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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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Comparing Copy Number Variations and SNPs02:26

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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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Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

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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...
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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.
GWAS does not require the identification of the target gene involved in...
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Point and Frameshift Mutations01:30

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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...
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Histone Variants at the Centromere02:30

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Annotating rare variants: A challenge that has not been completely resolved.

Snaigune Miskinyte1, Clemence Delcour2, Rihab Makhlouf1

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Summary

Advances in genomic sequencing have improved rare disease diagnosis, but identifying the impact of specific DNA variants remains a challenge. Further research is needed to link genetic variations to patient phenotypes.

Keywords:
ACMGRare diseaseVariants

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Area of Science:

  • Genetics and Genomics
  • Rare Diseases
  • Molecular Diagnostics

Background:

  • Significant progress in rare disease molecular diagnosis and management since the mid-1980s, driven by molecular genetics and genome research.
  • Whole genome sequencing is now integrated into patient care due to simplified techniques and investment in genome structure understanding.

Purpose of the Study:

  • To review human genome organization.
  • To discuss challenges in confirming DNA variant pathogenicity.
  • To illustrate these challenges using congenital gonadotropin deficiency as an example.

Main Methods:

  • Review of advancements in molecular genetics and genomic sequencing techniques.
  • Analysis of the current limitations in variant interpretation.
  • Case study approach using congenital gonadotropin deficiency.

Main Results:

  • While genome sequencing is accessible, determining the clinical significance of identified DNA variants is the primary hurdle.
  • The complexity of linking specific genetic variants to observed phenotypes is increasingly apparent.

Conclusions:

  • The focus in genetic diagnostics has shifted from sequencing to variant interpretation.
  • Confirming pathogenicity of DNA variants is crucial for effective patient management, particularly in rare genetic disorders like congenital gonadotropin deficiency.