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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%...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
Single Nucleotide Polymorphisms-SNPs01:05

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,...
Genetic Variation01:25

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Mechanistic Models: Compartment Models in Individual and Population Analysis01:23

Mechanistic Models: Compartment Models in Individual and Population Analysis

Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least squares (OLS)...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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: May 24, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Population structure analysis using rare and common functional variants.

Tesfaye M Baye1, Hua He, Lili Ding

  • 1Division of Asthma Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA. tesfaye.mersha@cchmc.org.

BMC Proceedings
|March 1, 2012
PubMed
Summary
This summary is machine-generated.

Rare genetic variants reveal finer population substructure than common variants. Understanding this genetic variation is crucial for accurate disease genetics studies and controlling for population structure.

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Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Next-generation sequencing enables large-scale genotyping of rare genetic variations.
  • Population structure is critical in common variant studies, but its role in rare variant analysis is less understood.

Purpose of the Study:

  • To analyze population structure using both common and rare functional variants.
  • To compare the effectiveness of rare variants versus common variants in characterizing fine-scale population substructure.

Main Methods:

  • Utilized mini-exome sequence data from the Genetic Analysis Workshop 17.
  • Performed principal component analysis on common and rare functional variants to assess population structure.
  • Compared the number of principal components required to explain variation in population structure.

Main Results:

  • Analysis of common variants required 388 principal components for 90% variation explanation.
  • Analysis of rare variants required 532 principal components for similar variation explanation.
  • Rare variants identified finer population substructure not captured by common variants.

Conclusions:

  • The level of population structure differs between rare and common variant data.
  • Rare variants offer a more detailed resolution for population structure analysis.
  • Accurate control for population structure depends on the chosen variant set and desired correction level.