Han’s work allowed for differentiation among H1N1 and other strains of flu and bacterial and viral illnesses in less than six hours. The test used proprietary molecular technology developed by Han and made available by Diatherix, a HudsonAlpha associate company located less than 50 yards from Han’s lab.

The advantage of target enriched multiplex polymerase chain reaction, or tem-PCR, technology is its ability to quickly check for multiple pathogens all at once.Because the majority of H1N1 deaths involved patients who had swine flu plus another type of infection, the capability of the HudsonAlpha-developed test to quickly check for nearly two dozen other viruses and bacteria while checking for H1N1 better equipped doctors with information about how to best treat patients with multiple infections.

Through Diatherix, the test was made available quickly to hospitals, private physician practices and public health departments.

Easing the pain of childhood cancer

Researchers at HudsonAlpha care about diseases that affect children and invest daily in learning more about the genomics of cancer to aid in finding a cure, or at least to find better treatments and earlier diagnosis.

In a cancer like Burkitt lymphoma – one of the most common cancers in children –there is no time to waste. It is one of the fastest-growing cancers, spreading quickly to other organs, and rapidly fatal if not treated.

By sequencing the exomes — or the three percent of the genome that contains genes — of Burkitt lymphoma tumors, HudsonAlpha is identifying new gene targets for these youngest of cancer patients. This research, in the lab of Shawn Levy and in collaboration with the Duke Institute for Genome Sciences and Policy and others, is identifying the genetic mutations that allow the cancer cells to grow so uncontrollably in the lymphatic system.

Equipped with this information, the scientific community may be able to pinpoint more and better targets for diagnostics and therapeutics for a disease that is now primarily treated with aggressive chemotherapy.

Sequencing for superior chocolate

While genomic research has the potential to improve people’s lives through medical discoveries, it can also be applied to improving the foods we eat, even foods to satisfy a sweet tooth like chocolate.

In partnership with one of the world’s leading chocolate manufacturers, Mars, Inc., the U.S. Department of Agriculture, and others, HudsonAlpha husband-and-wife team Jane Grimwood and Jeremy Schmutz sequenced the genome of cacao, from which cocoa and chocolate are made. The information may improve the way breeders and farmers around the world raise and harvest the tasty crop.

Farming of cacao trees and beans provides a livelihood for more than 5 million farmers, approximately two-thirds of whom are in West Africa. So raising productivity and income is an important step towards improving poverty in communities dependent on cacao.
“Cacao is a major export of many African and Asian countries and is a high value crop,” said Schmutz. “The genomics work, combined with breeding programs, forms the basis for maintaining and improving the stability of the cacao supply.”

Schmutz and Grimwood run the Genome Sequencing Center at HudsonAlpha where the assembly of the cacao genome took place, as well as the chromosome scale reconstructions to produce the final reference sequence.

Through cacao genome sequencing, researchers have learned why some cacao variations are optimal for breeding, yet produce an undesirable flavor or aroma. Other variations, when combined with different beans, increase flavor and color yet decrease the quality. Additionally, sequencing has identified resistance to various diseases and other horticultural traits.

This project is especially beneficial for cacao farmers and breeders in West Africa, Asia and South America who are using the genetic information to improve planting stocks and protect often-fragile incomes. Unlike food products such as corn or wheat, which are often grown on large, industrial farms, cacao is almost exclusively grown on small, individual farms.