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Related Concept Videos

Cancer02:18

Cancer

Cancers arise due to mutations in genes involved in the regulation of cell division, which leads to unrestricted cell proliferation. Modern science and medicine have made great strides in the understanding and treatment of cancer, including eradicating cancer in some patients. However, there is still no cure for cancer. This is largely due to the fact that cancer is a large group of many diseases.
Targeted Cancer Therapies02:57

Targeted Cancer Therapies

The targeted cancer therapies, also known as “molecular targeted therapies,” take advantage of the molecular and genetic differences between the cancer cells and the normal cells. It needs a thorough understanding of the cancer cells to develop drugs that can target specific molecular aspects that drive the growth, progression, and spread of cancer cells without affecting the growth and survival of other normal cells in the body.
There are several types of targeted therapies against specific...
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...

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Related Experiment Video

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Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
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Beyond basics: Key mutation selection features for successful tumor-informed ctDNA detection.

Marijana Nesic1,2, Mads H Rasmussen1,2, Tenna V Henriksen1,2

  • 1Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.

International Journal of Cancer
|April 16, 2024
PubMed
Summary

Prioritizing mutations by cancer cell fraction (CCF), multiplicity, and error rate significantly enhances circulating tumor DNA (ctDNA) detection. This study developed a pipeline to identify optimal ctDNA markers for improved tumor-informed analysis.

Keywords:
clonalityctDNA markerserror ratemultiplicitysomatic mutationstumor‐informed ctDNA analysis

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Area of Science:

  • Oncology
  • Genetics
  • Biotechnology

Background:

  • Tumor-informed mutation-based approaches are standard for detecting circulating tumor DNA (ctDNA).
  • However, not all mutations are equally effective as ctDNA markers, impacting detection sensitivity.
  • Optimizing marker selection is crucial for improving the success rate of ctDNA analysis.

Purpose of the Study:

  • To investigate if prioritizing mutations based on features like cancer cell fraction (CCF), multiplicity, and error rate improves ctDNA detection.
  • To develop a practical analysis pipeline for identifying and prioritizing candidate mutations from whole-exome sequencing (WES) data.

Main Methods:

  • Analysis of WES and ctDNA data from 390 patients across three studies (bladder and colorectal cancer).
  • Utilized the PureCN tool to assess CCF and multiplicity of mutations.
  • Evaluated the impact of mutation prioritization based on CCF, multiplicity, and error rate on ctDNA detection likelihood.

Main Results:

  • High-CCF mutations were significantly more frequently detected than low-CCF mutations across all cohorts.
  • Selecting mutations with multiplicity of two or higher also improved detection likelihood.
  • Prioritizing mutations with lower error rates further enhanced detection, especially for low plasma tumor fractions (<0.1%).

Conclusions:

  • Prioritizing mutations with high CCF, high multiplicity, and low error rates significantly improves ctDNA detection likelihood in tumor-informed analyses.
  • A free, accessible analysis pipeline is provided to facilitate qualified mutation prioritization for ctDNA studies.