The Genetic Link

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Article by: Rafal Iwasiow

DNA saliva samples for SNP and CNV analysis on microarrays

2010-10-05

For any type of genetic analysis (e.g. population studies, clinical genetic testing, paternity testing, pharmacogenomic testing), non-invasive and easy-to-use sample collection techniques are preferred because they increase compliance rates and reduce costs. Oragene•DNA is a DNA self-collection kit that is completely non-invasive, intuitive to use, and stabilizes DNA at elevated temperatures which facilitates transport and storage by eliminating the need for refrigeration.

For these reasons, Oragene•DNA is often used as a convenient method for collecting high quality genomic DNA (gDNA) from saliva. Numerous studies have shown that DNA from Oragene•DNA/saliva samples gives equivalent results to DNA from blood for applications such as PCR, SNPgenotyping and microarrays. Furthermore, of all oral collection methods (e.g. swabs, mouthwash, cytobrush), Oragene•DNA provides the highest yield and highest quality of human genomic DNA. Genetic research into common and complex human diseases continues to benefit from advances in DNA microarray technology.

CNV, microarray, Oragene, DNA kit

In recent years, DNA microarrays such as the Affymetrix Genome-Wide Human SNP Array 6.0 (Affy 6.0) have evolved to provide higher resolution through higher density arrays and now also include probes for detection of copy number variation. The Affy 6.0 microarray features more than 1.8 million markers for genetic variation, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 additional probes for the detection of copy number variation (CNVs). Previous studies, have shown that genomic DNA from saliva performs just as well as genomic DNA from blood when evaluating SNPs. Similarily, our new study reports saliva samples generated call rates >96% and had a >99% concordance with results from blood samples. In our present study we investigated using saliva as a source of gDNA for the evaluation of genotyping and CNV analysis. Furthermore we demonstrated the intra-donor reproducibility of such results.

I invite you to review the results of this study in this scientific poster. The poster will provide evidence of the following:

  • Saliva collected using the Oragene•DNA Self-Collection Kit provides genomic DNA of sufficient quality for genotyping and CNV analysis on the Affymetrix Genome-Wide Human SNP Array 6.0
  • DNA from saliva does not vary over time as demonstrated through intra-donor genotyping concordance and CNV reproducibility of samples taken from the same donor on three different days
  • DNA from saliva generates highly concordant data compared with DNA from blood for the same donor as demonstrated by the genotyping concordance and CNV reproducibility

I'd also like to thank our partner companies: The Centre for Applied Genomics and the Hospital for Sick Children, Toronto, Canada for their work on this study.

To download the complete poster, please click here.

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