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Related Concept Videos

Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

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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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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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Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

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Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
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Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
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Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu01:29

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

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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...
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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.
GWAS does not require the identification of the target gene involved in...
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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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BALL-SNPgp-from genetic variants toward computational diagnostics.

Sabine C Mueller1, Christina Backes2, Alexander Gress3

  • 1Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany Department of Human Genetics, Saarland University, Homburg 66421, Germany.

Bioinformatics (Oxford, England)
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Summary

BALL-SNPgp is a new tool that analyzes non-synonymous single nucleotide variants (nsSNVs) to understand their impact on protein structure and function. This aids in assessing disease-causing potential for genetic alterations.

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Area of Science:

  • Computational Biology
  • Genomics
  • Medical Informatics

Background:

  • Understanding the functional impact of genetic variations, particularly non-synonymous single nucleotide variants (nsSNVs), is critical in medical research.
  • NsSNVs are implicated in various human diseases, but analyzing their combined effects in complex disorders remains challenging.
  • Current methods for assessing the pathogenicity of multiple genetic factors are limited.

Purpose of the Study:

  • To present BALL-SNPgp, a computational tool for the structural and functional characterization of nsSNVs.
  • To enhance the pathogenicity assessment of nsSNVs in computational diagnostics.
  • To provide insights into the potential synergistic effects of multiple genetic factors.

Main Methods:

  • BALL-SNPgp utilizes the C++ framework Biochemical Algorithms Library (BALL) and its visualization tool BALLView.
  • The tool processes annotated SNV data to generate 3D protein visualizations.
  • It integrates information on disease relevance, functional annotations, performs cluster analysis, predicts binding pockets, and identifies interaction sites.

Main Results:

  • BALL-SNPgp provides a comprehensive structural and functional characterization of nsSNVs.
  • The tool facilitates the integration of diverse data sources for improved pathogenicity assessment.
  • It enables visualization and analysis of protein alterations relevant to disease.

Conclusions:

  • BALL-SNPgp offers a valuable resource for researchers studying the functional consequences of nsSNVs.
  • The tool can improve the accuracy of computational diagnostics for genetic diseases.
  • It aids in understanding the complex genetic basis of diseases by analyzing individual nsSNVs.