title: Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies.
abstract: Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at -20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies.
authors.affiliation: Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and ; Louvain Center for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, Brussels, Belgium.
authors.forename: Latifa
authors.initials: L
authors.lastname: El Bali
authors.affiliation: Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Diman
authors.affiliation: Louvain Center for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, Brussels, Belgium.
authors.forename: Alfred
authors.initials: A
authors.lastname: Bernard
authors.affiliation: Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and.
authors.forename: Nancy H C
authors.initials: NH
authors.lastname: Roosens
authors.affiliation: Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and.
authors.forename: Sigrid C J
authors.initials: SC
authors.lastname: De Keersmaecker
mesh_terms: D015415:Biomarkers / Q000032:analysis; D004247:DNA / Q000235:genetics / Q000302:isolation & purification*; D005260:Female; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011634:Public Health; D060888:Real-Time Polymerase Chain Reaction; D011978:Receptors, Nicotinic / Q000235:genetics; D013048:Specimen Handling; D014556:Urine / Q000737:chemistry*
chemical_list: D015415:Biomarkers; D004247:DNA; D011978:Receptors, Nicotinic
keywords: 16S; epidemiological studies; real-time polymerase chain reaction; species specificity