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Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

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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Updated: Oct 11, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Recommendations by the ClinGen Rett/Angelman-like expert panel for gene-specific variant interpretation methods.

Dianalee McKnight¹, Lora Bean², Izabela Karbassi³

¹Invitae, San Francisco, California, USA.

|November 27, 2021

Summary

This summary is machine-generated.

Gene-specific variant interpretation guidelines for Rett and Angelman-like disorders were tested. The customized criteria showed high accuracy and consistency among curators, improving variant classification for rare genetic disorders.

Keywords:

Angelman syndrome Christianson syndrome Pitt-Hopkins syndrome Rett syndrome guidelines variant interpretation

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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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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

Area of Science:

Genetics
Clinical Genetics
Bioinformatics

Background:

The American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines face challenges in interpreting variants for specific genes like MECP2, CDKL5, FOXG1, UBE3A, SLC9A6, and TCF4.
These genes are associated with complex neurodevelopmental disorders, necessitating refined interpretation strategies.

Purpose of the Study:

To evaluate the clarity and accuracy of gene-specific modifications to ACMG/AMP variant interpretation criteria developed by the Rett and Angelman-like Disorders Variant Curation Expert Panel (Rett/AS VCEP).
To assess the impact of these customized criteria on variant classification consistency and clinical relevance.

Main Methods:

A pilot study involving multiple curators was conducted to apply the Rett/AS VCEP's gene-specific variant interpretation criteria.
Curators independently interpreted 87 variants in the specified genes using the modified guidelines.
Results were compared to original classifications and ClinVar entries.

Main Results:

Approximately 90% of variants (78 out of 87) achieved consistent interpretation among curators using the modified guidelines.
The classification of 13 variants changed compared to previous curations, influenced by internal data and updated criteria strength.
No two-step classification changes occurred, and only one clinically significant change (Likely pathogenic to Variant of Unknown Significance) was observed.

Conclusions:

The gene-specific variant curation rules developed by the Rett/AS VCEP demonstrate high inter-curator reliability and accuracy.
These customized criteria enhance the interpretation of variants in MECP2, CDKL5, FOXG1, UBE3A, SLC9A6, and TCF4, aiding clinical decision-making.
The Rett/AS VCEP's approach offers a valuable framework for interpreting variants in other fully penetrant, early-onset genes associated with rare disorders.