Research at HudsonAlpha is grouped into five broad categories: cancer, neurological and psychological disorders, childhood genetic disorders, immunogenomics, and agriculture and bioenergy.

Cancer

All cancers involve genetic changes, most of which are not inherited but acquired, often by environmental exposures. Genetic changes influence how fast the cancer grows, how likely it is to spread, and what medications are most effective.

Recent breakthroughs in cancer research at HudsonAlpha include:

• using genomic analysis to differentiate which women with breast cancer will or will not respond to specific drug regimens
• investigating molecular differences in cancerous tissues and healthy tissues for the purpose of identifying biomarkers to aid with earlier detection of some of the deadliest and hardest-to-treat cancers: pancreatic cancer, kidney cancer and prostate cancer
• identifying a special population of intestinal stem cells that respond to damage and help prevent intestinal and colon cancer
• discovering new gene targets so that new diagnostics and therapeutics can be found for cancer patients with Burkitt lymphoma, a type of cancer most often affecting children

Neurological and Psychological Disorders

More than 600 neurological diseases –  including Alzheimer’s, Parkinson’s, ALS, bipolar disorder, and autism – impact more than 16 million Americans. Worldwide the number affected is even greater. The risk factors for these diseases are poorly identified, but evidence suggests multiple genetic and environmental factors. Untangling these puzzles with genomic technologies is critical for identifying better drugs for treatment.

One such project currently happening at HudsonAlpha is whole genome sequencing of individuals diagnosed with bipolar disorder to increase understanding of the disease, to identify genes and pathways that contribute to the risk for bipolar disorder, and to identify targeted therapies and approaches for treatment. HudsonAlpha faculty investigators Rick Myers, Ph.D., Devin Absher, Ph.D., and Shawn Levy, Ph.D., are collaborating on the research, along with the National Institute of Mental Health, the Center for Statistical Genetics at the University of Michigan and other colleagues.

Childhood Genetic Disorders

Two out of every 100 children are born with an intellectual or physical disability or developmental delay, many of which arise from genetic factors. These children, their families and their physicians are actively seeking a specific diagnosis, but often without resolution; current technologies have only been capable of delivering diagnoses for 10 to 15 percent of affected children.

Revolutionary DNA sequencing and analysis techniques pioneered by HudsonAlpha are now being applied to families with affected children in a large-scale HudsonAlpha project that inspires hope that diagnoses are in reach, and with it, new possibilities for treatment. HudsonAlpha faculty investigators Rick Myers, Ph.D., Greg Barsh, M.D., Ph.D., Greg Cooper, Ph.D., Neil Lamb, Ph.D, Shawn Levy, Ph.D., and genetic counselor Kelly East are working with physicians, scientists and genetic counselors at partner institutions using samples from hundreds of North Alabama children and their families to determine if new technologies that look at people’s DNA can explain why some children have problems with the development of their brain and body.

Immunogenomics

Using genomics technology to understand the human immune system and related diseases (such as lupus, rheumatoid arthritis, pancreatitis, psoriasis, and non-alcoholic fatty liver disease) is a burgeoning field called immunogenomics. It brings together experts in genomics and genetics, immunology, computational biology, and clinical research in a search for biomarkers to guide diagnosis and treatment. At HudsonAlpha, these research efforts — led by faculty investigators Rick Myers, Ph.D., Jian Han, M.D., Ph.D., Devin Absher, Ph.D. and Shawn Levy, Ph.D. — are exploring how the immune system drives disease and how genomics might predict which patients should benefit most from new classes of drugs.

One project underway at HudsonAlpha is using high-throughput sequencing of T-cell receptor genes in the immune repertoire to create a “snapshot” of the functional status of the immune system. Known as “R10K,” these snapshots are being compiled into a repertoire of 10,000 individuals, representing 100 important diseases. Because the immune system is directly involved with many diseases, a personalized immune repertoire can identify diseases that specify repertoire changes, evaluate safety and efficacy of new vaccines, identify new treatment targets, and develop new therapeutics.

Agriculture and Bioenergy

HudsonAlpha’s Genome Sequencing Center is one of only a handful of centers around the world that performs de-novo sequencing – which is the assembling of short reads to create full-length sequences – of important plants and organisms. In addition to bio-fuel plants and staple crops, such as soybean, cotton and cacao, the center examines the genome of common pests that wreak havoc on harvests.

The HudsonAlpha Genome Sequencing Center recently responded to a need to facilitate better and targeted cotton strains for an industry that is of great importance to the cotton farmers of Alabama, where HudsonAlpha is located, and around the world. Cotton is not only used in the textile industry but also in biofuel production and in bioremediation. Under the direction of HudsonAlpha faculty investigators Jane Grimwood, Ph.D., and Jeremy Schmutz, the Genome Sequencing Center partnered with colleagues to compare the high quality draft assembly of the simplest cotton genome against other cotton species and traced the evolution of cotton over millions of years, from wild varieties to what is currently grown. Their findings have the potential to reduce pesticide use in farming, improve disease resistance of cotton plants, and promote more efficient water usage.