BRCA testing in a genomic diagnostics referral center during the COVID-19 pandemic

Unexpected finding of a rare pathogenic germline BRCA1 variant in an intrahepatic cholangiocarcinoma using the Oncomine Focus DNA assay: clinical and diagnostic implications

BACKGROUND

Cholangiocarcinoma (CCA) is a malignant tumor arising from the epithelial cells of the bile ducts and is the second most common liver cancer after hepatocellular carcinoma. Recently, our Institution launched a Comprehensive Genomic Profiling (CGP) program (named FPG500 program), set up to provide a complete molecular characterization through the TruSight Oncology 500 High Throughput (TSO500HT) solution and samples that do not reach pre-set sample quantity and/or quality thresholds required for TSO500HT, are addressed to Oncomine Focus DNA Assay (OFA) and the Archer's FusionPlex Lung Panel (AFL).

METHODS AND RESULTS

Here we report the case of a patient with iCCA enrolled in the FPG500 program and screened by the orthogonal workflow (OFA/AFL). Although BRCA1 is not among the genes declared in the OFA panel, we unexpectedly detected a pathogenic variant in this gene (c.5278-2del, rs878853285).

CONCLUSIONS

This case highlights the diagnostic capabilities of CGP, now widely used in both clinical practice and academic setting. The incidental involvement of BRCA1 focuses attention on the role of BRCA genes in biliary tract cancers. Finally, as an orthogonal test confirmed the germline origin of BRCA1 c.5278-2del variant, the germline implications of CGP need to be considered.

Changes in the quality of cancer care as assessed through performance indicators during the first wave of the COVID-19 pandemic in 2020: a scoping review

BACKGROUND

Cancer comprises a high burden on health systems. Performance indicators monitoring cancer outcomes are routinely used in OECD countries. However, the development of process and cancer-pathway based information is essential to guide health care delivery, allowing for better monitoring of changes in the quality of care provided. Assessing the changes in the quality of cancer care during the COVID-19 pandemic requires a structured approach considering the high volume of publications. This study aims to summarize performance indicators used in the literature to evaluate the impact of the COVID-19 pandemic on cancer care (January-June 2020) in OECD countries and to assess changes in the quality of care as reported via selected indicators.

METHODS

Search conducted in MEDLINE and Embase databases. Performance indicators and their trends were collated according to the cancer care pathway.

RESULTS

This study included 135 articles, from which 1013 indicators were retrieved. Indicators assessing the diagnostic process showed a decreasing trend: from 33 indicators reporting on screening, 30 (91%) signalled a decrease during the pandemic (n = 30 indicators, 91%). A reduction was also observed in the number of diagnostic procedures (n = 64, 58%) and diagnoses (n = 130, 89%). The proportion of diagnoses in the emergency setting and waiting times showed increasing trends (n = 8, 89% and n = 14, 56%, respectively). A decreasing trend in the proportion of earliest stage cancers was reported by 63% of indicators (n = 9), and 70% (n = 43) of indicators showed an increasing trend in the proportion of advanced-stage cancers. Indicators reflecting the treatment process signalled a reduction in the number of procedures: 79%(n = 82) of indicators concerning surgeries, 72%(n = 41) of indicators assessing radiotherapy, and 93%(n = 40) of indicators related to systemic therapies. Modifications in cancer treatment were frequently reported: 64%(n = 195) of indicators revealed changes in treatment.

CONCLUSIONS

This study provides a summary of performance indicators used in the literature to assess the cancer care pathway from January 2020 to June 2020 in OECD countries, and the changes in the quality of care signalled by these indicators. The trends reported inform on potential bottlenecks of the cancer care pathway. Monitoring this information closely could contribute to identifying moments for intervention during crises.

COVID-19 GPH: tracking the contribution of genomics and precision health to the COVID-19 pandemic response

The scientific response to the COVID-19 pandemic has produced an abundance of publications, including peer-reviewed articles and preprints, across a wide array of disciplines, from microbiology to medicine and social sciences. Genomics and precision health (GPH) technologies have had a particularly prominent role in medical and public health investigations and response; however, these domains are not simply defined and it is difficult to search for relevant information using traditional strategies. To quantify and track the ongoing contributions of GPH to the COVID-19 response, the Office of Genomics and Precision Public Health at the Centers for Disease Control and Prevention created the COVID-19 Genomics and Precision Health database (COVID-19 GPH), an open access knowledge management system and publications database that is continuously updated through machine learning and manual curation. As of February 11, 2022, COVID-GPH contained 31,597 articles, mostly on pathogen and human genomics (72%). The database also includes articles describing applications of machine learning and artificial intelligence to the investigation and control of COVID-19 (28%). COVID-GPH represents about 10% (22983/221241) of the literature on COVID-19 on PubMed. This unique knowledge management database makes it easier to explore, describe, and track how the pandemic response is accelerating the applications of genomics and precision health technologies. COVID-19 GPH can be freely accessed via https://phgkb.cdc.gov/PHGKB/coVInfoStartPage.action.

The Impact of the SARS-CoV-2 Pandemic on Healthcare Provision in Italy to non-COVID Patients: a Systematic Review

BACKGROUND

Italy has been one of the countries most affected by the SARS-CoV-2 pandemic, and the regional healthcare system has had to quickly adapt its organization to meet the needs of infected patients. This has led to a drastic change in the routine management of non-communicable diseases with a potential long-term impact on patient health care. Therefore, we investigated the management of non-COVID-19 patients across all medical specialities in Italy.

METHODS

A PRISMA guideline-based systematic review of the literature was performed using PubMed, Embase, and Scopus, restricting the search to the main outbreak period in Italy (from February 20 to June 25 2020). We selected articles in English or Italian that detailed changes in the Italian hospital care for non-COVID-19 patients due to the pandemic. Our keywords included all medical specialities combined with our geographical focus (Italy) and COVID-19.

RESULTS

Of the 4643 potentially eligible studies identified by the search, 247 were included. A decrease in the management of emergencies in non-COVID patients was found together with an increase in mortality. Similarly, non-deferrable conditions met a tendency toward decreased diagnosis. All specialities have been affected by the re-organization of healthcare provision in the hub-and-spoke system and have benefited from telemedicine.

CONCLUSIONS

Our work highlights the changes in the Italian public healthcare system to tackle the developing health crisis due to the COVID-19 pandemic. The findings of our review may be useful to analyse future directions for the healthcare system in the case of new pandemic scenarios.

Special aspects of medical care for cancer patients during COVID-19 pandemic

The biggest challenge for the World Health Organization today is the fight against the COVID-19 pandemic. The current situation prompted major adjustments in the system of cancer care. In this review, we investigate the aspects of cancer treatment and care during the pandemic, since in this setting oncological services face challenges in determining the feasibility of anticancer treatments while minimizing the risk of infection. Cancer patients are at a higher risk from COVID-19 disease. Therefore, oncological community is discussing on the priorities for providing cancer therapies and care and at the same time minimizing the risk of infection.

Impact of the COVID-19 Pandemic on the Appropriateness of Diagnostic Pathways of Autoimmune Rheumatic Diseases

OBJECTIVE

Early diagnosis of autoimmune rheumatic diseases (ARDs) is key to achieving effective treatment and improving prognosis. The coronavirus disease 2019 (COVID-19) pandemic has led to major changes in clinical practice on a global scale. We aimed to evaluate the impact of the COVID-19 pandemic on rheumatological clinical practice and autoimmunity testing demands.

METHODS

Data regarding the first rheumatological visits and new diagnoses, together with the autoimmunity laboratory testing volumes related to the COVID-19 pandemic phase (January-December 2020), were collected from medical records and the laboratory information system of a regional reference hospital (Basilicata, Italy) and compared with those obtained during the corresponding period in 2019.

RESULTS

A significant decrease in the 2020 autoimmunity laboratory test volume was found when compared with the same period in 2019 (9912 vs 14,100; P < 0.05). A significant decrease in first rheumatological visits and diagnosis (1272 vs 2336; P < 0.05) was also observed. However, an equivalent or higher percentage of positive autoimmunity results from outpatient services was recorded during 2020 when compared to the prepandemic state. Of note, COVID-19-associated decline in new diagnoses affected mainly less severe diseases. In contrast, ARDs with systemic involvement were diagnosed at the same levels as in the prepandemic period.

CONCLUSION

The COVID-19 pandemic has affected access to health services. However, our study highlighted that during the outbreak, greater appropriateness of the requests for laboratory tests and visits emerged, as shown by a greater percentage of positive test results and new diagnoses of more severe ARDs compared to the prepandemic period.

Tumor BRCA testing in ovarian cancer and EQA scheme: our experience of a critical evaluation

Next generation sequencing (NGS) is a widespread molecular biology method integrated into clinical practice to detect genetic variants, for diagnostic and prognostic purposes. The scheduled external quality assessments (EQA) is integral part of clinical molecular laboratory quality assurance. The EQA provides an efficient system to compare analytic test performances among different laboratories, which is essential to evaluate consistency of molecular test. EQA failures demands targeted corrective action plans. In this context, the complexity of the NGS techniques requires careful and continuous quality control procedures. We report a tumor BRCA1/2 (tBRCA) testing benchmark discrepancy provided by the European Molecular Genetics Quality Network in our laboratory during a round of EQA for somatic mutation testing of BRCA genes in relation to ovarian cancer. The critical analysis emerging from the tBRCA EQA is presented. We underline that harmonization processes are still required for the EQA in the molecular biology field, especially if applied to the evaluation of methods characterized by high complexity.

Recent advances in detection technologies for COVID-19

Corona Virus Disease 2019 (COVID-19) is a highly infectious respiratory illness that was caused by the SARS-CoV-2. It spread around the world in just a few months and became a worldwide pandemic. Quick and accurate diagnosis of infected patients is very important for controlling transmission. In addition to the commonly used Real-time reverse-transcription polymerase chain reaction (RT-PCR) detection techniques, other diagnostic techniques are also emerging endlessly. This article reviews the current diagnostic methods for COVID-19 and discusses their advantages and disadvantages. It provides an important reference for the diagnosis of COVID-19.

Delays and Disruptions in Cancer Health Care Due to COVID-19 Pandemic: Systematic Review

PURPOSE

There has been noteworthy concern about the impact of COVID-19 pandemic on health services including the management of cancer. In addition to being considered at higher risk for worse outcomes from COVID-19, people with cancer may also experience disruptions or delays in health services. This systematic review aimed to identify the delays and disruptions to cancer services globally.

METHODS

This is a systematic review with a comprehensive search including specific and general databases. We considered any observational longitudinal and cross-sectional study design. The selection, data extraction, and methodological assessment were performed by two independent reviewers. The methodological quality of the studies was assessed by specific tools. The delays and disruptions identified were categorized, and their frequency was presented.

RESULTS

Among the 62 studies identified, none exhibited high methodological quality. The most frequent determinants for disruptions were provider- or system-related, mainly because of the reduction in service availability. The studies identified 38 different categories of delays and disruptions with impact on treatment, diagnosis, or general health service. Delays or disruptions most investigated included reduction in routine activity of cancer services and number of cancer surgeries; delay in radiotherapy; and delay, reschedule, or cancellation of outpatient visits. Interruptions and disruptions largely affected facilities (up to 77.5%), supply chain (up to 79%), and personnel availability (up to 60%).

CONCLUSION

The remarkable frequency of delays and disruptions in health care mostly related to the reduction of the COVID-19 burden unintentionally posed a major risk on cancer care worldwide. Strategies can be proposed not only to mitigate the main delays and disruptions but also to standardize their measurement and reporting. As a high number of publications continuously are being published, it is critical to harmonize the upcoming reports and constantly update this review.

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.

Droplet digital PCR for large genomic rearrangements detection: A promising strategy in tissue BRCA1 testing

BACKGROUND AND AIMS

With the introduction of Olaparib as target therapy for High Grade Serous Ovarian Cancer (HGSOC) patients with germline and somatic BRCA1/2 mutations, the genetic test performed on tumor tissue has become important like the germline test. In somatic testing the evaluation of Large Genomic Rearrangements (LGRs) represents the main challenge. We describe a droplet digital PCR (ddPCR) assay for the evaluation of target BRCA1 LGRs on blood and formalin-fixed paraffin-embedded (FFPE)/Fresh Frozen Tissue (FFT) samples.

MATERIALS AND METHODS

We analyzed blood, FFPE and FFT samples in a validation setting of n = 78 HGSOC patients. We applied the ddPCR to BRCA1 exons 2, 20 and 21 as some of the most common BRCA1 exons involved in LGRs in our cohort of patients.

RESULTS

The ddPCR custom assays allowed the identification of LGRs in all sample types, including FFPE specimens. Moreover, we were able to clearly detect LGRs accounted as somatic event.

CONCLUSION

The introduction of ddPCR in a comprehensive workflow, encompassing both germline and somatic tests, represents an improvement in BRCA1/2 testing. ddPCR can overcome challenges related to BRCA testing, especially on FFPE analysis. Finally, ddPCR represents a promising alternative strategy to the established standard methods currently used in clinical setting.

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.

Challenges and issues surrounding the use for translational research of human samples obtained during the COVID-19 pandemic from lung cancer patients

In only a few weeks after the eruption of the pandemic caused by syndrome coronavirus 2 (SARS-CoV-2), the number of associated research projects worldwide increased dramatically. The continual and almost daily improvement in the information associated with this viral infection has been spectacular, notably in the areas of epidemiology, pathophysiology and therapy. This knowledge but also the many uncertainties concerning coronavirus disease 2019 (COVID-19), in particular with respect to the level of contagiousness of different samples sent to pathology and biology laboratories, rapidly effected the collection for translational research projects, notably of samples from patients with thoracic cancers. However, it is still difficult to evaluate the current and the near impact of the COVID-19 pandemic on this domain. It is essential in this context to be reminded of good practice for the management of biological samples for research, notably concerning the biosafety and security procedures. Moreover, new recommendations concerning the traceability and use of human lung cancer samples from tissue and different biofluids may rapidly be issued in the near future. This review aims to discuss the new challenges and constraints encountered by pathologists, biobankers and researchers within the framework of collection and the use of samples from patients with lung cancer for research while taking into account the COVID-19 pandemic.

Impact of COVID-19 on cancer diagnosis and management in Slovenia - preliminary results

Background The COVID-19 pandemic has disrupted the provision and use of healthcare services throughout the world. In Slovenia, an epidemic was officially declared between mid-March and mid-May 2020. Although all non-essential health care services were put on hold by government decree, oncological services were listed as an exception. Nevertheless, as cancer control depends also on other health services and additionally major changes in people's behaviour likely occurred, we aimed to analyse whether cancer diagnosis and management were affected during the COVID-19 epidemic in Slovenia. Methods We analysed routine data for the period November 2019 through May 2020 from three sources: (1) from the Slovenian Cancer Registry we analysed data on pathohistological and clinical practice cancer notifications from two major cancer centres in Ljubljana and Maribor; (2) from the e-referral system we analysed data on all referrals in Slovenia issued for oncological services, stratified by type of referral; and (3) from the administrative data of the Institute of Oncology Ljubljana we analysed data on outpatient visits by type as well as on diagnostic imaging performed. Results Compared to the November 2019 - February 2020 average, the decrease in April 2020 was about 43% and 29% for pathohistological and clinical cancer notifications; 33%, 46% and 85% for first, control and genetic counselling referrals; 19% (53%), 43% (72%) and 20% (21%) for first (and control) outpatient visits at the radiotherapy, surgery and medical oncology sectors at the Institute of Oncology Ljubljana, and 48%, 76%, and 42% for X-rays, mammograms and ultrasounds performed at the Institute, respectively. The number of CT and MRI scans performed was not affected. Conclusions Significant drops in first referrals for oncological services, first visits and imaging studies performed at the Institute, as well as cancer notifications in April 2020 point to a possibility of a delayed cancer diagnosis for some patients during the first surge of SARS-CoV-2 cases in Slovenia. The reasons for the delay cannot be ascertained with certainty and could be linked to health-seeking behaviour of the patients, the beliefs and practices of doctors and/ or the health system management during the epidemic. Drops in control referrals and control visits were expected and are most likely due to the Institute of Oncology Ljubljana postponing non-essential follow-ups through May 2020.

The Impact of the COVID-19 Pandemic and the Associated Belgian Governmental Measures on Cancer Screening, Surgical Pathology and Cytopathology

Introduction

The severe acute respiratory syndrome coronavirus 2 caused a pandemic of coronavirus disease 2019 (COVID-19). Unprecedented public health actions were introduced, including social distancing, travel restrictions and quarantine. The Belgian government announced a national emergency plan, thereby postponing all non-urgent medical consultations and operations. This report analyses the impact of these measures on cancer screening, through assessment of the workload of a laboratory for histopathology and cytopathology.

Methods

Data on monthly numbers of histological and cytological samples, immunohistochemistry and molecular tests were extracted from the laboratory information management system.

Results

The global histopathological and cytological workload was substantially reduced. The impact on oncology-related surgical procedures was rather limited. The anti-COVID-19 measures significantly diminished all screening-related samples, such as colon biopsies, breast biopsies and cervical cytology, and strongly reduced the number of samples related to “functional” pathology, such as thyroidectomies and gastric biopsies.

Conclusions

Since many health care interventions are reflected in the workload of a pathology laboratory, this study enabled us to identify areas for “deconfinement” health care actions. Our findings indicate that various areas in medicine were affected, but the impact seemed largest for cancer screening. Health care professionals should assure that consultations related to cancer screening are postponed instead of cancelled.