生物技术与生物材料

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Is Saliva a Good Alternative to Blood for High Density Genotyping Studies: SNP and CNV Comparisons?

Alban Fabre, Emilie Thomas, Sylvain Baulande, Emilie Sohier, Lyan Hoang, Pascal Soularue, Stéphane Ragusa, Françoise Clavel-Chapelon and David G. Cox

Modern molecular genetic epidemiology is scaled towards large-scale analyses, including genome wide association studies (GWAS) containing hundreds of thousands to millions of single nucleotide polymorphisms. In addition to generating information on alleles at each SNP, GWAS can also be used to evaluate copy number variation (CNVs) across the genome. Traditionally, these studies have been carried out using DNA extracted from lymphocytes in blood samples. More recently, the use of DNA extracted from less invasive methods has become attractive in epidemiological studies. Here, we examine the feasibility of using DNA from saliva to assess CNVs in a pangenome study. We have compared SNP and CNV genotypes among 30 individuals genotyped with the Affymetrix GeneChip NspI genotyping array using DNA from blood and saliva samples of the same individual. In general, while we find that the DNA extracted from these cells is of sufficient quantity and quality to genotype SNPs in a GWAS setting, the results of CNV analyses differed between blood and saliva samples from the same individual, particularly for shorter CNV regions.