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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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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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Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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Related Experiment Video

Updated: Nov 16, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Detecting SARS-CoV-2 variants with SNP genotyping.

Helen Harper1, Amanda Burridge1, Mark Winfield1

  • 1School of Biological Sciences, University of Bristol, Bristol, United Kingdom.

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Summary

Genotyping SARS-CoV-2 samples using a SNP identification pipeline offers a rapid, low-cost method for tracking variants. This approach enables efficient population-scale monitoring of viral genetic variations and transmission lines.

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Area of Science:

  • Virology
  • Genetics
  • Epidemiology

Background:

  • Tracking SARS-CoV-2 genetic variations is vital for understanding outbreaks and transmission.
  • Whole-genome sequencing of all positive samples is prohibitively expensive for large-scale operations.
  • Genotyping presents a cost-effective, high-throughput alternative for variant screening.

Purpose of the Study:

  • To design and evaluate a SNP identification pipeline for SARS-CoV-2 variant genotyping.
  • To identify a minimal marker panel for defining distinct viral genotypes.
  • To assess the cost-effectiveness and reliability of SNP genotyping for population-scale surveillance.

Main Methods:

  • Developed a SNP identification pipeline to analyze sequenced SARS-CoV-2 samples.
  • Created a genotyping panel targeting variants from March-May 2020.
  • Tested the panel on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples from the UK.

Main Results:

  • The pipeline identified a minimal marker panel capable of defining distinct genotypes.
  • The genotyping panel successfully differentiated 15 distinct genotypes among 50 samples.
  • There was a 61.9% probability of distinct genotypes between randomly chosen samples.
  • Screening costs were estimated at < £1.50 per sample in a high-throughput setting.

Conclusions:

  • SNP genotyping is a rapid, cost-effective, and reliable method for monitoring SARS-CoV-2 variants.
  • The developed analysis pipeline is publicly available and adaptable to emerging viral genotypes.
  • This approach supports population-scale test and trace operations by enabling efficient variant surveillance.