Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Background

Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized diploid cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified.

Results

Tissue sections that fail more frequently show low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces are more likely to show FFPE-specific errors, akin to “edge effects” seen in histology, while the inner samples display no quality degradation related to fixation time.

Conclusions

To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02709-8.

Abstract 529: SNAQ-SEQ™: Use of synthetic internal standards in conjunction with poisson exact test to call variants in contrived circulating tumor DNA specimens

Background: Targeted next generation sequencing (NGS) analysis of circulating tumor (ct) DNA promises to significantly advance targeted therapy and potentially early diagnosis of cancer. However, targeted NGS has poor accuracy for calling known variants with VAF below 0.5%. The goal of this study from the FDA-Sequencing and Quality Control Phase 2 (SEQC2) consortium was to develop and validate bioinformatic and biostatistical methods that enable incorporation of synthetic competitive internal standards (IS) in targeted NGS analysis of actionable tumor mutations.

Methods: A synthetic IS spike-in was designed for each actionable mutation target, suitable for use in NGS following targeted PCR or hybrid-capture enrichment and either with unique molecular index (UMI) or non-UMI library preparation. Contrived ctDNA reference samples developed by the SEQC2 consortium containing actionable mutations at known variant allele fraction were used. An aliquot of each sample was mixed with a mixture of IS. Following Illumina TST170 enrichment and library preparation, each library was sequenced, then native template (NT) sequences were separated from IS sequences bioinformatically. In SNAQ-SEQ™ analysis, Poisson Exact Test (PET) analysis was used to calculate the statistical difference between each sample library NT variant VAF and respective IS variant VAF. Analysis was based on NT variant count and position coverage (i.e., copies recovered in library preparation) and IS count and position coverage. PET performed an exact test of a simple null hypothesis about the ratio between two rate parameters in Poisson distribution.

Results: Stochastic sampling effect on IS error detection was minimized by ensuring an IS/NT ratio of 2.5 or greater. Under the specified conditions, in which a minimum of two NT variant observations were required for a call, the IS was able to estimate NGS background error for each sample when a minimum IS:NT ratio of 2.5:1 was used. Without use of IS information, the Illumina pipeline called 73% (41/56) of known TP variants in the 0.1% - 0.3% VAF range. In contrast, SNAQ-SEQ™ analysis (PET analysis of IS and NT information) increased TP detection sensitivity to 86% (48/56), for a 13% increase in sensitivity, with no false positives.

Conclusion: Following mixture of contrived ctDNA reference samples with IS, PET analysis enabled calculation of technical error rate, limit of blank, and limit of detection for each variant at each nucleotide position, in each sample. Using this SNAQ-SEQ™ analysis, true positive mutations with variant allele fraction too low for detection by current practice were detected with this method, thereby increasing sensitivity. SNAQ-SEQ™ provides QC that is already standard operating procedure in clinical laboratories for analysis by high pressure liquid chromatography and mass spectrometry.

Citation Format: James C. Willey, Erin Crawford, Daniel J. Craig, Joshua Xu, Nathan Haseley, Jennifer Lococo, Tom Morrison. SNAQ-SEQ™: Use of synthetic internal standards in conjunction with poisson exact test to call variants in contrived circulating tumor DNA specimens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 529.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

BACKGROUND

Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.

RESULTS

All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.

CONCLUSION

This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

Homocystinuria patient and caregiver survey: experiences of diagnosis and patient satisfaction

Background

The main genetic causes of homocystinuria are cystathionine beta-synthase (CBS) deficiency and the remethylation defects. Many patients present in childhood but milder forms may present later in life. Some countries have newborn screening programs for the homocystinurias but these do not detect all patients.

Results

HCU Network Australia is one of the very few support groups for patients with homocystinurias. Here we report the results of its survey of 143 patients and caregivers from 22 countries, evaluating current diagnostic pathways and management for the homocystinurias. Most (110) of the responses related to patients with CBS deficiency. The diagnosis was made by newborn screening in 20% of patients and in 50% of the others within 1 year of the initial symptom but in 12.5% it took over 15 years. The delay was attributed mainly to ignorance of the disease. Physicians need to learn to measure homocysteine concentrations in children with neurodevelopmental problems, and in patients with heterogeneous symptoms such as thromboembolism, dislocation of the optic lens, haemolytic uraemic syndrome, and psychiatric disease. Even when the diagnosis is made, the way it is communicated is sometimes poor. Early-onset CBS deficiency usually requires a low-protein diet with amino acid supplements. More than a third of the participants reported problems with the availability or cost of treatment. Only half of the patients always took their amino acid mixture. In contrast, good adherence to the protein restriction was reported in 98% but 80% said it was hard, time-consuming and caused unhappiness.

Conclusions

There is often a long delay in diagnosing the homocystinurias unless this is achieved by newborn screening; this survey also highlights problems with the availability and cost of treatment and the palatability of protein substitutes.

Report of the 2019 NIST-FDA workshop on standards for next generation sequencing detection of viral adventitious agents in biologics and biomanufacturing

Adventitious virus testing assures product safety by demonstrating the absence of viruses that could be unintentionally introduced during the manufacturing process. The capabilities of next-generation sequencing (NGS) for broad virus detection in biologics have been demonstrated by the detection of known and novel viruses that were previously missed using the recommended routine assays for adventitious agent testing. A meeting was co-organized by the National Institute of Standards and Technology and the U.S. Food and Drug Administration on September 18-19, 2019 in Gaithersburg, Maryland, USA, to facilitate standardization of NGS technologies for applications of adventitious virus testing in biologics. The goal was to assess the currently used standards for virus detection by NGS and their public availability, and to identify additional needs for different types of reference materials and standards (natural and synthetic). The meeting focused on the NGS processes from sample preparation through sequencing but did not thoroughly cover bioinformatics, since this was considered to be the topic of a separate meeting.

Predictors to Private Practice Occupational Therapy Fieldwork Opportunities in Canada: New Evidence suggests New Solutions

The study examined predictors to increasing and enhancing fieldwork education opportunities provided by occupational therapists working in private practice. A cross-sectional design that used a self-administered questionnaire was provided to Canadian occupational therapists in private practice. Participants receiving funding from the workers' compensation sector, those with between 11 and 20 years of work experience, and therapists working full-time hours were more likely to accept a student in fieldwork placement. Respondents who indicated that physical space and resources were not barriers to taking students on placement were more likely to accept students. Therapists more comfortable with the criteria and methods for appropriate and effective student teaching and supervision were also more likely to accept a student for fieldwork placement. The study findings can inform academic programs on how best to support preceptorship and guide university fieldwork coordinators' strategies for outreach and education for private practitioners.

Lyman-α source for laser cooling antihydrogen

We present a Lyman-α laser developed for cooling trapped antihydrogen. The system is based on a pulsed Ti:sapphire laser operating at 729 nm that is frequency doubled using an LBO crystal and then frequency tripled in a Kr/Ar gas cell. After frequency conversion, this system produces up to 5.7 μW of average power at the Lyman-α wavelength. This laser is part of the ATRAP experiment at the antiproton decelerator in CERN.

Search for Narrow Resonances in the b-Tagged Dijet Mass Spectrum in Proton-Proton Collisions at sqrt[s]=8 TeV

A search for narrow resonances decaying to bottom quark-antiquark pairs is presented, using a data sample of proton-proton collisions at sqrt[s]=8  TeV corresponding to an integrated luminosity of 19.7  fb^{-1}. The search is extended to masses lower than those reached in typical searches for resonances decaying into jet pairs at the LHC, by taking advantage of triggers that identify jets originating from bottom quarks. No significant excess of events is observed above the background predictions. Limits are set on the product of cross section and branching fraction to bottom quarks for spin 0, 1, and 2 resonances in the mass range of 325-1200 GeV. These results improve on the limits for resonances decaying into jet pairs in the 325-500 GeV mass range.

The changing practice of transurethral resection of the prostate

Introduction Transurethral resection of the prostate (TURP) is considered the gold standard surgical treatment for lower urinary tract symptoms (LUTS) secondary to benign prostatic hyperplasia. The number of TURPs performed has declined significantly over the last three decades owing to pharmaceutical therapy. TURP data from a single institution for the years 1990, 2000 and 2010 were compared to assess the difference in performance. Methods A retrospective analysis was undertaken of all patients who underwent TURP between January and December 2010. These findings were compared with historical data for the years 1990 and 2000: 100 sets of case notes were selected randomly from each of these years. Results The number of TURPs performed fell from 326 in 1990 to 113 in 2010. The mean age of patients increased from 70.6 years to 74.0 years. There was also a significant increase in the mean ASA grade from 1.9 to 2.3. The most common indication for TURP shifted from LUTS to acute urinary retention. No significant change in operating time was observed. The mean resection weight remained constant (22.95g in 1990, 22.55g in 2000, 20.76g in 2010). A reduction in transfusion rates was observed but there were higher rates of secondary haematuria and bladder neck stenosis. There was an increase from 2% to 11.5% of patients with long-term failure to void following TURP. Conclusions The number of TURPs performed continues to decline, which could lead to potential training issues. Urinary retention is still by far the most common indication. However, there has been a significant rise in the percentage of men presenting for TURP with high pressure chronic retention. The number of patients with bladder dysfunction who either have persistent storage LUTS or eventually require long-term catheterisation or intermittent self-catheterisation has increased markedly, which raises the question of what the long-term real life impact of medical therapy is on men with LUTS secondary to benign prostatic hyperplasia who eventually require surgery.

Mesenchymal stromal cells for treatment of the acute respiratory distress syndrome: The beginning of the story

In spite of decades of research, the acute respiratory distress syndrome (ARDS) continues to have an unacceptably high mortality and morbidity. Mesenchymal stromal cells (MSCs) present a promising candidate for the treatment of this condition and have demonstrated benefit in preclinical models. MSCs, which are a topic of growing interest in many inflammatory disorders, have already progressed to early phase clinical trials in ARDS. While a number of their mechanisms of effect have been elucidated, a better understanding of the complex actions of these cells may pave the way for MSC modifications, which might enable more effective translation into clinical practice.

"Bored out of my gourd": a cancer survivor's return-to-work experience

“The cancer had to accommodate my life. My life was not going to be built around this diagnosis.”[...]

High performance multilayered nano-crystalline silicon/silicon-oxide light-emitting diodes on glass substrates

A low-temperature hydrogenation-assisted sequential deposition and crystallization technique is reported for the preparation of nano-scale silicon quantum dots suitable for light-emitting applications. Radio-frequency plasma-enhanced deposition was used to realize multiple layers of nano-crystalline silicon while reactive ion etching was employed to create nano-scale features. The physical characteristics of the films prepared using different plasma conditions were investigated using scanning electron microscopy, transmission electron microscopy, room temperature photoluminescence and infrared spectroscopy. The formation of multilayered structures improved the photon-emission properties as observed by photoluminescence and a thin layer of silicon oxy-nitride was then used for electrical isolation between adjacent silicon layers. The preparation of light-emitting diodes directly on glass substrates has been demonstrated and the electroluminescence spectrum has been measured.

Low mood and challenging behaviour in people with severe and profound intellectual disabilities

BACKGROUND

We investigated the relationship between low mood and challenging behaviour in people in the severe and profound range of intellectual disability, while controlling for the presence of potentially confounding variables such as diagnosis of autism, physical and sensory problems and ill health.

METHODS

The key workers of 52 people with severe and profound intellectual disability completed measures of depression, communication, challenging behaviour and provided information on relevant demographic and health variables.

RESULTS

Using the Mood, Interest and Pleasure Questionnaire for classification of mood, a significant difference was found between a 'low mood' and 'normothymic' group in the reported occurrence of challenging behaviour. This difference remained even when confounding variables such as the presence of autism, health and sensory difficulties were controlled. The frequency and severity of challenging behaviour was predicted by measures indicating the presence of low mood.

CONCLUSION

People with severe and profound show clear and measurable signs of low mood, and in this relatively small sample of institutionalised individuals, low mood was associated with challenging behaviour.

Roles of the primary cilium component Polaris in synchondrosis development

Primary cilia regulate several developmental processes and mediate hedgehog signaling. To study their roles in cranial base development, we created conditional mouse mutants deficient in Polaris, a critical primary cilium component, in cartilage. Mutant post-natal cranial bases were deformed, and their synchondrosis growth plates were disorganized. Expression of Indian hedgehog, Patched-1, collagen X, and MMP-13 was reduced and accompanied by decreases in endochondral bone. Interestingly, there was excessive intramembranous ossification along the perichondrium, accompanied by excessive Patched-1 expression, suggesting that Ihh distribution was wider and responsible for such excessive response. Indeed, expression of heparan sulfate proteoglycans (HS-PGs), normally involved in restricting hedgehog distribution, was barely detectable in mutant synchondroses. Analyses of the data provides further evidence for the essential roles of primary cilia and hedgehog signaling in cranial base development and chondrocyte maturation, and point to a close interdependence between cilia and HS-PGs to delimit targets of hedgehog action in synchondroses.

Wnt/beta-catenin signaling regulates cranial base development and growth

Wnt proteins and beta-catenin signaling regulate major processes during embryonic development, and we hypothesized that they regulate cranial base synchondrosis development and growth. To address this issue, we analyzed cartilage-specific beta-catenin-deficient mice. Mutant synchondroses lacked typical growth plate zones, and endochondral ossification was delayed. In reciprocal transgenic experiments, cartilage overexpression of a constitutive active Lef1, a transcriptional mediator of Wnt/beta-catenin signaling, caused precocious chondrocyte hypertrophy and intermingling of immature and mature chondrocytes. The developmental changes seen in beta-catenin-deficient synchondroses were accompanied by marked reductions in Ihh and PTHrP as well as sFRP-1, an endogenous Wnt signaling antagonist and a potential Ihh signaling target. Thus, Wnt/beta-catenin signaling is essential for cranial base development and synchondrosis growth plate function. This pathway promotes chondrocyte maturation and ossification events, and may exert this important role by dampening the effects of Ihh-PTHrP together with sFRP-1.

Nanoliter high throughput quantitative PCR

Understanding biological complexity arising from patterns of gene expression requires accurate and precise measurement of RNA levels across large numbers of genes simultaneously. Real time PCR (RT-PCR) in a microtiter plate is the preferred method for quantitative transcriptional analysis but scaling RT-PCR to higher throughputs in this fluidic format is intrinsically limited by cost and logistic considerations. Hybridization microarrays measure the transcription of many thousands of genes simultaneously yet are limited by low sensitivity, dynamic range, accuracy and sample throughput. The hybrid approach described here combines the superior accuracy, precision and dynamic range of RT-PCR with the parallelism of a microarray in an array of 3072 real time, 33 nl polymerase chain reactions (RT-PCRs) the size of a microscope slide. RT-PCR is demonstrated with an accuracy and precision equivalent to the same assay in a 384-well microplate but in a 64-fold smaller reaction volume, a 24-fold higher analytical throughput and a workflow compatible with standard microplate protocols.

High throughput, nanoliter quantitative PCR

The recent completion of the human genome sequence has increased the need for high throughput quantitative transcription analysis. Quantitative PCR is an alternative to microarrays for accurate and precise expression analysis with single transcript copy sensitivity. A review of current research in miniaturized, high throughput qPCR suggests this technique will soon be a viable option to hybridization microarrays for large-scale genetic analyses.:

MR imaging and histologic features of capillary telangiectasia of the basal ganglia

Capillary telangiectasias are being recognized with increasing frequency on MR imaging studies. Most are located in the brain stem and show slightly increased signal intensity on T2-weighted images, low signal intensity on T2*-weighted images (reflecting the presence of deoxyhemoglobin), and contrast enhancement. These findings are considered fairly typical for capillary telangiectasia, and pathologic correlation is not generally pursued. We present a case of a proven capillary telangiectasia in the basal ganglia. The imaging features of the lesion were identical to those described for capillary telangiectasias in the brain stem.

Carbohydrate modifications of the NDV fusion protein heptad repeat domains influence maturation and fusion activity

The amino acid sequence of the fusion protein (F) of Newcastle disease virus (NDV) has six potential N-linked glycosylation addition sites, five in the ectodomain (at amino acids 85, 191, 366, 447, and 471) and one in the cytoplasmic domain at amino acid 542. Two of these sites, at positions 191 and 471, are within heptad repeat (HR) domains implicated in fusion activity of the protein. To determine glycosylation site usage as well as the function of added carbohydrate, each site was mutated by substituting alanine for the serine or threonine in the addition signal. The sizes of the resulting mutant proteins, expressed in Cos cells, showed that sites at amino acids 85, 191, 366, and 471 are used. This conclusion was verified by comparing sizes of mutant proteins missing all four used sites with that of unglycosylated F protein. The role of each added oligosaccharide in the structure and function of the F protein was determined by characterizing stability, proteolytic cleavage, surface expression, and fusion activity of the mutant proteins. Elimination of the site in F(2) at amino acid 85 had the most detrimental effect, decreasing cleavage, stability, and surface expression as well as fusion activity. The protein missing the site at 191, at the carboxyl terminus of the HR1 domain, also showed modestly reduced surface expression and negligible fusion activity. Proteins missing sites at 366 and 471 (within HR2) were expressed at nearly wild-type levels but had decreased fusion activity. These results suggest that all carbohydrate side chains, individually, influence the folding or activity of the NDV F protein. Importantly, carbohydrate modifications of the HR domains impact fusion activity of the protein.

Psychiatrists disciplined by a state medical board

OBJECTIVE

This study determined the risk of discipline by a medical board for psychiatrists relative to other physicians and assessed the contributions to such risk.

METHOD

Physicians disciplined by the California Medical Board in a 30-month period were compared with matched groups of nondisciplined physicians.

RESULTS

Among 584 disciplined physicians, there were 75 (12.8%) psychiatrists, nearly twice the number of psychiatrists among nondisciplined physicians. Female psychiatrists were underrepresented in the disciplined group. Psychiatrists were significantly more likely than nonpsychiatrist physicians to be disciplined for sexual relationships with patients and about as likely to be charged with negligence or incompetence. The disciplined and nondisciplined psychiatrists did not differ significantly from a group of 75 nondisciplined psychiatrists on years since medical school graduation, international medical graduate status, or board certification. The disciplined group included significantly more psychiatrists who claimed child psychiatry as their first or second specialty and significantly fewer psychoanalysts.

CONCLUSIONS

Organized psychiatry has an obligation to address sexual contact with patients and other causes for medical board discipline. This obligation may be addressable through enhanced residency training, recertification exams, and other means of education.

Nongenomic action of progesterone: activation of Xenopus oocyte phospholipase C through a plasma membrane-associated tyrosine kinase

Using a plasma membrane-cortex preparation (wherein the nucleus and >90% of the total cell protein are removed), progesterone stimulated tyrosine kinase activity that stimulated phospholipase C. Although it has been known for over 20 yr that progesterone acts at the plasma membrane of Xenopus oocytes to induce oocyte maturation, this is the first report that progesterone stimulates this tyrosine kinase activity that is associated with the oocyte plasma membrane and cortex. A tyrosine kinase inhibitor (tyrphostin B46) inhibited steroid stimulation of tyrosine kinase and phospholipase C (PLC) activities, but did not block lipase C stimulation by G protein activators. A fusion protein that contains tandem N- and C-terminal SH2 domains of PLCgamma also blocked progesterone stimulation of PLC (a fusion protein with the SH2 domain from Shc was ineffective). Lowering the Ca2+ concentration in the medium inhibited progesterone, but not guanosine 5'-O-(3-thiotriphosphate), stimulation of PLC, and the effects of progesterone and a G protein agonist were additive. However, neither progesterone nor insulin increased phosphotyrosine on PLCgamma. To evaluate another tyrosine kinase path involving phosphatidylinositol 3-kinase, we added wortmannin to our membrane preparation, but wortmannin did not inhibit progesterone's ability to activate PLC.

Local Structure Analysis of Strontium Sorption to Hydrous Manganese Oxide

To develop mechanistic models of contaminant distribution processes, we conducted an X-ray absorption fine structure analysis of strontium sorption to hydrous manganese oxide (HMO). Sr K-edge measurements were performed at 298, 220, and 77 K, and at sample loadings from 10(-4) to 10(-2) mol Sr/g HMO. Results from fitting the first shell in the sorbed samples indicate that strontium is surrounded by 10-12 oxygen atoms at an average distance of 2.58 Å. This coordination environment is consistent with the strontium atom remaining hydrated upon sorption to the oxide, where in water hydrated strontium has approximately 9 atoms of oxygen at 2.62 Å. Furthermore, the temperature dependence of the strontium-oxygen bond also suggests physical adsorption due to the large contribution of the dynamic component of the Debye Waller factor. Although second-shell data are consistent with either 3 manganese atoms at 4.12 Å or 6 strontium atoms at 3.88 Å, both the near-edge and fine structure data for the manganese K-edge indicate that the local coordination environment of the manganese ion remains intact as a function of time or strontium sorption. Furthermore, the local structure of amorphous manganese oxide is highly ordered. Copyright 2000 Academic Press.

Counseling youth in tobacco-use prevention: determinants of clinician compliance

OBJECTIVE

The rate and determinants of tobacco prevention and cessation counseling to youth were examined for orthodontists participating in a controlled trial to decrease the incidence of tobacco use among adolescents.

METHODS

A cross-sectional interview design in private practice offices throughout Southern California was used. The survey was completed with 126 (82%) orthodontists. Clinicians randomly assigned to the experimental group (N = 77) received a 1.5 h workshop, anti-tobacco materials, reimbursement for provision of anti-tobacco prescriptions, and quarterly checkup visits. Control group clinicians (N = 77) did not receive training, materials, or visits.

RESULTS

Experimental group clinicians talked to more adolescent nonsmokers about never beginning tobacco use than did control group clinicians (P < 0.05). Experimental group clinicians talked to more adolescent tobacco users than did control group clinicians; however, the difference was not statistically significant. Content and determinants of counseling were affected by participation in the intervention.

CONCLUSIONS

Though training and support increased prevention and cessation counseling, absolute rates remained less than optimal. Social learning factors were associated with prevention and cessation counseling.

A study to determine the acceptability in patients and dentists of toluidine blue in screening for oral cancer

Opportunistic screening for oral cancer has been advocated as a possible beneficial procedure, especially with high-risk individuals. To assist in the identification of malignant lesions a dye has been developed which can be used routinely. Issues of acceptability for both patient and practitioner are raised. The adoption of this procedure for employees in a large retail chain in the UK has enabled an investigation into the use of the dye. The objective of the study was to determine the acceptability of toluidine blue in aiding the screening for oral cancer in regular attending dental patients who are at high-risk. A two-stage study design was conducted. The first stage consisted of a patient survey in which 10 patients from each of 14 stores of the retail chain were invited to complete a questionnaire. The level of embarrassment, taste and anxiety about the procedure was assessed. The second stage included a clinician questionnaire and telephone interview on the difficulties, if any, of conducting the screening procedure with the aid of the dye. The oral health screen (OHS) with OraScreen procedure was conducted in the retail store medical room. The participants consisted of 140 employees attending the routine dental examination at the store of their workplace. All employees in the survey reported that they smoked tobacco, drank alcohol and were over the age of 40 years. Fourteen dentists visited the stores to complete examinations, screening, questionnaires and telephone interview. The main outcome measures consisted of dentist and patient rating scales of acceptability developed for the study. Of the respondents 89% (n = 124) gave usable questionnaire data. The patients found the dye acceptable (for example 83% rated the oral health screen 'a comfortable experience') and 93% expected the examiner to give an opinion of the state of their mouths. A wish was expressed by 95% to take part in future oral health screens. The dentist-respondents were in favour of the use of the dye. In conclusion, the acceptability of toluidine blue dye to assist in the screening for oral cancer is good according to both patient and clinician. The use of this dye should now be encouraged more extensively by trained clinicians in the identification of oral cancerous and precancerous lesions.

Effect of cleavage mutants on syncytium formation directed by the wild-type fusion protein of Newcastle disease virus

The effects of Newcastle disease virus (NDV) fusion (F) glycoprotein cleavage mutants on the cleavage and syncytium-forming activity of the wild-type F protein were examined. F protein cleavage mutants were made by altering amino acids in the furin recognition region (amino acids 112 to 116) in the F protein of a virulent strain of NDV. Four mutants were made: Q114P replaced the glutamine residue with proline; K115G replaced lysine with glycine; double mutant K115G, R113G replaced both a lysine and an arginine with glycine residues; and a triple mutant, R112G, K115G, F117L, replaced three amino acids to mimic the sequence found in avirulent strains of NDV. All mutants except Q114P were cleavage negative and fusion negative. However, addition of exogenous trypsin cleaved all mutant F proteins and activated fusion. As expected for an oligomeric protein, the fusion-negative mutants had a dominant negative phenotype: cotransfection of wild-type and mutant F protein cDNAs resulted in an inhibition of syncytium formation. The presence of the mutant F protein did not inhibit cleavage of the wild-type protein. Furthermore, evidence is presented that suggests that the mutant protein and the wild-type protein formed heterooligomers. By measuring the syncytium-forming activity of the wild-type protein at various ratios of expression of mutant and wild-type protein, results were obtained that are most consistent with the notion that the size of the functionally active NDV F protein in these assays is a single oligomer, likely a trimer. That a larger oligomer, containing a mix of both wild-type and mutant F proteins, has partial activity cannot, however, be ruled out.

Partnership and collaboration: rhetoric and reality

Multidisciplinary collaboration in child protection work in the UK is facing considerable strains resulting from major organizational changes across public welfare systems, budgetary cuts, and severe resource deficits. In parallel with this there has been a powerful impetus through new legislation to recast the management of child protection in order to involve clients far more in decision making, reduce the removal of children from families, and to redirect resources towards a more preventive approach. This paper considers the nature of effective partnerships both between clients and agencies, and between agencies in the child protection field. The need for clear definitions of "partnership" is emphasized as well as the necessity for partnerships to be underpinned by a continuum of supportive and protective services. A framework for interagency collaboration is offered.

Oral mucosal screening as an integral part of routine dental care

The principal aim of this study was to assess the feasibility of conducting a systematic examination of the oral mucosa, as an integral part of the routine dental check-up and in conditions comparable with those in NHS dental practice. A total of 1949 individuals, who were already registered as patients with an industrial dental clinic, were invited to attend for an oral screen as part of their dental examination. Of these, 1947 patients agreed to participate and were also asked to complete a 'habits' questionnaire relating to their tobacco and alcohol use. A systematic examination of the oral mucosa was undertaken as part of the routine dental inspection and mucosal lesions were recorded as either a positive or negative screening result. Lesions included as a positive result were those which may be associated with early cancer or precancer. Four patients (0.2%) were considered to have a positive screening result and these were referred for specialist evaluation. Of these, two had tobacco-related leukoplakia, one had oral lichen planus and the other had an early squamous cell carcinoma. This study has confirmed that a systematic and thorough examination of the oral mucosa can realistically be carried out as part of the routine dental inspection in NHS dental practice.

The Modified Dental Anxiety Scale: validation and United Kingdom norms

The Corah Dental Anxiety Scale (CDAS) has been used extensively in epidemiology and clinical research. It is brief and is claimed to have good psychometric properties. However, it does not include any reference to local anaesthetic injections, a major focus of anxiety for many. Also, the multiple choice answers for three of the four questions are not clearly in order of severity of anxiety as the CDAS intends. The answers differ among the questions thus making them difficult to compare. They include descriptions of physiological reactions and anxiety, confusing two loosely related components of the experience. The Modified Dental Anxiety Scale (MDAS) described, added a question on anxiety about oral injections. New multiple choice answers, in clear order of anxiety and the same for each question, were provided. Twenty five dental personnel all confirmed independently the order of the multiple choice answers for the MDAS. They disagreed among themselves however, about the appropriate sequence for the answers denoting intermediate anxiety in the CDAS. Therefore the CDAS, unlike the MDAS, can provide meaningful measures only of extremely high or extremely low dental anxiety. Of 1392 subjects tested, 13 per cent expressed extreme anxiety about injections on the MDAS but were only 'fairly' or less anxious about drilling. Thus, the CDAS, unlike the MDAS, must overlook subjects very afraid of injections only. Data confirm the high reliability and validity of the MDAS and provide norms for phobic and nonphobic subjects.

Mutations in the fusion peptide and heptad repeat regions of the Newcastle disease virus fusion protein block fusion

Nonconservative mutations were introduced by site-specific mutagenesis into the fusion peptide and the adjacent heptad repeat region of the fusion protein of Newcastle disease virus in order to determine the role of both regions in the fusion activity of the protein. Mutations in both regions that allowed for proper folding and intracellular transport of the protein blocked the fusion activity of the protein when assayed in the presence of the hemagglutinin-neuraminidase protein.

Which port in the storm? Can a contract management system alone meet all your managed care requirements?

For the past decade, contract management was synonymous with managed care for hospitals. Today, managed care is taking on new meaning, especially as hospital administrators and clinicians begin to think "outside the four walls." To address the increasing demands managed care is placing on hospitals, the vendors of contract management software are adding HMO-like functionality to their systems. The vendors claim their products can confirm eligibility, track referrals, process claims and even calculate capitation, in addition to managing contract administration. How do these enhanced contract management systems differ from managed care information systems used by managed care organizations to perform essentially the same functions?

Role of a conserved sequence in the maturation and function of the NDV HN glycoprotein

The hemagglutinin-neuraminidase (HN) proteins of viruses in the Paramyxovirus genus have a short conserved sequence, G(A, S)EGR(I, L, V). The role of this sequence in the intracellular processing and function of the Newcastle disease virus HN protein was explored by site directed mutagenesis. Mutations in this region fall into two categories. One set of mutants (G398A, E400D, R402K, and a deletion removing amino acids 400-403) was defective in folding. These mutant proteins formed little or no mature, disulfide linked oligomer. They had few or no antigenic sites found on the mature protein and they were transported to the cell surface poorly or not at all. The second class of mutants (A399G, G401A, G401L) was minimally affected in folding and intracellular transport. When normalized to surface expression, this group of mutant proteins had wild type levels of attachment activity, neuraminidase activity, and fusion promotion activity. Thus mutations in this region directly affect intracellular processing but not the biological activities of the protein. This sequence may, therefore, be conserved in the HN proteins of Paramyxoviruses because it is critical to the folding of the molecule.

Mutations in the transmembrane domain of the HN protein of Newcastle disease virus affect the structure and activity of the protein

To explore the role of the transmembrane domain of the HN protein in the structure and function of the molecule, three conserved leucine residues in this domain which occur in a heptad-repeat motif were changed to alanine singly or in combination by site-specific mutagenesis. None of the mutant proteins were defective in translocation and intracellular transport. All mutant proteins formed disulfide-linked dimers. However, tetrameric structures of proteins with mutations in the third or most carboxy-terminal leucine could not be detected by sucrose gradient analysis, and mutant proteins with changes in both the first and second leucine formed less-stable tetramers. These results suggest that the transmembrane domain plays a role in the tetrameric structure of the HN protein. These mutations also altered the biological activities of the protein. Mutant proteins with alterations in the third leucine were very defective in attachment activity and somewhat defective for neuraminidase activity while all other mutant proteins had wild-type levels of attachment and neuraminidase activity. While all mutant proteins showed diminished fusion-promotion activity, proteins with mutations in the third leucine and proteins with changes in both the first and second leucines were very defective in fusion promotion. These results suggest that elimination or destabilization of the tetrameric structure affects attachment activity and fusion-promotion activity of the HN protein.

Perception of risk of HIV infection from regular attenders to an industrial dental service

The advent of the HIV pandemic has necessitated the introduction of consistent cross-infection procedures for dentistry. Suprisingly little is known of patient reactions to some of these changes. A structured questionnaire was administered (in 1988/9, n = 613) to regular-attending patients of an industrial dental service to assess their views towards cross-infection procedures. Approximately a third of the study sample believed that there was a slight risk or more of contracting HIV infection at the dentist. This risk perception attenuated with further visits to the dentist. Some patients (13%) claimed to be aware from the media of someone having been cross-infected with the HIV virus from a dental visit. The majority of patients prefer the dentist to adopt the barrier methods of mask and glove wearing. Over 60% of patients would like their dentist to wear a mask when in fact a mask had not been worn. Accuracy of recall by patients for mask wearing was only 70% and for glove wearing 88%. The possibility that drawing the patient's attention to cross-infection control may be reassuring for the patient was not supported with some evidence to suggest that in instances where the dentist provided treatment, the patient's perception of risk was increased.

The role of the amino terminus of F1 of the Newcastle disease virus fusion protein in cleavage and fusion

Phenylalanine is the amino acid at the amino terminus of the F1 protein of all paramyxovirus fusion proteins with the exception of the avirulent strains of Newcastle disease virus, which have a leucine residue in this position (Toyoda et al. (1989) Virology 169, 273-282). To explore the role of this phenylalanine in the fusion activity of the protein, this residue, amino acid 117 in the fusion protein sequence, was changed to leucine (F117L) or to glycine (F117G) by site-specific mutagenesis while maintaining the cleavage site sequence of virulent strains of NDV. While both wild-type and the F117G protein were proteolytically cleaved and F1 was detected, the F117L protein was not cleaved. In the presence of the HN protein, both wild-type F and F117G proteins stimulated fusion, but the F117L protein was inactive in fusion. However, incubation in trypsin activated the fusion activity of the protein. Thus the phenylalanine at the amino terminus of the F1 component of the fusion protein is not required for the fusion activity of the protein. The presence of a leucine at this position blocks cleavage even though the cleavage site sequence is unchanged.