Related Experiment Video
Updated: Feb 8, 2026
10:41
Wild-type Blocking PCR Combined with Direct Sequencing as a Highly Sensitive Method for Detection of Low-Frequency Somatic Mutations
Published on: March 29, 2017
12.4K
PIK3CA mutation profiling in patients with breast cancer, using a highly sensitive detection system
Tatsunori Shimoi1,2, Akinobu Hamada3, Marifu Yamagishi4
1Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo.
Cancer Science
|June 16, 2018
Summary
A new quenching probe (QP) system effectively detects PIK3CA mutations in breast cancer DNA, showing high accuracy with formalin-fixed paraffin-embedded (FFPE) tissues. These mutations are linked to patient relapse-free survival, highlighting the QP system
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- PIK3CA mutations are prevalent in breast cancer (20-30% of cases) and predict response to PI3K inhibitors.
- Accurate detection of these mutations is crucial for guiding treatment decisions.
- Existing detection methods may have limitations in sensitivity and applicability to clinical samples.
Purpose of the Study:
- To develop and validate a novel, sensitive quenching probe (QP) system for detecting PIK3CA mutations in breast cancer.
- To assess the performance of the QP system using DNA from both fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissues.
- To investigate the prognostic significance of PIK3CA mutations in breast cancer patient outcomes.
Main Methods:
- A quenching probe (QP) system was developed to detect PIK3CA mutations.
- DNA from 309 breast cancer tissue samples (fresh-frozen and FFPE) was analyzed.
- The QP system's performance was evaluated against direct sequencing (DS) and droplet digital PCR (ddPCR) in a blinded validation cohort.
Main Results:
- The QP system demonstrated high concordance (96%) between fresh-frozen and FFPE DNA.
- In the validation cohort, the QP system (via ddPCR) achieved 100% sensitivity and 100% specificity for PIK3CA mutation detection.
- Direct sequencing (DS) showed lower sensitivity (60%) compared to the QP system.
- PIK3CA mutations, particularly H1047R, were identified as prognostic factors for relapse-free survival.
Conclusions:
- The novel QP system offers a sensitive and reliable method for detecting PIK3CA mutations in breast cancer, outperforming direct sequencing.
- The system is effective with FFPE tissues, making it suitable for clinical diagnostics.
- PIK3CA mutational status is a significant prognostic indicator for relapse-free survival in breast cancer patients.
Related Concept Videos
01:39Mutations
94.6K
Overview
94.6K
01:35Mutations
44.6K
Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
44.6K
02:21Cancers Originate from Somatic Mutations in a Single Cell
14.9K
Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
14.9K
00:36Viral Mutations
39.9K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
39.9K
01:09Mutation, Gene Flow, and Genetic Drift
64.5K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
64.5K
01:30Point and Frameshift Mutations
1.2K
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
1.2K