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[Online ahead of print]

Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?

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Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?

Sarah J D Nauwelaerts et al. J Biomol Tech.

Abstract

Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.

Keywords: biomarkers; children; genetic epidemiology; genotype; real-time PCR.

Figures

FIGURE 1.
FIGURE 1.
Integrity of DNA extracted from urine and saliva. TapeStation results and concentrations (ng/μl) obtained from β-globin qPCR of DNA extracted form urine (A) and saliva (B) on a selection of 6 samples (boys: A, B, C, E; girls: D, F). The corresponding yields (nanograms per microliter biofluid) are for urine (A): sample A, B, C, D, F: undetermined; sample E: 11.1 ng/ml; and for saliva (B): sample A: 8495 ng/ml, sample B: 6244 ng/ml, sample C: 12,577 ng/ml, sample D: 10,008 ng/ml, sample E: 33,527 ng/ml, sample F; 17,977 ng/ml.

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