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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
09:16

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Published on: February 21, 2015

Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics.

Nicolien M Hanemaaijer1, Birgit Sikkema-Raddatz, Gerben van der Vries

  • 1Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands.

European Journal of Human Genetics : EJHG
|September 22, 2011
PubMed
Summary

Interpreting copy number gains in developmental disorders is challenging. New guidelines using a 200 kb threshold and considering heritability improve accuracy for copy number variations (CNVs) in clinical diagnostics.

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Area of Science:

  • Genetics
  • Clinical Diagnostics
  • Genomic Variation

Background:

  • Interpreting copy number gains (CNVs) in developmental delay and congenital anomalies is difficult due to high CNV frequency in healthy individuals.
  • Phenotypic variability and lack of consensus on inheritance, size, and presence in healthy individuals complicate CNV interpretation.

Purpose of the Study:

  • To develop and evaluate guidelines for interpreting copy number gains detected by array comparative genomic hybridization (aCGH).
  • To establish clear criteria for distinguishing benign from pathogenic CNVs in a diagnostic setting.

Main Methods:

  • Analysis of array CGH data from 300 patients with developmental delay/congenital anomalies using a 105K Agilent oligo array.
  • Evaluation of developed interpretation guidelines in an independent cohort of 300 patients.
  • Assessment of gain size, heritability, and de novo occurrence in relation to clinical relevance.

Main Results:

  • Out of 797 observed gains, 45.4% were de novo and 54.6% were familial.
  • A high percentage of both de novo (94.8%) and familial (87.1%) gains were classified as benign CNVs.
  • Clinically relevant gains were significantly larger (288–7912 kb) than benign gains (P < 0.001).
  • A 200 kb size threshold was found acceptable, and heritability did not rule out pathogenicity.

Conclusions:

  • Established guidelines provide a clear, easy-to-follow, and efficient method for interpreting copy number gains in clinical diagnostics.
  • A 200 kb threshold is a reliable parameter, and familial inheritance should not preclude a pathogenic classification of a gain.