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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

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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.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Related Experiment Video

Updated: Oct 20, 2025

Infinium Assay for Large-scale SNP Genotyping Applications
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Published on: November 19, 2013

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Study on the concordance between different SNP-genotyping platforms in sheep.

H Marina1, P Chitneedi1, R Pelayo1

  • 1Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain.

Animal Genetics
|September 13, 2021
PubMed
Summary
This summary is machine-generated.

Genotyping accuracy in sheep was evaluated using Affymetrix and Illumina SNP-chip technologies against whole-genome resequencing (WGR) data. Illumina showed higher concordance (99.51%) than Affymetrix (96.59%), informing marker reliability for genomic selection.

Keywords:
AffymetrixIlluminagenotype concordancehigh-throughput genotyping technologiessheepwhole-genome resequencing

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Area of Science:

  • Animal Genomics
  • Molecular Genetics
  • Bioinformatics

Background:

  • Single Nucleotide Polymorphism (SNP) genotyping is crucial for quantitative trait loci (QTL) detection, genotype imputation, and genomic predictions in animal breeding.
  • Genotyping errors can significantly reduce the accuracy of genomic selection, leading to false positives in genome-wide association studies.
  • Whole-genome resequencing (WGR) offers high-throughput genotyping but is limited by cost for large populations, necessitating evaluation of array-based technologies.

Purpose of the Study:

  • To assess the accuracy of two popular SNP-chip technologies (Affymetrix and Illumina) for high-throughput sheep genotyping.
  • To compare SNP-chip data concordance against high-coverage whole-genome resequencing (WGR) datasets.
  • To evaluate the impact of different sheep genome assemblies on genotype concordance rates.

Main Methods:

  • Genotyping data from Affymetrix and Illumina SNP-chip platforms were compared with reference whole-genome resequencing (WGR) datasets in sheep.
  • Analyses were conducted using two sheep genome assemblies: Oar_v3.1 and Oar_rambouillet_v1.0.
  • An efficient pipeline was developed to test marker reliability against WGR data from public databases.

Main Results:

  • Both Affymetrix and Illumina SNP-chip technologies demonstrated high concordance rates with WGR data.
  • Illumina technology achieved a higher concordance rate (99.51%) compared to Affymetrix (96.59%).
  • Genome assembly quality was shown to influence genotype concordance rates across different genotyping platforms.

Conclusions:

  • SNP-chip technologies provide reliable high-throughput genotyping data in sheep, with Illumina showing superior concordance.
  • The findings help identify low-reproducibility markers across platforms, crucial for accurate genomic selection.
  • The developed pipeline aids in validating SNP markers, improving the reliability of genomic information for gene mapping and prediction.