Twenty-five Years After the Human Genome Project, a New Era is Dawning
Written by Rose Miyatsu
Twenty-five years ago today, on July 7, 2000, the world got its very first look at a human genome—the 3 billion letter code that controls how our bodies function. Posted online by a small team at the University of California, Santa Cruz, on behalf of the global Human Genome Project, this goldmine of data forever changed how we understand biology, medicine, evolution, and what it means to be human.
“I will always remember this moment. There was a sense of awe, excitement and fulfillment as we watched people around the world download and marvel at the genetic code of our species, receiving it for free and without any patent claims.”
That moment, powered by over a decade of global collaboration and more than $3 billion in public investment, laid the foundation for what is now precision medicine. Today, DNA sequencing is used to diagnose rare diseases, guide cancer therapies, trace pathogens, and predict health risks. Genomics has transformed fields as diverse as neuroscience, agriculture, and ecology—and now, with the help of artificial intelligence and machine learning, its impact is accelerating.
"Genomics is no longer just about reading the code," said Lauren Linton, who led the MIT/Whitehead Institute’s sequencing center during the Human Genome Project and is now Executive Director of the UC Santa Cruz Genomics Institute. "It’s about applying that knowledge to real-world challenges—whether that’s finding treatments for a child with cancer or preserving the genetic diversity of endangered wildlife."
A race between academia and industry
Although 2000 was the year that the first human genome was published online, the Human Genome Project continued on well after that date. The sequence was not presented in a peer-reviewed academic publication until 2001, and the project did not end until 2003. Even then, roughly 8% of the human genome was left unsequenced. It was not until 2022, when the Telomere to Telomere Consortium, co-led by UC Santa Cruz and the National Institutes of Health (NIH), released the first completely sequenced human genome that the full genetic code for a human being was unveiled.
Among the possible anniversaries of the genome’s unveiling, however, July 7 stands out. That was the day it was made freely available to the public, a milestone that had been far from guaranteed just weeks before. It is symbolic of an ethos of collaborative, open science that has fueled the last 25 years of innovation, and without which the rapid progress we have made in biotech and precision medicine would be unimaginable.
When the NIH and Department of Energy had announced they would be pursuing the Human Genome Project in 1990, with a 15-year timetable and three billion dollar price tag, there were members of the scientific community who complained that it was a waste of money because they believed that large portions of the genome were just “junk DNA” that had little value. By the end of the decade, however, the biggest threat to the public project came not from those who disputed its value, but from a company that wanted to capitalize on it.
In the late 1990s, a former member of the public project had launched a private company, Celera Genomics, and promised to finish the genome before the public consortium. With fears that Celera would lock the data behind paywalls or patents—as Myriad Genomics had famously done with the BRCA 1 and 2 genes that influence breast cancer risk—urgency skyrocketed. The Human Genome Project, which was originally scheduled to be completed in 2005, suddenly found itself in a dramatic race to finish their genome sequence five years early.
The sequencing centers involved in the project ramped up their production, creating over 400,000 DNA fragments, but no one in the project had yet worked out how to string them together in the correct order to create a completed sequence. The situation seemed dire. The solution came at the final hour, not from an established scientist at one of the project’s prestigious centers, but an unlikely underdog—a graduate student at a small public university.
UC Santa Cruz professor David Haussler had joined the public project the year before to help identify genes, but quickly realized that assembling the genome sequence from the data that was being hurriedly gathered in the race with Celera would require new computer algorithms, and the project had no clear plan to create these. Informed that other centers were working on the sequence assembly problem, he formed a team to prepare to identify the genes after the sequence was assembled. This team included Jim Kent, a former computer software engineer who had gone back to school at UC Santa Cruz to get his Ph.D. in biology.
When no method for assembling the genome sequence appeared and Celera was rapidly closing in on a victory, Kent stopped preparing for gene finding and instead went to work coding an algorithm for genome sequence assembly. In just a month, he created a working assembly program. Days later, Celera and the public project declared a tie, and on July 7, UCSC had the great honor of being the institution that released the Human Genome Project’s first draft of the human genome sequence into the public domain by posting it on the Internet.
Kent then launched the UCSC Genome Browser to make it possible for researchers to annotate and share data about the genes they found in the sequence, a resource that remains one of the most important platforms in genomics today, helping researchers around the world explore genes, mutations, and their implications for human health.
Transforming data into action
After the Human Genome Project, Haussler founded the UC Santa Cruz Genomics Institute. He and his team have served as leaders in a number of major genomics projects over the years, serving as the data and coordination center for nationwide and global initiatives to push the field forward. Kent also stayed at UC Santa Cruz, directing the UCSC Genome Browser as it became a resource not only for studying human DNA, RNA, and multi-omic data, but for nearly 5,000 plant, animal, and pathogen species as well.
Kent is retired now, but Haussler and Linton have recently teamed up on another project—accelerating the applications of genomics for precision medicine and conservation. Linton was recruited as the UC Santa Cruz Genomics Institute’s Executive Director in 2023 to apply her experience in biotech and product development to help the Institute bring these exciting applications to more people. The Genomics Institute has developed a number of applications of genomics to improve human health, including clinical tests for pediatric cancer drivers, a pathogen-tracing platform used by state and federal public health agencies to track the spread of diseases, and more complete and rapid sequencing methods for identifying rare diseases that had previously taken years to diagnose.
An era of faster, smarter genomics is here
The pace of genomics today would have been unimaginable even a decade ago, let alone at the start of the human genome project. While it took years to first sequence the human genome, UC Santa Cruz has contributed to a world record that saw one sequenced in a clinic in just over five hours. This speed is transforming care for patients with rare diseases and aggressive cancers, enabling diagnoses in days rather than years.
New tools like the human pangenome—an inclusive reference genome sequence set that captures global genomic diversity, built by the leaders of the Telomere-to-Telomere Consortium and experts from many other institutes—are improving our ability to detect rare conditions. At the same time, artificial intelligence and machine learning are accelerating the interpretation of genomic data, allowing researchers to more quickly identify which mutations may cause disease.
Multidisciplinary collaboration has brought the field into new areas that can seem like science fiction. For example, a team at UC Santa Cruz is combining genomics with live cell technologies to find out exactly how genetic variations impact the growth of different cell types and tissues. They are using stem cells to grow organoids, miniature 3D “brains in a dish” that mimic real brain development, and are introducing genes linked to neurological disorders into these models to observe their effects in real time. These models allow scientists an ethical, scalable way of studying living neural connections that were previously unobservable outside of a living human subject, offering unprecedented insight into conditions like autism, epilepsy, and schizophrenia.
Beyond human health, genomics has become a vital tool in conservation biology. Environmental DNA taken from soil and water samples is being used to track which species of plants and animals are living in a given area—information that is guiding conservation efforts and helping protect endangered species. Population sequencing is also helping to identify what genetic variations might help key species like salmon and kelp better adapt to changing climates, and new tools will help introduce genetic diversity to endangered species that have been weakened by rapid population losses.
A legacy of public science
If you don’t yet know anyone who has benefited from a genetic test or personalized treatment, chances are that you will in the next decade as precision medicine becomes mainstream, particularly in the treatment of cancer and rare disease. For these life-saving interventions, we owe a debt of gratitude to the Human Genome Project. Its success was only possible because of the vision of—and investment in—public institutions, researchers, and funders who believed in science for the common good.
That ethos and commitment to open science continues at UC Santa Cruz, where researchers are turning genomic insights into real-world impact—and training the next generation to do the same.
The 25th anniversary of the human genome sequence is a celebration of science in the public interest, and a reminder of what we can accomplish when we invest in shared knowledge for the benefit of a healthier world.
