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Related Concept Videos

Genomics02:02

Genomics

41.1K
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

Evolutionary Relationships through Genome Comparisons

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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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Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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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...
16.0K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.9K
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 Variation01:25

Genetic Variation

1.5K
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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Related Experiment Video

Updated: Mar 2, 2026

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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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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GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

R Jay Mashl1,2, Adam D Scott1,2, Kuan-Lin Huang1,2

  • 1McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA.

Genome Research
|May 20, 2017
PubMed
Summary

GenomeVIP is an open-source cloud platform for genomic variant discovery and annotation. It streamlines analysis of whole-genome and exome data, overcoming data download challenges for researchers.

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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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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic variant identification is crucial for understanding disease.
  • Increasing sequencing data volume creates data download bottlenecks.
  • Demand for cloud-computing solutions in genomics analysis is rising.

Purpose of the Study:

  • Introduce Genome Variant Investigation Platform (GenomeVIP), an open-source framework.
  • Provide a cloud-based solution for genomics variant discovery and annotation.
  • Facilitate analysis of whole-genome and exome sequence data.

Main Methods:

  • GenomeVIP orchestrates popular tools (VarScan, GATK, Pindel, etc.) via a web interface.
  • Supports cloud or local high-performance computing infrastructure.
  • Demonstrates high-confidence variant annotation for somatic, germline, and de novo variants.

Main Results:

  • GenomeVIP successfully analyzed large-scale genomics projects (TCGA PanCanAtlas, ICGC Pilots).
  • The platform provides high-confidence annotated variants.
  • Demonstrated utility using publicly available datasets.

Conclusions:

  • GenomeVIP offers an efficient, cloud-based solution for genomic variant analysis.
  • It addresses the challenges of large-scale sequencing data processing.
  • Enables robust discovery and annotation of biologically significant variants.