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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%...
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,...
Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger theirĀ  survival. Therefore, the copying errors are checked and repaired at three levels.
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The pharmacogenetics of drug transporters is increasingly recognized as a critical factor influencing interindividual variability in drug absorption, distribution, and elimination. These membrane-bound proteins regulate drugs' movement across cellular barriers by actively pumping them out (efflux) or facilitating their uptake (influx). Among the major transporter families, ATP-binding cassette (ABC) and solute carrier (SLC) transporters play particularly prominent roles. Genetic polymorphisms...
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...
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Karyotyping

Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by special staining techniques that produce a particular banding pattern on each chromosome. State-of-the-art techniques make this approach even more powerful, enabling the detection of individual genes that cause disease.A Simple Chromosome Staining Technique Provides Valuable Scientific InsightSome genetic diseases can be detected by looking at...

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Related Experiment Video

Updated: Jun 28, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Population-specific GSTM1 copy number variation.

R Stephanie Huang1, Peixian Chen, Steve Wisel

  • 1Section of Hematology-Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., PB Box MC2115, Chicago, IL 60637, USA.

Human Molecular Genetics
|October 25, 2008
PubMed
Summary
This summary is machine-generated.

HapMap SNP rs366631 is a pseudo-SNP indicating GSTM1 deletion, not a true polymorphism. Its frequency and upstream copy number variation vary significantly between Caucasian and African populations.

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Area of Science:

  • Pharmacogenomics
  • Human Genetics
  • Molecular Biology

Background:

  • Glutathione S-transferase mu 1 (GSTM1) is a key enzyme in drug and xenobiotic detoxification.
  • GSTM1 activity is linked to cancer risk and drug resistance.
  • A genome-wide association study identified a potential link between HapMap SNP rs366631 and GSTM1 expression.

Purpose of the Study:

  • To investigate the association between HapMap SNP rs366631 and GSTM1 expression.
  • To clarify the nature of HapMap SNP rs366631 and its utility as a marker for GSTM1 gene alterations.
  • To analyze population-specific copy number variations (CNVs) in the GSTM1 upstream region.

Main Methods:

  • Genotyping assays for rs366631 and a homologous GSTM1 upstream site in CEU and YRI lymphoblastoid cell lines.
  • Copy number variation (CNV) assays for three GSTM1 gene regions.
  • Analysis of SNP genotyping and CNV data for population-specific patterns.

Main Results:

  • HapMap SNP rs366631 is a non-polymorphic pseudo-SNP due to sequence homology and platform limitations.
  • The rs366631 genotype accurately reflects GSTM1 upstream region deletion, serving as a marker for GSTM1 gene deletion.
  • Significant population-specific CNVs were observed: >75% of CEU samples showed GSTM1 deletion, while 25% of YRI samples had two copies.

Conclusions:

  • HapMap SNP rs366631 is a reliable pseudo-SNP marker for GSTM1 deletion.
  • GSTM1 deletion prevalence and upstream CNV patterns exhibit distinct population-specific distributions between CEU and YRI groups.
  • These findings have implications for understanding population differences in drug metabolism and disease susceptibility.