Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA

Area of Science:

• Genetics and Genomics
• Molecular Diagnostics

Background:

• Chromosomal microarray (CMA) is crucial for diagnosing copy number aberrations in developmental delay and congenital anomalies.
• Peripheral blood DNA is the standard source, but saliva DNA offers a less invasive alternative.
• The impact of bacterial content in saliva on CMA accuracy requires validation.

Purpose of the Study:

• To validate saliva DNA as a reliable source for CMA testing.
• To assess saliva DNA quality and CMA performance across different platforms.
• To compare CMA results from paired blood and saliva samples.

Main Methods:

• Validation study using six saliva DNA samples with varying bacterial content (3-21%).
• Analysis of 20 paired blood and saliva specimens using Agilent, Illumina, and Affymetrix CMA platforms.
• Comparison of DNA quality, CMA quality, SNP genotyping, and copy number variant detection between sample types.

Main Results:

• Saliva DNA quality was equivalent to blood DNA, irrespective of bacterial load.
• CMA and single-nucleotide polymorphism (SNP) genotyping quality were comparable between saliva and blood DNA across all platforms.
• All 13 clinically significant copy number aberrations (deletions and duplications) were accurately detected in saliva DNA.

Conclusions:

• Saliva DNA is a high-quality, reliable alternative to blood DNA for clinical CMA testing.
• Bacterial content in saliva does not compromise DNA quality or CMA diagnostic accuracy.
• Saliva DNA enables accurate detection of copy number aberrations, supporting its use in genetic diagnostics.