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Related Concept Videos

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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Genetic Variation01:25

Genetic Variation

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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,...
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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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Interpreting R Charts01:22

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R chart, or range chart, is a fundamental tool in statistical process control used to monitor the variability within a process. It complements the X-bar (x̄) chart by focusing on the range of the data, rather than individual values, providing a clear picture of the process dispersion over time.
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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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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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Related Experiment Video

Updated: Jul 16, 2025

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

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VCFshiny: an R/Shiny application for interactively analyzing and visualizing genetic variants.

Tao Chen1, Chengcheng Tang1, Wei Zheng1

  • 1Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China.

Bioinformatics Advances
|September 13, 2023
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Summary

VCFshiny is a new R package that simplifies the analysis of genetic variants. It provides an interactive web interface for researchers to easily interpret and visualize data from variant call format (VCF) files.

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

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Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing generates vast amounts of genetic variant data.
  • Variant Call Format (VCF) files are standard for documenting these variants.
  • Analyzing VCF data requires specialized bioinformatics and programming skills, posing a challenge for many researchers.

Purpose of the Study:

  • To develop a user-friendly tool for interactive analysis and visualization of VCF files.
  • To enable researchers without extensive bioinformatics expertise to interpret genetic variant data.
  • To facilitate the annotation, interpretation, and visualization of variant information.

Main Methods:

  • Introduction of VCFshiny, an R package with a web interface.
  • Integration of Annovar and VariantAnnotation for variant annotation (genes, functional impact).
  • Development of visualization tools for variant summaries (e.g., variant counts, indel lengths, gene mutations).

Main Results:

  • VCFshiny enables interactive annotation and interpretation of VCF files.
  • The package visualizes key variant metrics including variant counts, indel length distributions, and gene mutation frequencies.
  • It supports analysis of variant overlaps, base alterations, and cancer-related genetic features.

Conclusions:

  • VCFshiny enhances the intelligibility and accessibility of VCF file analysis.
  • The tool empowers researchers to gain insights from genetic variant data through interactive visualization.
  • It democratizes the analysis of next-generation sequencing data for a broader scientific audience.