Evaluation of the new cobas® HCV genotyping test based on real-time PCRs of three different HCV genome regions.

BACKGROUND: Determination of the hepatitis C virus (HCV) genotype and discrimination between HCV subtypes 1a and 1b is still mandatory prior to anti-HCV treatment initiation. The aim of this study was to evaluate the performance of the recently introduced cobas® HCV GT assay (Roche) and to compare it to two comparator assays. METHODS: The cobas® HCV GT assay is based on primer-specific real-time polymerase chain reaction (PCR). For comparison, the TRUGENE® HCV 5'NC Genotyping Kit (Siemens) and the VERSANT® HCV Genotype 2.0 Assay (Siemens) were employed. Accuracy of the new assay was determined using proficiency panels. For clinical evaluation, 183 residual clinical samples obtained from patients with chronic hepatitis C infection were included. RESULTS: When accuracy was tested, panel members containing HCV subtypes 1a, 1b, and 3a were identified as expected; however, the new assay failed to identify low titer panel members containing HCV subtype 5a correctly. Of 183 clinical samples, 160 gave concordant results. For seven samples, an indeterminate result was reported with the cobas® HCV GT assay and the remaining 16 samples were found discordant with one of the comparator assays. When time-to-results of the assays were compared, the new assay showed shorter total time and similar hands-on time per sample. CONCLUSIONS: The cobas® HCV GT assay showed a good performance and proved to be suitable for use in the routine diagnostic laboratory. Due to the high level of automation, fast and reliable results are obtained with short hands-on time.

Armored DNA in recombinant Baculoviruses as controls in molecular genetic assays.

The widespread use of molecular PCR-based assays in analytical and clinical laboratories brings about the need for test-specific, stable, and reliable external controls (EC) as well as standards and internal amplification controls (IC), in order to arrive at consistent test results. In addition, there is also a growing need to produce and provide stable, well-characterized molecular controls for quality assurance programs. In this study, we describe a novel approach to generate armored double-stranded DNA controls, which are encapsulated in baculovirus (BV) particles of the species Autographa californica multiple nucleopolyhedrovirus. We used the well-known BacPAK™ Baculovirus Expression System (Takara-Clontech), removed the polyhedrin promoter used for protein expression, and generated recombinant BV-armored DNAs. The obtained BV-armored DNAs were readily extracted by standard clinical DNA extraction methods, showed favorable linearity and performance in our clinical PCR assays, were resistant to DNase I digestion, and exhibited marked stability in human plasma and serum. BV-armored DNA ought to be used as ECs, quantification standards, and ICs in molecular assays, with the latter application allowing for the entire monitoring of clinical molecular assays for sample adequacy. BV-armored DNA may also be used to produce double-stranded DNA reference materials for, e.g., quality assurance programs. The ease to produce BV-armored DNA should make this approach feasible for a broad spectrum of molecular applications. Finally, as BV-armored DNAs are non-infectious to mammals, they may be even more conveniently shipped than clinical specimen.

Conditions of High Resolution Melting Analysis on the Cobas z480 Instrument for the Genotyping of VKORC1 in the Clinical Routine Laboratory.

BACKGROUND: High resolution melting (HRM) of amplicons is a simple method for genotyping of single nucleotide polymorphisms (SNPs). Albeit many applications reported, HRM seems to be rarely used in clinical laboratories. The suitability of HRM-PCR for the clinical laboratory was investigated for genotyping of SNPs of the vitamin K epoxide reductase complex unit 1 gene. METHODS: About 100 DNA samples were analyzed by two different HRM-PCRs on the Cobas z480 instrument and compared with a PCR with fluorescently labeled probes (HybProbe-PCR) on the LightCycler 2.0 instrument as reference. RESULTS: Reliable genotyping with 100% matching results was obtained, when the amplicon size was small (63 bp) and DNA input was limited by e.g., sample dilution with salt-free water. CONCLUSIONS: DNA extracted by differing methods may be used for genotyping by HRM-PCR. Compared with HybProbe-PCR, HRM-PCR on the Cobas z480 instrument allows for higher through-put, however, at the cost of a higher degree of laboratory standardization and a slower turnaround.

Reliable analysis of the single nucleotide polymorphism of lactase persistence LPH(-13910) C/T from saliva derived DNA: validation of a standardized saliva collection system.

BACKGROUND: The purpose of this study was to investigate the applicability of the Greiner Saliva Collection System (SCS) to obtain human genomic DNA for the analysis of single nucleotide polymorphisms (SNP) in the clinical routine laboratory. METHODS: Saliva and EDTA-blood were collected pair-wise from 112 participants. DNA was prepared by two automated procedures (MagNA Pure LC or MagNa Pure compact) and analyzed by UV-spectrophotometry and real-time PCR. RESULTS: Mean saliva derived DNA concentration was 52.7 ng/µL ± 36.4 (1000 µL, MagNA Pure LC) and 9.2 ng/µL ± 5.6 (200 µL, MagNA Pure compact) with A260/A280 ratios of 1.9 ± 0.1 and 2.1 ± 0.3 for MagNA Pure LC and MagNA Pure compact, respectively. SNP analysis for caucasian adult type lactase persistence showed a 100% success rate from saliva derived DNA and as reference from blood derived DNA. Matching genotypes were obtained in each sample pair. CONCLUSIONS: Saliva obtained with the standardized SCS yielded sufficient amounts of DNA in high purity and was found to represent a suitable and reliable source of human DNA for SNP analysis in the clinical routine laboratory.

Genotypic prediction of human immunodeficiency virus type 1 tropism by use of plasma and peripheral blood mononuclear cells in the routine clinical laboratory.

We developed a sequencing assay for genotypic HIV-1 tropism determination. The assay allows examination of HIV RNA from plasma and HIV DNA from peripheral blood mononuclear cells (PBMC), including PBMC samples from patients with undetectable viral loads. Assessment of 100 pairs of plasma and PBMC samples showed a high concordance of 90%. With the limitations of population-based sequencing, the assay was found to be robust and suitable for the routine clinical laboratory.

Lymphocyte imbalance in vitiligo patients indicated by elevated CD4+/CD8+ T-cell ratio.

Vitiligo is a disorder of pigmentation associated with an autoimmune-mediated loss of melanocytes from the epidermis. Humoral immunity and the involvement of cellular immunity have been investigated in the pathogenesis of vitiligo. We evaluated the role of pro-inflammatory cytokines and lymphocyte fractions in peripheral blood in a cohort of Austrian patients with vitiligo. Morning blood samples from 40 patients with vitiligo were collected. Twenty-one patients had active and 19 had stable vitiligo disease. All patients were suffering from non-segmental vitiligo at different stages of the disease. Sixteen persons presented with an additional autoimmune thyroid disease. To evaluate a possible involvement of proinflammatory cytokines in vitiligo we measured sTNF-RI (soluble tumour necrosis factor receptor I), IL-6 and additionally CIC (circulating immune complexes). We compared these findings to the data from matched normal persons. To investigate the mechanisms of cellular immunity, peripheral blood cell count and lymphocyte subtype analysis by flow cytometry were done. sTNF-RI, IL-6 and CIC serum levels were in the normal range. In the patient group median sTNF-RI level was 1.5 ng/ml and median CIC level was 35.2 microg/ml, and no statistically significant differences to the control group were observed. Median IL-6 level in vitiligo patients was 2.7 pg/ml and in the normal range-but higher than the median level of 0.5 pg/ml observed in normal persons (p < 0.001). Absolute and relative counts of lymphocyte subtypes were normal. The ratio of CD4+/CD8+ T-cells had an elevated median value of 2.6 [quartiles 2.0; 3.1]. 61% of the vitiligo patients had a ratio higher than 2.4, which was the normal cut-off point. In most vitiligo patients the balance of cytotoxic/suppressor and helper/inducer T-cells in peripheral blood is disturbed which might lead to a predominance of T-cell subtypes in the intracutaneous site of autoimmune melanocyte loss.

Genotypic antiretroviral resistance testing for human immunodeficiency virus type 1 integrase inhibitors by use of the TruGene sequencing system.

A sequencing assay for detection of mutations conferring resistance to human immunodeficiency virus type 1 (HIV-1) integrase inhibitors raltegravir and elvitegravir was developed using the automated TruGene sequencing system. The assay returned clear sequencing results for samples with >or=500 RNA copies/ml for mutation detection and HIV-1 subtyping across a spectrum of HIV-1 subtypes.

Prevalence, severity and predictors of HOMA-estimated insulin resistance in diabetic and nondiabetic patients with end-stage renal disease.

BACKGROUND: Prevalence of insulin resistance (IR) is increased in type 2 diabetes and in end-stage renal disease (ESRD). IR is associated with advanced atherosclerosis and is an independent predictor for cardiovascular disease in diabetes and ESRD patients. We investigated prevalence, severity, predictors and relation to vascular diseases by the homeostasis model assessment (HOMA-IR) in diabetic and nondiabetic ESRD patients. METHODS: ESRD patients with type 2 diabetes (n = 27) and nondiabetic ESRD patients (n = 35) were included in the study. IR was assessed with the HOMA-IR using fasting glucose and insulin levels. Additionally, serum levels of C-peptide, HbA1c, triglycerides, cholesterol and C-reactive protein and blood pressure were assessed. RESULTS: Median HOMA-IR was significantly higher in the diabetic ESRD patients than in the nondiabetic ESRD patients (6.3 [range 0.7-61.7] vs. 2.4 [range 0.3-5.7]; p < 0.001). Systolic blood pressure and triglycerides were significantly higher in patients with higher HOMA-IR, whereas HDL cholesterol was significantly lower in those patients. Only nondiabetic patients with increased HOMA-IR had significantly higher C-peptide levels than those with lower HOMA-IR (14.9 + 5.7 vs. 9.0 + 4.3, p = 0.004). Vascular disease prevalence was significantly higher in diabetic patients with higher HOMA-IR than in those with lower HOMA-IR. CONCLUSIONS: Prevalence and severity of HOMA-IR was greater in diabetic ESRD patients than in those without diabetes. In diabetic patients low HDL cholesterol was the only predictor for higher HOMA-IR, whereas in nondiabetic patients a high C-peptide level was the only predictor for higher HOMA-IR. The prevalence of vascular diseases is associated with higher HOMA-IR in ESRD patients.

Single-run, parallel detection of DNA from three pneumonia-producing bacteria by real-time polymerase chain reaction.

A molecular assay for parallel detection of three bacteria, Chlamydia (C.) pneumoniae, Legionella (L.) spp., and Mycoplasma (M.) pneumoniae, in clinical specimens by a set of real-time polymerase chain reactions (PCRs) in a single run was evaluated. Bacterial DNAs were extracted by an automated DNA extraction protocol on the MagNA Pure LC System. Amplification and detection were done by real-time PCR on the LightCycler (LC) instrument. For amplification, specific oligonucleotides derived from the 16s rRNA genes of C. pneumoniae, L. spp., and M. pneumoniae were used. The three assays were complemented with an internal control (IC), a specially designed DNA fragment which contains the specific primer binding sites for the three PCRs. The IC was added to the samples, co-extracted, and co-amplified. Primers and hybridization probes were designed to suit one LC PCR program. LC PCRs were established, detection limits were determined, and clinical samples were tested. The detection limits were found between 5.0 and 0.5 IFU/CFU per PCR reaction for each of the bacteria. A total number of 100 clinical specimens were tested for validation of the molecular assay. Tested samples included 63 bronchoalveolar lavages (BALs) and 37 induced sputa specimens. The internal control was detected in all negative and low-positive samples; no inhibition was found throughout the whole study. Additionally, samples underwent testing by culture for L. spp., and M. pneumoniae; for C. pneumoniae, the serological microimmunofluorescence (MIF) test was used. In conclusion, the developed set of LC PCR assays permits parallel detection of C. pneumoniae, L. spp., and M. pneumoniae in a single LC run. This molecular assay may lead to accurate and early diagnosis of pneumonia produced by these three types of bacteria. The assay proved to be suitable for the high-throughput routine diagnostic laboratory.

Rapid diagnosis of adenoviral keratoconjunctivitis by a fully automated molecular assay.

OBJECTIVE: To establish and evaluate a new test system for rapid detection and diagnosis of adenoviral keratoconjunctivitis. DESIGN: After establishment of the molecular assay, 52 conjunctival smears were studied. PARTICIPANTS: Samples were derived from patients with a clinical presentation compatible with keratoconjunctivitis. METHODS: A molecular assay for detection of human adenovirus (HAdV) based on automated nucleic acid extraction and real time polymerase chain reaction was established and evaluated. The new assay included a heterologous internal control. MAIN OUTCOME MEASURES: Statement about the presence or absence of adenoviral DNA in the specimen. RESULTS: The amplification efficiency was found to be 100%. The detection limit was calculated to be 116 copies per LightCycler capillary. When clinical specimens were tested, 15 of 52 conjunctival smears were found to be positive for HAdV DNA. The internal control was detected in all samples. CONCLUSIONS: The new molecular assay proved to be suitable for rapid diagnosis of adenoviral keratoconjunctivitis in the routine diagnostic laboratory.

Hypoplastic thyroid, growth hormone deficiency, corneal opacities, cataract and hyperkeratotic skin disease: a possible new ichthyosis syndrome associated with endocrinopathies.

A 56 year old man presented with ichthyosis vulgaris since early childhood, clinically characterised by fine scaling of the trunk and hyperkeratotic scales on the exterior surfaces of the upper and lower extremities. The patient also showed hypothyroidism due to hypoplastic thyroid, cataract, hypercholesterinemia with concommitant arcus cornealis and biliary concrements. Renal lithiasis caused by calcio-oxalate was additionally present. Endocrinological screening revealed growth hormone deficiency in the 1.55 m tall man-(secondary) osteoporosis was observed. The clinical symptomatology indicates that this case cannot be considered as a subtype of the inherited ichthyosis group, but suggests a new syndrome as a separate nosologic entity.

Diurnal variation of arterial stiffness and subendocardial perfusion noninvasively assessed using applanation tonometry in healthy young men.

BACKGROUND: Arterial stiffness is at least partially controlled by vascular tone. Vascular tone and underlying physiological processes, e.g. sympathetic activity, have been shown to follow diurnal variations. METHODS: This study investigated whether arterial stiffness and perfusion of subendocardial myocardium relative to cardiac workload show diurnal variations under physiological conditions. The aortic augmentation index (AIx) and subendocardial viability ratio (SEVR) were measured noninvasively in 26 healthy young men (27.6 +/- 3.4 years) using applanation tonometry at three different times (8:00, 12:00, 17:00) during one day. RESULTS: Mean AIx was significantly higher and mean SEVR significantly lower at 8:00 than at the later times. No significant differences were found between mean AIx and mean SEVR at 12:00 and at 17:00. CONCLUSIONS: The observed diurnal variations of AIx and SEVR will be of value when applanation tonometry is used in human research. In order to arrive at comparable data in longitudinal investigations, measurements should be made at similar times during the course of a day. In addition, our observation should assist in studies in which novel pharmacological compounds with activity on the vasculature are investigated.

Automated detection of five human herpes virus DNAs by a set of LightCycler PCRs complemented with a single multiple internal control.

BACKGROUND: Herpes viruses represent important causes of morbidity and mortality especially in immuno-compromised patients. To assist in rapid diagnosis real-time PCR assays have been developed for the detection of herpes virus DNA in patient specimens. A recently described set of real-time PCR assays using LightCycler technology enabled parallel detection of DNA from cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus type 1 and 2 (HSV-1/-2), and varicella-zoster virus (VZV) by using a single LightCycler program [J. Clin. Virol. 26 (2003) 85]. The set of assays lacked automation of DNA purification and of PCR mixture preparation, and was not furnished with measures to monitor for sample adequacy. OBJECTIVES: Development of a set of automated LightCycler-PCR assays for the detection CMV-, EBV-, HSV-1/-2- and VZV-DNA in plasma samples and complementation of the assays with internal amplification controls (ICs). STUDY DESIGN: The MagNA Pure LC instrument was used for automated DNA purification and automated preparation of PCR mixtures. A single multiple IC-DNA specific for all four herpes virus type-specific PCRs was generated and used in all four LightCycler assays. Detection limits were determined and clinical samples were evaluated. RESULTS: With quantified herpes virus type-specific reference DNA spiked into EDTA plasma, the detection limits were found at 250 copies/ml of CMV-, EBV-, HSV-1/-2-DNA and at 500 copies/ml of VZV-DNA. The novel set of assays was evaluated by testing 112 EDTA plasma samples. The use of the IC led to the detection of PCR-inhibited samples. CONCLUSION: The set of automated LightCycler assays was found rapid, markedly labour saving and suitable for the routine diagnostic laboratory. The use of the one internal control molecule simplified the assay protocol and allowed monitoring for sample adequacy.

A simple approach to the generation of heterologous competitive internal controls for real-time PCR assays on the LightCycler.

BACKGROUND: The real-time PCR technology allows convenient detection and quantification of virus derived DNA. This approach is used in many PCR based assays in clinical laboratories. Detection and quantification of virus derived DNA is usually performed against external controls or external standards. Thus, adequacy within a clinical sample is not monitored for. This can be achieved using internal controls that are co-amplified with the specific target within the same reaction vessel. OBJECTIVES: We describe a convenient way to prepare heterologous internal controls as competitors for real-time PCR based assays. STUDY DESIGN: The internal controls were devised as competitors in real-time PCR, e.g. LightCycler-PCR. The bacterial neomycin phosphotransferase gene (neo) was used as source for heterologous DNA. Within the neo gene a box was chosen containing sequences for four differently spaced forward primers, one reverse primer, and a pair of neo specific hybridization probes. Pairs of primers were constructed to compose of virus-specific primer sequences and neo box specific primer sequences. Using those composite primers in conventional preparative PCR four types of internal controls were amplified from the neo box and subsequently cloned. RESULTS: A panel of the four differently sized internal controls was generated and tested by LightCycler PCR using their virus-specific primers. All four different PCR products were detected with the single pair of neo specific FRET-hybridization probes. CONCLUSION: The presented approach to generate competitive internal controls for use in LightCycler PCR assays proved convenient und rapid. The obtained internal controls match most PCR product sizes used in clinical routine molecular assays and will assist to discriminate true from false negative results.

Genotyping of hepatitis C virus-comparison of three assays.

BACKGROUND: Genotyping of hepatitis C virus (HCV) is clinically relevant to epidemiology, prognosis, and therapeutical management of HCV infection. OBJECTIVES: Accuracy and specificity of three assays for HCV genotyping/subtyping were determined. The TruGene HCV 5'NC Genotyping Kit (TruGene), which is a direct sequencing test and two assays based on reversed hybridization, Inno-LiPA HCV II assay and ViennaLab HCV Strip Assay, were compared. Amplification products generated by the Cobas Amplicor HCV Test were used. STUDY DESIGN: A total of 100 consecutive HCV RNA positive samples derived from patients with chronic hepatitis C were examined for their genotypes/subtypes by the three assays. RESULTS: Identification of genotypes and subtypes by the TruGene assay as reference test for the Inno-LiPA HCV II assay and the ViennaLab HCV Strip Assay or Inno-LiPA HCV II assay as reference test for the TruGene and the ViennaLab HCV Strip Assay showed similar results for overall accuracies (TruGene as reference test for Inno-LiPA HCV II and ViennaLab HCV Strip Assay, genotypes/subtypes: 100%/95.5% and 97%/92%; Inno-LiPA HCV II as reference test for TruGene and ViennaLab HCV Strip Assay, genotypes/subtypes: 99%/85.9% and 97%/87.9%) and specificities (TruGene as reference test for Inno-LiPA HCV II and ViennaLab HCV Strip Assay, genotypes/subtypes: 100%/97.8% and 99%/97.7%; Inno-LiPA HCV II as reference test for TruGene and ViennaLab HCV Strip Assay, genotypes/subtypes: 100%/99.4% and 99.7%/98%). CONCLUSIONS: The three assays were found to be reliable for the detection and discrimination of all HCV genotypes common in Europe and in North America and to be suitable for the routine diagnostic laboratory.

Parallel detection of five human herpes virus DNAs by a set of real-time polymerase chain reactions in a single run.

BACKGROUND: Human herpes viruses cause a spectrum of diseases that are usually self-limiting but can be reactive during immuno-suppression and may then lead to severe or even life-threatening diseases. The LightCycler technology allows rapid polymerase chain reaction (PCR) including product analysis within a closed system. This approach has been demonstrated to be suitable for routine diagnostic virus detection. Several LightCycler PCR assays have been established to the detection of human herpes viruses. The assays vary in their detection formats and PCR cycling protocols. So, they cannot be performed within a single LightCycler run. OBJECTIVES: Development of four LightCycler PCR assays for parallel detection of DNA derived from human cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), and varicella-zoster virus (VZV) in a single run. STUDY DESIGN: Primers and hybridization probes were tailored to suit one LightCycler PCR program. LightCycler PCRs were established, detection limits were determined, and clinical samples were evaluated. RESULTS: With quantified herpes virus type specific DNA spiked into cerebrospinal fluid, serum or EDTA plasma the detection limits were found either at 500 or 250 viral DNA copies per ml depending on the virus DNA specific PCR and on the specimen type used. The applicability of the new LightCycler assays for routine molecular testing was evaluated by testing 96 clinical samples. CONCLUSION: The developed set of LightCycler PCRs permits parallel detection of CMV, EBV, HSV-1, HSV-2, and VZV in a single LightCycler run. The new molecular assays can easily be used to the rapid, simple, and convenient detection of herpes virus DNA in cerebrospinal fluid, serum and EDTA plasma in the routine diagnostic laboratory.

Detection of transfusion transmitted virus DNA by real-time PCR.

BACKGROUND: Little is known about the pathogenic role and the endemic situation of transfusion transmitted virus (TTV). OBJECTIVES: In this study, a molecular assay for detection of TTV based on automated nucleic acid extraction and real-time PCR was developed and evaluated. The new assay includes an internal control. STUDY DESIGN: After optimization of the molecular assay, 103 clinical samples were studied retrospectively. All sera had been tested for anti-HCV and anti-HIV-1 antibodies earlier. RESULTS: The amplification efficiency was found to be 102%. When clinical specimens were tested, 79 of 103 serum samples were found to be positive for TTV. There was no significant difference between various groups of patients. The internal control was detected in all negative and weak positive samples. CONCLUSIONS: This molecular assay proved to be suitable for routine detection of TTV in clinical samples. Moreover, a relative statement on the TTV serum load can be done.

Proinflammatory parameters as CRP and IL-6 do not discriminate between post-PCI cardiac patients with and without exercise-induced ischemia as indicated by Tl-201 myocardial scintigraphy.

INTRODUCTION: Atherosclerosis is looked upon as an inflammatory disease. The production of proinflammatory markers may indicate activity in this inflammatory state. METHODS: We prospectively evaluated a range of proinflammatory serum parameters in 136 cardiac patients who had previously undergone percutaneous coronary intervention (PCI). RESULTS: By means of myocardial scintigraphy, an ischemia group (A; n=49) and a group with stable cardiovascular disease without exercise induced ischemia (B; n=87) were distinguished. Risk factors and lipoprotein profile of both groups were comparable. Serum levels of serum C-reactive protein (CRP), IL-6, sTNF-RI, IGF-I, neopterin, serotonin and prolactin did not present any significant difference between the two groups. CONCLUSIONS: We conclude that measurement of these (inflammatory) parameters does not help to delineate post-PCI cardiac patients with and without exercise-induced ischemia.