By adding 119 million bases — the “letters” in DNA sequences — to the existing genomics reference, the pangenome provides a representation of human genetic diversity that was not possible with a single reference genome. It is highly accurate, more complete and dramatically increases the detection of variants in the human genome, as shown in a collection of groundbreaking papers published today in the journals Nature, Genome Research, Nature Biotechnology, and Nature Methods.

The pangenome was produced by the Human Pangenome Reference Consortium (HPRC), which is co-led by UCSC’s Associate Professor of Biomolecular Engineering Benedict Paten and Assistant Professor of Biomolecular Engineering Karen Miga and is now available for use in an assembly hub on the UCSC Genome Browser. More than a dozen UCSC researchers and students are contributors to this project, which will continue into 2024 when the researchers plan to release a final pangenome with genomic information from 350 individuals.

“We are introducing more diversity and equity into the reference by sampling diverse human beings and including them in this structure that everyone can use,” said Paten, who is the senior author on the main marker paper. “One genome isn’t enough to represent everybody — the pangenome will ultimately be something that is inclusive and representative.”

Understanding genomic variation

Each person’s genome varies slightly — by about 0.4 percent compared to the next person, on average — and understanding these differences can provide insight into their health, help to diagnose disease, predict medical outcomes, and guide treatments. Using the pangenome reference will improve scientists’ ability to detect and understand variation in future studies.

Typically when scientists and clinicians study an individual’s genome to look for variation, they compare that individuals’ DNA to that of a standard reference to determine where there are differences of one or more base pairs. Until now, the reference genome has primarily been represented by a single sequence for each human chromosome, mostly sourced from one individual. But, this reference is nearly 20 years old and fundamentally limited in that it can not represent the wealth of genetic variations present in the human population. This introduces an issue called reference bias into genome analysis.

In contrast, the new pangenome is a reference that combines the genomes of 47 individuals from various ancestral backgrounds. The pangenome looks like a linear reference in areas where the sequences have the same bases, and expands to show the areas where there are differences. It represents many different versions of the human genome sequence at the same time, and gives scientists a more accurate point of comparison for variation that is present in some populations but not others.

“One genome can’t possibly represent all of the rich variation we know can be observed and studied around the world,” said Miga, Director of the HPRC Production Center at UCSC. “The No. 1 goal of the human pangenome reference is to try to broaden the representation of a reference resource to be more inclusive and more equitable for studying the human species, as a collection of references and not just one.”

Genomic variation can be small, consisting of differences of just one or a few DNA bases, or it can be large structural variants, classified as variants that are 50 base pairs or larger. These larger, structural variants can have important health implications. Until now, researchers have been unable to identify more than 70 percent of the structural variants that exist in human genomes due to limited technologies and the bias of using a single reference sequence.

Of the 119 million new bases added to the reference with the pangenome, roughly 90 million of these derive from structural variation. Structural variants are complex and may be inversions of sequences, insertions, deletions, or tandem repeats — a segment of two or more bases repeated numerous times. These new bases will help researchers to study regions in the genome for which there was previously no reference, and potentially be able to associate structural variants with disease in future studies.

“Now, we can map to more structural variants, so we’re finding features and areas in the genome that just weren’t there before,” Miga said. “That’s exciting because it’s allowing us to look at gene regulation in a unique way that we couldn’t study before, because those areas probably would have been inappropriately mapped or just ignored altogether.”

Using the pangenome reference for genomic analysis increases the detection of structural variants by 104 percent as compared to detection using the standard reference. The pangenome reference also increases the accuracy of calling small variants, those just a few bases long, by about 34 percent because of the increased amount of data present in the pangenome.

Each human carries a paired set of chromosomes — one set inherited from the mother and one from the father. The individual genomes present in the pangenome reference contains haplotype-resolved information, meaning it can confidently distinguish the two parental sets of chromosomes — a major scientific feat. Having this information will help scientists better understand how various genes and diseases are inherited.

This also means the current reference actually includes 94 distinct genome sequences, with the goal of getting to 700 by 2024.

Creating the pangenome

The pangenome was made possible through the development of advanced computational techniques to align the multiple genome sequences into one, usable reference in a structure called a pangenome graph. Paten and researchers in the UCSC Computational Genomics lab helped lead the HPRC efforts to develop the algorithmic methods needed to create this pangenome graph structure.

Because of the methods used in this project, all of the genomes within the pangenome reference are of extremely high quality and accuracy, covering more than 99 percent of each human genome with more than 99 percent accuracy.

“In the linear reference, we had only one sequence, one representation of each gene,” said Mobin Asri, a bioinformatics Ph.D. candidate at UCSC and co-first author on the main paper. “But we know that our genes have different variations in the human population. Using the pangenome graph, we want to have all of those variations in a single structure — and a graph is a natural way to do this.”

The HPRC project relies heavily on long- and ultra long-read sequencing technology to read DNA from biological samples. With recent advances, these techniques can now decode thousands to millions of base pairs of the genome at once. The long stretches of DNA reads are then assembled via specialized algorithms into more complete genomic sequences. Ideally each assembled sequence should represent the sequence of one chromosome.

Long reads contain errors about one percent of the time and current assembly algorithms are not perfect, which can cause the assembled sequences to be erroneous in some locations. To check for and correct these errors, the individual genomes that have been sequenced and assembled move through multiple tools, including a reliability pipeline developed by Asri. Once having been processed by these tools, the researchers can ensure the assemblies are accurate and complete.

After moving through Asri’s pipeline, the various genomes are compiled via complex algorithmic methods into the pangenome graph structure. Visually, the graph genome allows researchers to view differences in the various reference sequences as diverging areas in otherwise shared paths.

Building an accessible resource

All of the first 47 diploid genomes in the draft pangenome were sourced from individuals who participated in the 1000 Genomes Project (1000G), an influential effort which created a catalog of common human genetic variation from openly consented samples and was completed in 2015. The open consent status of these samples allow any researcher to access the resource without the privacy barriers that typically accompany genome research, with the aim of making the pangenome accessible to as many people as possible.

“Becoming a common resource is something that’s fundamental to the success of a human pangenome reference,” Miga said. “It has to have the ability to be accessible and open around the world to all researchers so we can use it as the foundation.”

The HPRC team is focused on outreach to ensure that the pangenome is a useful resource that will be utilized in clinics around the world. This means facilitating annotations, feedback, and input from the researchers carrying out studies using the pangenome reference.

“The draft pangenome is an important proof of principle that we hope is going to influence a lot of people and get them thinking about the pangenome and how it might affect their work,” Paten said. “Looking ahead, we see a lot of engagement with other groups — it takes a lot of different people to build something that is going to become a big community resource.”

Along with a focus on accessibility, the HPRC project has a dedicated ethics team focused on the social and legal implications of this project. They are working to anticipate challenging issues and help guide informed consent, prioritize the study of different samples, explore possible regulatory issues pertaining to clinical adoption, and work with international and Indigenous communities to incorporate their genome sequences in these broader efforts.

Continuing the legacy and future work

The human pangenome is a continuation of decades-long efforts from scientists at UC Santa Cruz to understand the biological code that underlies human life.

In 2000, Jim Kent, then a UCSC graduate student and now a research scientist at the Genomics Institute and director of the UCSC Genome Browser, wrote the code that assembled the first working draft of the human genome. UCSC scientists published it with open access to anyone who wanted to use it. Since then, UCSC has been at the forefront of genomics research.

In April 2022, UCSC’s Karen Miga co-led the Telomere-to-Telomere consortium to assemble the first complete sequencing of a human genome, filling in missing, complex regions of reference that had long eluded scientists.

“Since 2000, we’ve had a series of increasingly more accurate representations of one genome,” said David Haussler, Scientific Director of the UCSC Genomics Institute who led the UCSC team on the original Human Genome Project and advises on the pangenome project. “But no matter how accurately you represent one genome, that’s not going to represent all of humanity. Now is a turning point: no longer genomics of the one standard human genome, but genomics for everybody.”

The researchers are making progress toward the goal of completing the full pangenome by 2024. The team is in the process of recruiting new individuals to represent some populations not included in the 1000 Genomes Project, particularly people of Middle Eastern and African ancestry. Miga, as the director of the Data Production Center at UCSC, will spearhead these efforts going forward.

In addition to completing the final pangenome reference, the researchers are working toward forming an international human pangenome project that would establish partnerships with researchers across the world. These partnerships would include a two-way skills and knowledge exchange, aimed to bring the skills and technology needed to create high-quality reference genomes into the hands of researchers worldwide so they can carry out their own research.

Other UCSC researchers on the main paper include Marina Haukness, Glenn Hickey, Julian Lucas, Jean Monlong, Xian Chang, Jordan Eizenga, Charles Markello, Adam Novak, Hugh Olsen, and Trevor Pesout.

Other institutions involved in the Human Pangenome Reference Consortium may be found on the project’s main page.

Funding for the HPRC was primarily provided by the National Human Genome Research Institute.

But it has always been a flawed tool. One of its biggest problems is that about 70 percent of its data came from a single man of predominantly African-European background whose DNA was sequenced during the Human Genome Project, the first effort to capture all of a person’s DNA. As a result, it can tell us little about the 0.2 to one percent of genetic sequence that makes each of the seven billion people on this planet different from each other, creating an inherent bias in biomedical data believed to be responsible for some of the health disparities affecting patients today. Many genetic variants found in non-European populations, for instance, aren’t represented in the reference genome at all.

For years, researchers have called for a resource more inclusive of human diversity with which to diagnose diseases and guide medical treatments. Now scientists with the Human Pangenome Reference Consortium have made groundbreaking progress in characterizing the fraction of human DNA that varies between individuals. As they recently published in Nature, they’ve assembled genomic sequences of 47 people from around the world into a so-called pangenome in which more than 99 percent of each sequence is rendered with high accuracy.

Layered upon each other, these sequences revealed nearly 120 million DNA base pairs that were previously unseen.

While it’s still a work in progress, the pangenome is public and can be used by scientists around the world as a new standard human genome reference, says The Rockefeller University’s Erich D. Jarvis, one of the primary investigators.

“This complex genomic collection represents significantly more accurate human genetic diversity than has ever been captured before,” he says. “With a greater breadth and depth of genetic data at their disposal, and greater quality of genome assemblies, researchers can refine their understanding of the link between genes and disease traits, and accelerate clinical research.”

Sourcing diversity

Completed in 2003, the first draft of the human genome was relatively imprecise, but it became sharper over the years thanks to filled-in gaps, corrected errors, and advancing sequencing technology. Another milestone was reached last year, when the final eight percent of the genome — mainly tightly coiled DNA that doesn’t code for protein and repetitive DNA regions — was finally sequenced.

Despite this progress, the reference genome remained imperfect, especially with respect to the critical 0.2 to one percent of DNA representing diversity. The Human Pangenome Reference Consortium (HPRC), a government-funded collaboration between more than a dozen research institutions in the United States and Europe, was launched in 2019 to address this problem.

At the time, Jarvis, one of the consortium’s leaders, was honing advanced sequencing and computational methods through the Vertebrate Genomes Project, which aims to sequence all 70,000 vertebrate species. His and other collaborating labs decided to apply these advances for high-quality diploid genome assemblies to revealing the variation within a single vertebrate: Homo sapiens.

To collect a diversity of samples, the researchers turned to the 1000 Genomes Project, a public database of sequenced human genomes that includes more than 2500 individuals representing 26 geographically and ethnically varied populations. Most of the samples come from Africa, home to the planet’s largest human diversity.

“In many other large human genome diversity projects, the scientists selected mostly European samples,” Jarvis says. “We made a purposeful effort to do the opposite. We were trying to counteract the biases of the past.”

It’s likely that gene variants that could inform our knowledge of both common and rare diseases can be found among these populations.

Mom, dad, and child

But to broaden the gene pool, the researchers had to create crisper, clearer sequences of each individual-and the approaches developed by members of the Vertebrate Genome Project and associated consortiums were used to solve a longstanding technical problem in the field.

Every person inherits one genome from each parent, which is how we end up with two copies of every chromosome, giving us what’s known as a diploid genome. And when a person’s genome is sequenced, teasing apart parental DNA can be challenging. Older techniques and algorithms have routinely made errors when merging parental genetic data for an individual, resulting in a cloudy view. “The differences between mom’s and dad’s chromosomes are bigger than most people realize,” Jarvis says. “Mom may have 20 copies of a gene and dad only two.”

With so many genomes represented in a pangenome, that cloudiness threatened to develop into a thunderstorm of confusion. So the HPRC homed in a method developed by Adam Phillippy and Sergey Koren at the National Institutes of Health on parent-child “trios” — a mother, a father, and a child whose genomes had all been sequenced. Using the data from mom and dad, they were able to clear up the lines of inheritance and arrive at a higher-quality sequence for the child, which they then used for pangenome analysis.

New variations

The researchers’ analysis of 47 people yielded 94 distinct genome sequences, two for each set of chromosomes, plus the sex Y chromosome in males.

They then used advanced computational techniques to align and layer the 94 sequences. Of the 120 million DNA base pairs that were previously unseen or in a different location than they were noted to be in the previous reference, about 90 million derive from structural variations, which are differences in people’s DNA that arise when chunks of chromosomes are rearranged — moved, deleted, inverted, or with extra copies from duplications.

It’s an important discovery, Jarvis notes, because studies in recent years have established that structural variants play a major role in human health, as well as in population-specific diversity. “They can have dramatic effects on trait differences, disease, and gene function,” he says. “With so many new ones identified, there’s going to be a lot of new discoveries that weren’t possible before.”

Filling gaps

The pangenome assembly also fills in gaps that were due to repetitive sequences or duplicated genes. One example is the major histocompatibility complex (MHC), a cluster of genes that code proteins on the surface of cells that help the immune system recognize antigens, such as those from the SARS-CoV-2 virus.

“They’re really important, but it was impossible to study MHC diversity using the older sequencing methods,” Jarvis says. “We’re seeing much greater diversity than we expected. This new information will help us understand how immune responses against specific pathogens vary among people.” It could also lead to better methods to match organ transplant donors with and patients, or identify people at risk for developing autoimmune disease.

The team has also uncovered surprising new characteristics of centromeres, which lie at the cruxes of chromosomes and conduct cell division, pulling apart as cells duplicate. Mutations in centromeres can lead to cancers and other diseases.

Despite having highly repetitive DNA sequences, “centromeres are so diverse from one haplotype to another, that they can account for more than 50 percent of the genetic differences between people or maternal and paternal haplotypes even within one individual,” Jarvis says. “The centromeres seem to be one of the most rapidly evolving parts of the chromosome.”

Relationship building

The current 47-people pangenome is just a starting point, however. The HPRC’s ultimate goal is to produce high-quality, nearly error-free genomes from at least 350 individuals from diverse populations by mid-2024, a milestone that would make it possible to capture rare alleles that confer important adaptive traits. Tibetans, for example, have alleles related to oxygen use and UV light exposure that enable them to live at high altitudes.

A major challenge in collecting this data will be to gain trust from communities that have seen past abuses of biological data; for example, there are no samples in the current study from Native American nor Aboriginal peoples, who have been long been disregarded or exploited by scientific studies. But you don’t have to go far back in time to find examples of unethical use of genetic data: Just a few years ago, DNA samples from thousands of Africans in multiple countries were commercialized without the donors’ knowledge, consent, or benefit.

These offenses have sown mistrust against scientists among many populations. But by not being included, some of these groups could remain genetically obscure, leading to a perpetuation of the biases in the data — and to continued disparities in health outcomes.

“It’s a complex situation that’s going to require a lot of relationship building,” Jarvis says. “There’s greater sensitivity now.”

And even today, many groups are willing to participate. “There are individuals, institutions, and governmental bodies from different countries who are saying, ‘We want to be part of this. We want our population to be represented,'” Jarvis says. “We’re already making progress.”

NASA’s new James Webb Space Telescope (JWST) solved that issue. The telescope’s infrared technology allows it to see planetary objects and features that were previously obscured by hazes, clouds or space dust, aiding astronomers in their search for habitable planets and early galaxies.

A team of researchers used JWST to observe GJ 1214b’s atmosphere by measuring the heat it emits while orbiting its host star. Their results, published in the journal Nature on May 10, 2023, represent the first time anyone has directly detected the light emitted by a sub-Neptune exoplanet — a category of planets that are larger than Earth but smaller than Neptune.

Though GJ 1214b is far too hot to be habitable, researchers discovered that its atmosphere likely contains water vapor — possibly even significant amounts — and is primarily composed of molecules heavier than hydrogen. University of Maryland Associate Professor of Astronomy Eliza Kempton, lead author of the Nature study, said their findings mark a turning point in the study of sub-Neptune planets like GJ 1214b.

“I’ve been on a quest to understand GJ 1214b for more than a decade,” Kempton said. “When we received the data for this Nature paper, we could see the light from the planet just disappear when it went behind its host star. That had never before been seen for this planet or for any other planet of its class, so JWST is really delivering on its promise.”

A ‘new light’

Sub-Neptunes are the most common type of planet in the Milky Way, though none exist in our solar system. Despite the murkiness of GJ 1214b’s atmosphere, Kempton and her co-authors determined the planet was still their best chance of observing a sub-Neptune’s atmosphere because of its bright but small host star.

In their Nature paper, the researchers measured the infrared light that GJ 1214b emitted over the course of about 40 hours — the time it takes the planet to orbit its star. As day turns to night, the amount of heat that shifts from one side of a planet to the other depends largely on what its atmosphere is made of. Known as a phase curve observation, this research method opened a new window into the planet’s atmosphere.

“JWST operates at longer wavelengths of light than previous observatories, which gives us access to the heat emitted by the planet and allows us to create a map of the planet’s temperature,” Kempton said. “We finally got to see GJ 1214b in a new light.”

By measuring the movement and fluctuation of heat, the researchers determined that GJ 1214b does not have an atmosphere dominated by hydrogen.

Potential water world?

The question of whether GJ 1214b contains water has long interested astronomers. Previous observations by NASA’s Hubble Space Telescope suggested that GJ 1214b could be a water world — a loose term for any planet that contains a significant amount of water.

The latest JWST data revealed traces of water, methane or some mix of the two. These substances match a subtle absorption of light seen in the wavelength range observed by JWST. Further studies will be needed to determine the exact makeup of the planet’s atmosphere, but Kempton said the evidence remains consistent with the possibility of large amounts of water.

“GJ 1214b, based on our observations, could be a water world,” Kempton said. “We think we detect water vapor, but it’s challenging because water vapor absorption overlaps with methane absorption, so we can’t say 100% that we detected water vapor and not methane. However, we see this evidence on both hemispheres of the planet, which heightens our confidence that there really is water there.”

Reflecting on the findings

The researchers made another surprising discovery in their study: GJ 1214b is incredibly reflective. The planet was not as hot as expected, which tells researchers that something in the atmosphere is reflecting light.

Kempton said there is plenty of room for follow-up studies, including ones that take a closer look at the high-altitude aerosols that form the haze — or possibly clouds — in GJ 1214b’s atmosphere. Previously, researchers thought it might be a dark, soot-like substance that absorbs light. However, the discovery that the exoplanet is reflective raises new questions.

“Whatever is making up the hazes or clouds is not what we expected. It’s bright, it’s reflective and that’s confusing and surprising,” Kempton said. “This is going to point us toward a lot of further studies to try to understand what those hazes could be.”

Accidentally discovered as researchers were checking pygmy-possum and bat nest boxes on Kangaroo Island, a colony of Polyrhachis femorata ants appeared to be dead… until one moved.

Researchers believe the ants were ‘playing dead’ as a defensive strategy to avoid potential danger.

Published by CSIRO, this is the first time that a whole colony of ants has been recorded feigning death, and the first record of the Polyrhachis femorata ant species for South Australia.

Wildlife ecologist, UniSA’s Associate Professor S. ‘Topa’ Petit, says she was surprised to discover a colony of what appeared to be dead ants in one of the nest boxes.

“The mimicry was perfect,” Assoc Professor Petit says. “When we opened the box, we saw all these dead ants…and then one moved slightly.

“This sort of defensive immobility is known among only a few ant species — in individuals or specific casts — but we don’t know of other instances when it’s been observed for entire colonies.

“In some of the boxes containing colonies of Polyrhachis femorata, some individuals took a while to stop moving, and others didn’t stop. The triggers for the behaviour are difficult to understand.”

Assoc Prof Petit says that nest boxes may present an opportunity to study the ants’ death-feigning behaviours, which are of great interest to many behavioural ecologists investigating a diversity of animal species.

The discovery was made during the Kangaroo Island Nest Box Project, where 901 box cavities have been monitored across 13 diverse properties as part of wildlife recovery efforts following the devastating 2020 bushfires.

Co-researcher at the Kangaroo Island Research Station, Peter Hammond, says that he used to call the Nest Box Project ‘Friends of the Invertebrates’, because invertebrates were often the only occupants of the bat and pygmy-possum nest boxes.

“We are learning a lot about invertebrates as well as targeted vertebrates,” Hammond says.

“Most of our several hundred boxes are on burnt ground, but we also have some on unburnt properties as controls because our aim is to determine the value of nest boxes in bushfire recovery.

“Polyrhachis femorata is strongly associated with the critically endangered Narrow-Leaf Mallee community, where it colonised several boxes very quickly. However, we also have records for two other properties further west, indicating that the ants will use other habitats.

“We believe that the Polyrhachis femorata species was strongly affected by the bushfires.”

Assoc Prof Petit says there is a lot to discover about this species.

“Polyrhachis femorata is a beautiful arboreal ant that tends to be quite shy, but little else is known about its ecology or behaviour,” Assoc Prof Petit says.

“We have a relatively unknown world of ants under our feet and in the trees. Ants provide crucial ecosystem services and are a vital part of functional ecosystems on Kangaroo Island and elsewhere.

“It is very exciting that such an endearing species as Polyrhachis femorata is living on Kangaroo Island and we look forward to finding out more about its ecology.

“We have no doubt that other ants with similar death-feigning behaviours will be discovered in Australia, but it is thrilling to be among the pioneers.”

The study found that warm water pollution increased growth rates but also death rates, resulting in a population of younger, but larger fish. The finding is at odds in part with general predictions of the effect of warming on natural ecosystems and highlights that these need to be tested in large-scale experiments.

As aquatic ecosystems become warmer, it is predicted that animals such as fish will grow faster at a young age but reach smaller body sizes as adults. This pattern has mainly been observed in small-scale experiments, and although some studies have tested this prediction in natural environments, these have mostly been carried out on fish species subjected to fishing, where the process of fishing itself can influence growth rates and body size.

“Studies into the effects of warming waters on fish from large-scale, semi-controlled experiments in natural settings are rare, yet they can provide unique insights,” says lead author Max Lindmark, researcher at the Swedish University of Agricultural Sciences, Department of Aquatic Resources, Lysekil, Sweden. “We used a unique study system to investigate how warm water pollution has changed the death rates, growth rates and size of fish over many generations.”

The team carried out their study in an enclosed coastal bay that has received cooling water from a nuclear power plant, making it 5-10°C warmer than the surrounding waters. They compared the fish species Eurasian perch from the enclosed bay and from a reference area in the adjacent archipelago over a 24-year time period. They combined data on catches with measurements of the fishes’ length-at-age (back-calculated throughout their life from “age rings” in hard structures), and then analysed these using statistical models to investigate how the warm water pollution affected the age and size of the fish populations, as well as their growth and death rates.

While the researchers found statistically notable differences in estimated growth rates, death rates and sizes of the fish populations between the heated and reference areas, not all of these changes were as they expected. Although female perch in the warm area grew faster, as the team anticipated, they continued to do so throughout life. These fish therefore reached a large size-at-age — approximately 7-11% larger in the heated area at any age, when compared with the reference area. Moreover, the authors say the increase in growth rate of younger fish due to warm water was so pronounced that even if death rates were higher because of warming, and resulted in a younger overall population of fish, the average size and relative abundance of larger fish was still higher in the heated area. This trend conflicts with the prediction that global warming would shrink fish over time, especially the large and old ones. In essence, ecosystem warming instead led to younger, but larger fish in this study.

“Our study provides strong evidence for warming-induced differences in growth and death rates among a natural population of an unexploited temperate fish species exposed to 5-10°C water temperature increases for more than two decades. These effects largely, but not completely, counteract each other — while the fish are younger, they are also larger on average,” says co-author Malin Karlsson, Water Manager at the Department of Nature and Environment, County Administrative board of Västmanland, Sweden.

“These findings highlight that generalised predictions based on theories such as the temperature-size rule may have limited use for predicting changes at a population level, and that both death rates and growth rates are important when studying temperature effects,” concludes senior author Anna Gårdmark, Professor at the Swedish University of Agricultural Sciences, Department of Aquatic Resources, Uppsala, Sweden. “Although we only studied a single species, this unique climate change experiment suggests the effects of heating at the scale of a whole ecosystem, making its findings highly relevant in the context of global warming.”