UCSC researcher completes human genome sequencing


SANTA CRUZ – After nearly 40 years of work, scientists have finally completed sequencing the human genome and UC Santa Cruz was at the center of it all.

The completion of the sequence gives an idea for the baseline of all human genetics. Humans are 99.9% identical genetically, according to UCSC Genomics Institute Director David Haussler. Therefore, while scientists have only sequenced the DNA of a human once, anyone can look at it and get a near indistinguishable snapshot of their own genetic code.

UCSC Chancellor Emeritus Robert Sinsheimer embarked on the quest in 1985. Karen Miga, an assistant professor in biomolecular engineering, completed the task at the end of March.

“It’s the greatest honor of my life,” she said. “What it turned out to be was this amazing walking with a whole group of people towards a historic moment. I feel lucky to be a part of that legacy.”

The former chancellor had just finished sequencing the genome of a virus, which inspired him to gather a team to sequence the human genome in the mid-80s. However, that task would be much harder than the one he just completed.

The virus Sinsheimer sequenced only has a sequence of a few thousand DNA patterns, which is miniscule compared to the genome of human, according to Haussler. The human genome is comprised of 3 billion DNA sequences.

Haussler likened the task to a jigsaw puzzle, except this puzzle has 3 billion pieces and a corner piece is not as easy to find.

“It gives you a feel for how hard this problem of putting together all the little snippets of DNA into the right orientation and figure out what the actual chromosome looks like — how hard that problem is,” said Haussler, who worked on the original Human Genome Project.

In fact, the puzzle is so complex that scientists from 20 different countries joined forces to sequence the human genome. That team became known as the Human Genome Project, and it officially launched in 1990.

Those scientists spent the next 10 years working on sequencing the human genome. Along the way, the Human Genome Project even faced competition against a private company, Solara Genomics, that sought to accomplish the same task but also find a way to monetize it.

That competition lead to further innovations in technology, which gave researchers the power to sequence the genome faster. While technology advanced, the task at hand still remained daunting.

“That work was incredibly difficult because the genome was so huge and the technology could only read 1,000 bases at a time,” Haussler said.

To put that into perspective, the first chromosome in the human genome is 250 million bases long, Haussler noted. Subsequent chromosomes continue to get smaller, but there are still an additional 22 chromosomes adding up to more than 3 billion bases.

However, in July 2000, researchers at UCSC accomplished what seemed unachievable. A student at the university wrote a program that helped the Human Genome project complete a first draft of the sequence by July 7, 2000.

“That was incredibly important to us because now scientists got a glimpse of our human heritage,” Haussler said. “In fact, regular people got a glimpse at our human heritage without having to pay a subscription.”

That first draft displayed roughly 90% of the complete human genome. The remaining 10% of the human genome was just out of grasp with the state of technology at the time. As a result, many people in the project gave up, conceding that there is plenty of information for modern medicine in the 90% of the genome sequenced.

Technological advancements and perseverance would later help Miga, who was a grad researcher during the original project,  catalogue the remaining 10% of the human genome.

Miga formally launched her international consortium in 2019, co-led by Evan Eichler from the University of Washington and Adam Phillippy from the National Institute of Health. Unlike the Human Genome Project, this consortium was independently funded and achieved its success on the free time of each of the associates.

“It’s completely grass roots. This is just a bunch of scientists from around the world — using their spare time, using their own money — that decided that this was something that needed to happen,” Miga said.

The team really leaned into their research as the COVID-19 pandemic gripped the world.

While many people were learning to make banana bread, Miga and her team were completing the jigsaw puzzle of human genomics. However, what was left over from the Human Genome Project were some of the hardest pieces of the puzzle.

“It was really difficult to sequence these, put them together or just reconstruct the puzzle,” Miga said. “When you’re putting a puzzle together and you have all the blue-sky pieces that look the same, that’s what we were up against.”

But of course, the hardest pieces to solve were some of the most important parts of human genetics. The parts of the human genome that Miga catalogued are some of the fastest changing genetics through history, Haussler said. They are also parts of genetics that are vital to human life.

The parts of the genome Miga focused on focused on the centromere of cells, which makes sure cells separate properly during mitosis. When this part of cell does not function properly, it leads to cancer and birth defects.

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