Clinical-grade computational pathology using weakly supervised deep learning on whole slide images

The development of decision support systems for pathology and their deployment in clinical practice have been hindered by the need for large manually annotated datasets.
To overcome this problem, the authors present a multiple instance learning-based deep learning system that uses only the reported diagnoses as labels for training, thereby avoiding expensive and time-consuming pixel-wise manual annotations. We evaluated this framework at scale on a dataset of 44,732 whole slide images from 15,187 patients without any form of data curation. Tests on prostate cancer, basal cell carcinoma and breast cancer metastases to axillary lymph nodes resulted in areas under the curve above 0.98 for all cancer types. Its clinical application would allow pathologists to exclude 65-75% of slides while retaining 100% sensitivity. The results show that this system has the ability to train accurate classification models at unprecedented scale, laying the foundation for the deployment of computational decision support systems in clinical practice.
NCBIwww.ncbi.nlm.nih.gov/pubmed/31308507

Renal disease diagnosis

Elevated hormone flags liver problems in mice with methylmalonic acidemia. Researchers have discovered that a hormone, fibroblast growth factor 21 (FGF21), is extremely elevated in mice with liver disease that mimics the same condition in patients with methylmalonic acidemia (MMA), a serious genomic disorder. Based on this finding, medical teams treating patients with MMA will be able to measure FGF21 levels to predict how severely patients’ livers are affected and when to refer patients for liver transplants.

The findings also might shed light on more common disorders such as fatty liver disease, obesity and diabetes by uncovering similarities in how MMA and these disorders affect energy metabolism and, more specifically, the function of mitochondria, the cells’ energy powerhouses. The study was conducted by researchers at the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health.

“Findings from mouse studies usually take years to translate into health care treatment, but not in this case,” said Charles P. Venditti, M.D., Ph.D., senior author and senior investigator in the NHGRI Medical Genomics and Metabolic Genetics Branch. “We can use this information today to ensure that patients with MMA are treated before they develop severe complications.”

MMA is a genomic disease that impairs a person’s ability to break down food proteins and certain fatty acids. The condition affects roughly 1 in 50,000 children born in the United States and can be detected through newborn screening. Children with MMA suffer from frequent life-threatening metabolic crises when they encounter a minor viral illness or other stressors like trauma, dietary imbalance or surgery. They must adhere to a special low-protein diet and take various supplements their entire lives.

The NHGRI team created a new mouse model and used it to discover key pathways that were affected during a fasting challenge to model a metabolic crisis in a patient with MMA. It enabled them to identify markers that they could then measure in MMA patients to assess the severity of the dysfunction in their mitochondria, specifically in the liver.
The MMA mice also allowed them to study the response to liver-directed gene therapy and to compare the findings in patients after liver transplant surgery. Liver transplants give patients with MMA a missing enzyme and ease some of the symptoms, but do not cure the disease. Kidney transplantation, on the other hand, is necessary when these patients reach terminal stages of renal failure, an expected chronic complication of MMA. Selecting which patients would benefit from a liver or combined liver/kidney transplant as opposed to just a kidney transplant is an important clinical decision for families and their clinicians.

“We found that having MMA, whether in a mouse or person, causes stress pathways to be chronically activated and can impair their ability to respond to acute stress,” said Irini Manoli, M.D., Ph.D., lead author and associate investigator in NHGRI’s Medical Genomics and Metabolic Genetics Branch. “Our new markers can accurately predict how effective a therapy, whether cellular or genomic, might be for the patients.”
National Human Genome Research Institutewww.genome.gov/news/news-release/Elevated-hormone-flags-liver-problems-in-mice-with-methylmalonic-acidemia-MMA

Horiba Yumizen hematology analysers minimize microscopy slide reviews

Horiba has recently announced the publication of scientific studies which demonstrate the excellent performance of its new HELO high throughput fully automated hematology platform on body fluid and pathological samples. Horiba’s Yumizen® H2500 and H1500 automated hematology analysers within the HELO platform deliver enhanced precision for complete blood counts and white blood cell (WBC) differential testing, with body fluid analysis included as standard. This improves diagnosis, minimizes unnecessary manual microscopy slide reviewing and enhances laboratory workflow, as highlighted by two recent scientific evaluation studies.
The first study was undertaken by Nantes University Hospital (CHU de Nantes) focusing on the need for automated analysis of biological fluids for robust and reliable results reporting. Hematological analysis of body fluids (BF) can provide clinicians with valuable diagnostic information as it can indicate a number of serious medical conditions. Manual microscopy has traditionally been used to determine total and differentiated WBC in BFs, however, results can be affected by inter-operator variability and take time to undertake. By using an automated method of analysis of WBC in a body fluid smear, this can improve turnaround times and accuracy.
To ensure the robustness and reliability of automated BF analysis in routine laboratory workflows, the evaluation study was undertaken on the performance of the automated body fluid analysis cycle on the Yumizen H2500. The study included 98 samples from cerebro-spinal, pleural, ascitic, pericardic and bronchoalveolar liquid (BAL) fluids which were used for comparative leukocyte and erythrocyte counts, as well as differential. This confirmed the good analytical performance of Yumizen analyser in comparison with conventional microscopic count, as well as a reference analyser.
The second study explored the flagging efficiency of the new analyser. Pathological samples, coming from patients with altered hematopoiesis, often trigger a WBC-Diff flag; this is due to poor cell separation and requires a manual slide review (MSR) by microscopy to confirm the WBC differential. Laboratory workload would be optimized if MSR could be reduced without compromising patient care. Therefore, the study undertaken by the Institut Bergonié Comprehensive Cancer Centre compared the flagging performance in the WBC differential of the Yumizen H1500/H2500 to a routine analyser. This included patients with pathology or treatment affecting hematopoiesis, such as those undergoing chemotherapy or with onco-hematologic disorders.
The study on 228 pathological samples (100 from patients on chemotherapy for solid tumours and 128 from patients with malignant blood disease) demonstrated an improvement in the WBC-diff analysis and reliability of the Yumizen H1500/2500 analyser compared to a routine analyser. It delivered better precision and specificity, due to improved cell separation, and a significant decrease (-21%) in unnecessary morphology reviewing by microscopy, thus saving significant time in the laboratory.
Commenting on the successful outcome of the studies, Mandy Campbell, Horiba Medical said, “These evaluation studies undertaken by recognized authorities in hematological analysis, demonstrate the excellent performance of our new Yumizen H1500/H2500 automated hematology analysers with both body fluid and pathological samples. Body fluid analysis is available as standard on these analysers which have been shown to enhance diagnoses and lower film review rates to improve laboratory workflow.” www.horiba.com/medical

Zika virus study reveals possible causes of brain pathology

In healthy individuals, the Zika virus causes flu-like symptoms. If a pregnant woman becomes infected, the unborn child can suffer from severe brain abnormalities as a result of mechanisms that have not yet been explained. A study by the Technical University of Munich (TUM) and the Max Planck Institute of Biochemistry (MPI-B) shows that Zika virus proteins bind to cellular proteins that are required for neural development.

A few years ago, Zika virus spread across South America, posing a health issue with global impact. A significant number of South American women who came into contact with the virus for the first time at the start of their pregnancy by a mosquito bite subsequently gave birth to children with severe disabilities. The babies suffered from a condition known as microcephaly; they were born with a brain that was too small. This can lead to intellectual disabilities and other serious neurological disorders.

Scientists succeeded in proving that these deformities are caused by Zika virus infections, but so far they have been unable to explain why. Andreas Pichlmair, Chair for Viral Immunopathology at TUM and his team from the TUM Institute of Virology and MPI-B have examined how Zika virus influences human brain cells. They identified the virus proteins with the potential to affect neuronal development in the developing brain.

 “Zika virus is closely related to the Hepatitis C virus and certain tropical diseases such as Dengue and West Nile virus. It is, however, the only virus that causes brain damage in newborns,” explains Pichlmair, who headed the recent study.

The researchers discovered that the virus uses certain cellular proteins to replicate its own genome. These molecules are also important neurological factors in the process of a stem cell developing into a nerve cell. “Our findings suggest that the virus takes these factors away from brain development and uses them to replicate its genome, which prevents the brain from developing properly,” explains the virologist.

When the team headed by Pichlmair removed the factors in the cells, the virus found it much harder to replicate. The researchers were able to demonstrate which virus proteins come in contact with these development factors and cause the brain defects. “Previous studies revealed the virus proteins necessary for the packaging or replication of the viral genome but it was enigmatic to understand how these proteins influence neuronal development. It appears that viral proteins are responsible for causing the serious defects in the unborn – unintentionally we presume,” says Pichlmair.

In their comprehensive proteomics survey, the research team identified cellular proteins that were altered chemically or numerically by the virus or which bound to virus proteins. In this way, they were not only able to illustrate possible reasons for the caused deformities, but also obtained a very clear picture of how the virus reprograms the cell to use it for its own replication. www.tum.de/nc/en/about-tum/news/press-releases/details/34920/

Astell Scientific at Medica

Astell Scientific is a world renowned manufacturer and supplier of steam sterilizers. Astell Scientific autoclaves, steam generators and effluent decontamination systems (EDS) are designed to meet the exacting demands of modern Laboratory, Research and Medical professionals, and as such incorporate innovations such as colour touchscreen controllers as standard throughout the range.

We manufacture:
•    Circular section autoclaves from 30-330 litres
•    Square Section autoclaves from 125 – 2000 litres
•    Steam Generators up to 72 kW
•    Effluent Decontamination Systems (EDS)
•    Customized steam sterilizers to meet the most challenging of applications

All Astell autoclaves are manufactured in accordance with standards and directives including ISO 9001:2015, Pressure Equipment Directive (PED 2014/68/EU) and CE (Conformité Européenne).www.astell.com

Oncimmune at Medica

The battle against cancer hinges on the early detection and then delivery of effective treatment. Oncimmune is working to revolutionise both the detection of cancer and its treatment by harnessing the sophisticated disease-detecting capabilities of the immune system to find cancer in its early stages. Oncimmune’s range of diagnostic tests assist clinicians to identify the presence of cancer on average four years before standard clinical diagnosis, whilst its technology platform and sample biobanks are helping healthcare companies to develop new cancer treatments.

www.oncimmune.com

Jackson ImmunoResearch at Medica

Jackson ImmunoResearch manufactures secondary antibodies and conjugates, with an outstanding reputation for quality, earned over 30 years. Our products are used in Western Blotting, IHC/ICC/IF, Flow Cytometry, ELISA, Electron Microscopy and many other immunological techniques. From our UK office we serve Europe with euro pricing, technical service and fast delivery. www.jacksonimmuno.com

Starna Scientific at Medica

Starna, established 1964, has a worldwide reputation for quality, service and innovation in the production and supply of spectrophotometer cells, optical components and Certified Reference Materials (CRMs). World-leader with over 50 years’ experience in the production of Certified Reference Materials for UV-Vis-NIR & Fluorescence spectroscopy; it is the only company to achieve both ISO/IEC 17025 and ISO 17034 for this range of products. A highly regarded manufacturer of high precision quartz and glass Cells/Cuvettes for Photometers and Fluorimeters. Starna sells worldwide to instrument manufacturers, pharmaceuticals, life-biosciences, R&D laboratories, medical companies and universities.

www.starna.com

GAMBICA at Medica

GAMBICA is the Trade Association for Instrumentation, Control, Automation and Laboratory Technology in the UK. Our insight and influence help our members to be more competitive by increasing their knowledge and impact. Together we remove barriers and maximise the market potential in our industry.
GAMBICA members are active in the following sectors:
•    Industrial automation products and systems
•    Process instrumentation and control
•    Laboratory technology
•    Test and measurement equipment for electrical and electronics industries

www.gambica.org.uk

Scientists develop test for uncommon brain diseases

National Institutes of Health (NIH) scientists have developed an ultrasensitive new test to detect abnormal forms of the protein tau associated with uncommon types of neurodegenerative diseases called tauopathies.  This advance gives them hope of using cerebrospinal fluid, or CSF – an accessible patient sample – to diagnose these and perhaps other, more common neurological diseases, such as Alzheimer’s disease.

Scientists have linked the abnormal deposition of tau in the brain to at least 25 different neurodegenerative diseases. However, to accurately diagnose these diseases, brain tissue often must be analysed after the patient has died. For their study, the researchers used the same test concept they developed when using postmortem brain tissue samples to detect the abnormal tau types associated with Pick disease, Alzheimer’s disease and chronic traumatic encephalopathy (CTE). They adapted the test to use CSF for the detection of abnormal tau of progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and other less common tauopathies.

They detected abnormal tau in CSF from both living and deceased patients. In one case, the test led to a corrected diagnosis in a patient who had died from CBD, but who was initially diagnosed with PSP. The new test is called 4R RT-QuIC – which stands for 4-repeat tau protein amplified in a real-time, quaking-induced conversion process.

The researchers plan to continue evaluating the clinical performance of 4R RT-QuIC by analysing larger sets of CSF samples. One focus will be to compare test results from tauopathy patients who agree to provide CSF samples both before and after death. The scientists hope this type of evaluation will help them better understand how abnormal tau in CSF evolves during brain disease.

NIHwww.niaid.nih.gov/news-events/nih-scientists-develop-test-uncommon-brain-diseases