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Related Concept Videos

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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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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Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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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

18.4K
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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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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Related Experiment Video

Updated: Nov 26, 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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AVIA 3.0: interactive portal for genomic variant and sample level analysis.

Hue V Reardon1, Anney Che1, Brian T Luke1

  • 1Advanced Biomedical Computational Science, Biomedical Informatics & Data Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.

Bioinformatics (Oxford, England)
|December 8, 2020
PubMed
Summary

The Annotation, Visualization and Impact Analysis (AVIA) tool simplifies genomic variant analysis. This web application allows users to easily annotate, visualize, and analyze genetic alterations without needing prior expertise or software installation.

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic variant analysis is crucial for understanding genetic diseases.
  • Existing tools often require significant technical expertise and software management.
  • There is a need for accessible, integrated platforms for variant annotation and visualization.

Purpose of the Study:

  • To introduce AVIA version 3.0, an enhanced web application for genomic variant data analysis.
  • To provide users with intuitive tools for exploring the functional significance of genetic alterations.
  • To facilitate data management, sharing, and comparative analysis.

Main Methods:

  • AVIA integrates annotation and visualization features.
  • Interactive charts and linked disease data sources enable filtering.
  • New services include reporting, correlation analysis, and cohort building.

Main Results:

  • AVIA 3.0 offers advanced filtering and data linking capabilities.
  • Users can perform gene, variant, and sample level reporting.
  • Comparative analysis against public datasets like TCGA and ClinVar is supported.

Conclusions:

  • AVIA 3.0 is a comprehensive, user-driven portal for variant analysis.
  • The application simplifies the exploration of genomic alterations for researchers.
  • Its web-based nature eliminates the need for software installation and maintenance.