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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.6K
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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Adapting ACMG/AMP sequence variant classification guidelines for single-gene copy number variants.

Tracy Brandt1, Laura M Sack2, Dolores Arjona2

  • 1GeneDx, Gaithersburg, MD, USA. tbrandt@genedx.com.

Genetics in Medicine : Official Journal of the American College of Medical Genetics
|September 20, 2019
PubMed
Summary

Modified American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) criteria improve the interpretation of single-gene copy number variants (CNVs). This adaptation enhances concordance and usability for a unified classification system.

Keywords:
ACMG/AMP criteriaPVS1copy number variant (CNV)variant classification guidelinesvariant interpretation

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Area of Science:

  • Clinical Genetics
  • Molecular Diagnostics
  • Genomic Variation Analysis

Background:

  • Next-generation sequencing enables simultaneous detection of sequence and copy number variants (CNVs), merging clinical cytogenetics and molecular genetics.
  • The distinction between sequence variants and CNVs is often blurred, with existing guidelines having limited scope for CNV classification.

Purpose of the Study:

  • To adapt the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) criteria for the interpretation of single-gene copy number variants (CNVs).

Main Methods:

  • Developed CNV-specific modifications to the 2015 ACMG/AMP criteria.
  • Tested the utility of these modified criteria across three independent diagnostic laboratories interpreting 12 single-gene CNVs.
  • Validated the modified criteria through a replication study involving 12 additional CNVs.

Main Results:

  • The adapted criteria system demonstrated improved concordance and usability for single-gene CNV interpretation compared to standard ACMG/AMP guidelines.
  • The modified criteria facilitated a more streamlined workflow for variant classification.

Conclusions:

  • The proposed single-gene CNV criteria modifications can supplement existing ACMG/AMP guidelines for sequence variants.
  • These adaptations contribute to a more uniform classification system for both sequence and copy number alterations in clinical genetics.