Effect of mismatch between types of viral nucleic acid and intended targets of extraction kits on polymerase chain reaction-based testing

Lab personnel generally select an extraction kit based on the nucleic acid (NA) type of the target. This study investigated the effect of mismatch between the NA type of the target and the intended target NA of the extraction kit on the polymerase chain reaction outcome. DNA, RNA and total NA extraction kits manufactured by the same company were used to isolate NA from serial dilutions of four viruses representing different genome types. All extracts were tested for the viruses by either conventional or real-time polymerase chain reactions with and without reverse transcription. While the DNA kit specifically isolated DNA from samples, the RNA kit extracted both DNA and RNA as efficiently as the total NA kit, suggesting that RNA kits can be an economical alternative.

Simple DNA extraction of urine samples: Effects of storage temperature and storage time

Urine samples are commonly analysed in cases with suspected illicit drug consumption. In events of alleged sample mishandling, urine sample source identification may be necessary. A simple DNA extraction procedure suitable for STR typing of urine samples was established on the Promega Maxwell^® 16 paramagnetic silica bead platform. A small sample volume of 1.7mL was used. Samples were stored at room temperature, 4°C and -20°C for 100days to investigate the influence of storage temperature and time on extracted DNA quantity and success rate of STR typing. Samples stored at room temperature exhibited a faster decline in DNA yield with time and lower typing success rates as compared to those at 4°C and -20°C. This trend can likely be attributed to DNA degradation. In conclusion, this study presents a quick and effective DNA extraction protocol from a small urine volume stored for up to 100days at 4°C and -20°C.

Assessment of the stability of DNA in specimens collected under conditions for drug testing-A pilot study

For forensic biological sample collections, the specimen donor is linked solidly to his or her specimen through a chain of custody (CoC) sometimes referenced as a chain of evidence. Rarely, a donor may deny that a urine or oral fluid (OF) specimen is his or her specimen even with a patent CoC. The goal of this pilot study was to determine the potential effects of short-term storage on the quality and quantity of DNA in both types of specimen under conditions that may be encountered with employment-related drug testing specimens. Fresh urine and freshly collected oral fluid all produced complete STR profiles. For the "pad" type OF collectors, acceptable DNA was extractable both from the buffer/preservative and the pad. Although fresh urine and OF produced complete STR profiles, partial profiles were obtained after storage for most samples. An exception was the DNA in the Quantisal OF collector, from which a complete profile was obtained for both freshly collected OF and stored OF.

Profiling a multiplex short tandem repeat loci from human urine with use of low cost on-site technology for verification of sample authenticity

This work focuses on the development of a sophisticated technique via STR typing to unequivocally verify the authenticity of urine samples before sent to laboratories. STR profiling was conducted with the CSF1PO, TPOX, TH01 Multiplex System coupled with a smartphone-based detection method. The promising capability of the method to identify distinct STR profiles from urine of different persons opens the possibility to conduct sample authenticity tests. On-site STR profiling could be realized with a self-contained autonomous device with an integrated PCR microchip shown hereby.

Individual identification of racehorses from urine samples using a 26-plex single-nucleotide polymorphism assay

To construct a system for identifying individual horses from urine samples that are submitted for postracing doping tests, we developed a genotyping assay based on 26-plex single-nucleotide polymorphisms (SNPs). DNA was isolated from urine using a commercially available DNA/RNA extraction kit, and SNP genotyping was achieved with a SNaPshot(™) technique. DNA profiles including 26 SNPs were acquired from urine samples and blood/hair samples. Within the studied Thoroughbred population, the 26-plex assay showed a probability of identity of 5.80 × 10(-11). Compared to the conventional short tandem repeat assay, the SNP assay used less DNA, and the rate of successful genotyping was improved to 97% using aliquots of horse urine as small as 140 μL. The urinary DNA could be successfully genotyped under proper storage concerning refrigeration or freeze-thawing. This SNP assay can be used for individual identification when suspicious results are obtained from horse doping tests.

A solid-phase method for preparing human DNA from urine for diagnostic purposes

OBJECTIVES

To develop a simple method using paramagnetic beads for isolation of human DNA from small volumes of urine. The method should be amendable for automation. The purified DNA is intended to be used in downstream diagnostics and screening studies using nucleic acid amplification techniques.

DESIGN AND METHODS

Unspecific capture of cells present in urine to magnetic particles, lysis and subsequent binding of the DNA to the same bead surface.

RESULTS

DNA isolated using the method could be used as template for sensitive real-time PCR and end-point PCR using primers targeted to the GAPDH, K-ras, DD3 and p53 genes. Compared to silica spin column-based extraction, the method showed equal or higher DNA yields. The method performed reliably when automated using a liquid handling robot equipped with a magnetic workstation.

CONCLUSIONS

The method generates purified DNA free from inhibitors, applicable for sensitive applications such as real-time PCR, genotyping, and for sequence variant analysis. The use of magnetic beads allows for automation, reducing hands-on time and creating a high throughput and reproducible protocol for the purpose of large-scale screening and diagnostics.

Accuracy of multiplexed Illumina platform-based single-nucleotide polymorphism genotyping compared between genomic and whole genome amplified DNA collected from multiple sources

Association studies designed to identify the genetic determinants underlying complex disease increasingly require sustainable high-quality DNA resources for large-scale single-nucleotide polymorphism (SNP) genotyping. Recent studies have shown that genomic DNA (gDNA) suitable for SNP genotyping can be obtained from buccal cells and from dried blood spots on Guthrie cards. Further, successful SNP genotyping has been done using the reaction product of multiple displacement amplification of gDNA. We evaluated genotype consistency on the Illumina genotyping platform for 717 to 1,744 SNP loci between replicate samples of gDNA and whole genome amplified DNA (wgaDNA) from a variety of sources. Nine healthy adults provided peripheral blood via venipuncture and buccal cells by mouth rinse. DNA was also obtained from urothelial cells in urine samples from five of the nine subjects. gDNA was extracted from all samples, wgaDNA was generated from each gDNA, and all samples were genotyped. To assess SNP genotyping accuracy of DNA obtained from dried blood spots, gDNA was extracted, amplified, and genotyped from peripheral blood samples and paired Guthrie card samples were obtained from eight childhood leukemia patients. Call rates and replicate concordances for all sample types, regardless of amplification, were >97%, with most sample types having call rates and replicate concordances >99%. Using the gDNA from blood samples as the reference for concordances calculated for all other sample types, we observed concordances >98% regardless of sample type or amplification. We conclude that highly multiplexed Illumina genotyping may be done on gDNA and wgaDNA obtained from whole blood, buccal samples, dried blood spots on Guthrie cards, and possibly even urine samples, with minimal misclassification.

Detection of manipulation in doping control urine sample collection: a multidisciplinary approach to determine identical urine samples

Manipulation of urine sampling in sports drug testing is considered a violation of anti-doping rules and is consequently sanctioned by regulatory authorities. In 2003, three identical urine specimens were provided by three different athletes, and the identity of all urine samples was detected and substantiated using numerous analytical strategies including gas chromatography-mass spectrometry with steroid and metabolite profiling, gas chromatography-nitrogen/phosphorus detector analysis, high-performance liquid chromatography-UV fingerprinting, and DNA-STR (short tandem repeat) analysis. None of the respective athletes was the donor of the urine provided for doping analysis, which proved to be a urine sample collected from other unidentified individual(s). Samples were considered suspicious based on identical steroid profiles, one of the most important parameters for specimen individualization in sports drug testing. A database containing 14,224 urinary steroid profiles of athletes was screened for specific values of 4 characteristic parameters (ratios of testosterone/epitestosterone, androsterone/etiocholanolone, androsterone/testosterone, and 5alpha-androstane-3alpha,17beta-diol/5beta-androstane-3alpha,17beta-diol) and only the three suspicious samples matched all criteria. Further metabolite profiling regarding indicated medications and high-performance liquid chromatography-UV fingerprinting substantiated the assumption of manipulation. DNA-STR analyses unequivocally confirmed that the 3 urine samples were from the same individual and not from the athletes who provided DNA from either buccal cell material or blood specimens. This supportive evidence led to punishment of all three athletes according to the rules of the World Anti-Doping Agency. Application of a new multidisciplinary strategy employing common and new doping control assays enables the detection of urine substitution in sports drug testing.

Determinants of the variability of aflatoxin-albumin adduct levels in Ghanaians

Hepatocellular carcinoma (HCC) is a multifactorial disease with various host and environmental factors involved in its etiology. Of these, aflatoxin exposure has been established as an important risk factor in the development of HCC; the presence of aflatoxin-albumin (AA) adducts in the blood serves as a valuable biomarker of human exposure. In this study, the relationship between a variety of different HCC host factors and the incidence of AA adduct levels was examined in a Ghanaian population at high risk for HCC. These factors included age, gender, hepatitis virus B (HVB) and hepatitis C virus (HCV) status, and genetic polymorphisms in both microsomal epoxide hydrolase (mEH) and glutathione S-transferases (GSTs). Blood samples were analyzed for AA adducts and HBV and HCV status. GSTM1 and GSTT1 deletion polymorphisms and mEH exon 3 and exon 4 single-nucleotide polymorphisms (SNPs) were determined from urine samples. In univariate analysis, age, HBV and HVC status, and GSTT1 and mEH exon 3 genotypes were not associated with AA adduct levels. However, mean adduct levels were significantly higher in both females and individuals typed heterozygous for mEH exon 4 (vs. wild types). Stratification analysis also showed that gender along with mEH exon 4 genotype and HBV status had a significant effect on adduct levels. Both females typed HBsAg+ and males with mEH exon 4 heterozygote genotypes showed significantly higher adduct levels as compared to the HBsAg- and wild types, respectively. Understanding the relationships between these host factors and the variability in aflatoxin-adduct levels may help in identifying susceptible populations in developing countries and for targeting specific public health interventions for the prevention of aflatoxicoses in populations with HCC and chronic liver diseases.

Noninvasive identification of interindividual variation in xenobiotic-metabolizing enzymes: implications for cancer epidemiology and biomarker studies

In this study, DNA extracted from frozen urine was used in the analysis of polymorphisms in genes coding for xenobiotic-metabolizing enzymes (XMEs). These included single-nucleotide polymorphisms (SNP) in microsomal epoxide hydrolase (mEH), that is, substitutions of tyrosine by histidine in codon 113 (Y113H) and histidine by arginine in codon 139 (H139R), and deletion polymorphisms in glutathione S-transferase (GST) M1 and T1 genes. The concentration of DNA extracted from urine of a Ghanaian population (n = 91) exposed to aflatoxins in their diet ranged from 82.5 to 573 ng/ml urine. Polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) procedures were used for the characterization of mEH polymorphisms, whereas a multiplex PCR method was utilized to identify GST deletion polymorphisms. In total, 91% and 94% of 91 samples were genotyped for mEH exon 3 and exon 4 polymorphisms, respectively. In the multiplex analysis of GST polymorphisms, 94% and 91% of 91 individuals were genotyped for GSTM1 and GSTT1 polymorphisms, respectively. The polymorphisms in the mEH exon 4, GSTM1 and GSTT1, were not in Hardy-Weinberg equilibrium (HWE) except for mEH exon 3. Representative genotypes identified by PCR-RFLP were cloned and sequenced, then confirmed by comparison with reference sequences of human DNA published in the GenBank BLAST database. These results demonstrate that XMEs can be genotyped from urine with reliable accuracy and may be useful in cancer and molecular epidemiology studies.

Transrenal DNA testing: progress and perspectives

Transrenal DNA (Tr-DNA) is a recently discovered class of extracellular urinary DNA that originates from cells dying throughout the body. Postapoptotic DNA is known to appear in the circulating plasma, but it is now recognized that a portion of these fragments cross the kidney barrier and appear in urine in the form of 150-200-bp fragments. Tr-DNA containing fetal sequences has been isolated from the urine of pregnant women, tumor-specific mutations have been detected in Tr-DNA from patients with colon and pancreatic tumors, and donor DNA has been found in Tr-DNA isolated from recipient urine. Furthermore, proviral HIV DNA, bacterial and parasite DNA sequences have been detected in Tr-DNA from infected patients. Potential applications of Tr-DNA-based tests cover a very broad area of molecular diagnostics and genetic testing, including prenatal detection of inherited diseases, tumor diagnostics and therapeutic monitoring and detection of infectious agents. The Tr-DNA test is expected to have utility in treatment monitoring, transplantation monitoring, drug development and broad public health screening, where a noninvasive, common-platform diagnostic technology has particular value. This review describes some of the highlights of Tr-DNA technology applications, advantages over existing technologies and potential problems anticipated in test development.

Forensic identification of urine samples: a comparison between nuclear and mitochondrial DNA markers

Urine samples from 20 male volunteers of European Caucasian origin were stored at 4 degrees C over a 4-month period in order to compare the identification potential of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) markers. The amount of nDNA recovered from urines dramatically declined over time. Consequently, nDNA likelihood ratios (LRs) greater than 1,000 were obtained for 100, 70 and 55% of the urines analysed after 6, 60 and 120 days, respectively. For the mtDNA, HVI and HVII sequences were obtained for all samples tested, whatever the period considered. Nevertheless, the highest mtDNA LR of 435 was relatively low compared to its nDNA equivalent. Indeed, LRs obtained with only three nDNA loci could easily exceed this value and are quite easier to obtain. Overall, the joint use of nDNA and mtDNA markers enabled the 20 urine samples to be identified, even after the 4-month period.

Usefulness of deoxyribonuclease I (DNase I) polymorphism for individualization from small aged urine stains

We devised a procedure that combines a simple extraction method, isoelectric focusing and activity staining using the dried agarose film overlay method, for deoxyribonuclease I (DNase I) typing from aged urine stains. DNase I types were determined without difficulty from urine stains kept at room temperature for 3 months or more in all of the samples tested. The amounts of urine stains required for typing after 3 months of storage were estimated to be equivalent to 60-120 microl of liquid urine. Therefore, considering that useful PCR-based DNA typing has not yet been developed for urine stains, DNase I polymorphism could be considered the first biochemical marker found to be well suited for individualization from small aged urine stains.