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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

Comparing Copy Number Variations and SNPs

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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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Human Genetics01:28

Human Genetics

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Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
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Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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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Mismatch Repair01:20

Mismatch Repair

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
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Incomplete Dominance01:43

Incomplete Dominance

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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
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Related Experiment Video

Updated: Jun 25, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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ProtVar: mapping and contextualizing human missense variation.

James D Stephenson1, Prabhat Totoo1, David F Burke2

  • 1EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, UK.

Nucleic Acids Research
|May 20, 2024
PubMed
Summary
This summary is machine-generated.

ProtVar simplifies the interpretation of human missense genetic variations by integrating diverse data. This tool provides rapid mapping across genomic, protein, and structural data for comprehensive variant analysis.

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In Vivo Modeling of the Morbid Human Genome using Danio rerio
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Related Experiment Videos

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Understanding genomic variation's impact on biological function is complex.
  • Increasing data volume and diverse standards complicate variant analysis across genomic, coding, protein, and structural levels.
  • Investigating variants and assimilating annotations from disparate resources presents significant challenges.

Purpose of the Study:

  • To develop a flexible and accessible tool for contextualizing and interpreting human missense variation.
  • To address the complexity of mapping variants across different data types and integrating diverse annotations.
  • To facilitate the broadest possible researcher access to variant interpretation tools.

Main Methods:

  • Pre-calculation of all possible human proteome variants for instantaneous data mapping.
  • Integration of genomic, protein sequence, function annotations, and structural data.
  • Development of an intuitive web server and programmatic API for data exploration and access.

Main Results:

  • ProtVar enables near-instantaneous mapping between genomic, coding, protein, and structure positions.
  • The tool consolidates data from numerous resources, offering comprehensive insights into missense variation.
  • Provides a unified platform for exploring and downloading variant data and analyses.

Conclusions:

  • ProtVar significantly enhances the ease and flexibility of human missense variation interpretation.
  • The integrated approach provides deeper understanding of variant effects by combining multiple data types.
  • Offers a valuable resource for researchers studying the impact of genetic variation on human health.