Clinical and molecular practice of European thoracic pathology laboratories during the COVID-19 pandemic. The past and the near future.

BACKGROUND: This study evaluated the consequences in Europe of the COVID-19 outbreak on pathology laboratories orientated toward the diagnosis of thoracic diseases. MATERIALS AND METHODS: A survey was sent to 71 pathology laboratories from 21 European countries. The questionnaire requested information concerning the organization of biosafety, the clinical and molecular pathology, the biobanking, the workload, the associated research into COVID-19, and the organization of education and training during the COVID-19 crisis, from 15 March to 31 May 2020, compared with the same period in 2019. RESULTS: Questionnaires were returned from 53/71 (75%) laboratories from 18 European countries. The biosafety procedures were heterogeneous. The workload in clinical and molecular pathology decreased dramatically by 31% (range, 3%-55%) and 26% (range, 7%-62%), respectively. According to the professional category, between 28% and 41% of the staff members were not present in the laboratories but did teleworking. A total of 70% of the laboratories developed virtual meetings for the training of residents and junior pathologists. During the period of study, none of the staff members with confirmed COVID-19 became infected as a result of handling samples. CONCLUSIONS: The COVID-19 pandemic has had a strong impact on most of the European pathology laboratories included in this study. Urgent implementation of several changes to the organization of most of these laboratories, notably to better harmonize biosafety procedures, was noted at the onset of the pandemic and maintained in the event of a new wave of infection occurring in Europe.

Molecular screening in a longitudinal cohort of young men who have sex with men and young transgender women: associations with focus on the emerging sexually transmitted pathogen Mycoplasma genitalium.

OBJECTIVES: This investigation sought to characterise risk factors associated with acquisition of traditional and emerging agents of sexually transmitted infection (STI) in a cohort of young men who have sex with men and transgender women. METHODS: 917 participants provided urine and rectal swab submissions assessed by transcription-mediated amplification (TMA)-based assays for Chlamydia trachomatis and Neisseria gonorrhoeae and by off-label TMA-based Trichomonas vaginalis and Mycoplasma genitalium testing. A subset provided specimens at 6-month and 12-month follow-up visits. RESULTS: Prevalence of M. genitalium from rectal and urine specimens (21.7% and 8.9%, respectively) exceeded that of C. trachomatis (8.8% and 1.6%) and other STI agents. Black participants yielded higher prevalence of M. genitalium (30.6%) than non-black participants (17.0%; χ²=22.39; p<0.0001). M. genitalium prevalence from rectal specimens was 41.5% in HIV-positive participants vs 16.3% in HIV-negative participants (χ²=57.72; p<0.0001). Participant age, gender identity, condomless insertive anal/vaginal sexual practice and condomless receptive anal sexual practice were not associated with rectal C. trachomatis (p≥0.10), N. gonorrhoeae (p≥0.29), T. vaginalis (p≥0.18) or M. genitalium (p≥0.20) detection. While prevalence of T. vaginalis was calculated at ≤1.0%, baseline rectal and urine screening status was predictive of detection/non-detection at follow-up. A non-reactive M. genitalium baseline rectal or urine screening result was less predictive of non-reactive follow-up versus C. trachomatis, N. gonorrhoeae and T. vaginalis. CONCLUSIONS: Rectal M. genitalium detection is associated with black race and HIV seropositivity. Baseline M. genitalium infection influences subsequent detection of the organism.

Advanced cancer patient preferences for receiving molecular profiling results.

OBJECTIVE: This study aimed to discern preferences for receiving somatic molecular profiling (MP) results in cancer patients who have given consent to undergo testing. METHODS: We conducted a mixed-methods study to explore patients' views on which MP results they would like to receive and why. Advanced cancer patients (n = 1299) completed questionnaires after giving consent to participate in a parent genomics study and undergoing MP. A subset of patients (n = 20) participated in qualitative interviews. RESULTS: Almost all (96%) participants were interested in receiving results which would direct cancer treatment (ie, were actionable). A smaller majority wanted to access results which were not actionable (64%) or were variants of unknown significance (60%). Most (86%) were interested in finding out about germline findings, though not as a priority. Themes identified in interview data were: (a) Cancer is the focus; (b) Trust in clinicians; and (c) Respect for a right not to know. CONCLUSIONS: The majority of advanced cancer patients undergoing MP prioritised results which would lead to treatment options. They trusted their oncologists to help them navigate the results return process. While there was interest in knowing about other results, this was a lesser priority. Nevertheless, given high levels of interest in receiving all results, ethical aspects of not providing uninformative results requires further research, including a consideration of patient rationales for desiring this information and what health professionals can and should do to support patients in the absence of meaningful information being available.

Support of a molecular tumour board by an evidence-based decision management system for precision oncology.

BACKGROUND: Reliable and reproducible interpretation of molecular aberrations constitutes a bottleneck of precision medicine. Evidence-based decision management systems may improve rational therapy recommendations. To cope with an increasing amount of complex molecular data in the clinical care of patients with cancer, we established a workflow for the interpretation of molecular analyses. METHODS: A specialized physician screened results from molecular analyses for potential biomarkers, irrespective of the diagnostic modality. Best available evidence was retrieved and categorized through establishment of an in-house database and interrogation of publicly available databases. Annotated biomarkers were ranked using predefined evidence levels and subsequently discussed at a molecular tumour board (MTB), which generated treatment recommendations. Subsequent translation into patient treatment and clinical outcomes were followed up. RESULTS: One hundred patients were discussed in the MTB between January 2016 and May 2017. Molecular data were obtained for 70 of 100 patients (50 whole exome/RNA sequencing, 18 panel sequencing, 2 immunohistochemistry (IHC)/microsatellite instability analysis). The MTB generated a median of two treatment recommendations each for 63 patients. Thirty-nine patients were treated: 6 partial responses and 12 stable diseases were achieved as best responses. Genetic counselling for germline events was recommended for seven patients. CONCLUSION: The development of an evidence-based workflow allowed for the clinical interpretation of complex molecular data and facilitated the translation of personalized treatment strategies into routine clinical care. The high number of treatment recommendations in patients with comprehensive genomic data and promising responses in patients treated with combination therapy warrant larger clinical studies.

Patient perspectives on molecular tumor profiling: "Why wouldn't you?"

AIM: This study explored the attitudes of patients with advanced cancer towards MTP and return of results, prior to undergoing genomic testing within a research program. METHODS: Participants were recruited as part of the longitudinal PiGeOn (Psychosocial Issues in Genomics in Oncology) study involving patients with advanced/metastatic solid cancer who had exhausted therapeutic options and who were offered MTP in order to identify cognate therapies. Twenty patients, selected by purposive sampling, were interviewed around the time they gave consent to MTP. Interviews were audio recorded, transcribed and analysed using thematic analysis. Themes identified in the transcripts were cross-validated via qualitative responses to the PiGeOn study survey (n = 569; 63%). RESULTS: All interviewed participants gave consent to MTP without reservation. Three themes were identified and further supported via the survey responses: (1) Obvious agreement to participate, primarily because of desire for new treatments and altruism. (2) The black box - while participant knowledge of genomics was generally poor, faith in their oncologists and the scientific process encouraged them to proceed with testing; and (3) Survival is the priority - receiving treatment to prolong life was the priority for all participants, and other issues such as identification of a germline variant were generally seen as ancillary. CONCLUSION: Having advanced cancer seemed to abrogate any potential concerns about MTP. Participants valued the research for varied reasons, but this was secondary to their priority to survive. While no negative attitudes toward MTP emerged, limitations in understanding of genomics were evident.

Quality of molecular detection of vancomycin resistance in enterococci: results of 6 consecutive years of Quality Control for Molecular Diagnostics (QCMD) external quality assessment.

The quality of PCR to detect vancomycin-resistant enterococci (VRE) was evaluated by analysing their performance in six consecutive external quality assessment (EQA) schemes, organized annually since 2013 by Quality Control for Molecular Diagnostics. VRE EQA panels consisted of 12-14 heat-inactivated samples. Sensitivity was tested with vanA-positive Enterococcus faecium (E. faecium), vanB-positive E. faecium, E. faecalis or E. gallinarum or vanC-positive E. gallinarum in different concentrations. Vancomycin-susceptible enterococci, Staphylococcus aureus or sample matrix was used to study the specificity. Participants were asked to report the VRE resistance status of each sample. The detection rate of vanA-positive samples was already 95% in the 2013 EQA panel (range 94-97%) and remained stable over the years. The 2013 detection rate of vanB-positive samples was 82% but increased significantly by more than 10% in subsequent years (96% in 2014, 95% in 2015, 92% in 2016 and 93% in 2017/2018, p < 0.05). The vanC detection rate by the limited number of assays specifically targeting this gene was lower compared to vanA/B (range 55-89%). The number of false positives in the true-negative sample (8% in 2013 to 1.4% in 2018) as well as the van-gene-negative bacterial samples (4% in 2013 to 0% in 2018) declined over the years. In the six years of VRE proficiency testing to date, the detection of vanA-positive strains was excellent and an increased sensitivity in vanB detection as well as an increase in specificity was observed. Commercial and in-house assays performed equally well.

Gridlock from diagnosis to treatment of multidrug-resistant tuberculosis in Tanzania: low accessibility of molecular diagnostic services and lack of healthcare worker empowerment in 28 districts of 5 high burden TB regions with mixed methods evaluation.

BACKGROUND: Multidrug-resistant tuberculosis (MDR-TB) outcomes are adversely impacted by delay in diagnosis and treatment. METHODS: Mixed qualitative and quantitative approaches were utilized to identify healthcare system related barriers to implementation of molecular diagnostics for MDR-TB. Randomly sampled districts from the 5 highest TB burden regions were enrolled during the 4th quarter of 2016. District TB & Leprosy Coordinators (DTLCs), and District AIDS Coordinators (DACs) were interviewed, along with staff from all laboratories within the selected districts where molecular diagnostics tests for MDR-TB were performed. Furthermore, the 2015 registers were audited for all drug-susceptible but retreatment TB cases and TB collaborative practices in HIV clinics, as these patients were in principal targeted for drug susceptibility testing by rapid molecular diagnostics. RESULTS: Twenty-eight TB districts from the 5 regions had 399 patients reviewed for retreatment with a drug-susceptible regimen. Only 160 (40%) had specimens collected for drug-susceptibility testing, and of those specimens only 120 (75%) had results communicated back to the clinic. MDR-TB was diagnosed in 16 (13.3%) of the 120 specimens but only 12 total patients were ultimately referred for treatment. Furthermore, among the HIV/AIDS clinics served in 2015, the median number of clients with TB diagnosis was 92 cases [IQR 32-157] yet only 2 people living with HIV were diagnosed with MDR-TB throughout the surveyed districts. Furthermore, the districts generated 53 front-line healthcare workers for interviews. DTLCs with intermediate or no knowledge on the clinical application of XpertMTB/RIF were 3 (11%), and 10 (39%), and DACs with intermediate or no knowledge were 0 (0%) and 2 (8%) respectively (p = 0.02). Additionally, 11 (100%) of the laboratories surveyed had only the 4-module XpertMTB/RIF equipment. The median time that XpertMTB/RIF was not functional in the 12 months prior to the investigation was 2 months (IQR 1-4). CONCLUSIONS: Underutilization of molecular diagnostics in high-risk groups was a function of a lack of front-line healthcare workforce empowerment and training, and a lack of equipment access, which likely contributed to the observed delay in MDR-TB diagnosis in Tanzania.

Molecular diagnostics improves diagnosis and treatment of respiratory allergy and food allergy with economic optimization and cost saving.

BACKGROUND: Component resolved diagnosis (CRD) allows to precisely identify the sensitization to specific molecules of a given allergenic source, resulting in an important improvement in clinical management, particularly of polysensitized subjects. This will end in the correct prescription of allergen immunotherapy (AIT) for respiratory allergy and in adequate avoidance diets or prescription of self-injectable adrenaline in food allergy. OBJECTIVE: The aim of this multicenter, real life study is to evaluate the percentage change of the diagnostic-therapeutic choice in polysensitized patients with respiratory allergy and in patients with food allergy, after using CRD compared to a first level diagnosis, along with an economic analysis of the patient's overall management according to the two different approaches. METHODS: An overall number of 462 polysensitized patients, as suggested by skin prick tests (SPT), and with clinical symptoms related to a respiratory (275 pts) or food (187 pts) allergy, were recruited. All patients underwent CRD for specific IgE against food or inhalant recombinant molecules, which were chosen according to medical history and positivity to SPT. The first diagnostic-therapeutic hypothesis, based only on medical history and SPT, was recorded for each patient while the final diagnostic-therapeutic choice was based on the results from CRD. The rate of change of the diagnostic-therapeutic choice from the first hypothesis to the final choice was statistically evaluated. The economic impact of CRD on the overall management of the allergic patients was analyzed to evaluate whether the increase in the diagnostic costs would be compensated and eventually exceeded by savings coming from the improved diagnostic-therapeutic appropriateness. RESULTS: An approximate 50% change (k index 0.54) in the prescription of AIT for respiratory allergy as well as a change in the prescription of self-injectable adrenaline (k index 0.56) was measured; an overall saving of financial resources along with a higher diagnostic-therapeutic appropriateness was also detected. CONCLUSION: There is moderate agreement concerning prescription of AIT and self-injectable adrenaline before and after performing CRD: this highlights the usefulness of CRD, at least in polysensitized patients, in indicating the risk assessment and therefore the correct therapy of respiratory and food allergy, which results in a cost-saving approach.

Assessing the Incremental Contribution of Common Genomic Variants to Melanoma Risk Prediction in Two Population-Based Studies.

It is unclear to what degree genomic and traditional (phenotypic and environmental) risk factors overlap in their prediction of melanoma risk. We evaluated the incremental contribution of common genomic variants (in pigmentation, nevus, and other pathways) and their overlap with traditional risk factors, using data from two population-based case-control studies from Australia (n = 1,035) and the United Kingdom (n = 1,460) that used the same questionnaires. Polygenic risk scores were derived from 21 gene regions associated with melanoma and odds ratios from published meta-analyses. Logistic regression models were adjusted for age, sex, center, and ancestry. Adding the polygenic risk score to a model with traditional risk factors increased the area under the receiver operating characteristic curve (AUC) by 2.3% (P = 0.003) for Australia and by 2.8% (P = 0.002) for Leeds. Gene variants in the pigmentation pathway, particularly MC1R, were responsible for most of the incremental improvement. In a cross-tabulation of polygenic by traditional tertile risk scores, 59% (Australia) and 49% (Leeds) of participants were categorized in the same (concordant) tertile. Of participants with low traditional risk, 9% (Australia) and 21% (Leeds) had high polygenic risk. Testing of genomic variants can identify people who are susceptible to melanoma despite not having a traditional phenotypic risk profile.

Dual composite reference standards (dCRS) in molecular diagnostic research: A new approach to reduce bias in the presence of Imperfect reference.

A main challenge in molecular diagnostic research is to accurately evaluate the performance of a new nucleic acid amplification test when the reference standard is imperfect. Several approaches, such as discrepant analysis, composite reference standard (CRS) method, or latent class analysis (LCA), are commonly applied for this purpose by combining multiple imperfect (reference) test results. In discrepant analysis or LCA, test results from the new assay are often involved in the construction of a new pseudo-reference standard, which results in the potential risk of overestimating the parameters of interest. On the contrary, the CRS methods only combine the results of reference tests, which is more preferable in practice. In this article, we study the properties of two extreme CRS methods, i.e., combining multiple reference test results by the "any positive" rule or by the "all-positive" rule, and propose a new approach "dual composite reference standards (dCRS)" based on these two extreme methods to reduce the biases of the estimates. Simulations are performed for various scenarios and the proposed approach is applied to two real datasets. The results demonstrate that our approach outperforms other commonly used approaches and therefore is recommended for future applications.

Validation of Molecular Pathology Codes for the Identification of Mutational Testing in Lung and Colon Cancer.

BACKGROUND: Targeted therapy for patients with lung and colon cancer based on tumor molecular profiles is an important cancer treatment strategy, but the impact of gene mutation tests on cancer treatment and outcomes in large populations is not clear. In this study, we assessed the accuracy of an algorithm to identify tumor mutation testing in administrative claims data during a period before test-specific Current Procedural Terminology codes were available. MATERIALS AND METHODS: We used Pennsylvania Cancer Registry data to select patients with lung or colon cancer diagnosed between 2007 and 2011 who were treated at the University of Pennsylvania Health System, and we obtained their administrative claims. A combination of Current Procedural Terminology laboratory codes (stacking codes) was used to identify potential tumor mutation testing in the claims data. Patients' electronic medical records were then searched to determine whether tumor mutation testing actually had been performed. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. RESULTS: An algorithm using stacking codes had moderate sensitivity (86% for lung cancer and 81% for colon cancer) and high specificity (98% for lung cancer and 96% for colon cancer). Sensitivity and specificity did not vary significantly during 2007-2011. In patients with lung cancer, PPV was 98% and NPV was 92%. In patients with colon cancer, PPV was 96% and NPV was 83%. CONCLUSIONS: An algorithm using stacking codes can identify tumor mutation testing in administrative claims data among patients with lung and colon cancer with a high degree of accuracy.

Data-Driven Iterative Refinement of Bone Marrow Testing Protocols Leads to Progressive Improvement in Cytogenetic and Molecular Test Utilization.

OBJECTIVES: To determine the effect of iterative refinement of standard ordering protocols on test utilization and results for bone marrow biopsy specimens. METHODS: Eighteen months of test utilization and result data were used to revise the protocols that determine cytogenetic and molecular test selection on bone marrow specimens and then compared with data obtained following protocol revision. RESULTS: Revision of protocols resulted in reduction in total tests and associated charges, due to a decrease in tests both concordant and discordant with the protocols. These reductions only occurred in diseases for which revisions were made and were limited to cases in which reflex testing was performed. There was an increase in the fraction of positive tests, which was also limited to reflex testing. CONCLUSIONS: Data-driven iterative revision of protocols further improves test utilization and performance, while reducing cost. Analysis of testing data can be used to continuously improve test ordering decisions.

How much reproducibility do we need in human and veterinary pathology?

In diagnostic and research reports as well as text-books of human and veterinary pathology repeatability, reproducibility, inter- and intra-observer variation are mentioned rarely as a problem in preparing diagnosis from macroscopic and/or microscopic samples and discussed inconsistently. However, optimal care and restoration of health for a patient are dependent on reliability of diagnosis, therapy, prognosis and prophylaxis. This requires for all tests and procedures a maximal repeatability and reproducibility, a sensitivity and specificity of 85-95% for procedures and methodologies and a comparison of results procedures and methodologies to a gold standard. Looking at the various steps on the road to diagnosis in pathology this is influenced by a series of laboratory steps preparing tissue samples but most importantly reproducibility depends on the handling of visual information in the central nervous system of the individual diagnostician. Thus reproducibility in this context has to be divided into at least three levels: individual (epistemological, organoleptic, inter- and intra-observer variation, and formal/technological- and normative reproducibility). The aim of the present manuscript is to stimulate the reflection among the pathology experts on this most important topic.

[Molecular surveillance shows progress in measles elimination process]. / Molekulare Surveillance belegt Fortschritt im Eliminationsprozess der Masern.

Measles is a severe disease caused by infection with the measles virus. Complications after the onset of infection lead to 1-3 fatalities per 1,000 cases in industrialized countries. If more than 95 % of the global population were vaccinated twice with the measles, mumps, and rubella (MMR) vaccine, measles could be eliminated worldwide. The elimination of measles and rubella should be reached in the WHO Europe region in 2015. One important criterion for elimination of the measles virus consists in the analysis of the duration of transmission chains initiated by the import of measles virus. To assign measles viruses to outbreaks and transmission chains, genetic characterization is necessary. These investigations have been performed continually at the National Reference Center Measles, Mumps, Rubella since 1999, when the German Intervention Program was launched. This article summarizes our experiences with measles virus genotyping and new developments with respect to measles elimination in Germany.

Nonadherence to imatinib adversely affects event free survival in chronic phase chronic myeloid leukemia.

There is limited data on the impact of treatment interruptions due to nonadherence in patients with chronic phase chronic myeloid leukemia (CP-CML) treated with Imatinib. We looked at factors (including adherence to therapy) affecting the outcome in a large cohort of patients with CP-CML. All the 516 patients received Imatinib free-of-cost through a company sponsored scheme, which mandated regular three monthly visits for drug procurement. Data regarding the disease characteristics, adherence to treatment and outcomes, were obtained from patients records. Unwarranted interruption of treatment for more than 1 week was defined as nonadherence. With a median follow-up of 39 months, the estimated 5-year event free survival (EFS) was 70.8% (95%, CI = 63.3-78.3). Nearly one-third of the patients (29.6%) were found to be nonadherent at some point during their treatment. On univariate analysis, the factors adversely affecting the EFS were prolonged symptom duration before diagnosis, treatment with hydroxyurea for more than 1 month before start of Imatinib, and nonadherence to therapy. Only nonadherence was significant in multivariate analysis (HR1.6; P = 0.048). The 5-year EFS in adherent and nonadherent patients was 76.7% and 59.8% respectively (P = 0.011, log rank test). Nonadherent patients were less likely to achieve complete cytogenetic responses (26% versus 44%; P = 0.004; χ(2) test) at any point. A significant proportion of patients with CP-CML have drug interruptions due to nonadherence during therapy and this compromises the EFS. Adherence to therapy must be included as an important evaluation parameter in all future studies of CML.

Unique marker finder algorithm generates molecular diagnostic markers.

By taking advantage of the power of comparative genomics, we devised an algorithm, Unique Marker Finder (U-MarFin), to generate a collection of unique DNA sequences from a target organism. The whole target genome is partitioned into a scoring pool of less 4000 base-pair fragments, which are then subjected to elimination of homologous sequences in other bacterial genomes by BLAST alignment, and looked for all open reading frames as they may be applied as unique markers. Through regular, nested, multiplex and real time PCR and microarray technology, we empirically demonstrated that the sequences discovered were highly specific to the species that they are derived from, and they can serve as molecular biomarkers for diagnostic purpose.