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Related Concept Videos

Multiple Comparison Tests01:13

Multiple Comparison Tests

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Multiple comparison test, abbreviated as MCT, is a post hoc analysis generally performed after comparing multiple samples with one or more tests. An MCT will help identify a significantly different sample among multiple samples or a factor among multiple factors.
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Related Experiment Video

Updated: Oct 16, 2025

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
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Oncomine™ Comprehensive Assay v3 vs. Oncomine™ Comprehensive Assay Plus.

Lau K Vestergaard1, Douglas N P Oliveira1, Tim S Poulsen1

  • 1Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark.

Cancers
|October 23, 2021
PubMed
Summary
This summary is machine-generated.

The Oncomine™ Comprehensive Assay Plus (OCA-Plus) shows 91% concordance with OCAv3 for detecting cancer gene mutations. This new assay effectively identifies genomic variants in ovarian cancer samples, with specific filters for improved PTEN gene coverage.

Keywords:
Oncomine Comprehensive Assay PlusOncomine Comprehensive Assay v3biomarker discoveryclinical researchgenomic profilingtargeted NGS

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

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Area of Science:

  • Genomic medicine
  • Cancer genomics
  • Next-generation sequencing (NGS)

Background:

  • Next-generation sequencing and targeted gene panels enhance understanding of tumor composition.
  • Genomic biomarkers are vital for cancer diagnosis, prognosis, and treatment selection.
  • The Oncomine™ Comprehensive Assay v3 (OCAv3) is a standard clinical tool for cancer gene analysis.

Purpose of the Study:

  • To compare DNA sequencing results between the Oncomine™ Comprehensive Assay v3 (OCAv3) and the new Oncomine™ Comprehensive Assay Plus (OCA-Plus).
  • To validate the performance of OCA-Plus against OCAv3 for detecting cancer-associated gene mutations.
  • To assess the concordance of variant detection between the two assays in ovarian cancer samples.

Main Methods:

  • DNA sequencing was performed on 50 ovarian cancer formalin-fixed, paraffin-embedded samples using both OCAv3 and OCA-Plus.
  • A comparative analysis focused on 144 overlapping genes and 313,769 nucleotide positions.
  • Validation assessment included identifying likely-pathogenic or pathogenic variants and addressing poor gene coverage with rescue filters.

Main Results:

  • A 91% concordance rate was observed for variants classified as likely-pathogenic or pathogenic between OCAv3 and OCA-Plus.
  • The OCA-Plus assay demonstrated poor coverage in a specific region of the PTEN gene, necessitating the implementation of rescue filters.
  • The OCA-Plus assay generally reflects the mutational profile of overlapping genes compared to OCAv3 without performance compromise.

Conclusions:

  • The Oncomine™ Comprehensive Assay Plus (OCA-Plus) provides a reliable assessment of genomic variants compared to OCAv3 for overlapping genes.
  • The OCA-Plus assay demonstrates robust performance in detecting clinically relevant mutations in ovarian cancer.
  • Further validation and optimization, including specific filters for regions like PTEN, are important for clinical implementation of new assays.