complicating variant calling tool development.
  • Accurate benchmarking of somatic variant callers is challenging due to the lack of well-characterized simulated datasets.

Purpose of the Study:

  • To introduce tHapMix, a novel simulation framework for generating realistic tumor genomes.
  • To facilitate the creation of diverse simulated somatic genomes for benchmarking and training variant calling tools.

Main Methods:

  • Developed tHapMix, a simulation framework enabling control over ploidy, purity, and polyclonality.
  • Integrated real sequencing data to preserve platform-specific noise and biases.
  • Generated a benchmark set of 140 simulated somatic genomes.

Main Results:

  • tHapMix successfully simulates tumor samples with varying genomic features.
  • The framework scales efficiently for simulating hundreds of somatic genomes.
  • Demonstrated tHapMix utility in training and testing somatic copy number variant calling tools.

Conclusions:

  • tHapMix provides a versatile and scalable solution for generating simulated somatic genomes.
  • This framework enhances the development and evaluation of variant calling tools.
  • The open-source availability promotes reproducible research in cancer genomics.