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Related Concept Videos

T Cell Activation and Clonal Selection01:22

T Cell Activation and Clonal Selection

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T cells are integral to our adaptive immune system, recognizing and effectively responding to foreign antigens. T cell activation and clonal selection are pivotal in orchestrating this immune response. This article elucidates these mechanisms, detailing the roles of cluster of differentiation (CD) markers, major histocompatibility complex (MHC) molecules, costimulatory signals, and the process of clonal selection.
Naive T cells that have not yet encountered an antigen express two primary CD...
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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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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.
The recognition sites for Cre recombinase called LoxP...
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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Reproductive Cloning01:27

Reproductive Cloning

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Reproductive cloning is the process of producing a genetically identical copy—a clone—of an entire organism. While clones can be produced by splitting an early embryo—similar to what happens naturally with identical twins—cloning of adult animals is usually done by a process called somatic cell nuclear transfer (SCNT).
Somatic Cell Nuclear Transfer
In SCNT, an egg cell is taken from an animal and its nucleus is removed, creating an enucleated egg. Then a somatic...
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Synteny and Evolution02:31

Synteny and Evolution

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
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Related Experiment Video

Updated: Oct 3, 2025

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

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Exploring Current Challenges and Perspectives for Automatic Reconstruction of Clonal Evolution.

Sarah Sandmann1, Silja Richter2, Xiaoyi Jiang3

  • 1Institute of Medical Informatics, University of Münster, Münster, Germany; sarah.sandmann@uni-muenster.de.

Cancer Genomics & Proteomics
|February 19, 2022
PubMed
Summary
This summary is machine-generated.

Reconstructing cancer clonal evolution automatically is challenging. While 17 of 51 tools showed potential, further research is needed for accurate tumor development analysis and prediction.

Keywords:
Clonal evolutionclusteringtree reconstructionvariant integrationvisualization

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Characterizing Mutational Load and Clonal Composition of Human Blood
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Characterizing Mutational Load and Clonal Composition of Human Blood

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Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM
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Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM

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Related Experiment Videos

Last Updated: Oct 3, 2025

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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Characterizing Mutational Load and Clonal Composition of Human Blood
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Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM
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Area of Science:

  • Oncology
  • Computational Biology
  • Genomics

Background:

  • Reconstructing cancer clonal evolution is crucial for understanding tumor development and prediction.
  • Current methods based on mutational data face significant challenges.
  • Automated tools offer potential but require further validation.

Purpose of the Study:

  • To evaluate the applicability and performance of existing computational tools for reconstructing cancer clonal evolution.
  • To identify challenges and limitations in current automated approaches.

Main Methods:

  • Extensive literature research identified 51 available tools for clonal evolution reconstruction.
  • Analysis of two cancer datasets (n=21) to assess tool performance.
  • Investigation of variant clustering and phylogenetic tree accuracy.

Main Results:

  • Seventeen out of 51 tools were applicable to the analyzed cancer datasets.
  • Accurate variant clustering was achieved for 4 patients with specific data characteristics (≤3 clusters, ≥5 time points).
  • Correct phylogenetic trees were determined for 10 patients, with visualization improvements possible through algorithm adjustments.

Conclusions:

  • Automated reconstruction of cancer clonal evolution, while promising, remains a complex challenge.
  • Further research, including systematic error analysis with simulation tools, is necessary to improve accuracy and reliability.
  • Development of robust automated methods could reduce the need for manual reconstruction.