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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Related Experiment Video

Updated: Jan 1, 2026

Comparative Lesions Analysis Through a Targeted Sequencing Approach
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[Reconstruction of tumor clonal haplotypes based on an improved spanning algorithm].

Yu Geng1,2, Zhongmeng Zhao2, Jianye Liu2

  • 1School of Health Management, Jinzhou Medical University, Jinzhou 121001, China.

Nan Fang Yi Ke Da Xue Xue Bao = Journal of Southern Medical University
|December 20, 2019
PubMed
Summary

This study introduces a novel algorithm for reconstructing tumor clonal haplotypes from sequencing data, effectively identifying tumor heterogeneity and evolution. The method achieves over 97% accuracy, aiding clinical decision-making.

Keywords:
clonal haplotypedepth stripping methodmaximum spanning treethird-generation sequencing datatumor heterogeneity

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Area of Science:

  • Genomics
  • Computational Biology
  • Cancer Research

Background:

  • Tumor heterogeneity poses a significant challenge in cancer research and treatment.
  • Accurate reconstruction of tumor clonal haplotypes is crucial for understanding tumor evolution.

Purpose of the Study:

  • To develop and validate an algorithm for reconstructing tumor subclonal haplotypes using third-generation sequencing data.
  • To effectively identify and analyze tumor heterogeneity and clonal evolution.

Main Methods:

  • Developed a novel algorithm integrating somatic mutation extraction, probability-based connection weight determination, and maximum spanning tree for haplotype reconstruction.
  • Employed depth stripping method to estimate subclone number, ratio, and evolutionary dynamics.

Main Results:

  • The algorithm demonstrated robustness across simulation experiments evaluating coverage, read length, subclone number, and somatic variant rate.
  • Achieved a mean subclonal haplotype accuracy exceeding 97%, outperforming existing methods.

Conclusions:

  • The proposed method accurately reconstructs tumor subclonal haplotypes and elucidates clonal evolution processes.
  • Provides a theoretical foundation for tumor heterogeneity research and supports clinical decision-making.