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Related Concept Videos

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.
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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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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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

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.
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant

Michael T Watkins1, Wendy K Kohlmann2, Therese S Berry2

  • 1University of Utah, Salt Lake City, UT.

AMIA ... Annual Symposium Proceedings. AMIA Symposium
|May 2, 2023
PubMed
Summary

LocalVar is an open-source tool that helps manage local genetic variant collections, addressing challenges in data upkeep and interpretation for clinical settings. It streamlines variant curation and ensures data integrity for research and diagnostics.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Clinical Genetics

Background:

  • Public repositories for biological sequence variation data exist, but open-source tools for maintaining local variant collections are scarce.
  • Clinics often curate local variant data, facing challenges with changing variant representations and clinical significance interpretations.

Purpose of the Study:

  • To develop an open-source tool, LocalVar, to assist in the upkeep of local collections of genetic variant data.
  • To address the burden of frequent changes in variant representation and interpretation for clinical curators.

Main Methods:

  • Analyzed a dictionary of genetic variants from the Huntsman Cancer Institute over two years.
  • Developed LocalVar using publicly available ClinVar files.
  • Implemented features such as auto-complete search, duplicate detection, and asynchronous update suggestions.

Main Results:

  • LocalVar provides functionality for efficient variant record entry and management.
  • The tool automatically detects duplicate and synonymous variant records.
  • It offers asynchronous suggestions for Human Genome Variation Society (HGVS) expression and interpretation updates.
  • Extensive edit history tracking and flexible data export options are included.

Conclusions:

  • LocalVar offers a robust solution for managing local variant data collections in clinical and research settings.
  • The tool enhances data integrity and reduces the manual effort required for variant curation.
  • It supports efficient workflows for handling evolving genetic variant information.