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Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Related Experiment Video

Updated: Nov 10, 2025

Genotyping of Plant and Animal Samples without Prior DNA Purification

Genotyping of Plant and Animal Samples without Prior DNA Purification

Published on: September 24, 2012

A New SNP-Based Genotyping Method for C. psittaci: Application to Field Samples for Quick Identification.

Fabien Vorimore¹, Rachid Aaziz¹, Bertille de Barbeyrac²

¹Laboratory for Animal Health, Bacterial Zoonosis Unit, ANSES Maisons-Alfort, Paris-Est University, 94706 Paris, France.

|April 3, 2021

Summary

A new PCR-high-resolution melting (HRM) assay quickly identifies Chlamydia (C.) psittaci lineages. This method aids in rapidly determining infection sources in avian chlamydiosis and human psittacosis outbreaks.

Keywords:

Chlamydia psittaci PCR-high-resolution melting (HRM)SNP avian chlamydiosis genotyping psittacosis

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Published on: August 2, 2011

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

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Last Updated: Nov 10, 2025

Genotyping of Plant and Animal Samples without Prior DNA Purification

Genotyping of Plant and Animal Samples without Prior DNA Purification

Published on: September 24, 2012

Rapid Diagnosis of Avian Influenza Virus in Wild Birds: Use of a Portable rRT-PCR and Freeze-dried Reagents in the Field

Rapid Diagnosis of Avian Influenza Virus in Wild Birds: Use of a Portable rRT-PCR and Freeze-dried Reagents in the Field

Published on: August 2, 2011

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

Area of Science:

Veterinary Microbiology
Infectious Diseases
Molecular Diagnostics

Background:

Chlamydia (C.) psittaci causes avian chlamydiosis and human psittacosis.
Accurate and rapid genotyping is crucial for understanding transmission and controlling outbreaks.
Existing methods like whole-genome sequencing and MLST are time-consuming and resource-intensive.

Purpose of the Study:

To develop a novel, rapid genotyping assay for C. psittaci.
To identify and characterize major C. psittaci lineages based on whole-genome data.
To validate the new assay's performance against established genotyping techniques.

Main Methods:

Whole-genome sequencing of 55 C. psittaci strains to identify single-nucleotide polymorphisms (SNPs).
Development of a combined PCR/high-resolution melting (HRM) assay targeting eight phylogenetically informative SNPs.
Validation using 11 reference strains and 118 field isolates, comparing results with ompA/MLST genotyping.

Main Results:

Eight major, often host-related, C. psittaci lineages were identified.
The PCR-HRM assay demonstrated high concordance with previous genotyping methods.
Application to clinical samples identified genotypes linked to common sources (ducks, pigeons) and a novel Mat116-like genotype.

Conclusions:

The developed PCR-HRM assay provides a rapid, cost-effective alternative for C. psittaci genotyping.
This method facilitates quick identification of infection sources in both animal and human cases.
The assay supports efficient epidemiological surveillance and outbreak investigation of C. psittaci.