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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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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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.
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Genetic Variation01:25

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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.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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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.
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Variant Review with the Integrative Genomics Viewer.

James T Robinson1, Helga Thorvaldsdóttir2, Aaron M Wenger3

  • 1School of Medicine, University of California San Diego, La Jolla, California. jrobinso@ucsd.edu.

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|November 3, 2017
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Manual review of next-generation sequencing (NGS) data using the Integrative Genomics Viewer (IGV) enhances variant call accuracy. IGV provides essential tools for validating single-nucleotide and structural variants in cancer and germline datasets.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Manual review of aligned reads is crucial for interpreting variant calls in next-generation sequencing (NGS) pipelines.
  • Visual inspection of genomic data improves confidence in variant calls and helps identify false positives and complex events.

Purpose of the Study:

  • To provide an overview of the variant review features of the Integrative Genomics Viewer (IGV).
  • To demonstrate IGV's utility in validating both single-nucleotide variants and structural variants.

Main Methods:

  • Utilized the Integrative Genomics Viewer (IGV) for visualization and analysis of next-generation sequencing (NGS) data.
  • Presented examples of variant review using both cancer and germline datasets.

Main Results:

  • IGV offers a comprehensive set of tools for the inspection, validation, and interpretation of NGS and other genomic datasets.
  • The software facilitates the review of single-nucleotide variants and structural variants.

Conclusions:

  • The Integrative Genomics Viewer (IGV) is a valuable tool for manual review and interpretation of variant calls in NGS data.
  • IGV aids in increasing confidence of variant calls and characterizing complex genomic events.