The integration of gene expression data to predict systemic lupus erythematosus (SLE) disease activity is a significant challenge because of the high degree of heterogeneity among patients and study cohorts, especially those collected on different microarray platforms. Here we deployed machine learning approaches to integrate gene expression data from three SLE data sets and used it to classify patients as having active or inactive disease as characterized by standard clinical composite outcome measures. Both raw whole blood gene expression data and informative gene modules generated by Weighted Gene Co-expression Network Analysis from purified leukocyte populations were employed with various classification algorithms. Classifiers were evaluated by 10-fold cross-validation across three combined data sets or by training and testing in independent data sets, the latter of which amplified the effects of technical variation. A random forest classifier achieved a peak classification accuracy of 83 percent under 10-fold cross-validation, but its performance could be severely affected by technical variation among data sets. The use of gene modules rather than raw gene expression was more robust, achieving classification accuracies of approximately 70 percent regardless of how the training and testing sets were formed. Fine-tuning the algorithms and parameter sets may generate sufficient accuracy to be informative as a standalone estimate of disease activity.
At BioBuzz, we’re dedicated to bringing you interesting and important stories that emerge from the thriving life sciences ecosystem that is the BioHealth Capital Region (BHCR).
The heart of the BHCR biohealth cluster is Maryland, with its vast network of government research agencies, the strong university system, and a deep network of established, emerging, and startup life science companies across a wide range of fields, including cell and gene therapy, advanced biomanufacturing, phage therapy, medical devices and more traditional biotech and pharma organizations. That’s not even to mention the remarkable efforts of myriad Maryland vaccine companies to develop the first approved, safe, and efficacious SARS-CoV-2 vaccine.
Maryland is certainly the most mature market within the wider BHCR, and the one we tend to cover the most, especially recently, but it isn’t the only growing and thriving BHCR sector.
In addition to exciting developments in Washington, DC, Charlottesville, Virginia is quietly emerging as an exciting hub for life science companies and promising startups that have spun out of the University of Virginia (UVA). UVA and CVilleBioHub, which was founded in 2016 by biotech industry leaders to support the growing biohealth ecosystem in and around Charlottesville, Virginia, have been catalysts for growth in what they call the CVille ecosystem. CVilleBioHub’s mission is to double the size of the biohealth cluster it serves by 2030 through strong engagement, deft resourcing, valuable programming, and grassroots advocacy.
It seems the collaboration between UVA and CVilleBioHub is working. There are a host of exciting, innovative startup companies that call Charlottesville home. We’re excited to highlight these nine innovative Charlottesville, Virginia startup companies and look forward to telling their stories well into the future.
Charlottesville-based company develops COVID-19 test
CHARLOTTESVILLE, Va. (CBS19 NEWS) — A Charlottesville-based precision medical company has developed a new approach to predicting the severity of the coronavirus. Link to the full broadcast: https://www.cbs19news.com/clip/15082777/ample-biosolutions-test
AMPEL BioSolutions has developed technology to determine how severely a person will react to coronavirus and identify the best, FDA-approved treatment options. The company has been working since March to develop a new test amid the COVID-19 pandemic.
“AMPEL’s goal is to accelerate getting effective treatments to COVID patients to be able to blunt that serious illness that leads to lung damage and death,” said Dr. Amrie Grammer, Co-Founder, COO, and CSO of AMPEL BioSolutions.
Grammer, a double University of Virginia-graduate, said the company began work quickly to get results, publishing a paper in just five weeks.
“We started working around the clock and were able to get some results in five weeks to be able to suggest drugs that would blunt that very serious illness that leads to lung damage,” she said.
The genomic test, CovGENE, uses bodily fluids from a nasal swab or blood for testing. A partnership with a diagnostic company could expedite the test’s timeline.
“To partner with an existing diagnostic company that has a test on the market for COVID, to be able to license that, and they could very quickly bring this to market, with the right company it could be available in a matter of months,” Grammer said.
AMPEL’s focus has shifted slightly over the past few months.
“Our goal was bringing new drugs to patients with serious illness, initially Lupus, a very serious auto-immune disease that affects women,” Grammer said.
Amidst the coronavirus pandemic, she felt an obligation to focus on COVID-19 research.
“A contribution to the scientific community and we felt an obligation to bring that forward, especially in these very difficult COVID-19 pandemic times,” Grammer said.
AMPEL BioSolutions is working to get its lupus treatment, LuGENE, a gene-based diagnostic for patients to determine disease status, predict flares ups, and match patients with the best drug options, to market by 2022. The company is currently securing funding.
Charlottesville Based Companies Technology Predicts Severity of COVID-19 Illness in Patients and Identifies Treatments. Aired June 9, 2020
Les Sinclair talks with Dr. Amrie Grammer about AMPEL BioSolutions, a Charlottesville Virginia company that has reengineered the gene-based technology they developed for lupus to COVID19.
Aired June 10, 2020 – Virginia Public Radio’s Sandy Hausman
A Charlottesville biotech company says it’s come up with a test that predicts the most severe cases of COVID-19 and could guide doctors in their choice of medications to save lives.
Scientists at AMPEL Biosolutions had been studying lupus – an auto-immune disease in which the body’s white blood cells cause inflammation of joints and organs. What they heard about the most serious cases of COVID-19 sounded familiar.
“There are certain white blood cells that normally would fight off the COVID that are out of control and are actually propagating damage to the lungs and other organs,” says Amrie Grammar, AMPEL’s Chief Scientific Officer. “These uncontrolled white blood cells are secreting a variety of inflammatory compounds that are driving the severe symptoms and the lung damage.”
Not everyone who gets COVID suffers that symptom, but those who do may end on a ventilator and many will die. So AMPEL developed a test that identifies those at greatest risk for serious complications and could guide doctors to use certain medications that would reduce or prevent inflammation of the lungs. The company hopes it can collaborate with a firm that makes diagnostic kits for the coronavirus, so that doctors can identify patients and plan treatment strategies with just one test.
Link to full interview: https://www.wvtf.org/post/cville-company-develops-new-covid-test#stream/0