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Saliva-Derived DNA Performs Well in Large-Scale, High-Density Single-Nucleotide Polymorphism Microarray Studies


Bahlo, M and Stankovich, J and Danoy, P and Hickey, PF and Taylor, BV and Browning, SR and Booth, DR and Broadley, SA and Foote, SJ and Griffiths, LR and Kilpatrick, TJ and Lechner-Scott, J and Moscato, P and Perreau, VM and Scott, RJ and Stewart, GJ and Wiley, J and Clarke, G and Cox, MB and Csurhes, PA and Dickinson, JL and Drysdale, K and Field, J and Greer, JM and Guru, P and Hadler, J and Hoban, E and McMorran, BJ and Jensen, CJ and Johnson, LJ and McCallum, R and Merriman, M and Merriman, T and Polanowski, A and Pryce, K and Tajouri, L and Whittock, L and Wilkins, EJ and Browning, BL and Perera, D and Butzkueven, H and Carroll, WM and Chapman, C and Kermode, AG and Marriott, M and Mason, D and Heard, RN and Pender, MP and Slee, M and Tubridy, N and Willoughby, E and Brown, MA and Rubio, JP, Saliva-Derived DNA Performs Well in Large-Scale, High-Density Single-Nucleotide Polymorphism Microarray Studies, Cancer Epidemiology, Biomarkers and Prevention, 19, (3) pp. 794-798. ISSN 1055-9965 (2010) [Refereed Article]

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©2010 American Association for Cancer Research.

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DOI: doi:10.1158/1055-9965.EPI-09-0812


As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both salivaand blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the "GCScore," an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Item Details

Item Type:Refereed Article
Research Division:Chemical Sciences
Research Group:Analytical chemistry
Research Field:Bioassays
Objective Division:Manufacturing
Objective Group:Human pharmaceutical products
Objective Field:Human diagnostics
UTAS Author:Stankovich, J (Dr Jim Stankovich)
UTAS Author:Taylor, BV (Professor Bruce Taylor)
UTAS Author:Foote, SJ (Professor Simon Foote)
UTAS Author:Dickinson, JL (Professor Joanne Dickinson)
UTAS Author:Drysdale, K (Ms Karen Drysdale)
UTAS Author:Guru, P (Mrs Preethi Mayura Guru)
UTAS Author:Hoban, E (Ms Ella Hoban)
UTAS Author:McMorran, BJ (Associate Professor Brendan McMorran)
UTAS Author:Polanowski, A (Ms Andrea Polanowski)
UTAS Author:Whittock, L (Dr Lucy Whittock)
UTAS Author:Perera, D (Miss Devindri Perera)
ID Code:65374
Year Published:2010
Web of Science® Times Cited:37
Deposited By:Menzies Institute for Medical Research
Deposited On:2010-11-10
Last Modified:2011-06-15

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