NTRK fusions in solid tumours: what every pathologist needs to know.

Fusions involving the Neurotrophic tropomyosin receptor kinase (NTRK) gene family (NTRK1, NTRK2 and NTRK3) are targetable oncogenic alterations that are found in a diverse range of tumours. There is an increasing demand to identify tumours which harbour these fusions to enable treatment with selective tyrosine kinase inhibitors such as larotrectinib and entrectinib. NTRK fusions occur in a wide range of tumours including rare tumours such as infantile fibrosarcoma and secretory carcinomas of the salivary gland and breast, as well as at low frequencies in more common tumours including melanoma, colorectal, thyroid and lung carcinomas. Identifying NTRK fusions is a challenging task given the different genetic mechanisms underlying NTRK fusions, their varying frequency across different tumour types, complicated by other factors such as tissue availability, optimal detection methods, accessibility and costs of testing methods. Pathologists play a key role in navigating through these complexities by determining optimal approaches to NTRK testing which has important therapeutic and prognostic implications. This review provides an overview of tumours harbouring NTRK fusions, the importance of identifying these fusions, available testing methods including advantages and limitations, and generalised and tumour-specific approaches to testing.

ROS1 rearrangements in lung adenocarcinomas are defined by diffuse strong immunohistochemical expression of ROS1.

A small subset of lung adenocarcinomas harbour ROS1 gene arrangements and are amenable to tyrosine kinase inhibitor therapy. Current practice in Australia involves screening for ROS1 rearrangements in adenocarcinomas using ROS1 immunohistochemistry (IHC) followed by confirmatory molecular testing such as fluorescence in situ hybridisation (FISH), if other known genetic driver alterations are absent. The best threshold to determine ROS1 IHC positivity is not well defined, however, and this study aims to determine the optimal threshold for ROS1 IHC screening to identify ROS1-rearranged lung adenocarcinomas. A total of 177 lung adenocarcinomas tested for a ROS1 rearrangement by FISH at our institution between 2017 and 2020 due to presence of ROS1 IHC staining were included in the study. ROS1 IHC staining was assessed by scoring the staining intensity (0, 1, 2, or 3+) and multiplying by the percentage of positive cells to generate an H-score. IHC H-scores were compared with FISH. Of 177 cases, 32 (18%) were ROS1 FISH-positive and 145 (82%) were negative. FISH-positive cases had a median H-score of 300 (range 200-300; mean 290.3) and negative cases had a median H-score of 40 (range 0-300; mean 63). All FISH-positive cases showed strong and diffuse IHC positivity. Using a threshold H-score of 200, the sensitivity of identifying ROS1 rearrangements was 100% and the specificity was 95% amongst cases referred with ROS1 IHC positivity. Adenocarcinomas with a FISH-confirmed ROS1 rearrangement demonstrate diffuse, strong (2-3+) IHC staining. Cases with weak, patchy ROS1 IHC staining are not associated with ROS1 rearrangements and in these cases FISH testing is of little to no utility.

Standardized phenology monitoring methods to track plant and animal activity for science and resource management applications.

Phenology offers critical insights into the responses of species to climate change; shifts in species' phenologies can result in disruptions to the ecosystem processes and services upon which human livelihood depends. To better detect such shifts, scientists need long-term phenological records covering many taxa and across a broad geographic distribution. To date, phenological observation efforts across the USA have been geographically limited and have used different methods, making comparisons across sites and species difficult. To facilitate coordinated cross-site, cross-species, and geographically extensive phenological monitoring across the nation, the USA National Phenology Network has developed in situ monitoring protocols standardized across taxonomic groups and ecosystem types for terrestrial, freshwater, and marine plant and animal taxa. The protocols include elements that allow enhanced detection and description of phenological responses, including assessment of phenological "status", or the ability to track presence-absence of a particular phenophase, as well as standards for documenting the degree to which phenological activity is expressed in terms of intensity or abundance. Data collected by this method can be integrated with historical phenology data sets, enabling the development of databases for spatial and temporal assessment of changes in status and trends of disparate organisms. To build a common, spatially, and temporally extensive multi-taxa phenological data set available for a variety of research and science applications, we encourage scientists, resources managers, and others conducting ecological monitoring or research to consider utilization of these standardized protocols for tracking the seasonal activity of plants and animals.

Blood transfusion practice in a rural hospital in Northern Ghana, Damongo, West Gonja District.

BACKGROUND: Blood transfusion in rural sub-Saharan Africa presents special challenges. Transfusions are primarily given for emergencies--life-threatening blood loss or anemia; blood is usually collected from family or replacement donors; and facilities to store an adequate reserve in a hospital bank are constrained. We report the everyday and organizational practices in a medium-sized district hospital in Northern Ghana. STUDY DESIGN AND METHODS: Information and data on blood transfusion practices at West Gonja Hospital, Damongo, were available from the laboratory reports, from day books and workbooks, and from direct observation in the following four areas: blood collection and blood donors; blood donation testing; blood storage and logistics; and clinical transfusion practice, adverse events, and follow-up. RESULTS: The hospital serves a rural community of 86,000. In 2009, a total of 719 units of whole blood were collected, a rate of 8.36 units per 1000 population. All donors were family or replacement donors. Positivity rates for infectious disease markers were 7.5% (64/853) for hepatitis B surface antigen, 6.1% (50/819) for hepatitis C virus, 3.9% (33/846) for human immunodeficiency virus, and 4.7% (22/468) for syphilis. Supply of laboratory materials was sometimes problematic, especially for temperature-critical materials. Difficulties in sample labeling, storage of blood and laboratory supplies, and disposal of waste were also incurred by operational, material, and financial constraints. Follow-up for outcomes of transfusion is not currently feasible. CONCLUSIONS: The operational, demographic, and financial environment pertaining in a rural hospital in Northern Ghana differs substantially from that in which much of current blood transfusion practice and technology evolved. Considerable effort and innovation will be needed to address successfully the challenges posed.