The cobas® 6800/8800 System: a new era of automation in molecular diagnostics

INTRODUCTION

Molecular diagnostics is a key component of laboratory medicine. Here, the authors review key triggers of ever-increasing automation in nucleic acid amplification testing (NAAT) with a focus on specific automated Polymerase Chain Reaction (PCR) testing and platforms such as the recently launched cobas® 6800 and cobas® 8800 Systems. The benefits of such automation for different stakeholders including patients, clinicians, laboratory personnel, hospital administrators, payers, and manufacturers are described. Areas Covered: The authors describe how molecular diagnostics has achieved total laboratory automation over time, rivaling clinical chemistry to significantly improve testing efficiency. Finally, the authors discuss how advances in automation decrease the development time for new tests enabling clinicians to more readily provide test results. Expert Commentary: The advancements described enable complete diagnostic solutions whereby specific test results can be combined with relevant patient data sets to allow healthcare providers to deliver comprehensive clinical recommendations in multiple fields ranging from infectious disease to outbreak management and blood safety solutions.

Long-term alterations in monocyte function after elective cardiac surgery

Optimal immunological homoeostasis determines the long-term recovery of patients in the postoperative period. The functional adaptability of monocytes plays a pivotal role in adjusting the host's response to an insult, immunostasis and long-term health, and may help to determine successful recovery. We undertook a longitudinal analysis of the functional adaptability of monocytes in 20 patients undergoing heart surgery with cardiopulmonary bypass, as a model of severe stress. Using each patient's pre-cardiopulmonary bypass data as a baseline, we investigated the characteristics of peripheral blood monocytes' functional plasticity in-vitro before elective bypass, and three months afterwards. Approximately 30% of subjects showed diminished monocyte plasticity, as demonstrated by decreased monocyte differentiation into dendritic cells three months after bypass. Diminished monocyte functional plasticity was related to over-production of macrophage colony-stimulating factor. Adding a neutralising antibody to macrophage colony-stimulating factor corrected the monocytes' differentiation defect. Finally, patients with reduced monocyte plasticity had significantly elevated serum C-reactive protein, with a concomitant increase in cytomegalovirus IgG antibody titres, suggestive of the acquisition of immuno-suppressive traits. Our study shows that severe surgical stress resulted in a lasting immunological defect in individuals who had seemingly recovered.

Programmed intermittent epidural boluses for maintenance of labor analgesia: an impact study

INTRODUCTION

The aim of this impact study was to compare the analgesic efficacy and side effect profile of programmed intermittent epidural boluses (PIEB)+patient-controlled epidural analgesia (PCEA) to continuous epidural infusion (CEI)+PCEA for maintenance labor analgesia after the introduction of PIEB at our institution.

METHODS

We conducted a retrospective analysis after replacing the background CEI with PIEB for our labor PCEA. Pre-change pump settings were CEI 12mL/h with PCEA (12mL bolus, lockout 15min); PIEB settings were a 9mL bolus every 45min with PCEA (10mL bolus, lockout 10min). We compared medical records of all women receiving epidural or combined spinal-epidural labor analgesia for vaginal delivery for two months before PIEB implementation to a two-month period of PIEB utilization following a five-month introductory familiarization period. The primary outcome was the proportion of women requiring rescue clinician boluses.

RESULTS

Fewer patients in the PIEB group required rescue clinician boluses compared to the CEI group (12% vs. 19%, P=0.012). Time to first rescue bolus request and total bolus dose were not different. Peak (median [IQR]) pain scores were 2[0-5] with CEI and 0[0-4] with PIEB. There was no difference in instrumental delivery rates.

CONCLUSIONS

Using PIEB compared to CEI as the background maintenance epidural analgesia method in conjunction with PCEA reduced the number of women requiring clinician rescue boluses while providing comparable labor analgesia. The findings of this clinical care impact study confirm the results of randomized controlled studies and suggest PIEB may be a preferable technique to CEI for the maintenance of labor analgesia.

Spatial atmospheric atomic layer deposition of InxGayZnzO for thin film transistors

We have investigated the nucleation and growth of InGaZnO thin films by spatial atmospheric atomic layer deposition. Diethyl zinc (DEZ), trimethyl indium (TMIn), triethyl gallium (TEGa), and water were used as Zn, In, Ga and oxygen precursors, respectively. The vaporized metal precursors have been coinjected in the reactor. The metal composition of InGaZnO has been controlled by varying the TMIn or TEGa flow to the reactor, for a given DEZ flow and exposure time. The morphology of the films changes from polycrystalline, for ZnO and In-doped ZnO, to amorphous for In-rich IZO and InGaZnO. The use of these films as the active channel in TFTs has been demonstrated and the influence of In and Ga cations on the electrical characteristics of the TFTs has been studied.

Molecular diagnostics in the management of chronic hepatitis C: key considerations in the era of new antiviral therapies

Molecular tests that detect and/or quantify HCV RNA are important in the diagnosis and management of patients with chronic hepatitis C (CHC) undergoing anti-viral therapy. The primary goal of anti-HCV therapy is to achieve a sustained virologic response (SVR) defined as "undetectable" Hepatitis C Virus (HCV) RNA in the serum or plasma at 12 to 24 weeks following the end of treatment.

Comparative performances of HIV-1 RNA load assays at low viral load levels: results of an international collaboration

Low-level viremia during antiretroviral therapy and its accurate measurement are increasingly relevant. Here, we present an international collaboration of 4,221 paired blood plasma viral load (pVL) results from four commercial assays, emphasizing the data with low pVL. The assays compared were the Abbott RealTime assay, the Roche Amplicor assay, and the Roche TaqMan version 1 and version 2 assays. The correlation between the assays was 0.90 to 0.97. However, at a low pVL, the correlation fell to 0.45 to 0.85. The observed interassay concordance was higher when detectability was defined as 200 copies/ml than when it was defined as 50 copies/ml. A pVL of ∼100 to 125 copies/ml by the TaqMan version 1 and version 2 assays corresponded best to a 50-copies/ml threshold with the Amplicor assay. Correlation and concordance between the viral load assays were lower at a low pVL. Clear guidelines are needed on the clinical significance of low-level viremia.

Detection of low HCV viraemia by repeated HCV RNA testing predicts treatment failure to triple therapy with telaprevir

BACKGROUND

Early on-treatment virological response is one of the most important predictors for sustained virological response (SVR) to treatment of chronic hepatitis C virus (HCV) genotype 1 infection with triple therapy including HCV protease inhibitors (PI). Treatment duration (24 vs. 48 weeks) is based on HCV RNA results at weeks 4 and 12 of PI therapy when HCV RNA must be 'undetectable' to allow shorter therapy.

AIM

To analyse the reliability of HCV RNA measurements at key decision time points (weeks 4 and 12) and the predictive value of concordant or discordant assay results for SVR.

METHODS

Weeks 4 and 12 samples of patients receiving telaprevir-containing triple therapy were initially tested with the AmpliPrep/COBAS-TaqMan_HCV-Test-v1.0 (limit of detection; LOD = 15IU/mL) and retested with the AmpliPrep/COBAS-TaqMan_HCV-Test-v2.0 (LOD = 15IU/mL) and the High_Pure/COBAS-TaqMan_HCV-Test-v2.0 (LOD = 20IU/mL).

RESULTS

Concordance among the three test results in classifying samples as HCV RNA 'undetectable' or 'detectable' was only 55% at week 4, but 85% at week 12. Retesting of 'undetectable' week 4 samples with the respective other assays revealed positive HCV RNA results in 32-50%. In 30%, HCV RNA was 'undetectable' by all three tests at week 4 and all of these patients achieved SVR. In contrast, treatment failure occurred in 62% of patients with at least one 'detectable' result, including cases with one or two other 'undetectable' tests at week 4.

CONCLUSIONS

A single 'undetectable' HCV RNA result at week 4 is not always associated with achieving SVR. Repeated testing in difficult-to-treat patients may identify those at risk for treatment failure.

Genome-wide copy number variation analysis of a Branchio-oto-renal syndrome cohort identifies a recombination hotspot and implicates new candidate genes

Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by branchial arch anomalies, hearing loss and renal dysmorphology. Although haploinsufficiency of EYA1 and SIX1 are known to cause BOR, copy number variation analysis has only been performed on a limited number of BOR patients. In this study, we used high-resolution array-based comparative genomic hybridization on 32 BOR probands negative for coding-sequence and splice-site mutations in known BOR-causing genes to identify potential disease-causing genomic rearrangements. Of the >1,000 rare and novel copy number variants we identified, four were heterozygous deletions of EYA1 and several downstream genes that had nearly identical breakpoints associated with retroviral sequence blocks, suggesting that non-allelic homologous recombination seeded by this recombination hotspot is important in the pathogenesis of BOR. A different heterozygous deletion removing the last exon of EYA1 was identified in an additional proband. Thus, in total five probands (14 %) had deletions of all or part of EYA1. Using a novel disease-gene prioritization strategy that includes network analysis of genes associated with other deletions suggests that SHARPIN (Sipl1), FGF3 and the HOXA gene cluster may contribute to the pathogenesis of BOR.

HCV RNA viral load assessments in the era of direct-acting antivirals

Recent regulatory approvals of the NS3/4A protease inhibitors boceprevir and telaprevir launched a new therapeutic era for hepatitis C virus (HCV) genotype 1 infection. Decisions to shorten, extend, or stop treatment with these direct-acting antiviral (DAA) regimens require accurate quantification of serum HCV RNA levels. To effectively use DAA therapies, clinicians must understand performance characteristics of HCV RNA real-time PCR assays and the clinical significance of HCV RNA that is detectable below the lower limit of quantification. This review summarizes terms used to report HCV RNA viral load results, explains the analytical performance of the PCR assay used in the clinical trials of boceprevir and telaprevir, and compares currently available commercial assays.

An international multicenter performance analysis of cytomegalovirus load tests

BACKGROUND

Quantification of cytomegalovirus (CMV) load is central to the management of CMV infections in immunocompromised patients, but quantitative results currently differ significantly across methods and laboratories.

METHODS

The COBAS AmpliPrep/COBAS TaqMan CMV Test (CAP/CTM CMV test), developed using the first World Health Organization CMV standard in the calibration process, was compared to local assays used by 5 laboratories at transplant centers in the United States and Europe. Blinded plasma panels (n = 90) spiked with 2.18-6.7 log(10) copies/mL and clinical plasma samples from immunocompromised patients (n = 660) were tested.

RESULTS

Observed mean panel member concentrations by site and 95% confidence intervals (CIs) of the data combined across sites were narrower for CAP/CTM CMV test compared with local assays. The 95% CI in log(10) copies/mL of the combined data per panel member for CAP/CTM CMV test vs comparator assays was .17 vs 1.5 at 2.18 log(10) copies/mL; .14 vs .52 at 2.74 log(10) copies/mL; .16 vs .6 at 3.3 log(10) copies/mL; .2 vs 1.11 at 4.3 log(10) copies/mL; .21 vs 1.13 at 4.7 log(10) copies/mL; and .18 vs 1.4 at 6.7 log(10) copies/mL. In clinical specimens, constant and variable quantification differences between the CAP/CTM CMV test and comparator assays were observed.

CONCLUSIONS

High interlaboratory agreement and precision of CAP/CTM CMV test results across 5 different laboratories over 4 orders of magnitude suggest that this assay could be valuable in prospective studies identifying clinical viral load thresholds for CMV treatment.

C8orf13/BLK association with systemic lupus erythematosus across different ethnicities (136.28)

SLE is a complex autoimmune disease with immunological abnormalities that targets B cell functions and development. Previous genome-wide association studies identified C8orf13/BLK as a novel SLE risk factor. BLK (B lymphoid tyrosine kinase) has been shown to have potential effects on B cell develoment. The main objectives of this study are to: 1.) assess this association in independent populations and 2.) determine if BLK risk alleles correlate with alteration in peripheral blood B cell development and protein expression. We genotyped 52 SNPs within the C8orf13/BLK region in European-derived, Asian and African American populations. rs13277113 is associated with SLE in all three populations. A few novel upstream SNPs within the intergenic region demonstrate a stronger association in Asians. Flow cytometry data suggests there is a significant difference in BLK expression and T2 cells B cell numbers between high-risk and non-risk individuals based on the risk haplotype. Our results suggest that the BLK genetic polymorphisms alter immune system development and function to increase the risk for SLE development. Supported by NIH RR020143, RR015577, NIAID-DAIT-BAA-05-11, AI031584, AR053483, AR48940, AI063274, AR052125, AR043247 and OCAST # HR08-037.

Activation of airway cl- secretion in human subjects by adenosine

We investigated cystic fibrosis (CF) transmembrane conductance regulator (CFTR) regulation by A2 adenosine (Ado) receptors and beta2 adrenergic receptors in CFTR-corrected CFBE41o- airway cells and human subjects. CFBE41o- cells stimulated with Ado (10 microM), isoproterenol (Iso, 10 microM), or Ado + Iso (10 microM each) elevated cyclic AMP (cAMP) above control conditions (P < 0.001), with the Iso conditions increasing cAMP approximately 10-fold above that produced by Ado alone (P < 0.001). All agonist conditions had similar effects on short circuit current at 10 and 25 microM, with no further currents produced by subsequent stimulation with forskolin (20 microM). CFTR dependence was demonstrated by glybenclamide block of agonist-stimulated currents. Nasal potential difference studies in normal (n = 50) subjects demonstrated that Ado (10 microM) and Ado + Iso (10 microM each) produced more polarization compared with Iso (10 microM Ado increase = 44%, 10 microM Ado + Iso increase = 52%, P < 0.05 for each condition compared with Iso alone). Studies completed in patients with CF (n = 10, "severe" genotypes) confirmed that Ado-stimulated polarization was CFTR-dependent. Together, these results indicate that Ado is a potent Cl- secretagogue in vivo, with relatively small effects on cAMP levels despite strong effects on CFTR-dependent short circuit current and nasal Cl- transport. These findings support growing evidence indicating a role for Ado regulation of CFTR-dependent Cl- secretion in vivo.

A macromolecular complex of beta 2 adrenergic receptor, CFTR, and ezrin/radixin/moesin-binding phosphoprotein 50 is regulated by PKA

It has been demonstrated previously that both the cystic fibrosis transmembrane conductance regulator (CFTR) and beta(2) adrenergic receptor (beta(2)AR) can bind ezrinradixinmoesin-binding phosphoprotein 50 (EBP50, also referred to as NHERF) through their PDZ motifs. Here, we show that beta(2) is the major adrenergic receptor isoform expressed in airway epithelia and that it colocalizes with CFTR at the apical membrane. beta(2)AR stimulation increases CFTR activity, in airway epithelial cells, that is glybenclamide sensitive. Deletion of the PDZ motif from CFTR uncouples the channel from the receptor both physically and functionally. This uncoupling is specific to the beta(2)AR receptor and does not affect CFTR coupling to other receptors (e.g., adenosine receptor pathway). Biochemical studies demonstrate the existence of a macromolecular complex involving CFTR-EBP50-beta(2)AR through PDZ-based interactions. Assembly of the complex is regulated by PKA-dependent phosphorylation. Deleting the regulatory domain of CFTR abolishes PKA regulation of complex assembly. This report summarizes a macromolecular signaling complex involving CFTR, the implications of which may be relevant to CFTR-dysfunction diseases.

Family dynamics, parental-fetal attachment and infant temperament

Family dynamics, parental-fetal attachment and infant temperament The purpose of this longitudinal study of families having their first or second baby was to explore relationships among family dynamics, paternal- and maternal-fetal attachment, and infant temperament. Data were collected from 156 women and 62 of their partners during the third trimester of pregnancy. One year later, when the infant was 8-9 months old, 75 of the women and 30 of their partners participated. In a hierarchical multiple regression analysis, after controlling for demographic variables, mutuality in the family was associated with greater maternal- and paternal-fetal attachment. Family dynamics were stable across the transition to parenthood except for an increase in role conflict reported by mothers. Sensitivity to specific family experiences by clinicians can provide assistance to families during these periods.

Formation of the compact confomer of kinesin requires a COOH-terminal heavy chain domain and inhibits microtubule-stimulated ATPase activity

Full-length Drosophila kinesin heavy chain from position 1 to 975 was expressed in Escherichia coil (DKH975) and is a dimer. The sedimentation coefficient of DKH975 shifts from 5.4 S at 1 M NaCl to approximately 6.9 S at <0.2 M NaCl. This transition of DKH975 between extended and compact conformations is essentially identical to that for the heavy chain dimer of bovine kinesin (Hackney, D. D., Levitt, J. D., and Suhan, J. (1992) J. Biol. Chem. 267, 8696-8701). Thus the capacity for undergoing the 7 S/5 S transition is an intrinsic property of the heavy chains and requires neither light chains nor eukaryotic post-translational modification. DKH960 undergoes a similar transition, indicating that the extreme COOH-terminal region is not required. More extensive deletions from the COOH-terminal (DKH945 and DKH937) result in a shift in the midpoint for the transition to lower salt concentrations. DKH927 and shorter constructs remaining extended even in the absence of added salt. Thus the COOH-terminal approximately 50 amino acids are required for the formation of the compact conformation. Separately expressed COOH-terminal tail segments and NH2-terminal head/neck segments interact in a salt-dependent manner that is consistent with the compact conformer being produced by the interaction of domains from these regions of the heavy chain dimer. The microtubule-stimulated ATPase rate of DKH975 in the compact conformer is strongly inhibited compared with the rate of extended DKH894 (4 s-1 and 35 s-1, respectively, for kcat at saturating microtubules).

The role of the serotonin transporter gene in cigarette smoking

Data from twin studies have suggested that cigarette smoking has a significant heritable component. The serotonin transporter gene (5-HTT) is a plausible candidate gene for smoking predisposition because of its association with psychological traits relevant to smoking behavior. The present investigation evaluated the associations of smoking practices and smoking cessation with a common polymorphism in the upstream regulatory region of 5-HTT that is manifested as either an inserted (long) variant or a deleted (short) variant. The short variant of the polymorphism is associated with reduced transcription of the gene promoter and diminished uptake. A case-control study design (268 smokers and 230 controls) was used to evaluate the associations of 5-HTT genotype with smoking status. Case series analysis of smokers was used to evaluate the role of 5-HTT in age at smoking initiation, previous quitting history, current smoking rate, and 12-month quit rate following a minimal-contact smoking cessation program. There were no significant differences in the distribution of 5-HTT genotypes in smokers as compared with nonsmokers in either Caucasians or African Americans, nor was the 5-HTT genotype associated with the smoking outcome variables. However, the results did reveal significant racial differences in the distribution of 5-HTT genotypes: Caucasians were significantly more likely to carry the short variant of the 5-HTT gene than were African Americans (P = 0.005). These findings suggest that the 5-HTT gene may not play a significant role in cigarette smoking practices.

Advantages and limitations of current soft intraocular lenses

We report our clinical experience with six soft intraocular lenses: (1) STAAR silicone, (2) CooperVision/Schlegel silicone, (3) IOLAB silicone, (4) Allergan Medical Optics (AMO) silicone, (5) Fyodorov silicone, and (6) Alcon hydrogel (IOGEL). We found that these soft intraocular lenses have several common design problems. The single-size design of five of the six soft lenses can lead to a windshield-wiper decentration effect in lenses too small for larger eyes. We observed several instances in which the one-piece lenses became decentered, subluxed, and vaulted anteriorly against the iris or posteriorly away from the iris as postoperative capsulozonular changes occurred. We found that the insertion methods for these soft lenses need refining to reduce the risk of intraocular damage and wound stretching if the lenses are to be folded and inserted through a small 3.0 mm to 3.5 mm incision. The surface and physical characteristics of these lenses may also require further study. We observed folding grooves, sebacium deposits, and rust from the insertion instrument on some lenses inside the postoperative eye and pigment dispersion associated with hydrogel lenses. We conclude that small diameter polymethylmethacrylate implants are the best choice for small incision cataract surgery at this time.

Glare disability devices for cataractous eyes: a consumer's guide

We evaluated five commercially available glare testers to determine how accurately each device predicted outdoor Snellen acuity in cataract patients. Predicted outdoor Snellen acuity was compared to actual Snellen outdoor acuity for the Miller-Nadler glare tester, the brightness acuity tester (BAT), the InnoMed true vision analyzer (TVA), the VisTech VCT 8000, and the EyeCon 5. All five devices were evaluated in a single series of eyes. We ranked the five glare testers as follows based upon their ability to predict outdoor Snellen acuity within one Snellen line: (1) BAT (73%), (2) TVA (69%), (3) VisTech VCT 8000 (56%), (4) Miller-Nadler (47%), and (5) EyeCon 5 (15%). All five devices were also evaluated for their capacity to provide false negative or false positive results and for testing time per eye, test difficulty level for the patient, versatility, upgrading capacity, examining room adaptability, and price. We concluded that glare testing of cataract patients is necessary to measure visual disability and that glare testing devices vary in their ability to predict outdoor vision.