Each year, the Muscular Dystrophy Association (MDA) awards are granted to the world’s best scientists to help accelerate treatments and cures for families living with neuromuscular diseases. Among the grant recipients this year are two HudsonAlpha Institute for Biotechnology faculty investigators.

Greg Cooper, PhD, and CO-PI Jane Grimwood, PhD, were recently awarded roughly $290,000 over three years from the MDA for their project titled, “Long-read sequencing to diagnose neuromuscular disorders.”

Cooper and his lab are not strangers to using genome sequencing to diagnose rare diseases. Over the past decade, Cooper’s lab, along with many collaborating labs, sequenced the genomes of more than 1,790 children with rare diseases. Most of the children were showing signs of neurodevelopmental disorders, with features such as intellectual disability, developmental delay, and seizures. However, about 18 percent of the sequenced cohort also exhibit features of neuromuscular disorders like muscle weakness, contractures, ataxia, and dysphagia.

“Both exome and genome sequencing are powerful diagnostic tools for many diseases,” Cooper said. “Across all our patient cohorts, we found pathogenic or likely pathogenic variants in about 27 percent of patients, with about 17 percent of variants leading to a precise neuromuscular diagnosis. However, genome sequencing fails to identify genetic contributors to most neuromuscular disorders, despite severe, early onset phenotypes likely caused by genetic factors.”

Cooper and his lab believe that many neuromuscular disorders result from genetic variation that cannot be detected using the standard method of short-read sequencing. During short-read sequencing, long pieces of DNA are cut into shorter pieces that are sequenced and then pieced back together. Complicated DNA repeats, duplications, and expansions are often missed with this type of sequencing.

However, HudsonAlpha’s Genome Sequencing Center, of which Grimwood is the co-director, is an expert in another type of sequencing that could overcome the limitations of short-read sequencing: long-read sequencing. Long-read sequencing reads segments of DNA that are thousands of times longer than those produced using short-read sequencing. In an initial pilot study, the team used long-read sequencing on six patients whose genomes were previously sequenced with short-read technology. For two of the six patients, the team identified pathogenic/likely pathogenic variants missed by the short-read sequencing.

The goal of the recently funded grant is to refine the use of long-read sequencing to help diagnose neuromuscular disorders more frequently and effectively. The researchers will select patients with features of neuromuscular disorders from the pool of unsolved cases previously sequenced using short-read sequencing. The hope is that long-read sequencing will afford them a diagnosis. Researchers will also streamline the sequencing and diagnosis process for routine research and clinical use.

“Despite identifying hundreds of genes implicated in neuromuscular disease, there are still many people who lack a diagnosis,” said Sharon Hesterlee, Ph.D., MDA’s Chief Research Officer. “The work that Dr. Cooper and Dr. Grimwood have undertaken should help shed light on new causes of neuromuscular disease and represent the first step in developing meaningful treatments for these diseases.”

This has been quite a process in the making. When asked about the time given to this project, HudsonAlpha Faculty Member Greg Cooper, PhD explained, “Core pieces of this project really began in 2013 when we first started working with Dr. Martina Bebin, a UAB pediatric neurologist that works at North Alabama Children’s Specialists (NACS) in Huntsville and treats children that have undiagnosed developmental conditions. We collaborate with her to identify children in need of a diagnosis and to perform genomic testing to find that diagnosis.”

“The key technological piece unique to this proposal, i.e., a new type of ‘long-read sequencing’, first started to be used in 2019 by Jane Grimwood and Jeremy Schmutz’s team, the HudsonAlpha Genome Sequencing Center (GSC). The GSC is a collaborator with Pacific Biosciences, a sequencing company that specializes in long-read sequencing and was an early-access “beta-tester” for the specific type of DNA sequencing that we will use for this proposal, called “HiFi”. HiFi has gotten much better (more efficient, faster, higher-quality, etc.) since 2019 and is now at the point that we are ready to start using it on much larger numbers of patients; this is where the MDA grant will come in and help us to develop what we hope will one day be a better standard-of-care for genomic testing in the future.”

Cooper expressed that the most important goal now that HudsonAlpha has received the grant, is that the key long-term goal for is to better diagnose children with unexplained developmental disabilities, especially neuromuscular conditions like the ones that are focused on in this project. Towards that end, the researchers at HudsonAlpha believe that many of these conditions have genetic changes as their root cause but that current technologies cannot detect those genetic changes.

“This new technology is more powerful and can reveal many genetic changes that were previously missed. So, our key goal is to determine how much more effective it can be and maximize its utility; we believe in the next few years that it will replace our current methods and provide a significantly better diagnostic yield in clinical genetic testing for developmental conditions.”, said Cooper.

Many contributing factors live at the root of this research, but Cooper expressed, sharing the driving few, “[A]t a high level, at HudsonAlpha, we are committed to the idea that advances in scientific technology are essential for addressing many challenges in the world around us. Specifically, for this project, we are motivated by the fact that many children struggle with unexplained developmental conditions that impose considerable medical, financial, and emotional difficulties on them and their families. One of these challenges comes from the uncertainty of not having a diagnosis or understanding of what’s causing the child’s condition.”

“Genetic testing, by seeking out root causes, can help to alleviate that uncertainty and provide a specific diagnosis, which can in turn help affected families in a variety of ways. In this study we hope to demonstrate that this new technology will greatly improve upon our ability to find those root genetic causes and improve clinical diagnostic testing for these very challenging conditions.”, continued Cooper.

Cooper says that learning the grant had been received was exciting, but only further motivated the team to continue working to address what they view as a major unmet medical need.

Cooper and his team firmly believe this technology may be transformative for a variety of research and clinical applications and are eager to get to work to prove that.

When asked of any additional words he had to share with the public on this exciting opportunity for HudsonAlpha, Cooper concluded, “As always, we are grateful to the families that participate in our research programs and work with us to make progress to a better future for families affected by developmental conditions. It is also important to note that this project, and other studies going on related to it, would not be possible without the excellent teams of scientists, with various backgrounds and disciplines, at HudsonAlpha that come together to tackle big challenges.”