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Related Concept Videos

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,...
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%...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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...
Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu01:29

Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu

Genetic variations significantly influence drug response through pharmacokinetics, receptor interactions, and biologic milieu modifications. Pharmacokinetic alterations impact drug metabolism and clearance, affecting efficacy and toxicity. Variants in drug-metabolizing enzymes, such as CYP2C9 and CYP2C19, alter drug activation and elimination. For example, CYP2C9 loss-of-function variants require lower warfarin doses to prevent excessive bleeding, while CYP2C19 variants reduce clopidogrel...
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...

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic

Eric Arehart1, Scott Gleim1, Bill White2

  • 1Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, NH, USA.

Biodata Mining
|April 1, 2009
PubMed
Summary
This summary is machine-generated.

Specific nucleotide combinations in DNA flanking regions are associated with single nucleotide polymorphisms (SNPs). This study used multifactor dimensionality reduction (MDR) to identify these patterns, potentially predicting future mutation sites.

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Published on: August 21, 2016

Area of Science:

  • Genomics
  • Molecular Biology
  • Computational Biology

Background:

  • DNA replication fidelity is crucial for genetic evolution and disease.
  • Single nucleotide polymorphisms (SNPs) account for most human genetic variation.
  • A new theory posits DNA replication selectivity is governed by base-pair geometry.

Purpose of the Study:

  • To investigate the hypothesis that specific nucleotide combinations in flanking regions of SNP fragments are associated with mutation.
  • To model the relationship between DNA sequence and observed polymorphisms.

Main Methods:

  • Utilized the multifactor dimensionality reduction (MDR) approach, originally developed for detecting synergistic SNP interactions.
  • Analyzed pilot data from the Broad Institute (n=2194) and expanded with human SNPs from the NCBI database (n=29967).
  • Included a control set of non-SNP coding sequences from NCBI (n=29967).

Main Results:

  • Identified seven significant flanking region pattern associations in the pilot dataset (p ≤ 0.05).
  • Detected significant models (p << 0.001) for each SNP type in the larger NCBI dataset.
  • Found that flanking region models varied in length based on nucleotide change and nucleotide distributions differed significantly at motif sites.

Conclusions:

  • This study is the first to apply MDR for modeling nonlinear patterns in molecular genetics.
  • MDR successfully identified distinct nucleotide patterns around mutation sites, dependent on the nucleotide change.
  • These findings may enable prediction of future SNP sites and polymorphism types by scanning genomic databases for specific nucleotide clusters.