Implications of storing urinary DNA from different populations for molecular analyses

PLoS ONE

Volumn 4, Issue 9, 2009, Pages

  Cannas, Angela ^a   Kalunga, Glendah ^b   Green, Clare ^b,c   Calvo, Ludovica ^a   Katemangwe, Patrick ^b   Reither, Klaus ^d,f   Perkins, Mark D ^e   Maboko, Leonard ^d   Hoelscher, Michael ^d,f   Talbot, Elizabeth A ^e   Mwaba, Peter ^b   Zumla, Alimuddin I ^b,c   Girardi, Enrico ^a   Huggett, Jim F ^b,c  

^a NATIONAL INSTITUTE FOR INFECTIOUS DISEASES L SPALLANZANI   (Italy)

^b UNIVERSITY TEACHING HOSPITAL   (Zambia)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d NIMR Mbeya Medical Research Programme   (Tanzania)

^e FOUNDATION FOR INNOVATIVE NEW DIAGNOSTICS   (Switzerland)

^f LUDWIG MAXIMILIANS UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; EDETIC ACID; TOLL LIKE RECEPTOR 2;

ADOLESCENT; ADULT; ALU SEQUENCE; ARTICLE; CHILD; CONTROLLED STUDY; DIAGNOSTIC TEST; DNA CONTENT; DNA DEGRADATION; DNA DETERMINATION; ETHNIC DIFFERENCE; FEMALE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC STABILITY; HUMAN; HUMAN EXPERIMENT; ITALY; MALE; NORMAL HUMAN; POPULATION GENETICS; PROGNOSIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SCHOOL CHILD; SEX DIFFERENCE; STORAGE TEMPERATURE; URINALYSIS; ZAMBIA; DIAGNOSIS, MEASUREMENT AND ANALYSIS; LABORATORY DIAGNOSIS; METHODOLOGY; MIDDLE AGED; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TEMPERATURE; TIME; URINE;

ADOLESCENT; ADULT; CHILD; DNA; FEMALE; HUMANS; LABORATORY TECHNIQUES AND PROCEDURES; MALE; MIDDLE AGED; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPECIMEN HANDLING; TEMPERATURE; TIME FACTORS;

EID: 70349297651     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006985     Document Type: Article

References (32)

1. Cairns P (2004) Detection of promoter hypermethylation of tumor suppressor genes in urine from kidney cancer patients. Circulating Nucleic Acids in Plasma/Serum Iii and Serum Proteomics 1022: 40-43.
2. Mehta TK, Hoque MO, Ugarte R, Rahman MH, Kraus E, et al. (2006) Quantitative detection of promoter hypermethylation as a biomarker of acute kidney injury during transplantation. Transplantation Proceedings 38: 3420-3426.
3. Murdoch DR, Walford EJ, Jennings LC, Light GJ, Schousboe MI, et al. (1996) Use of the polymerase chain reaction to detect Legionella DNA in urine and serum samples from patients with pneumonia. Clinical Infectious Diseases 23: 475-480.
4. Chapin KC (2006) Molecular tests for detection of the sexually-transmitted pathogens Neisseria gonorrhoeae and Chlamydia trachomatis. Med Health R I 89: 202-204.
5. Cannas A, Goletti D, Giradi E, Chiacchio T, Calvo L, et al. (2008) Mycobacterium tuberculosis DNA Detection in Soluble Fraction of Urine from Pulmonary Tuberculosis Patients. International Journal of Tuberculosis and Lung Disease 12: 146-151.
6. Fisa R, Riera C, Lopez-Chejade P, Molina I, Gallego M, et al. (2008) Leishmania infantum DNA detection in urine from patients with visceral Leishmaniasis and after treatment control. American Journal of Tropical Medicine and Hygeine 78: 741-744.
7. Mharakurwa S, Simoloka C, Thuma PE, Shiff CJ, Sullivan DJ (2006) PCR detection of Plasmodium falciparum in human urine and saliva samples. Malaria Journal 5: 103.
8. Aceti A, Zanetti S, Mura MS, Sechi LA, Turrini F, et al. (1999) Identification of HIV Patients with Active Pulmonary Tuberculosis using Urine Based Polymerase Chain Reaction Assay. Thorax 54: 145-146.
9. Kafwabulula M, Ahmed K, Nagatake T, Gotoh J, Mitarai S, et al. (2002) Evaluation of PCR-based Methods for the Diagnosis of Tuberculosis by Identification of Mycobacterial DNA in Urine Samples. International Journal of Tuberculosis and Lung Disease 6: 732-737.
10. Rebollo MJ, San Juan Garrido R, Folgueria D, Palenque E, Diaz-Pedroche C, et al. (2006) Blood and Urine Samples as Useful Sources for the Direct Detection of Tuberculosis by Polmerase Chain Reaction. Diagnostic Microbiology and Infectious Disease 56: 141-146.
11. Sechi LA, Piera Pinna M, Sanna A, Pirina P, Ginesu F, et al. (1997) Detection of Mycobacterium tuberculosis by PCR Analysis of Urine and Other Clinical Samples from AIDS and Non-HIV Infected Patients. Molecular and Cellular Probes 11: 281-285.
12. Torrea G, Van de Perre P, Ouedraogo M, Zougba A, Sawadogo A, et al. (2005) PCR-based Detection of the Mycobacterium tuberculosis Complex in Urine of HIV-infected and Uninfected Pulmonary and Extrapulmonary Tuberculosis Patients in Burkina Faso. Journal of Medical Microbiology 54: 39-44.
13. Gopinath K, Singh S (2008) Urine as an adjunct specimen for the diagnosis of active pulmonary tuberculosis. International Journal of Infectious Diseases.
14. Green C, Huggett JF, Talbot E, Mwaba P, Reither K, et al. (2009) Rapid diagnosis of tuberculosis through the detection of mycobacterial DNA in urine by nucleic acid amplification methods. The Lancet Infectious Diseases 9: 505-511.
15. Ingersoll J, Bythwood T, Abdul-Ali D, Wingood GM, Diclemente RJ, et al. (2008) Stability of Trichomonas vaginalis DNA in Urine Specimens. Journal of Clinical Microbiology 46: 1628-1630.
16. Morré SA, van Valkengoed IGM, de Jong A, Boeke AJP, van Eijk JTM, et al. (1999) Mailed, Home-obtained Urine Specimens: a Reliable Screening Approach for Detecting Asymptomatic Chlamydia trachomatis Infections. Journal of Clinical Microbiology 1999: 976-980.
17. Vu NT, Chaturvedi AK, Canfield DV (1999) 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 Science International 102: 23-34.
18. Milde A, Haas-Rochholz H, Kaatsch HJ (1999) Improved DNA Typing of Human Urine by Adding EDTA. International Journal of Legal Medicine 112: 209-210.
19. van der Hel OL, van der Luijt RB, de Mesquita HBB, van Noord PAH, Slothouber B, et al. (2002) Quality and quantity of DNA isolated from frozen urine in population-based research. Analytical Biochemistry 304: 206-211.
20. Prinz M, Grellner W, Schmitt C (1993) DNA typing of urine samples following several years of storage. International Journal of Legal Medicine 106: 75-79.
21. Garringer LA, Simkins MR, Chomiszewski CK, Palisano C, Zimmerman SJ (2002) Evaluation of the DNA/RNA Protect System to Preserve Urine for Testing Using BDProbeTec for Neisseria gonorrhoeae and Chlamydia trachomatis. Abstracts of the General Meeting of the American Society for Microbiology 102: 129.
22. Swartz B, Bourbeau P (2007) Comparative evaluation of UriSwab urine collection transport and preservative and BD vacutainer C&S preservative plus plastic tube for preservation of urine specimens. Abstracts of the General Meeting of the American Society for Microbiology 107: 217.
23. McMillian RA, Fort TL (2004) Evaluation of a new urine transport tube with preservative for use in the BD ProbeTec (TM) ET system. Abstracts of the General Meeting of the American Society for Microbiology 104: 173-174.
24. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett JF, et al. (2009) The MIQE guidelines: Minimum Information for publication of Quantitative realtime PCR Experiments. Clinical Chemistry 55: doi:10.1373/ clinchem.2008.112797.
25. Nolan T, Hands RE, Ogunkolade W, Bustin SA (2006) SPUD: a quantitative PCR assay for the detection of inhibitors in nucleic acid preparations. Analytical Biochemistry 351: 308-310.
26. Huggett JF, Novak T, Garson JA, Green C, Morris-Jones SD, et al. (2008) Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon. BMC Research Notes 1.
27. Johnson DJ, Calderaro AC, Roberts KA (2004 Oct 29) Variation in nuclear DNA concentrations during urination; Ventura, CA. pp 110-113.
28. Bryzgunova OE, Skvortsova TE, Kolesnikova EV, Starikov AV, Rykova EY, et al. (2006) Isolation and comparative study of cell-free nucleic acids from human urine. Annals of the New York Academy of Sciences 1075: 334-340.
29. Gu Z, Wang H, Nekrutenko A, Li W-H (2000) Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene 259: 81-88.
30. Kanavarioti A, Monnard P-A, Deamer DW (2001) Eutectic phases in ice facilitate nonenzymatic nucleic acid synthesis. Astrobiology 1: 271-281.
31. Elliott P, Peakman TC, Biobank UK (2008) The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. International Journal of Epidemiology 37: 234-244.
32. Peakman TC, Elliott P (2008) The UK Biobank sample handling and storage validation studies. Int J Epidemiol 37 Suppl 1: i2-6.