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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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: Jul 3, 2026

Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

Segmental Copy Number Variant Detection Using an Amplicon-Based Next-Generation Sequencing Panel for Integrated

Kajeetha Sarvananthan1, Stephanie Santos1, Brent Saylor1

  • 1Molecular Diagnostics Division, Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario.

The Journal of Molecular Diagnostics : JMD
|July 1, 2026
PubMed
Summary

This study introduces a custom analysis for detecting copy number variants (CNVs) in glioma using next-generation sequencing (NGS). The method accurately identifies key biomarkers, improving diagnostic efficiency and reducing costs.

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

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

Related Experiment Videos

Last Updated: Jul 3, 2026

Comparative Lesions Analysis Through a Targeted Sequencing Approach
08:16

Comparative Lesions Analysis Through a Targeted Sequencing Approach

Published on: November 5, 2019

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

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

Area of Science:

  • Molecular oncology
  • Genomics
  • Cancer diagnostics

Background:

  • Next-generation sequencing (NGS) is crucial for molecular oncology, detecting sequence variants (SVs) and copy number variants (CNVs).
  • Amplicon-based gene panels, while not primarily designed for segmental chromosomal CNVs, can infer them.
  • Accurate CNV detection is vital for classifying gliomas and guiding treatment.

Purpose of the Study:

  • To describe and validate a custom analysis for CNV detection using the amplicon-based Oncomine Comprehensive Assay v3 (OCAv3).
  • To assess the assay's performance for critical glioma biomarkers: 1p/19q co-deletion, +7/-10, EGFR amplification, and CDKN2A/B homozygous deletion.
  • To evaluate the clinical utility and workflow impact of integrated SV and CNV analysis in glioma diagnostics.

Main Methods:

  • Developed a custom CNV calling algorithm using vendor-normalized gene-level CNV data with inter-sample normalization.
  • Assessed assay performance across three cohorts: discovery (N=52), validation (N=39) against FISH, and clinical (N=53).
  • Defined positive thresholds for 100% specificity and permissive thresholds for reflex FISH to ensure 100% sensitivity; excluded samples with <30% tumor cellularity.

Main Results:

  • The custom analysis achieved 100% concordance with FISH testing in the validation cohort for all evaluated glioma biomarkers.
  • The OCAv3 assay enabled integrated classification of glioma subtypes, particularly oligodendroglioma and glioblastoma, by simultaneously assessing SVs and CNVs.
  • Implementation in a clinical cohort reduced FISH studies by 90%, shortened turnaround times, and decreased molecular testing costs.

Conclusions:

  • The custom amplicon-based NGS analysis provides accurate and efficient detection of critical glioma CNV biomarkers.
  • Integrated SV and CNV analysis using OCAv3 streamlines glioma classification and improves diagnostic workflow.
  • This approach offers a cost-effective and time-saving alternative to traditional methods, enhancing molecular oncology diagnostics.