Predictive molecular pathology in the time of coronavirus disease (COVID-19) in Europe

Rapid and reliable testing for clinically actionable EGFR mutations in non-small cell lung cancer using the IdyllaTM platform: a real-world two-center experience in Greece

BACKGROUND

Limited information exists on epidermal growth factor receptor (EGFR) molecular epidemiology in Greece. Next-generation sequencing (NGS) is the recommended method for EGFR genotyping in NSCLC. The Idylla Biocartis platform is a fully automated system for actionable EGFR mutation detection.

RESEARCH DESIGN AND METHODS

We describe the prevalence of EGFR mutations in NSCLC patients in two high-volume clinical centers in Greece and compare key methods used for their determination. Eight hundred and fifty-seven FFPE samples from NSCLC patients were tested for EGFR mutations at University of Crete (UoC; n = 324) and at Evangelismos Hospital, Athens (Evangelismos; n = 503).

RESULTS

The prevalence of EGFR mutations was 11.1% in the whole cohort (11.5% in non-squamous). The detection rate was 11.0% by NGS, 9.8% by Sanger and 11.3% by Idylla for the whole cohort (12.0% in non-squamous). The agreement between Idylla and Sanger was 93.2%. A targetable EGFR mutation was detected in 10.0% using tissue NGS alone, and in 16.0% using concurrent Idylla ctEGFR testing.

CONCLUSION

The frequency of EGFR mutations was as expected for a Caucasian population. The Idylla EGFR test performance is comparable to reference methods and with a shorter TAT. Adding a concurrent plasma Idylla test to tissue NGS testing increases the detection rate of EGFR mutations in NSCLC.

FACILITATE: A real-world, multicenter, prospective study investigating the utility of a rapid, fully automated real-time PCR assay versus local reference methods for detecting epidermal growth factor receptor variants in NSCLC

Accurate testing for epidermal growth factor receptor (EGFR) variants is essential for informing treatment decisions in non-small cell lung cancer (NSCLC). Automated diagnostic workflows may allow more streamlined initiation of targeted treatments, where appropriate, while comprehensive variant analysis is ongoing. FACILITATE, a real-world, prospective, multicenter, European study, evaluated performance and analytical turnaround time of the Idylla™ EGFR Mutation Test compared with local reference methods. Sixteen sites obtained formalin-fixed paraffin-embedded biopsy samples with ≥ 10% neoplastic cells from patients with NSCLC. Consecutive 5 μm sections from patient samples were tested for clinically relevant NSCLC-associated EGFR variants using the Idylla™ EGFR Mutation Test and local reference methods; performance (concordance) and analytical turnaround time were compared. Between January 2019 and November 2020, 1,474 parallel analyses were conducted. Overall percentage agreement was 97.7% [n = 1,418; 95% confidence interval (CI): 96.8-98.3], positive agreement, 87.4% (n = 182; 95% CI: 81.8-91.4) and negative agreement, 99.2% (n = 1,236; 95% CI: 98.5-99.6). There were 38 (2.6%) discordant cases. Ninety percent of results were returned with an analytical turnaround time of within 1 week using the Idylla™ EGFR Mutation Test versus ∼22 days using reference methods. The Idylla™ EGFR Mutation Test performed well versus local methods and had shorter analytical turnaround time. The Idylla™ EGFR Mutation Test can thus support application of personalized medicine in NSCLC.

Evaluation of a fully closed real time PCR platform for the detection of SARS-CoV-2 in nasopharyngeal swabs: a pilot study

AIMS

To date, reverse transcriptase PCR (RT-PCR) on nasopharyngeal swabs is the 'gold standard' approach for the diagnosis of COVID-19. The need to develop easy to use, rapid, robust and with minimal hands-on time approaches are warranted. In this setting, the Idylla SARS-CoV-2 Test may be a valuable option. The aim of our study is to evaluate the analytical and clinical performance of this assay on previously tested SARS-CoV-2 people by conventional RT-PCR based approach in different settings, including initial diagnosis and clinical follow-up.

METHODS

To evaluate the sensitivity and specificity of the Idylla SARS-CoV-2 Test, we retrieved 55 nasopharyngeal swabs, previously analysed by a fully validated assay, from symptomatic patients or from people who have been in close contact with COVID-19 positive cases. Discordant or high discrepant cases were further analysed by a third technique. In addition, a second subset of 14 nasopharyngeal swab samples with uncertain results (cycle threshold between 37 and 40), by using the fully validated assay, from patients with viral infection beyond day 21, were retrieved.

RESULTS

Overall, Idylla showed a sensitivity of 93.9% and a specificity of 100.0%. In addition, in the additional 14 nasopharyngeal swab samples, only five (35.7%) featured a positive result by the Idylla SARS-CoV-2 Test.

CONCLUSIONS

We demonstrated that the Idylla SARS-CoV-2 Test may represent a valid, fast, highly sensitive and specific RT-PCR test for the identification of SARS-CoV-2 infection.

Thyroid and COVID-19: a review on pathophysiological, clinical and organizational aspects

BACKGROUND

Thyroid dysfunction has been observed in patients with COVID-19, and endocrinologists are requested to understand this clinical issue. Pandemic-related restrictions and reorganization of healthcare services may affect thyroid disease management.

OBJECTIVE AND METHODS

To analyze and discuss the relationship between COVID-19 and thyroid diseases from several perspectives. PubMed/MEDLINE, Google Scholar, Scopus, ClinicalTrial.gov were searched for this purpose by using free text words and medical subject headings as follows: "sars cov 2", "covid 19", "subacute thyroiditis", "atypical thyroiditis", "chronic thyroiditis", "hashimoto's thyroiditis", "graves' disease", "thyroid nodule", "differentiated thyroid cancer", "medullary thyroid cancer", "methimazole", "levothyroxine", "multikinase inhibitor", "remdesivir", "tocilizumab". Data were collected, analyzed, and discussed to answer the following clinical questions: "What evidence suggests that COVID-19 may induce detrimental consequences on thyroid function?"; "Could previous or concomitant thyroid diseases deteriorate the prognosis of COVID-19 once the infection has occurred?"; "Could medical management of thyroid diseases influence the clinical course of COVID-19?"; "Does medical management of COVID-19 interfere with thyroid function?"; "Are there defined strategies to better manage endocrine diseases despite restrictive measures and in-hospital and ambulatory activities reorganizations?".

RESULTS

SARS-CoV-2 may induce thyroid dysfunction that is usually reversible, including subclinical and atypical thyroiditis. Patients with baseline thyroid diseases are not at higher risk of contracting or transmitting SARS-CoV-2, and baseline thyroid dysfunction does not foster a worse progression of COVID-19. However, it is unclear whether low levels of free triiodothyronine, observed in seriously ill patients with COVID-19, may worsen the disease's clinical progression and, consequently, if triiodothyronine supplementation could be a tool for reducing this burden. Glucocorticoids and heparin may affect thyroid hormone secretion and measurement, respectively, leading to possible misdiagnosis of thyroid dysfunction in severe cases of COVID-19. High-risk thyroid nodules require a fine-needle aspiration without relevant delay, whereas other non-urgent diagnostic procedures and therapeutic interventions should be postponed.

DISCUSSION

Currently, we know that SARS-CoV-2 could lead to short-term and reversible thyroid dysfunction, but thyroid diseases seem not to affect the progression of COVID-19. Adequate management of patients with thyroid diseases remains essential during the pandemic, but it could be compromised because of healthcare service restrictions. Endocrine care centers should continuously recognize and classify priority cases for in-person visits and therapeutic procedures. Telemedicine may be a useful tool for managing patients not requiring in-person visits.

EGFR Status Assessment for Better Care of Early Stage Non-Small Cell Lung Carcinoma: What Is Changing in the Daily Practice of Pathologists?

The recent emergence of novel neoadjuvant and/or adjuvant therapies for early stage (I-IIIA) non-small cell lung carcinoma (NSCLC), mainly tyrosine kinase inhibitors (TKIs) targeting EGFR mutations and immunotherapy or chemo-immunotherapy, has suddenly required the evaluation of biomarkers predictive of the efficacy of different treatments in these patients. Currently, the choice of one or another of these treatments mainly depends on the results of immunohistochemistry for PD-L1 and of the status of EGFR and ALK. This new development has led to the setup of different analyses for clinical and molecular pathology laboratories, which have had to rapidly integrate a number of new challenges into daily practice and to establish new organization for decision making. This review outlines the impact of the management of biological samples in laboratories and discusses perspectives for pathologists within the framework of EGFR TKIs in early stage NSCLC.

Impact of the COVID-19 pandemic and related control measures on cancer diagnosis in Catalonia: a time-series analysis of primary care electronic health records covering about five million people

OBJECTIVE

Cancer care has been disrupted by the response of health systems to the COVID-19 pandemic, especially during lockdowns. The objective of our study is to evaluate the impact of the pandemic on the incidence of cancer diagnoses in primary care.

DESIGN

Time-series study of malignant neoplasms and diagnostic procedures, using data from the primary care electronic health records from January 2014 to September 2020.

SETTING

Primary care, Catalonia, Spain.

PARTICIPANTS

People older than 14 years and assigned in one of the primary care practices of the Catalan Institute of Health with a new diagnosis of malignant neoplasm.

MAIN OUTCOME MEASURES

We obtained the monthly expected incidence of malignant neoplasms using a temporary regression, where the response variable was the incidence of cancer from 2014 to 2018 and the adjustment variables were the trend and seasonality of the time series. Excess or lack of malignant neoplasms was defined as the number of observed minus expected cases, globally and stratified by sex, age, type of cancer and socioeconomic status.

RESULTS

Between March and September 2020 we observed 8766 (95% CI 4135 to 13 397) fewer malignant neoplasm diagnoses, representing a reduction of 34% (95% CI 19.5% to 44.1%) compared with the expected. This underdiagnosis was greater in individuals aged older than 64 years, men and in some types of cancers (skin, colorectal, prostate). Although the reduction was predominantly focused during the lockdown, expected figures have not yet been reached (40.5% reduction during the lockdown and 24.3% reduction after that).

CONCLUSIONS

Reduction in cancer incidence has been observed during and after the lockdown. Urgent policy interventions are necessary to mitigate the indirect effects of the COVID-19 pandemic and related control measures on other diseases and some strategies must be designed in order to reduce the underdiagnosis of cancer.

Cytopathology Practice in the COVID-19 Era: Focus on Sample Workload

Since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak was declared a pandemic, the magnitude of coronavirus disease 2019 (COVID-19) has continued to grow, putting an unprecedented strain on all medical fields. Its effects on cytopathology workloads have been dramatic. Indeed, despite the implementation of several laboratory biosafety recommendations, cytological screening activities and cytological sampling of patients at low risk of malignancy have been postponed to limit the risk of contagion and to lessen the strain on overwhelmed hospital facilities. In this scenario, a drastic reduction in the total number of cytological specimens has been observed worldwide. This review summarizes the current evidence of the impact of the COVID-19 pandemic on cytopathology practice by focusing on its impact on cytological sample workload.

Cytopathology practice during the COVID-19 postlockdown: An Italian experience

Background

During the current coronavirus disease 2019 (COVID‐19) pandemic, the cytopathology workload has decreased remarkably worldwide as all screening and elective procedures have been postponed to prioritize the clinical management of patients at high oncological risk. In the current study, the authors provide data on the lasting impact of COVID‐19 on cytopathology practice during the initial phases of the Italian postlockdown period.

Methods

The percentages of the cytological sample types processed at the University of Naples Federico II during the first 12 weeks of the Italian postlockdown period were compared with those of the same period in 2019. The study period was divided into four 3‐week periods. Differences in the rates of malignant diagnoses were also assessed.

Results

During the 12‐week study period, the overall cytological sample workload decreased by 41.6% in comparison with 2019. In particular, the workload significantly declined for each sample type: Pap smears, –33.3%; urine, –42.8%; serous fluids, –14.4%; thyroid, –54.5%; breast, –43%; lymph node, –27.3%; and salivary gland, –61%. By contrast, the overall malignancy rate was significantly increased (P = .0011).

Conclusions

The reduction in the cytological sample workload during the postlockdown period still represents an ongoing effect of the COVID‐19 pandemic. On the other hand, the rise in the overall malignancy rate reflects the importance of prioritizing diagnostic procedures for patients at high oncological risk.

The reduction in the cytological sample workload during the postlockdown period represents an ongoing effect of the COVID‐19 pandemic. On the other hand, the rise in the overall malignancy rate reflects the importance of prioritizing diagnostic procedures for patients at high oncological risk.

The Immunopathological and Histological Landscape of COVID-19-Mediated Lung Injury

A complete understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) physiopathology and related histopathologic lesions is necessary to improve treatment and outcome of coronavirus disease 2019 (COVID-19) patients. Many studies have focused on autopsy findings in COVID-19-related deaths to try and define any possible specific pattern. Histopathologic alterations are principally found within lungs and blood vessels, and these abnormalities also seem to have the highest clinical impact. Nevertheless, many of the morphological data collected so far are non-specific, fickle, and possibly associated with other co-existing factors. The aim of this minireview is to describe the main histopathological features related to COVID-19 and the mechanism known as "cytokine storm".

[Management of samples in pathology laboratories and biobanks during the Covid-19 pandemic]

La pandémie liée à la Covid-19 a brutalement bouleversé le fonctionnement des hôpitaux, en particulier les activités des services cliniques et des laboratoires de biologie, notamment de virologie. Cette pandémie a eu aussi une répercussion soudaine sur la prise en charge des échantillons tissulaires et cellulaires par les laboratoires de pathologie. Les conséquences ont été l’optimisation de mesures sanitaires au sein de ces laboratoires, mais aussi selon les institutions, une forte diminution dans différents secteurs d’activité de la pathologie clinique et moléculaire. Ainsi, les pathologistes ont dû s’adapter très rapidement à de nouvelles contraintes sanitaires, et organiser les laboratoires selon des recommandations internationales, afin de maintenir l’offre de soins aux patients hospitalisés, en particulier ceux atteints d’un cancer. Cette revue aborde les principales conséquences de la pandémie liée à la Covid-19 au niveau des laboratoires de pathologie et les mesures prises par ces laboratoires pour assurer leur fonctionnement durant cette période.

Exploring the real-world effect of the SARS-CoV-2 pandemic on the molecular diagnostics for cancer patients and high-risk individuals

Background: The SARS-CoV-2 pandemic introduced a global distraction effect in cancer patients' care. The aim of this study was to explore the effect of the pandemic on the largest molecular diagnostics center for cancer patients and high-risk individuals in Serbia.Research design and methods: EGFR, KRAS/NRAS, BRAF, and BRCA1/2 mutation testing were performed by qPCR and NGS. NGS was used for panel testing of hereditary breast/ovarian cancer and cancers associated with Lynch syndrome. The analytical output during the state of emergency (SoE) was compared to the period before and after the outbreak using one-way ANOVA. Statistical significance was set at p < 0.05.Results: A 38% reduction in the number of analysis was detected during the SoE. After the SoE, a 19% reduction was noted compared to SoE and 50% compared to the period before the SoE (p = 0.038). Three of the 48 scheduled appointments for pretest genetic counseling were carried out during the SoE, but the number of NGS tests increased by 50%.Conclusions: The SARS-CoV-2 pandemic had a profound negative effect on the diagnostic output of our centralized molecular diagnostics center. The only positive effect was shortening of waiting lists for hereditary cancer patients and high-risk individuals.

BRCA testing delay during the COVID-19 pandemic: How to act?

Recently, our lab, part of a referral center in Italy, reported its experience regarding the execution of germline BRCA1/2 (gBRCA) testing during the first months of the coronavirus disease-2019 (COVID-19) pandemic, which highlights a substantial reduction (about 60%) compared with the first 2 months of the current year. This evidence appeared to be a lockdown effect due to extraordinary restriction measures to slow down the spread of SARS-CoV-2. In this study, we aimed to evaluate the overall effects of the ongoing pandemic on gBRCA testing in our institution and to understand how COVID-19 has influenced testing after the complete lockdown (March 8-May 5, 2020). Additionally, we compared this year's trend with trends of the last 3 years to better monitor gBRCA testing progress. This detailed analysis highlights two important findings: (1) gBRCA testing did not increase significantly after the lockdown period (May-October 2020) compared with the lockdown period (March-April 2020), emphasizing that even after the lockdown period testing remained low. (2) Comparing the total tests per year (January-October 2017, 2018, 2019, with 2020), the impact of COVID-19 on gBRCA testing is apparent, with similarities of trends registered in 2017. These evidences reveal a gBRCA testing delay for cancer patients and healthy patients at this moment, and the new era of gBRCA testing in the management of ovarian, breast, pancreas and prostate cancer patients has been seriously questioned due to the COVID-19 pandemic. As consequence, we underline that measures to guarantee oncogenetic testing (e.g., gBRCA testing) along with new diagnostic/clinic strategies are mandatory. For these reasons, several proposals are presented in this study.

Juggling the COVID-19 pandemic: A cytopathology point of view

Since its first identification in China at the end of 2019, severe acute respiratory syndrome coronavirus 2 has rapidly spread all over the world, becoming an international healthcare emergency. In the era of coronavirus disease-2019 (COVID-19), several aspects of normal life, including those related to the medical activities, have been radically changed. Extraordinary measures have been adopted by different nations to cope with the rapid diffusion of COVID-19 all over the world. In hospitals, careful attention has been paid to manage infected patients with a possible detrimental effect for patients affected by other diseases. As with other medical fields, cytopathology laboratories have also drastically modified their activities to cope with the COVID-19 healthcare emergency. Here, the main effects of COVID-19 pandemic on the routine practice of cytopathology are summarised, focusing on the prioritisation policy adopted by cytopathologists worldwide.

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.

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Biosafety measures used in the first wave of the COVID-19 crisis were heterogeneous in 53 European pathology laboratories.

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A dramatic decrease of the workload in pathology laboratories was noted.

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No case of healthcare workers contaminated with SARS-CoV-2 associated with samples handling was identified.

A narrative review of lung cancer cytology in the times of coronavirus: what physicians should know

In the modern era of personalized and precision medicine, lung cancer management needs to be carried out in a multidisciplinary manner. Among other disciplines, also cytopathology is key in diagnosis and treatment management of these patients. Indeed, cytopathology specimens are often the only source of available tissue material for morphological diagnosis and molecular purposes in order to guarantee an adequate treatment decision making, since surgical resection specimens are not available when lung cancer is diagnosed at advanced disease stages. Today, as an effect of the current severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) pandemic, cytopathology is reorganizing and reshaping many of its procedures and workflows, in order to ensure the safety of cytopathologists and laboratory personnel. In particular, careful attention should be paid on biosafety procedures when pulmonary cytological specimens are handled. In addition, also molecular cytopathology, that provides relevant information on the molecular status and on the potential sensitivity to target treatments, is undergoing major changes. In this setting, fully automated technologies, requiring minimal hands-on work, may be a valid option. The aim of this narrative review is to keep updated all the different professional figures involved in lung cancer management and treatment on how SARS-CoV-2 is modifying lung cancer cytopathology.

How the COVID-19 Pandemic Impacted Oncological Molecular Diagnosis: A Picture from a National Reference Center for Molecular Pathology

Introduction

The Portuguese healthcare system had to adapt at short notice to the COVID-19 pandemic. We implemented workflow changes to our molecular pathology laboratory, a national reference center, to maximize safety and productivity. We assess the impact this situation had on our caseload and what conclusions can be drawn about the wider impact of the pandemic in oncological therapy in Portugal. Material and Methods. We reviewed our database for all oncological molecular tests requested between March and April of 2019 and 2020. For each case, we recorded age, sex, region of the country, requesting institution, sample type, testing method, and turnaround time (TAT). A comparison between years was made.

Results

The total number of tests decreased from 421 in 2019 to 319 in 2020 (p = 0.0027). The greatest reduction was in clinical trial-related cases. Routine cases were similar between years (267 vs. 256). TAT was higher in 2019 (mean 15 days vs. 12.3 days; p = 0.0003). Medium- to large-sized public hospitals in the north of the country were mostly responsible for the reduction in cases (p = 0.0153).

Conclusions

Case reduction was observed at hospitals that have mostly been involved in the treatment of COVID-19 and in the north of the country, the region worst-hit by the pandemic. Similar to other studies, our TAT decreased, even with a similar number of routine cases. Thus, we conclude that it is possible to successfully adapt the workflow of a molecular pathology laboratory to new safety standards without losing efficiency.