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Related Concept Videos

Genetic Variation01:25

Genetic Variation

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, which...
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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%...
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...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
10:57

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

Published on: August 14, 2018

Variant view: visualizing sequence variants in their gene context.

Joel A Ferstay1, Cydney B Nielsen, Tamara Munzner

  • 1University of British Columbia.

IEEE Transactions on Visualization and Computer Graphics
|September 21, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces Variant View, a novel visualization tool that simplifies assessing DNA sequence variant impact for disease research. It accelerates genetic analysis by providing an information-dense overview, reducing navigation needs.

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Published on: August 14, 2018

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
  • Human Genetics

Background:

  • Understanding the genetic basis of disease relies on analyzing DNA sequence variants against reference genomes.
  • Assessing variant impact is challenging due to the complexity of variant type, location, and biological context.
  • Current genome browsers often require extensive navigation, hindering efficient analysis.

Purpose of the Study:

  • To design and implement a visualization tool, Variant View, for assessing DNA sequence variant impact.
  • To support analysts in three specific variant impact assessment tasks.
  • To develop data and task abstractions for efficient analysis of large genomic datasets.

Main Methods:

  • A design study involving four analysts to create the Variant View tool.
  • Development of data and task abstractions tailored for variant impact assessment.
  • Implementation of Variant View with an information-dense visual encoding for overview-level analysis.

Main Results:

  • Variant View provides maximal information at the overview level, contrasting with traditional genome browsers.
  • Case studies demonstrated that Variant View simplified and accelerated variant impact assessment workflows.
  • The tool reduces the need for memory-intensive navigation through concise overviews of complex data.

Conclusions:

  • Variant View offers a promising approach to enhance the efficiency of genetic variant impact assessment.
  • The design emphasizes data and task abstractions for managing sprawling information spaces in genomics.
  • Lessons learned can inform the development of future visualization tools for complex biological data.