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Comparing Copy Number Variations and SNPs

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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Updated: Jun 16, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Criterion values for multiplex SNP genotyping by the invader assay.

Hiroaki Nakahara¹, Kazumasa Sekiguchi, Naoya Hosono

¹National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan. senju@nrips.go.jp

Forensic Science International. Genetics

|February 5, 2010

Summary

This study introduces a new method for forensic identification using single nucleotide polymorphism (SNP) typing. The improved Invader assay offers more reliable genotype analysis for forensic applications.

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Area of Science:

Forensic Science
Genetics
Biotechnology

Background:

Multiplex single nucleotide polymorphism (SNP) typing is crucial for forensic identification.
The Invader assay is a common method, but endpoint genotyping can lack clarity for some loci.

Purpose of the Study:

To develop a more reliable multiplex SNP typing system for forensic identification.
To enhance genotype analysis accuracy using the Invader assay.

Main Methods:

Developed a multiplex SNP typing system based on the Invader assay.
Collected and analyzed fluorescence data for 21 SNP loci.
Introduced new typing criteria beyond standard endpoint genotyping, including analysis of fluorescence curve climbing angles.

Main Results:

Identified specific criteria, like the climbing angle of fluorescence curves, for highly reproducible genotype identification.
Demonstrated that climbing angles strongly correlate with homozygous genotypes.
Found that heterozygote endpoint fluorescence ratios are highly reproducible with minimal aberration.
Achieved clearer SNP typing compared to using only endpoint fluorescence ratios.

Conclusions:

The developed criteria, easily calculated from raw fluorescence data, significantly improve multiplex SNP typing accuracy.
This enhanced Invader assay method offers greater reliability for forensic identification applications.
The study provides valuable tools for precise genetic analysis in forensic contexts.