This story originally appeared on the .
Cole Williams was crunched for time. The genetics and genomics senior was deep into the world of human population genetics. In the , Williams was trying to parse apart familial relationships in African hunter-gatherer and pastoralist groups, some of which are the most diverse human populations on Earth.
But he ran into a problem. The publicly available computer algorithms Williams used couldn鈥檛 make sense of his study population鈥檚 genomic data.
鈥淢ost [of the algorithms] were developed with European-descent groups in mind,鈥 said Henn, who holds appointments in the Department of Anthropology and the 新澳门六合彩内幕信息 Davis Genome Center. 鈥淭hey don鈥檛 work well for populations with multiple ancestries, cousin-cousin marriages or situations where there are many half-siblings in a population.鈥
Such was the case with the African populations Williams and Henn studied, like the Himba, from northern Namibia. To further emphasize Henn鈥檚 point, an article published in reported that 78 percent of individuals in 鈥済enome-wide association studies鈥 are of European descent. , Europeans make up only about 10 percent of the world鈥檚 population.
Williams needed a fix. He鈥檇 spent nearly eight months on a project with little more than an inkling of advancement. He knew an original algorithm was needed, but with graduation looming, he didn鈥檛 have time to write it. Then the California wildfires hit and the 新澳门六合彩内幕信息 Davis campus closed. Williams turned the closure into an opportunity and wrote the algorithm.
The result, according to Henn, was an algorithm capable of handling diverse populations, technical artifacts and complex family genealogies that runs rapidly on human genomic datasets.
鈥淐ole solved a major problem we were facing, in other words how to accurately construct multi-generational pedigrees in African genomes,鈥 said Henn. 鈥淗e really put the time into understanding the technical difficulties inherent in genomic data and how other research groups tackled the problem previously.鈥
For his outstanding research and service, Williams, who graduated this month, was named the 2019 College of Biological Sciences Undergraduate of the Year.
鈥淭his award is a testament to my passion for human genetics and all of my hard work of the past four years,鈥 said Williams. 鈥淚t has been such a privilege to be at 新澳门六合彩内幕信息 Davis studying and researching the subject I love; to be given this award is just the cherry on top of such an amazing time here.鈥
Preserving childhood wonder
Williams can trace his affinity for genetics back to fifth grade, when he was introduced to Punnett squares, diagrams used to predict the probability of heritable traits, such as eye or hair color. He became fascinated by the potential power of genetics to help solve diseases. Raised in Davis in an Aggie household, Williams followed his parents鈥 footsteps and enrolled at 新澳门六合彩内幕信息 Davis due to its strong reputation for genetics and because he wanted to stay close to home.
During his freshman year living in the Tercero Residence Hall, Williams learned about , a nationwide student-run organization that runs camps for children of cancer patients. As a child, Williams鈥 father was taken by cancer. He was all too familiar with the emotional toll surrounding such a loss and joined the program as a camp counselor. According to Williams, the camp is all about providing a space for kids to just be kids. He now serves as the 新澳门六合彩内幕信息 Davis chapter鈥檚 treasurer.
鈥淲hen your parent has cancer, you鈥檙e kind of forced to grow up,鈥 he said. 鈥淵ou kind of miss out on some of your childhood.鈥
Williams himself felt the experience was a struggle and now, he鈥檚 ensuring other children don鈥檛 feel as he did.
鈥淚t turned out it was the most impactful thing that I鈥檝e done,鈥 he said of volunteering. 鈥淚鈥檝e had a lot of success with my research and my academics, but I think I鈥檓 most proud of the work I鈥檝e done with Camp Kesem.鈥
Choreographing the ancestral dance of genetics and anthropology
When Williams found the during his junior year, he struck scientific gold.
鈥淚 knew that human population genetics was what I wanted to do when I came to Davis,鈥 he said. 鈥淚 had been looking for a lab like this my whole time here.鈥
Williams became familiar with the Himba and San populations Henn and her colleagues studied. But with populations like the Himba defining familial relationships with genetic data can be a daunting task.
鈥淭hey have arranged marriages, so that鈥檚 the first layer,鈥 said Williams. 鈥淭he second layer is that preferred pairings are between first cousins and the third layer is that they can have additional relationships outside of their marriage.鈥
Algorithms developed using European ancestry data couldn鈥檛 genetically delineate between grandparent-grandchild, half-sibling and avuncular (aunts/uncles-nieces/nephews) relationships. Since individuals in these relationships share about 25 percent of their genetic material with one another, they all looked the same to the publicly available algorithms.
To overcome this hurdle, Williams peered closer at the genomes, zeroing in on segments of DNA known as identical by descent (IBD) segments, which are measured in genetic metric called centiMorgans. It turned out that the three complex relationships differed in size and number of shared IBD segments.
鈥淎 grandparent-grandchild, they share fewer segments but they鈥檙e longer,鈥 said Williams. 鈥淎vuncular relationships, they share more segments of shorter length.鈥
With this new knowledge, Williams wrote an algorithm capable of delineating between grandparent-grandchild, half-sibling and avuncular relationships with greater accuracy. The algorithm learns and becomes more accurate with each new dataset.
鈥淗is solution is both really unique but practical,鈥 said Henn.
The algorithm could help researchers further understand disease spread in African hunter-gatherer and pastoralist populations by highlighting the inherited genetics that lead to disease susceptibility. This could help Henn and her colleagues understand the spread of tuberculosis in their study populations.
Focusing on genetic diseases in underrepresented populations
After graduation, Williams will head to the , where he will continue researching genetic diseases in underrepresented populations. He plans on later pursuing a Ph.D. degree.
鈥淚 would like to acknowledge Dr. Brenna Henn, who gave me a chance and afforded me the independence to become a better scientist; the campers and counselors at Camp Kesem 新澳门六合彩内幕信息 Davis who have taught me love and empathy and have made me a better person; and lastly, I would like to thank my mom for her endless support and instilling in me the work ethic needed to receive an award like this,鈥 said Williams.
鈥淎nd for letting me live with her rent-free for the past three years,鈥 he added.
is a science writer and communications specialist at the .