alexa Is Saliva a Good Alternative to Blood for High Density Genotyping Studies: SNP and CNV Comparisons? | OMICS International | Abstract
ISSN: 2155-952X

Journal of Biotechnology & Biomaterials
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Research Article

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

Alban Fabre1,2, Emilie Thomas3, Sylvain Baulande4, Emilie Sohier6, Lyan Hoang1,2, Pascal Soularue4, Stéphane Ragusa5, Françoise Clavel-Chapelon1,2* and David G. Cox6

1INSERM, Centre for Research in Epidemiology and Population Health, Gustave-Roussy Institute Villejuif, France

2Paris South University, UMRS 1018, France

3Fondation Synergie-Lyon Cancer, Lyon, France

4PartnerChip, Evry, France

5Statlife, Institut Gustave Roussy, Villejuif, France

6INSERM U1052, Lyon, France

Corresponding Author:
Françoise Clavel-Chapelon
INSERM E3N/U1018, Institut Gustave
Roussy, 117 rue Edouard Vaillant
94805 Villejuif Cedex, France
Tel: +33-14211-4148
Fax: +33-14211-4000
E-mail: [email protected]

Received date: August 11, 2011; Accepted date: December 14, 2011; Published date: December 16, 2011

Citation: Fabre A, Thomas E, Baulande S, Sohier E, Hoang L, et al. (2011) Is Saliva a Good Alternative to Blood for High Density Genotyping Studies: SNP and CNV Comparisons? J Biotechnol Biomaterial 1:119. doi:10.4172/2155-952X.1000119

Copyright: © 2011 Fabre A, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

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.

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