Comparative study of seven commercial kits for human dna extraction from urine samples suitable for dna biomarker-based public health studies

Journal of Biomolecular Techniques

Volumn 25, Issue 4, 2014, Pages 96-110

  El Bali, Latifa ^a,b   Diman, Aurélie ^a   Bernard, Alfred ^b   Roosens, Nancy H C ^a   Dekeersmaecker, Sigrid C J ^a  

^a SCIENTIFIC INSTITUTE OF PUBLIC HEALTH   (Belgium)

^b UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

16S; Epidemiological studies; Real time polymerase chain reaction; Species specificity

Indexed keywords

BACTERIAL DNA; GENOMIC DNA; HEMOGLOBIN BETA CHAIN; NICOTINIC RECEPTOR; OLIGONUCLEOTIDE; RNA 16S; BIOLOGICAL MARKER; DNA; NICOTINIC RECEPTOR SUBUNIT ALPHA3;

ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; DNA ISOLATION; DNA PURIFICATION; DNA TEMPLATE; ELECTROPHORESIS; EPIDEMIOLOGICAL MONITORING; FEMALE; GENE DOSAGE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPING TECHNIQUE; HUMAN; LACTOBACILLUS ACIDOPHILUS; LUNG CANCER; MALE; MOLECULAR DIAGNOSTICS; MRNA EXPRESSION ASSAY; NONHUMAN; NORMAL HUMAN; REAL TIME POLYMERASE CHAIN REACTION; SAMPLING; SINGLE NUCLEOTIDE POLYMORPHISM; SMOKING; SPECTROPHOTOMETER; SPECTROPHOTOMETRY; URINALYSIS; CHEMISTRY; COMPARATIVE STUDY; GENETICS; GENOTYPE; HUMAN GENOME; ISOLATION AND PURIFICATION; LABORATORY DIAGNOSIS; POLYMERASE CHAIN REACTION; PUBLIC HEALTH; URINE;

BIOMARKERS; DNA; FEMALE; GENOME, HUMAN; GENOTYPE; HUMANS; MALE; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PUBLIC HEALTH; REAL-TIME POLYMERASE CHAIN REACTION; RECEPTORS, NICOTINIC; SPECIMEN HANDLING; URINE;

EID: 84913589950     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: 10.7171/jbt.14-2504-002     Document Type: Article

References (57)

1. Ziegler A, Koch A, Krockenberger K, Grosshennig A. Personalized medicine using DNA biomarkers: a review. Hum Genet 2012;131:1627-1638.
2. Cleeren E, Van der Heyden J, Brand A, Van Oyen H. Public health in the genomic era: will Public Health Genomics contribute to major changes in the prevention of common diseases? Arch Public Health 2011;69:8.
3. Kendall TL, Byerley DJ, Dean R. Isolation of DNA from blood. Anal Biochem 1991;195:74-76.
4. Yoshizawa JM, Schafer CA, Schafer JJ, Farrell JJ, Paster BJ, Wong DT. Salivary biomarkers: toward future clinical and diagnostic utilities. Clin Microbiol Rev 2013;26:781-791.
5. Abraham JE, Maranian MJ, Spiteri I, et al. Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping. BMC Med Genomics 2012;5:19.
6. Bryzgunova OE, Skvortsova TE, Kolesnikova EV, et al. Isolation and comparative study of cell-free nucleic acids from human urine. Ann N Y Acad Sci 2006;1075:334-340.
7. Anker P, Mulcahy H, Stroun M. Circulating nucleic acids in plasma and serum as a noninvasive investigation for cancer: time for large-scale clinical studies? Int J Cancer 2003;103:149-152.
8. Botezatu I, Serdyuk O, Potapova G, et al. Genetic analysis of DNA excreted in urine: a new approach for detecting specific genomic DNA sequences from cells dying in an organism. Clin Chem 2000;46:1078-1084.
9. Yokota M, Tatsumi N, Tsuda I, Takubo T, Hiyoshi M. DNA extraction from human urinary sediment. J Clin Lab Anal 1998; 12:88-91.
10. Vu NT, Chaturvedi AK, Canfield DV. Genotyping for DQA1 and PM loci in urine using PCR-based amplification: effects of sample volume, storage temperature, preservatives, and aging on DNA extraction and typing. Forensic Sci Int 1999;102:23-34.
11. Johnson DJ, Calderaro AC, Roberts KA. Variation in nuclear DNA concentrations during urination. J Forensic Sci 2007;52: 110-113.
12. Bergallo M, Costa C, Gribaudo G, et al. Evaluation of six methods for extraction and purification of viralDNAfrom urine and serum samples. New Microbiol 2006;29:111-119.
13. Van der Hel OL, van der Luijt RB, Bueno de Mesquita HB, et al. Quality and quantity of DNA isolated from frozen urine in population-based research. Anal Biochem 2002;304:206-211.
14. Haufroid V, Clippe A, Knoops B, Bernard A, Lison D. Genotyping in urine: an interesting tool for epidemiological studies. Clin Chem 1998;44:2210-2211.
15. Milde A, Haas-Rochholz H, Kaatsch HJ. Improved DNA typing of human urine by adding EDTA. Int J Legal Med 1999;112: 209-210.
16. Yasuda T, Iida R, Takeshita H, et al. A simple method of DNA extraction and STR typing from urine samples using a commercially available DNA/RNA extraction kit. J Forensic Sci 2003;48: 108-110.
17. Siddiqui H, Nederbragt AJ, Jakobsen KS. A solid-phase method for preparing human DNA from urine for diagnostic purposes. Clin Biochem 2009;42:1128-1135.
18. Khan G, Kangro HO, Coates PJ, Heath RB. Inhibitory effects of urine on the polymerase chain reaction for cytomegalovirus DNA. J Clin Pathol 1991;44:360-365.
19. Hedman J, Radstrom P. Overcoming inhibition in real-time diagnostic PCR. Methods Mol Biol 2013;943:17-48.
20. Hedman J, Knutsson R, Ansell R, Radstrom P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2013;11(Suppl 1):S87-S101.
21. Alaeddini R. Forensic implications of PCR inhibition—a review. Forensic Sci Int Genet 2012;6:297-305.
22. Saulnier P, Andremont A. Detection of genes in feces by booster polymerase chain reaction. J Clin Microbiol 1992;30:2080-2083.
23. Kavaler E, Landman J, Chang Y, Droller MJ, Liu BC. Detecting human bladder carcinoma cells in voided urine samples by assaying for the presence of telomerase activity. Cancer 1998;82: 708-714.
24. Holland NT, Smith MT, Eskenazi B, Bastaki M. Biological sample collection and processing for molecular epidemiological studies. Mutat Res 2003;543:217-234.
25. Prinz M, Grellner W, Schmitt C. DNA typing of urine samples following several years of storage. Int J Legal Med 1993;106:75-79.
26. Cannas A, Kalunga G, Green C, et al. Implications of storing urinary DNA from different populations for molecular analyses. PLoS One 2009;4:e6985.
27. Zhang SH, Zhao SM, Zhao ZM, Li CT. Genotyping of urinary samples stored with EDTA for forensic applications. Genet Mol Res 2012;11:3007-3012.
28. Hilhorst M, Theunissen R, van Rie H., van Paassen P, Tervaert JW. DNA extraction from long-term stored urine. BMC Nephrol 2013;14:238.
29. Amos CI, Wu X, Broderick P, et al. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet 2008;40:616-622.
30. Sambrook J, Fritsch EF, Maniatis T., Maniatis T. Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press, 1989.
31. European Network of Genetically Modified Organism Laboratories. Definition of Minimum Performance Requirements for Analytical Methods of GMO Testing, European Commission, Brussels, Belgium, 2008;8.
32. Argentinian Meat (A19), Labo National Reference Laboratory Food Born Pathogen, Scientific Institute of Public Health (WIV-ISP), Brussels, 2010.
33. El-Osta YG, Hillier AJ, Dobos M. Construction of a combined physical and genetic map of the chromosome of Lactobacillus acidophilus ATCC 4356 and characterization of the rRNA operons. Microbiology 2005;151:875-892.
34. Altermann E, Russell WM, Azcarate-Peril MA, et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci USA 2005;102: 3906-3912.
35. Nakazono T, Kashimura S, Hayashiba Y, Hara K, Miyoshi A. Successful DNA typing of urine stains using a DNA purification kit following dialfiltration. J Forensic Sci 2005;50:860-864.
36. QIAamp DNA Micro Kit protocol, QIAamp Viral RNA Mini Kit protocol. Valencia, CA, USA: Qiagen, 2014.
37. Thermo Scientific. Assessment of Nucleic Acid Purity, T042 Technical Bulletin, NanoDrop Spectrophotometers. Wilmington, DE, USA: Thermo Fisher Scientific, 2011.
38. Huggett JF, Novak T, Garson JA, et al. Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon. BMC Res Notes 2008;1:70.
39. Nelson DE, Van Der Pol B, Dong Q, et al. Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLoS One 2010;5:e14116.
40. Dong Q, Nelson DE, Toh E, et al. The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. PLoS One 2011;6:e19709.
41. Siddiqui H, Nederbragt AJ, Lagesen K, Jeansson SL, Jakobsen KS. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol 2011;11:244.
42. Cole ST, Saint Girons I. Bacterial genomics. FEMS Microbiol Rev 1994;14:139-160.
43. Young M, Cole ST. Clostridium. In Sonenshein AL, Hoch JA, Losick R (eds): Bacillus subtilis and Other Gram-Positive Organisms. Washington, DC, USA: American Society for Microbiology, 1993;35-52.
44. Beskow LM, Khoury MJ, Baker TG, Thrasher JF. The integration of genomics into public health research, policy and practice in the United States. Community Genet 2001;4:2-11.
45. Wilson IG. Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 1997;63:3741-3751.
46. Wiedbrauk DL, Werner JC, Drevon AM. Inhibition of PCR by aqueous and vitreous fluids. J Clin Microbiol 1995;33:2643-2646.
47. Ghatak S, Muthukumaran RB, Nachimuthu SK. A simple method of genomic DNA extraction from human samples for PCR-RFLP analysis. J Biomol Tech 2013;24:224-231.
48. Rauter C, Mueller M, Diterich I, et al. Critical evaluation of urine-based PCR assay for diagnosis of Lyme borreliosis. Clin Diagn Lab Immunol 2005;12:910-917.
49. Merchant ML, Powell DW, Wilkey DW, et al. Microfiltration isolation of human urinary exosomes for characterization by MS. Proteomics Clin Appl 2010;4:84-96.
50. Sullivan PS, Chan JB, Levin MR, Rao J. Urine cytology and adjunct markers for detection and surveillance of bladder cancer. Am J Transl Res 2010;2:412-440.
51. Manoni F, Gessoni G, Alessio MG, et al. Mid-stream vs. firstvoided urine collection by using automated analyzers for particle examination in healthy subjects: an Italian multicenter study. Clin Chem Lab Med 2012;50:679-684.
52. Schaub S, Wilkins J, Weiler T, Sangster K, Rush D, Nickerson P. Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 2004;65:323-332.
53. Kishi K, Yasuda T, Takeshita H. DNase I: structure, function, and use in medicine and forensic science. Leg Med (Tokyo) 2001;3:69-83.
54. Tobacco Free Initiative, World Health Organization. WHO Report on the Global Tobacco Epidemic, 2009: Implementing Smoke-Free Environments. Geneva, Switzerland: World Health Organization, 2009.
55. De Viron S, Malats N, Van der Heyden J, Van Oyen H, Brand A. Environmental and genomic factors as well as interventions influencing smoking cessation: a systematic review of reviews and a proposed working model. Public Health Genomics 2013; 16:159-173.
56. Le Marchand L, Derby KS, Murphy SE, et al. Smokers with the CHRNA lung cancer-associated variants are exposed to higher levels of nicotine equivalents and a carcinogenic tobacco-specific nitrosamine. Cancer Res 2008;68:9137-9140.
57. Wassenaar CA, Dong Q, Wei Q, Amos CI, Spitz MR, Tyndale RF. Relationship between CYP2A6 and CHRNA5-CHRNA3-CHRNB4 variation and smoking behaviors and lung cancer risk. J Natl Cancer Inst 2011;103:1342-1346.