Category Archives: Genome

Genomics, the study of the entirety of an organisms genes called the genome, a much newer field compared to the well-known study of genetics, has progressed in the last couple of decades owing to technical advancements in DNA sequencing and computational biology. Genomics as a field is not only advancing healthcare but is also driving sustainable innovation across a whole variety of sectors, be it computing, agriculture, forensics, climate change, and more. Introducing IDCs new whitepaper commissioned by Lenovo & Intel, called Leveraging High-Performance Compute Infrastructure to Address the Genomic Data Challenge in Life Sciences,Sinisa Nikolic, Director - HPC & AI, Lenovo ISG AP, engaged in an informative discussion with Dr. Harsh Sheth, Assistant Professor and Head of Advanced Genomic Technologies Division, FRIGEs Institute of Human Genetics.The revolution of the genomics industry began in the 19th century, way back when genome sequencing required scientists to hold up an x-ray photograph and manually read 400-500 DNA letters a day from a base of 3.3 billion bases in the human genome. It is no surprise that it took 13 years to sequence one complete human genome, and at the cost of approximately $3 Billion. Speaking about how genome sequencing has evolved over the last few decades, Dr. Sheth explains that today genome sequencing of an individual is possible in 2-3 days and that in a span of 40 years, the cost of genome sequencing has reduced from $3 Billion to less than $1000. Elaborating further on the advancement of genome sequencing, Dr. Sheth said, For the last three of four decades, it has been a dream of a scientist or a doctor to provide results in a short time frame to the patients. The advancements in the last four decades have been so huge that genetic test results can be provided in a few days. Opining on the technological barriers impacting the genomics revolution, Sinisa said, Organizations have limited time and limited resources to develop some of these genomics technologies [...] what they want is a blend of pre-packaged technologies, and Lenovo was and is best positioned to work with these organizations given its long and storied history in HPC and very strong focus on genomics.

Elaborating on the challenges faced by genomics researchers, Sinisa recalls findings from the IDC report regarding infrastructure challenges across the industry. He explains that 28 per cent of Asian respondents said their existing infrastructure is not scalable enough, 20 per cent said their current solution is complex, and 20 per cent said too much customization is required. With a consistent focus to address some of these industry-wide challenges, Sinisa explained how Lenovo collaborated with Intel using Genome Analysis Toolkit (GATK) open-source code an HPC architecture poised to revolutionize genome sequencing. We optimized and tuned that for our hardware infrastructure, front of mind was to use off-the-shelf components, keeping the costs for our clients to minimum [] we call it GOAST, he adds. Sinisa further explains how with the Genomics Optimization and Scalability Tool (GOAST), Lenovo had reduced the processing time of a whole human genome from 60 - 150 hours to 24 48 minutes. He further elaborated how GOAST can increase lab productivity, improve time to data and potentially save lives through all the discoveries.

Lenovo ISG partnered with Delhi Universitys Center of Genetic Manipulation of Crop Plants (CGMCP), looking to improve and breed more nutritious, drought and disease-tolerant, high-yield plants to feed the world. Lenovo deployed its GOAST solution at CGMCP to accelerate time to insights - 48 hours to just 6 hours.

Dr. Sheth adds, The COVID-19 pandemic is a wonderful example of where genomics came to the rescue. Never in the history of mankind has a vaccine been developed within a year. He further explains how technological advancements in genomics helped create the genetic architecture of the COVID-19 virus even before it was declared a pandemic, which only helped rapidly accelerate the development of vaccines and begin Phase 1 trials early into the pandemic, which was spreading at a massive pace. He adds that genomics is also being used to address multi-drug resistance in various diseases, and oncology has changed how cancer treatment is delivered through personalized treatment. Lenovo has further collaborated with the CSIR Institute of Genomics, and Integrative Biology (CSIR-IGIB), New Delhi, in a unique partnership that uses GOAST to advance cancer research by digging deeper into the genetic roots of the disease.

In conclusion, Sinisa draws light on precision medicine as The Next Big Thing that will drive the genomics revolution on the back of technological advancements. He elaborated how genome sequencing and genome analytics tools (such as GOAST) are helping the world understand biology and genetics better and would allow faster and more accurate care for patients. In explaining how GOAST technology will evolve, he states that Lenovo is working closely with software development teams to build many technology efficiencies which will ultimately impact humanity positively.

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Lenovo ISGs GOAST Solution Powering genome sequencing with smarter IT - ETHealthWorld

As an associate professor in Genomic Medicine, Linghua Wang, M.D., Ph.D., studies how normal cells become cancerous and how cancer cells develop resistance to drugs.

She and her lab are working to identify the earliest events during tumor progression from precancerous diseases to discover new biomarkers and targets for the development of effective interception strategies.

The lab is also focused on understanding cellular plasticity, which is how cancer cells adapt to the microenvironment and avoid being attacked by the immune system or cancer treatments.

Cellular plasticity contributes to cancer development, progression and metastasis. If we can better understand this process, we can develop effective treatment strategies to overcome drug resistance, Wang says.

As she looks toward the future, she reflects on the challenges shes overcome to get to where she is today.

A desire for a different path

Growing up in a small village in China, Wang was expected to follow a traditional path for young women to become a housewife and take care of children. In fact, with three younger brothers at home to take care of, she wasnt supposed to advance beyond middle school.

I knew I wanted a different life for myself, Wang says. She worked hard and earned great grades, which caught the attention of her teachers and the school principal, who encouraged Wangs parents to let her continue her education.

Wang did so well in school that she earned scholarships to pay for college, where her love of learning grew. I never had books of my own to read growing up, she says. The first time I saw the library, I couldnt believe there were so many books.

Earning an M.D., then Ph.D.

Wang grew up with the goal of becoming a doctor so she could help people. After medical school, she earned a license to practice ophthalmology. But a few months later, her husband was admitted to a Ph.D. program in Tokyo, Japan.

I didnt want to live apart, but I knew I would have had to start my medical school all over again to be able to practice in Japan, so I decided to move with my husband and find a new career, she says.

For the first few months in Japan, Wang wasnt sure what she wanted to do with her life. But she did know one thing: I didnt want to be just a housewife, so I started looking for a job that would keep me constantly learning. She was hired as a research fellow in a cancer genetics laboratory.

I learned about cancer cells and couldnt wait to learn more, she says. So, she enrolled in a Ph.D. program in cancer genomics at the University of Tokyo, studying pancreatic cancer.

It opened a whole new world for me and fueled my passion, Wang says. I realized that studying the cancer genome can transform cancerdiagnosis and treatment and help cancer patients. After that, I was hooked on cancer genomics and data science.

Making connections at MD Anderson

After earning her Ph.D., Wang and her family moved to Houston in 2012, where she completed her postdoctoral training at Baylor College of Medicine and joined their research faculty.

She wanted to become an independent investigator so that she could build and grow her own lab. In 2016, she was invited to speak at the Annual Human Genome Meeting, where she met Andy Futreal, Ph.D., chair of Genomic Medicine at MD Anderson.

I walked up to him and asked if he had any tenure-track faculty positions, she recalls. I felt so lucky to meet Dr. Futreal, who recruited me to MD Anderson. He is always there whenever I need his support and he provided the platform for me to find my own way to shine.

Wang credits MD Andersons team science approach for her interest in establishing a lab here in 2017. MD Anderson is an exceptional place to work with resources and facilities unlike anywhere else. We have so many talented scientists here, and it is such a wonderful place to collaborate. Working closely as a team, were making meaningful contributions to patient care, she says.

Wangs lab aims to harness the potential of big data to fight cancer. Im thrilled about the future of big data in cancer care and the work were doing in the lab. I want to bring in new researchers who love the work and are just as motivated and ambitious as I am.

Finding a balance between work and home life

With three young kids at home, Wang says being a mother helps her be a better leader. Parenthood has taught me to communicate more effectively, and to be more compassionate with members of my lab, she says.

It also helps her manage her time. I have a very busy schedule, constantly going from one meeting to the next, and with tight deadlines for grants and manuscripts, she says. So, I have to manage my time wisely to make sure I can spend quality time with my family, too.

Outside the lab, she likes to travel with her family and finds that cooking meals for them feeds her creative side. I love testing new recipes and seeing my family enjoy trying something new, she says. Cooking is my mental break, and its nice to make something without having to look at a screen, like I do throughout the workday.

The future of genomic medicine

Wang believes the rise in data science, machine learning and artificial intelligence will advance precision and predictive oncology and accelerate drug development.

We will be able to accurately predict patients response to therapy as well as the risk of recurrence and adverse effects and choose the best possible treatment for patients, she says.

And, perhaps most importantly, by using big data and predictive analytics to determine cancer risk, Wang believes researchers will be able to identify better biomarkers to detect cancer early and develop better prevention strategies to reduce the risk of getting cancer.

I expect to see successful integration of data science and clinical practice in the near future, Wang says.

Request an appointment at MD Anderson online or by calling 1-877-632-6789.

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From a small village in China to MD Anderson: Genomic medicine researcher looks to the future of big data in cancer care - MD Anderson Cancer Center

And thats where the now-extinct thylacine comes in.

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Last month, US biotech Colossal Biosciences announced it would invest $10 million in a University of Melbourne team working to bring the Tasmanian tiger back from extinction.

The funding will allow a team of about 50 scientists across Melbourne and Texas to work on the project, initially for three years.

Some of the same techniques used to map the full genome for the smoky mouse will be used on the thylacine project, including growing living cells of threatened species, storing them in a cryobank, and using the DNA from those cells for ongoing research.

The Melbourne Museum has a liquid nitrogen facility called the Ian Potter Australian Wildlife Biobank the animal equivalent of a seed bank that houses the museums existing collection of more than 44,000 tissue, feather and fur samples at minus 185 degrees.

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Cryobanking, or cryopreservation, is the process of cooling and storing cells, tissues, or organs at very low or freezing temperatures to save them for future use.

Previously, the smoky mouse DNA was extracted from skin samples from the ear. But now the institute is growing living smoky mouse cells, so there will always be a store of living DNA from threatened species.

We can preserve living cells as an indefinite resource to maintain living genomic variation, should we require it as part of animal husbandry, said Dr Kevin Rowe from the Museum Victoria Research Institute.

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De-extinction and the recovery of nature lost will only succeed if we as a species are inspired to make the investments needed in nature research and in healing nature.

The smoky mouse genome, the thylacine project and the ethical debate around resurrecting extinct animals will be discussed at the museums next Future Forum on October 6.

Get to the heart of whats happening with climate change and the environment. Our fortnightly Environment newsletter brings you the news, the issues and the solutions. Sign up here.

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This little furball is helping to map a course toward the return of the thylacine - Sydney Morning Herald

An international course strengthened the capacities of laboratories in the region to monitor genetic changes in viruses.

Panama, Aug. 26, 2022 (PAHO)- Representatives from 17 public health laboratories in the region came together this week for the 26th edition of the Viral Evolution and Molecular Epidemiology (VEME) course in Panama. The training, which was organized by the Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES) in Panama, the Oswaldo Cruz Foundation (FIOCRUZ) in Brazil, and the Pan American Health Organization (PAHO), aims to strengthen genomic surveillance in the Americas.

"Studying the evolution of viruses is key to detecting mutations or variants that can modify the transmission rate or severity of a pathogen and affect the efficacy of diagnostic tests, vaccines and treatments," said Jairo Mndez, emerging viral disease advisor at PAHO. "This is something we experienced with SARS-CoV-2, so we must deepen genomic surveillance for any emerging or re-emerging viruses," he added.

More than 120 people from around the world participated in the 26th edition of VEME, a course that originated at the University of Leuven, Belgium, more than 25 years ago. Around 50 experts in bioinformatics from renowned scientific institutions from 15 countries delivered the training that took place from August 21 to 26 in Panama. Participants from the region were supported through PAHO with funds from the United States Government.

The course consisted of theoretical and practical sessions divided into four modules, ranging from the generation of data from genomic sequencing to more complex analysis of these sequences. For the first time, VEME also included a module aimed at managers and decision-makers.

Dr. Carlos Senz, Secretary General of the Nicaraguan Ministry of Health, considered the training to be "extremely important" both for the technicians who carry out genomic sequencing and for decision-makers like himself. "The course has provided tools to link the epigenetic situation, genomic sequencing and molecular epidemiology information to political and strategic decision-making at the level of each country," he said, highlighting the relevance of "integrating technical approaches with transdisciplinary participation for the resolution of complex problems."

Genetic sequencing and analysis provide insights into the evolution of a virus and its variants, as well as its geographic- and temporal dispersion. The timely analysis of the data serves to identify signs or changes that can have an impact on the behavior of the virus and on health tools and measures. In addition, the information obtained can be complementary to guide the response to an epidemic or pandemic.

"This type of bioinformatic analysis is not something that is commonly done in public health laboratories in the region because it requires training and education," said Alexander Martinez Caballero, Director of the Department of Genomics and Proteomics Research at the Gorgas Institute in Panama. "From now on, many laboratories will be able to perform these analyses in their facilities in a timely manner and for various viruses of interest, such as monkeypox and others that may appear," he said.

Since the beginning of the COVID-19 pandemic, the sequencing capacity to monitor SARS-CoV-2 and its variants has been expanded in the region with the support of PAHO and the Regional COVID-19 Genomic Surveillance Network (COVIGEN), which includes laboratories from more than 20 countries in the Americas.

PAHO has provided training to strengthen genomic sequencing and to integrate it into epidemiological surveillance in the countries. Since 2020, COVIGEN has performed more than 426,000 sequences of SARS-CoV-2 in Latin America and the Caribbean.

The VEME course is one more action to strengthen surveillance and is aligned with the Regional Genomic Surveillance Strategy for Epidemic and Pandemic Preparedness and Response, which will be discussed in September by health leaders of the Americas during PAHO's 30th Pan American Sanitary Conference in Washington.

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PAHO strengthens genomic surveillance in the Americas - Pan American Health Organization

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China Genome-Based Drug Industry Forecasts 2022: Demand to Grow by 9% Through 2031 - ResearchAndMarkets.com - Tullahoma News and Guardian

When the Smithsonian National Museum of Natural History opened its genomics exhibit in 2013, the field was just celebrating the 10th anniversary of the completed Human Genome Project. Sequencing that first genome cost over $500 million. The genomes since cost $10,000.

In 2022, as the museum prepares to wrap up the landmark exhibit, much has changed. Gene names such as BRCA1 and HER2 have entered the public consciousness. Sequencing DNA has become faster, cheaper, and smaller-scale. Portable sequencers that were not even being sold commercially in 2013 have since been used to trace the evolution of the Ebola virus as it wreaked havoc in West Africa. The development of CRISPR-Cas9 landed a Nobel Prize. The cost of genome sequencing is rapidly approaching $100.

What seemed cutting edge maybe in 2013, now in 2022, were just things that were somewhat more routine, said Carla Easter, who helped organize the exhibit while at the National Human Genome Research Institute, which partnered with the Smithonian to launch the project.

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Nobody knew what CRISPR was ten years ago, added Easter, now at the Smithsonian. But now, people will mention it and theyll know what that is. They may not know understand the science behind it, but at least theyve heard the word.

Before the exhibit closes its doors later this year, STAT spoke with curators, educators, and leading scientists involved in its creation about how genomics has changed in the past decade.

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The field of genomics has gone way beyond genomics experts, people who would call themselves genomicists, and its applied everywhere, said Lawrence Brody, who leads the NHGRI Division of Genomics and Society. Weve done these analyses of the NIH budget, and theres way more genomics being done outside of our institute than there is inside our institute, because its such a powerful tool. And thats a great thing.

Most of those improvements have been with sequencing, he said. Were now talking about what genetic variation might be. If you study people who have a disease, [and] find a genetic variant that seems to be common in those people, you dont really know anything until you ask yourself, How common is that variant in people who dont have the disease? And you need to look at large numbers of people to understand that. This also means involving people who are not normally represented in research, a task the NIH-funded All of Us program has taken up.

Another change he sees is the newfound ability to broadly study the entire genome, rather than only specific genes, and to analyze how various parts of the genome are being turned on or off in individual cells.

Even though all cells but sperm and egg share the same genome, they do not all make the same proteins. A decade or two ago, studying these differences involved an arduous process, and scientists could only study a few specific genes at a time. But Brody said that has changed thanks to advances in RNA sequencing, which allow you to ask questions about all the genes completely, objectively, and agnostically. And to me, thats really the power and has always been the power of genetics is to ask the question and have the organism tell you whats important, as opposed to guess and saying It must be this gene or it must be that gene.

Now, he said, the field needs to understand how diseases are caused by a combination of genes and environmental exposures, manipulate the genome to treat diseases, and survey life on the planet because, as a geneticist, its really important for me to know the variations out there.

We often say Oh, in ten years, well be doing this, and if you look back at those predictions, were wrong a lot, said Brody. But we will get there.

To Stephen Palumbi, a professor of marine sciences at Stanford who studies corals, the biggest change in genomics is the speed and cost of sequencing.

The same questions are there, the same approaches are there, said Palumbi. But its like you took a garden hose that you were plenty of water flow and everything and you turned it into a firehose of information. That deluge of data that you can get right now is incredible. So the whole field, not just natural history or oceans, but the whole field of genomics, has become more and more and more tuned to being a high-flow data-rich, incredible science of whats now called bioinformatics. Bioinformatics at the time, a decade ago, was really important. Its probably increased in importance 50-fold because the data sets have increased 100-fold, and being able to actually pull information out of these data sets has become one of the most interesting, challenging, and rewarding parts of how genomes are used.

The human genome is the most traveled, well-mapped genome in the known universe, no big surprise. But I study organisms that are not humans and have genomes anyway. And so were always sort of scrambling a little bit behind that technology, but adopting it and adapting it, he said.

He pointed to work he is doing to study corals living on reefs in an archipelago in Palau that look strikingly similar, but have turned out to be genetically different. Being able to deeply mine the genomes of those corals offers valuable clues about their genetic capacity to adapt to environmental change.

So genomics gives me a map to their current patterns of adaptation that I would not get in any other way, he said. When this exhibit opened, I couldnt have done what I just told you because it would have been prohibitively expensive. And the people who can do the bioinformatics really werent there. And the genetic, genomic resources that I need to do this work werent there. But theyre there now. So thats where the whole field has changed so much. In that period of time, 2011 till now, the entire landscape, seascape, forestscape changed.

He said the fields advances like enabling handheld sequencing will make it even easier to reveal DNA in the environment, whether that is samples pulled from a kelp forest or fungus living in the soil of wetlands. Those insights are more critical than ever, as they can offer insights on monitoring pathogens and endangered species.

What I dont want to see in 50 years in a genome exhibit, is a whole lot of genomes of extinct species that weve lost because of climate change.

Harvard professor and genetics pioneer George Church was involved in the Human Genome Project from its earliest days, having joined the effort in 1984, years before the National Institutes of Health got involved. He saw the project pique the interest first of lawmakers, and then the public at large. Some projects that are highly technical, whether theyre expensive or not, are unpopular or ignored, said Church. But this one actually captured Congresss interest, around 1987 was really when they started paying attention. They liked this and they committed to $3 billion, which was quite a lot in 1987. And then they proceeded to get excited in all kinds of science and they ended up doubling the NIH budget, which is almost unprecedented and hasnt happened since then.

And despite the celebration of the sequencing of the human genome, Church said, the work is far from over.

[It] had been sort of declared done in 2001, and then was re-declared done in 2004. And its actually still not done in my opinion. This year marks the first year that weve finished one genome, one human genome, but in a way that really isnt generally applicable we did it to a haploid cell. Haploid cells have only a single set of chromosomes, in contrast to the typical human cell which is diploid and has two. So if you want to diagnose a patient, you have to be able to do a diploid genome. And no ones ever completed a diploid genome yet, although we are on our way, Church said.

Church said genomics has already made an impact in medical care. It played a role in the development of the Covid-19 vaccines, and can give prospective parents insight about when they carry a recessive gene for certain diseases. It also enabled the development of the first gene therapy to be approved by the Food and Drug Administration. Even when the exhibit was being developed a decade ago, he said, the idea of gene therapy wasnt that popular. In fact, it just barely was recovering from its 2001 setback, or 1999 to 2001 setbacks, plural.

In the future, Church would like to see a bioweather map that uses genomics to keep tabs on and track the evolution of viruses and bacteria, akin to a weather forecast. What flu just flew in the town? And what is happening at the daycare? Should you take your kid? he asked.

But for all his big ideas about genomics, Church also has his sticking points. Among them: One of my pet peeves is when people say, Oh, you know that humans share fill in your favorite number with fill in your favorite organism. So itd be like 46% related to plants or bananas, he said. I mean, its a completely meaningless statistic.

(It is a battle he did not win with the Smithsonian exhibit, which tells viewers that the human genome is 41% similar to a bananas.)

For Joann Boughman, a senior vice chancellor at the University System of Maryland, advances in genomics have changed how people perceive genetic diseases. From the historical perspective, if you will, in human genetics, we have understood and have always looked at variability as an essential theme, said Boughman. It wasnt until the human genome started and people started understanding about the variations at the DNA level that they made the connection between genes and ultimate phenotype, what we look like. And it has been really fascinating to see how these two worlds, as you will, collide and hopefully come together.

During the pandemic, Boughman served as the point person for the Maryland university systems Covid response, which included a community of over 200,000 students, staff, and faculty. And I realize Im working with an educated population, but all kinds of people really understood when we started talking about viral variants, they understood what had changed was the DNA in the virus, that there had been a mutation. These were not absolutely foreign concepts to people, and they, with very little explanation, would understand why one vaccine might fight this virus, but not a mutated form of that virus, Boughman said.

This is part of a growing awareness she had seen unfolding long before the pandemic hit. The fact that the double strand of DNA is not a foreign concept, even to relatively small children, really makes our conversation different. And thats been an incredible thing to watch over the last 40 years. Today, if people see an image of DNA, theyll recognize it.

Boughman said that shift struck her recently when she saw a commercial for a treatment for a rare genetic disease. It hit me right between the eyes that they actually have an ad on TV and named a genetic syndrome and talked about that drug that was helping these children. But 20 years ago, the idea of putting on television a picture of a child who has physical abnormalities and labeling them as having a genetic disease or a genetic syndrome just would have been devastating. But now that we are getting to the point where we understand enough about the genetics that we can start to intervene and treat, it becomes a very different perspective than somebody who is simply doomed. They labeled it genetic and they labeled it as a syndrome, and then they talked about hope that they had. And that simply was not the case 20 or 30 years ago, at all.

As a geneticist and professor at the University of Pennsylvania, Sarah Tishkoff originally got involved in the exhibit to share her expertise on what genetics and genomics can tell us about the evolutionary history of humans. Given her research, she is keenly aware of how much the field has changed in the past few decades.

She is also aware of how far the field still needs to go specifically when it comes to securing better representation in genomics research, which is overwhelmingly centered on white and European populations. What we dont really have are good reference genomes, she said. So there are populations or people in different parts of the world that might have insertions or deletions in their genome or things that arent even in that reference.

But if the Smithsonian were to open the exhibit again in 50 years, she said, we will have unraveled far more mysteries and the public will be far more familiar with the science.

I think at that point, most people are going to have their genome sequenced, she said. That would give scientists a far deeper trove of data to understand structural variation large-scale differences across the DNA of individuals, including duplications of certain genes and, in turn, knowledge of how humans have adapted to different environments and develop different levels of risk for disease. She added that by that time, were going to know more about what the genome variation actually does, similar to her findings that multiple different gene mutations can cause lactose tolerance.

She is also hopeful that we will have wide-ranging insights into ancient DNA and the origins of human history, including a far more complete picture. Right now, she noted, we are limited by the fact that ancient DNA is often poorly preserved. Someday, somebody is going to get ancient DNA from a fossil in Africa thats 50,000 years old or 100,000 or 200,000. Thats going to really help shed light on human history in that region, which is where we all evolved, Tishkoff said. Im hoping that were going to know a lot more examples of how people adapted to different environments.

In addition to his day job at the E.O. Wilson Biodiversity Foundation, Dennis Liu serves on the board of the American Chestnut Foundation, which has funded efforts to introduce a gene into American chestnut trees that can help them resist a group of diseases known as blight. To Liu, there are clear benefits that advances in genomics can bring to conservation efforts like this one.

But as the field ages, he also sees a downside to the growing distance from the Human Genome Project.

When the initiative launched, Liu said, there was a sense of a moonshot at the time. And I think that kind of new excitement isnt necessarily here. I havent done a survey or a poll, but I imagine that these things are now kind of all lumped together with big pharma and the pharmaceutical industry and sort of high-tech medicine. And I would imagine that a lot of people still would wonder, Oh, I dont know, what does this do for me? I do think theyd hope, of course, that this kind of information is going to help cancer treatments, for example, and those sorts of things.

For example: To the field, the increase in sequencing speeds is a huge advance. But I dont think that means much of anything to the general public, Liu said. Instead of feeling that genomics completed with the sequencing of the genome, he hopes we will continue to wonder about genomics. It is not like Oh, the genome, we did that, its over. Its like, No, its both that this work has continued and it continues to matter, said Liu, who was then with the Howard Hughes Medical Institute, And you should know something about it even if youre not a professional scientist.

Eric Green has served as the director of the NHGRI since 2009. The biggest difference he sees in genomics then, and genomics now? At the time I started as director, when this exhibition was being created, there was a lot of clarity around what had been accomplished and a lot of growing knowledge about how the human genome works. But the idea of actually using genomic information for the practice of medicine was pretty hypothetical.

When he stepped into his role, he wanted to close that gap and figure out how to use genomic information to improve the practice of medicine. And the biggest difference between then and now is then it was hypothetical and, while it is certainly not pervasive in medicine, there are a number of just very clear areas where now genomics is mainstream. Green highlighted the use of genomics to diagnose rare diseases. They were like the very first home runs in those areas, he said. But now its just routine practice. Another notable change, he added, is the proliferation of DNA genealogy tests from companies such as 23andMe and Ancestry.

Looking ahead, Green said he is a realist about the role of genomics in medicine.

The implementation of some aspects of genomic medicine are no longer scientifically difficult. Theyre sociological, because of the societal challenges associated with health care, said Green, who trained as a physician-scientist. What I would say going forward is that, Im actually quite optimistic were going to figure out a lot of these really valuable uses of genomics. But I cant claim to be as optimistic about the effective use of those tools in health care, because we all appreciate that health care is really complicated.

It is a hurdle he had not considered early on in research, he said. Science drives some things, but its not the only thing.

See more here:
As the Smithsonian wraps a genome exhibit, leaders in the field reflect - STAT

UW-Madison scientists studying the genetics of orangutans in zoos were stumped. The lineages they found didnt match those made public when the orangutan genome was sequenced in 2011.

When they pulled a photo for one animal from the 2011 research, supposedly a female, it had cheek pads, a distinctly male trait. In further digging, they learned a label for one orangutan was really for a pig. Another orangutan, marked as Doris from Dallas Zoo, was actually Sibu from Zoo Atlanta.

Things just didnt add up, said Graham Banes, who now directs the Madison-based Orangutan Conservation Genetics Project. Our data just could not reconcile with what had already been published.

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At the same time, the related journal Nature Scientific Data included a paper by Banes and his colleagues detailing their finding that nine of 10 samples in the 2011 research were inadvertently switched.

I was aghast, said Michael Sweet, who researches coral genomes at the University of Derby in England and worries that recent examples of scientific fraud have already increased public skepticism about topics such as climate change. The general public is going to start mistrusting science.

Marc Tollis, whose research at Northern Arizona University involves bioinformatics and genomics, called the orangutan genome mishap a nightmare scenario for almost all scientists.

The revelation about the orangutan research doesnt only raise questions about scientific error, public trust and the validity of subsequent studies based on the genome work. Banes said it has implications for the management of orangutans in zoos, as there is now proof that at least several orangutans in American zoos are from a new third species announced only in 2017. Should they be prevented from breeding with other species, which he argues can increase the risk of disease and birth defects?

This is a really massive problem for zoos, Banes said. If zoos allow different species of the animals to mate freely, at that point, its not a conservation breeding program, he said. Its an experiment.

Rob Vernon, spokesperson for the American Association of Zoos and Aquariums, said the group would review the research and consult with experts for advice. Ronda Schwetz, leader of the associations Orangutan Saving Animals from Extinction program and director of Vilas Zoo in Madison where orangutan Chelsea had a baby in June did not respond to requests for comment.

Devin Locke, lead author of the 2011 genome paper and of the recent correction, could not be reached for comment. Formerly with Washington University Genome Center in St. Louis, which headed up the genome-sequencing project, Locke is now with the Massachusetts-based cancer research company Foundation Medicine, according to his LinkedIn profile.

Sweet, one of numerous scientists who have raised concerns about the new report on social media, is part of a group that published standards on sequencing coral genomes to help prevent such mistakes. He said misconduct recently identified in investigations of a University of Delaware coral scientist and a spider behavior ecologist at McMaster University in Canada have already damaged scientific credibility.

The whole mess (about the orangutan genome) underlines the need for careful curation of genomic data, including checking apparently solid identification in the genomic databases, said Michael Cobb, a zoologist at the University of Manchester in England.

Different species

It wasnt until the 1980s, decades after orangutans were first captured from the islands of Borneo and Sumatra in Southeast Asia for placement in zoos, that two distinct species were identified: Bornean orangutans and Sumatran orangutans.

Interbreeding was discouraged and zoos separated the populations, Banes said.

Graham Banes heads up theOrangutan Conservation Genetics Project, based in Madison, and was part of a research team that discovered orangutan genome mix-ups.

The genome published in 2011 was based on a Sumatran female. Ten other orangutans five identified as Sumatran and five as Bornean were also sequenced in less detail, serving as reference samples of the diversity of orangutan genetics.

The orangutan was the third nonhuman primate genome to be sequenced, after the chimp and the rhesus macaque. The analysis showed humans and orangutans share about 97% of their DNA, compared with 99% between humans and chimps.

Banes, who left UW-Madisons Wisconsin National Primate Research Center in May but still conducts primatology research in Madison, focuses on the effects of inbreeding, or mating between closely related groups, and outbreeding, or mating between divergent groups.

In 2016, his research showed a non-native subspecies of Bornean orangutan, released into Tanjung Puting National Park on Borneo in Indonesia, bred with apes in the park, creating a cocktail hybrid species. One of two non-native females rescued from the pet trade, Siswoyo, had fewer surviving offspring than any other female in the park.

Banes said preliminary data suggest outbreeding may be connected to birth defects he saw among intermixed orangutans at zoos in China and chronic respiratory disease found in some captive orangutans.

It appears theyre ill-adapted to each others novel pathogens, he said.

Science sleuths

In 2018, Banes UW-Madison research team was testing orangutans in U.S. zoos to determine the extent of interbreeding. Graduate student Alyssa Karklus, now a veterinarian with the Wisconsin Humane Society, noticed that the genetics of some animals didnt line up with the reference genomes from 2011.

A female orangutan reintroduced to the wild is pictured carrying her wild-born offspring. UW-Madison researchers found a mix-up in a genome-sequencing research project that could have implications for orangutan-breeding programs at zoos.

Banes and Karklus, along with post-graduate researcher Emily Fountain, became sleuths, sifting through volumes of data and eventually finding that even the sex reported for five animals in the 2011 paper was wrong. Three researchers from Washington University, who participated in the initial genome work, assisted the UW-Madison group and are co-authors of the paper about the mix-ups.

Its not clear who made the mistakes or how, Banes said. The errors likely occurred at several stages, from when samples were collected from animals and labeled in vials to when sequencing data was linked to individuals, he said.

It was probably multiple people, he said. It was a series of unfortunate events.

Banes said hes not out to vilify the genome researchers and is glad they agreed to do the correction. He said his goal is to improve the integrity of science.

Theres no shame in making mistakes. What is critically important is that we correct them, he said. I personally mixed up three samples on Wednesday last week, but I caught it.

Tapanuli orangutans

Banes said one of the switches in the genome samples has implications for managing Tapanuli orangutans the newly discovered third species, from part of Sumatra.

One of the five animals identified as Sumatran in the 2011 paper turned out to be Tapanuli, which scientists wouldnt have been expected to know at the time. But it wasnt Baldy, a long-deceased male animal from the Sacramento Zoo that had only two offspring and no second-generation offspring, as identified by the genome researchers, Banes said. The Tapanuli was Bubbles, from the San Diego Zoo, a female that had eight descendants, some of which are still alive and in zoos, he said.

That led Banes and his colleagues to discover additional Tapanulis in zoos in the U.S. and elsewhere, with studies underway in Europe. He plans to publish a report soon on the extent of Tapanulis found, which he said raises questions for the future of orangutans in zoos.

What are the zoos going to do if 50% of their population now has to be taken out of the breeding program? he asked.

Visitors enter Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Deynah Thao, 7, gets a close look at a grizzly bear during a trip to Henry Vilas Zoo on the first day of the reopening of the zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors to Henry Vilas Zoo follow one way walking paths on the first day of the reopening of the zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors stop to see the grizzly bears on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors follow the paw prints as they check out animal exhibits on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors enter Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

The first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Employee Ryan Brockner, right, shows off an umbrella cockatoo named Reggie to visitors Samia Sanders, 4, front, Nazilah Lites, 4, and Miyauna Sanders, 10, on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Nicole Josi Lema, with her daughters Arianna, 7, and Akemi, 5, right, are greeted by Courtney Cordova, educational specialist, as she explains the rules before entering Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Employee Debbie Scheffel cleans picnic tables after they are used by guests on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Dan Tortorice, center, sits with his grandchildren, Aria Oettiker, 9, left, and her brother, Anthony, 6, as they eat ice cream during a visit to Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Signs reminding visitors to social distance are seen at Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

The whole (genome) mess underlines the need for careful curation of genomic data, including checking apparently solid identification in the genomic databases.

Michael Cobb, University of Manchester zoologist

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Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals - Nature.com

For nearly 40 years, geneticists have looked to ancient DNA to find answers about our modern condition. And, beyond just ancient DNA, research institutionsincluding Penn Medicinehave sought to sequence current human DNA to better understand how genetic variations affect health and disease.

What Iain Mathieson wants to do is compare the past and present to understand how certain genes have evolved, in the process shining new light on some of today and yesterdays diseases.

What were interested in is, Can we say anything about the phenotypes of these ancient individuals? explains Mathieson, an assistant professor of genetics in the Perelman School of Medicine. A lot of people are trying to use present-day genomes to discover genetic variants in people today that are related to specific diseases. [We want to see if] we can take that information and use it to say anything about the ancient people and their diseases. What were doing is combining ancient genomes with information about genetic variants and diseases from present day people to learn about disease in ancient people.

This summer, Mathieson and postdoctoral researcher Samantha Cox are working with two rising second-year students to collate and analyze existing data from scientific literature conducted around the world. Carson Shin, of Herndon, Virginia, who is an anthropology major in the School of Arts & Sciences, conducts anthropological and archaeological literature reviews to find new archaeological and DNA data. Kaeli Kaymak-Loveless, a computer science major in the School of Engineering and Applied Science, then takes that data and tries to analyze it using the statistical computing program R. The students work is funded by the Center for Undergraduate Research and Fellowships.

While Mathieson is ultimately interested in answering big questions, like how the rise of agriculture influenced the genome, hes first looking to see if his method for comparison works. He and his team of CURF interns are collating DNA data, tracking down information on skeletons, and determining height. Theyre examining height in particular, Mathieson says, because theres already a lot known about genetic variants and their relationship to height in present-day people. If they can accurately predict the height of ancient people through genetics, then, the next question becomes, What else can we say?

What wed like is to be able to say things we cant measure in the skeletons, Mathieson says. One of the big technology changes in the last 10,000 years is the development of agriculture; before that, people lived by hunting and gathering, and in the last 6,000 to 8,000 years many transitioned to an agricultural diet. You might wonder if variants of diseases todayobesity, diabetes, or even some autoimmune diseasesmight have a genetic basis in that diet.

Shin began his first year at Penn as a global health major before switching to anthropology, concentrating in archaeology. Heading into the summer, he knew he wanted to work on a project thats hands-on and interdisciplinary; Mathiesons project felt like a perfect fit.

As an anthropology major, its fascinating to me that even though were so separated from our ancestors by time, so little has actually changed about us as humans, Shin muses. Biologically, were pretty much the same. If I met someone from 3,000 years ago, I wouldnt be looking down on them or looking uptheyd be almost the same height as me, eye to eye.

As hes worked, he says, hes realized that he needs more coding experience and plans to take a half-credit course on R in the Wharton School once he meets prerequisitesthe sort of flexibility he says brought him to Penn in the first place. He says he never expected to take a computer science course, coming to Penn, but has relented.

Ive got to know how to code, he says.

Kaymak-Loveless, meanwhile, began as a bioengineering major before switching to computer science. Shes been weighing what to concentrate in but says the internship has allowed her to settle on computational biology, with an aim to take more biostatistics courses.

Most freshmen struggle to find something meaningful to do in their first summer, and I honestly wasnt really expecting to be doing anything meaningful this summer, says Kaymak-Loveless. But I feel like Im applying myself and learningthis has been a great experience.

Mathieson says he usually works with fourth-year students, but has been really impressed with how quickly Kaymak-Loveless and Shin have learned. In the short-term, Mathieson plans to develop the project into a paper.

But once we establish this technique and the ability to do this [successfully], wed like to use this to learn about traits you cant see in skeletons, related to diet and disease, Mathieson says. Thats the end goal.

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What the genomes of ancient humans can teach us about modern health | Penn Today - Penn Today

More than half of all cancers have mutations in a gene called p53. The protein made from this gene is whats called a tumor suppressor: When working properly, it guards against cancer development in part, by detecting damaged DNA and alerting cells to repair it.

Cells without working p53 are unable to properly repair damaged DNA, leading to a buildup of mutations, including large chromosomal alterations. Because of its important role in maintaining DNA integrity, scientists long ago dubbed p53 the guardian of the genome.

But 30 years on from that christening, many questions remain about exactly how p53 guards the genome and how its loss promotes cancer.

One hotly debated question has been whether the guardian role of p53 is important for preventing cancer. While tumors with p53 mutations show evidence of chromosomal alterations, research has shown that the normal p53 protein controls several other processes that might explain why its inactivation promotes cancer. For example, p53 promotes apoptosis, or programmed cell death, in cells that have developed precancerous features.

Another question relates to how the genetic instability arises following p53 loss. One longstanding assumption has been that p53 loss acts as a kind of gateway to genetic chaos. In other words, losing the tumor suppressor leads to random buildup of genetic mutations without much rhyme or reason. But a new study from researchers at the Sloan Kettering Institute (SKI) challenges that assumption and brings some insight into p53s guardian role.

Rather than promoting genetic chaos, what we see when cells lose p53 is an orderly progression of genetic changes that is actually quite predictable, says Scott Lowe, Chair of the Cancer Biology and Genetics Program in SKI and the senior author on the study, which was published August 17, 2022, in the journal Nature. That came as a complete surprise to us and suggests a new way to think about possibly treating cancer.

Scientists have struggled to fully understand p53s role in cancer, particularly its effects on the genome, in part because there are few good laboratory models that allow the study of p53 function at the earliest (benign) stages of tumor development, well before cells have acquired obvious cancerous properties.

By staining cells taken from mouse models, researchers can learn about how the loss of the p53 gene leads to cancer. The image on the left shows tumor tissue. The red cells, which have lost p53, are cancerous, and the green cells are not cancerous. The image on the right is taken from normal tissue. It shows a few red cells that have the potential to become cancer interspersed among the green cells.

The vast majority of cancer genomic studies are based on analyzing human tumors, says Timour Baslan, the ONeil Charitable Trust Fellow in the Lowe Lab and one of the papers lead authors. The limited availability of patient tissue before and after tumor development means it has been impossible to gain a temporal picture of how p53 loss leads to cancer, starting from the earliest stages.

To bring those early changes into view, Drs. Baslan and Lowe along with former Lowe Lab members and cancer biologists Zhen Zhao and John P. Morris IV produced a unique mouse model of pancreatic cancer in which p53 mutational status can be detected, irrespective of tumor development, thereby allowing measurements of genetic changes as incipient cancer cells transition from a benign to malignant state.

The models key feature is a set of fluorescent tags that record specific genetic events and can be detected with a microscope. One tag is red and records the presence of a mutated KRAS gene known to be involved in promoting pancreatic cancer in both humans and mice. The other tag is green and records loss of p53. Cells with mutated KRAS but working p53 emit both red and green fluorescence, while cells that are missing p53 emit only red.

This visual trick allowed the scientists to identify specific populations of cells in the mouse that had lost p53 function but were still very far from being a full-fledged cancer. Its sort of like the first step when the wheels start to fall off the wagon, Dr. Lowe says.

By collecting these specific cells and then performing single-cell DNA sequencing on them, the scientists were able to identify the genetic changes that occurred immediately following p53 loss and continuing after.

The mouse really gave us the opportunity to look at a specific stage of cancer evolution, pull it out, and characterize it at a level thats has never been done before, Dr. Baslan says.

To the scientists surprise, the changes they observed always seemed to happen in a consistent pattern. First, the cells lost particular regions of chromosomes called deletions. Later on, genome doubling occurred, but only after a lot of deletions were accrued. Finally, following genome doubling, the cells continued to acquire further deletions but also uniquely gained additional copies of specific genes called gains and amplifications.

Since p53 mutations are often linked with genomic chaos, we were stunned to see there was a preferred order of events, says Dr. Morris, now an assistant professor at the University of North Carolina at Chapel Hill.

The mouse really gave us the opportunity to look at a specific stage of cancer evolution, pull it out, and characterize it at a level that's has never been done before.

Timour Baslan, research fellow

Even though cells from early stages had lost p53, the researchers were able to show that they were not yet cancerous, but instead, required these changes to look and act like cancer cells. Together, these observations suggested to the researchers that p53 loss by itself is not sufficient to cause cancer; instead, cells lacking p53 must acquire additional genetic changes, in an orderly manner, to fully go rogue.

Whats true of the mouse also seems to be true of humans: The scientists could see evidence that the same sorts of deletions, doublings, and amplifications that occur in the mouse also occur in human pancreas tumors.

And its likely not just pancreatic cancer that follows this pattern. Since the team has started discussing their results with colleagues at Memorial Sloan Kettering Cancer Center (MSK), others have been finding similar changes in cancer types besides pancreatic cancer.

Knowing that there are rules to the genetic evolution of tumors suggests a different way of thinking about treating them, the scientists say.

Many existing cancer drugs target gene amplifications in tumors. But because these are acquired late in tumor evolution, not all cells in the tumor will have them. This means that drugs targeting these amplifications may kill off only certain cancer cells, leaving others unscathed.

A more effective approach to treating cancer might be to target the gene deletions that occur very early in cancer development, since these changes will be found in all, or nearly all, tumor cells. (Changes that occur early in tumor evolution are called truncal changes because they are found in the trunk of the tumors evolutionary tree.)

Targeting these deletions could be tricky, but Dr. Lowe says the possibility is there: If its not genetic chaos, and theres order and rules to cancer development, then you might ultimately be able to exploit those rules against the cancer itself, he says.

Fittingly, this new paper comes just after the 30th anniversary of the publication of the original Nature paper, by scientist David Lane, that named p53 the guardian of the genome in the first place. Since that time, scientists have developed a much deeper understanding of p53s importance, with this latest paper bringing the multifaceted role of p53 into the sharpest focus yet.

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SKI Scientists Solve 30-Year-Old Mystery About p53 Protein Dubbed Guardian of the Genome - On Cancer - Memorial Sloan Kettering