B36
Successful paired blood and saliva DNA in high throughput genotyping and genome-wide association studies
Jean Abraham1, Mel Maranian1, Inma Spiteri2, Roslyn Russell2, Alison Dunning1, Carlos Caldas2
1University of Cambridge, Strangeways Research Laboratory, Cambridgeshire, UK, 2CRUK Cambridge Cancer Research Institute, Cambridgeshire, UK
Background
Increasingly phase III randomised controlled clinical trials are incorporating DNA sample collection into their trial structure. Most trials use either retrospective or prospective blood sample or paraffin embedded tumour block collections. PG-SNPS is a pharmacogenetics study collecting blood samples from breast cancer patients.
Aim
A pilot sub-study was set up to assess if saliva sample collection would be an effective method of DNA collection. A comparative analysis of the quality and quantity of DNA extracted from both the blood and saliva samples was undertaken. The feasibility of using DNA extracted from saliva in genome-wide association studies was assessed.
Method
After obtaining written, informed consent paired blood and saliva samples were collected from 80 patients with breast cancer. Blood was collected in 9ml EDTA tubes, and DNA extracted by Whatman plc. Saliva samples were collected using Oragene DNA Self Collection Kits (DNA Genotek) according to manufacturers instructions and processed using the PUREGENE DNA Purification Kit. High-throughput Taqman Assay by Design technique was used for genotypic analysis. Saliva DNA yield, number of samples with readable genotypes and reproducibility of results were assessed. In addition a sub-set of matched samples were genotyped in duplicate using the Illumina HumanHap550 Beadchip array.
Results and Conclusion
The average yield from saliva samples was 15g/ml. The paired samples showed exceptionally high concordance rates (100%) and an overall genotyping pass rate of 98.8%. The success of the pilot sub-study has lead to over 450 saliva samples being included as part of a genome-wide association study, which is currently being completed. This study shows that saliva DNA samples are an acceptable and more a patient-friendly method of DNA collection comparable with blood DNA collection for use in high throughput genotyping.
