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Related Concept Videos

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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Human Genetics01:28

Human Genetics

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Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
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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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Single Nucleotide Polymorphisms-SNPs01:05

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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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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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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.
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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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HGVA: the Human Genome Variation Archive.

Javier Lopez1, Jacobo Coll1, Matthias Haimel2,3,4

  • 1Genomics England, Charterhouse Square, London EC1M 6BQ, UK.

Nucleic Acids Research
|May 24, 2017
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Summary

The Human Genome Variation Archive (HGVA) simplifies access to large-scale human genomic variation data. It integrates diverse datasets, providing annotation and population frequencies for disease-causing genotype identification.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Large-scale genomic projects generate vast human variation data crucial for identifying disease-causing genotypes.
  • Current data access and integration from these projects are often cumbersome and inefficient.
  • A need exists for streamlined access to genomic variation knowledge bases.

Purpose of the Study:

  • To develop the Human Genome Variation Archive (HGVA) for simplified access to genomic variation data.
  • To address challenges in accessing, contrasting, and integrating data from major genomic projects.
  • To serve as a proof-of-concept for advanced genome analysis developments.

Main Methods:

  • Developed HGVA with an intuitive web interface and a comprehensive RESTful API.
  • Provided client libraries in Python, Java, and JavaScript for programmatic data access.
  • Integrated variant annotation using CellBase and calculated population frequencies for reference projects.

Main Results:

  • HGVA facilitates clean, fast, and integrated access to genomic data from key reference projects.
  • The platform offers efficient data mining and programmatic access to a knowledge base.
  • Enriched genomic data with variant annotation and population frequencies.

Conclusions:

  • HGVA effectively tackles challenges in accessing and utilizing large-scale human genomic variation data.
  • The archive enhances downstream analyses by providing integrated and annotated genomic information.
  • HGVA demonstrates the potential of open-source software platforms like OpenCB for massive genomic data analysis.