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The Evolutionary Perspective
Category Archives: Genome
Posted: January 22, 2020 at 6:44 pm
A visiting professor at Oakland University has spent the last six years mapping human genomes in Russia in an attempt to fill in the blanks for the worlds ninth most populous country.
Taras Oleksyk, assistant professor of biological sciences, and a team of international scientists launched the project with the goal of charting the genetic diversity of several populations in Russia. Their findings were recently published in the scientific journal Genomics.
As people have spread across the world over centuries, they have gained different genetic characteristics, either at random or due to adaptation to their local environments. These differences are crucial for understanding who people are and where they came from, Oleksyk said. Russia is a treasure trove of previously undescribed genetic variations. Mapping them will allow scientists to chart the vast genetic diversity of Russian populations and fill in the largest gap on the genetic map of humankind.
The DNA of 264 adults in six geographic areas has been so far mapped for the project, including Western Russia and the Yakutia region of Eastern Siberia.
We established the borders to show areas where people are more genetically similar to each other sort of like genetic countries, Oleksyk said. This shows that history and geography shape our genomes. Where we are from largely defines the genetic characteristics we carry. And that has important implications, particularly for genes that influence our health.
The study found correlations of higher risk for certain diseases to geographic proximity with neighboring regions. In Yakutia, the researchers found the population was at a higher risk for lactose intolerance and a slower response to blood thinners, matching with genome mapping results from east Asia.
The goal is to give doctors the ability to tailor medical treatments to their patients genetic profile, Oleksyk said. For example, making sure that patients dont have a genetic predisposition that prevents them from metabolizing certain drugs. We need genome maps in order to lay the groundwork for this type of personalized medicine.
The full study can be found at sciencedirect.com.
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Posted: at 6:44 pm
When asked whats so special about Drosophila melanogaster, or the common fruit fly, Gerry Rubin quickly gets on a roll. Rubin has poked and prodded flies for decades, including as a leader of the effort to sequence their genome. So permit him to count their merits. Theyre expert navigators, for one, zipping around without crashing into walls. They have great memories too, he adds. Deprived of their senses, they can find their way around a roommuch as you, if you were suddenly blindfolded, could probably escape through whichever door you most recently entered.
Fruit flies are very skillful, he appraises. And all that skill, although contained in a brain the size of a poppy seed, involves some neural circuitry similar to our own, a product of our distant common ancestor. Thats why, as director of Janelia Research Campus, part of the Howard Hughes Medical Institute, hes spent the last 12 years leading a team thats mapping out the fly brains physical wiring, down to the very last neuron.
Janelia researchers announced a major step in that quest on Wednesday, releasing a wiring diagram of the fly brain that contains 25,000 neurons and the 20 million connections between them. The so-called connectome corresponds to the flys hemibrain, a region thats about 250 micrometers acrossthe size of a dust mite, or the thickness of two strands of hair. Its about a third of the total fly brain, and contains many of the critical regions responsible for memory, navigation, and learning.
Rubin hopes wiring diagrams such as this one, showing neurons involved in navigation, will give researchers a better sense of how brain circuits work.
Researchers like Rubin believe a physical blueprint of the brain could become a foundational resource for neuroscientistsdoing for brain science what genome sequences have done for genetics. The argument is that to get anywhere with understanding brain circuits, you first need to know what the circuits are, and what kinds of cells they join. That physical schematic becomes a road map for all kinds of inquiries, Rubin says, anything from understanding the role of the brains wiring in psychiatric disorders to how our brains store memories.
Obviously, it would be nice to pursue those questions with a complete human connectome. But thats a long way off. Fully analyzing even the tiniest amount of brain matter requires an enormous amount of time and treasure.
Hence, the brain of the humble fruit fly, with one-millionth the number of neurons of our own. Drosophila is only the second adult animal to have its brain circuitry mapped at this level of detail, following the nematode C. elegans back in 1986. That task was far more modest. The entire nervous system spanned 302 neurons and 7,000 connectionssmall enough for researchers, with enough effort, to get the job done by physically shaving off layers of cells, printing off images taken with an electron microscope, and tracing them with colored pencils. The complexity of the fly brain is two orders of magnitude greaterthus the three-decade gap in getting it done.
Mutation Responsible for Tumors Are Discovered in Concealed Sequences in the Cancer Genome – Science Times
Posted: at 6:44 pm
(Photo : upload.wikimedia.org)
The search for a cancer cure has led researchers in the OICR, to stumble on a ground-breaking discovery. Previously unknown and undetected in the sequences of non-coding DNA, which can transform into cancer-causing agents in the host cell. Prior to this discovery, this was largely unknown until now.
An investigation into the mutagenic gene demonstrated new ways that it can multiply and advance cancer further. Since it was practically hidden, then specialists are pointing their crosshairs on where to begin. More data uncovered will give more clues on how to tame cancer, later on, better tests to detect it and devise better-targeted therapy for patients.
What made this study more conclusive than those before it, that only covered 2% of the gene for producing proteins needed inside the cell. Furthermore, it dug deeper into more mutation probabilities that weren't explored until this is study. Going further into unknown territory into the non-coding parts of the human genetic matrix. Trying to figure out what causes the genes to get tripped and activated. Which triggers the formation of cancer-causing mutation wholesale inside the host cell.
The lead of the study, Dr. Jri Reimanda, and investigator at OICRsaid that mutation caused by altered proteins are not common in large coding regions. It is this far proximity that does not make it suspect at all. Analyzing data based on these will be challenging to analyze too.
Armed with improved statistical tools and more complete genomic information makes it more accurate. Data that was collected from 1,800 patients is the base of the genomic data, that produced evidence of molecularly based ways that led to cancer, and worse tumors too.
Researchers had a go at 100,000 sections of each patient, now paying more attention to the unexplored non-coded location on the sequence to interact with. One location in the genome is determined to control and anti-tumor gene in cancerous cells. It was located as far as, 250,000 base pairs away from the gene located in the three-dimensional genome. To gain an idea of how it worked more, they did gene editing and experiments in host human cells. To test how potent cancer is in this non-coded location in the genetic sequencing.
Throughout the process of investigating the region involved, several conclusions about the non-coding region that is involved in the development of cancer cells. So far, with more specialized algorithms and data about cancer genomes will lead to analysis and cures. Just one of the findings that lead to a better cure for patients, or detecting it before it gets worse.
All the data gained from "Reimand's" study is free and for use by other scientists studying cancer. Everything from the statistical algorithms to overall methods is tried and tested for accuracy. Anyone has free access to add more to this relevant research.
It cannot be stressed enough that genes are grossly affected by non-coding gene sequences, with easy turning on or off. When a mutation happens, it will cause abnormal functions inside the cell to become cancerous. Another fellow, Helen Zhu a student and author as well, mentioned the method called "ActiveDriverWGS" zeroes in on cancer in the genome.
Finding the mutations that drive development to cancer is the key to track what causes it. Finding and digging up more about it should help in developing medicines to suppress it. This will give rise to better analyses and cures for patients that should be a good development for everyone.
Read: New tumor-driving mutations discovered in the under-explored regions of the cancer genome
LifeOmic Partners with Indiana University-based Healthy Breast Tissue Bank to Advance Breast Cancer Research – P&T Community
Posted: at 6:44 pm
INDIANAPOLIS, Jan. 22, 2020 /PRNewswire/ --LifeOmic, the creator of the LIFE mobile apps and the Precision Health Cloud (PHC) platform in use at major medical and cancer centers, today announced a partnership with the Susan G. Komen Tissue Bank, a unique resource established by researchers at Indiana University Melvin and Bren Simon Cancer Center and Indiana University School of Medicine, to improve breast cancer research. The Komen Tissue Bank at the IU Simon Cancer Center will utilize the PHC for genomic, clinical and imaging data aggregation and analysis, as well as its health care compliant survey capabilities.
The Komen Tissue Bank is the only repository in the world for normal breast tissue and matched serum, plasma and DNA. The tissue bank advances breast cancer research by offering high quality, richly annotated tissue samples to scientists worldwide. Scientists who access the Komen Tissue Bank's Virtual Tissue Bank can query the medical history of donors, request tissue and download existing data. The current system does not support genomic data.
"We are passionate about sharing our research resources with scientists worldwide," said Jill Henry, chief operating officer of the Komen Tissue Bank at the IU Simon Cancer Center. "Using LifeOmic's PHC will expand the Virtual Tissue Bank'scapabilities to help fuel ongoing treatment and prevention discovery."
LifeOmic and the Komen Tissue Bank will work together to deploy the Virtual Tissue Bank onto the PHC's secure, reliable and scalable platform. The new platform enables researchers around the world to query an extended data model including whole-genome sequencing data. The use of analytics tools in the PHC allows researchers to overlay data reported from participants' clinical history with all other data available in the PHC, including genomic, clinical and imaging data.
"The Precision Health Cloud was created to break down silos that exist between current systems, to help advance precision health," said Dr. Don Brown, CEO and founder of LifeOmic. "We are thrilled to partner with the Komen Tissue Bank because of our shared goal to break down silos and help its mission to end breast cancer by enabling advanced research using PHC."
For more information on LifeOmic's PHC, visit: https://lifeomic.com/products/precision-health-cloud/.
LifeOmic is the software company that leverages the cloud, machine learning and mobile devices to power precision health solutions for providers, researchers, health care IT, pharma and individuals. The company's cloud-based software securely aggregates, stores and analyzes patient data to accelerate the development and delivery of precision health treatments. LifeOmic's core competency is the Precision Health Cloud, a cloud-based repository of all patient data such as a basic profile, whole genome sequences, gene expression levels, lab results, medical images and more. The company's product lines also include security software platform JupiterOne and consumer-centric LIFE mobile apps.
Founded in 2016 and headquartered in Indianapolis, LifeOmic was created by serial entrepreneur Don Brown and boasts a team of highly experienced engineers, scientists and security specialists.
For more information, visit https://lifeomic.com.
About The Komen Tissue Bank at the IU Simon Cancer Center:
The Susan G. Komen Tissue Bank, a resource established by researchers at Indiana University Melvin and Bren Simon Cancer Center and Indiana University School of Medicine in Indianapolis, is uniquely positioned to characterize the molecular and genetic basis of normal breast development and compare it to the different types of breast cancer. The bank was established expressly for the acquisition of normal tissues from volunteer donors with no clinical evidence of breast disease and/or malignancy, providing a resource to investigators around the globe. More than 6,000 women have donated breast tissue since 2007. In all, more than 12,000 women also have donated DNA and blood to the tissue bank.
For more information, visit https://komentissuebank.iu.edu/
Katie GrantBAM Communications(858) email@example.com
Michael SchugIndiana University Melvin and Bren Simon Cancer Center(317) firstname.lastname@example.org
Hackensack Meridian Health Center for Discovery and Innovation to Host Genomic Medicine Symposium – The Trentonian
Posted: at 6:44 pm
NUTLEY, N.J., Jan. 17, 2020 /PRNewswire/ --Genomic medicine's groundbreaking treatments, and its future promise, will be the focus of a full-day symposium at the Hackensack Meridian Health Center for Discovery and Innovation (CDI) on Wednesday, February 19.
This emerging discipline for tailoring active clinical care and disease prevention to individual patients will be the focus of presentations given by eight experts from medical centers in the U.S.A. and Canada.
"The Genomic Medicine Symposium convenes a diverse group of scientific experts who help serve as a vanguard for precision medicine," said David Perlin, Ph.D., chief scientific officer and vice president of the CDI. "At the Center for Discovery and Innovation, we are working to make genomics a central component of clinical care, and we are delighted to host our peers and partners from other institutions."
"The event is one-of-a-kind," said Benjamin Tycko, M.D., Ph.D., a member of the CDI working in this area, and one of the hosts. "We are bringing together great minds with the hope it will help inform our planning for genomic medicine within Hackensack Meridian Health and inspire further clinical and scientific breakthroughs."
Cancer treatments, neuropsychiatric and behavioral disorders, cardiometabolic conditions, autoimmune disease, infectious disease, and a wide array of pediatric conditions are areas where DNA-based strategies of this type are already employed, and new ones are being tested and refined continually.
The speakers come from diverse medical institutions and will talk about a variety of clinical disorders in which prevention, screening, and treatment can be informed through genomic and epigenomic data.
Among the speakers are: Daniel Auclair, Ph.D., the scientific vice president of the Multiple Myeloma Research Foundation; Joel Gelernter, M.D., Ph.D., Foundations Fund Professor of Psychiatry and Professor of Genetics and of Neuroscience and Director, Division of Human Genetics (Psychiatry) at Yale University; James Knowles, M.D., Ph.D., professor and chair of Cell Biology at SUNY Downstate Medical Center in Brooklyn; Tom Maniatis, Ph.D., the Isidore S. Edelman Professor of Biochemistry and Molecular Biophysics, director of the Columbia Precision Medicine Initiative, and the chief executive officer of the New York Genome Center; Bekim Sadikovic, Ph.D., associate professor and head of the Molecular Diagnostic Division of Pathology and Laboratory Medicine at Western University in Ontario; Helio Pedro, M.D., the section chief of the Center for Genetic and Genomic Medicine at Hackensack University Medical Center; Kevin White, Ph.D., the chief scientific officer of Chicago-based TEMPUS Genetics; and Jean-Pierre Issa, M.D., Ph.D., chief executive officer of the Coriell Research Institute.
The event is complimentary, but registration is required. It will be held from 8 a.m. to 4:30 p.m. at the auditorium of the CDI, located at 111 Ideation Way, Nutley, N.J.
The event counts for continuing medical education (CME) credits, since Hackensack University Medical Center is accredited by the Medical Society of New Jersey to provide continuing medical education for physicians.
Hackensack University Medical Center additionally designates this live activity for a maximum of 7 AMA PRA Category 1 Credit TM. Physicians should claim only the credit commensurate with the extent of their participation in the activity.
For more information, visit https://www.hackensackmeridianhealth.org/CDIsymposium.
Hackensack Meridian Health is a leading not-for-profit health care organization that is the largest, most comprehensive and truly integrated health care network in New Jersey, offering a complete range of medical services, innovative research and life-enhancing care.
Hackensack Meridian Health comprises 17 hospitals from Bergen to Ocean counties, which includes three academic medical centers Hackensack University Medical Center in Hackensack, Jersey Shore University Medical Center in Neptune, JFK Medical Center in Edison; two children's hospitals - Joseph M. Sanzari Children's Hospital in Hackensack, K. Hovnanian Children's Hospital in Neptune; nine community hospitals Bayshore Medical Center in Holmdel, Mountainside Medical Center in Montclair, Ocean Medical Center in Brick, Palisades Medical Center in North Bergen, Pascack Valley Medical Center in Westwood, Raritan Bay Medical Center in Old Bridge, Raritan Bay Medical Center in Perth Amboy, Riverview Medical Center in Red Bank, and Southern Ocean Medical Center in Manahawkin; a behavioral health hospital Carrier Clinic in Belle Mead; and two rehabilitation hospitals - JFK Johnson Rehabilitation Institute in Edison and Shore Rehabilitation Institute in Brick.
Additionally, the network has more than 500 patient care locations throughout the state which include ambulatory care centers, surgery centers, home health services, long-term care and assisted living communities, ambulance services, lifesaving air medical transportation, fitness and wellness centers, rehabilitation centers, urgent care centers and physician practice locations. Hackensack Meridian Health has more than 34,100 team members, and 6,500 physicians and is a distinguished leader in health care philanthropy, committed to the health and well-being of the communities it serves.
The network's notable distinctions include having four hospitals among the top 10 in New Jersey by U.S. News and World Report. Other honors include consistently achieving Magnet recognition for nursing excellence from the American Nurses Credentialing Center and being named to Becker's Healthcare's "150 Top Places to Work in Healthcare/2019" list.
The Hackensack Meridian School of Medicine at Seton Hall University, the first private medical school in New Jersey in more than 50 years, welcomed its first class of students in 2018 to its On3 campus in Nutley and Clifton. Additionally, the network partnered with Memorial Sloan Kettering Cancer Center to find more cures for cancer faster while ensuring that patients have access to the highest quality, most individualized cancer care when and where they need it.
Hackensack Meridian Health is a member of AllSpire Health Partners, an interstate consortium of leading health systems, to focus on the sharing of best practices in clinical care and achieving efficiencies.
For additional information, please visit http://www.HackensackMeridianHealth.org.
About the Center for Discovery and Innovation:
The Center for Discovery and Innovation, a newly established member of Hackensack Meridian Health, seeks to translate current innovations in science to improve clinical outcomes for patients with cancer, infectious diseases and other life-threatening and disabling conditions. The CDI, housed in a fully renovated state-of-the-art facility, offers world-class researchers a support infrastructure and culture of discovery that promotes science innovation and rapid translation to the clinic.
Posted: January 18, 2020 at 10:13 am
All of us have a human genome, which is basically a composite of our genes. But we also have a screenome, a composite of our digital lives, according to a group of researchers from the United States. Their goal is to make sense of how the screens in our lives are affecting us.
A decade ago, the Human Genome Project worked to identify and map all of the genes of the human genome. In a nod to their research, academics Byron Reeves, Thomas Robinson and Nilam Ram created the concept of the screenome to describe the entity formed by all the digital activity individuals subject themselves to.
The three argued that everything we know about the effects of media use on individuals and societies could be incomplete, irrelevant or wrong. We are all doing more online and as this expanding form of behavior is digitalized, it is open to all forms of manipulation, they said.
In a comment article in the latest edition of the journal Nature, the authors argued that a large-scale analysis of detailed recordings of digital life could provide far greater insights than simply measuring screen time. Americans now spend over half of their day interacting with digital media.
The academics said most of the thousands of studies investigating the effects of media over the past decade used peoples estimates of the amount of time they spend engaging with technologies or broadly categorized platforms such as smartphone, social media or entertainment media.
Nevertheless, the range of content has become too broad, patterns of consumption too fragmented, information diets too idiosyncratic, experiences too interactive, and devices too mobile, for such simplistic characterization. Technologies now available can allow researchers to record digital life in exquisite detail, they said.
Digital life is life these days. As we spend more of our life on our devices, so more of our life is expressed through these screens. This gives us a tremendous opportunity to learn about all aspects of human behaviour, said Robinson to the Australian Financial Review.
Tracking our digital life has become much easier. Instead of using a range of devices for different things, applications have been consolidated into smartphones and other mobile devices. At the same time, there are now tools available to see what people are doing on their screens.
The researchers are using so-called screenomics technologies to observe and understand our digital lives, minute by minute. The result of their initial work is a call for the Human Screenome Project, a collection of large-scale data that will inform knowledge of and solutions to a wide variety of social issues.
Screenomics emerges from the development of systems for capturing and recording the details of individuals digital experiences, said Ram to Penn News. The system includes software that collects screenshots every five seconds on smartphones and laptop computers, extracts text and images, and allows analysis of the timing, content, function and context of digital life.
In their article in Nature, the researchers outlined the possibilities of the technology. Over 600 participants have so far consented to use screenomics software on laptops and Android smartphones that were linked to the researchers secure computational infrastructure.
Participants then went about their daily lives while the system unobtrusively recorded their device use. In their initial analyses of these data, the researchers found that participants quickly changed tasks, approximately every 19 seconds on a laptop, and every 10 seconds on a smartphone.
All the information collected includes indicators of health and well-being and can be shared with larger interdisciplinary projects. Reeves, Robinson and Ram suggested that researchers wishing to study digital life could even create a repository that everyone can contribute to and use.
That type of large interdisciplinary project they call for would have far-reaching benefits for all areas of life touched by digital technology. In the future, it might be possible for various apps to interact with an individuals screenome and to deliver interventions that alter how people think, learn, feel and behave, said Ram.
The rest is here:
First was the genome. Now, its time for the screenome - ZME Science
Posted: at 10:13 am
How did the monstrous giant squid reaching school-bus size, with eyes as big as dinner plates and tentacles that can snatch prey 10 yards away get so scarily big?
Today, important clues about the anatomy and evolution of the mysterious giant squid (Architeuthis dux) are revealed through publication of its full genome sequence by a University of Copenhagen-led team that includes scientist Caroline Albertin of the Marine Biological Laboratory (MBL), Woods Hole.
Giant squid are rarely sighted and have never been caught and kept alive, meaning their biology (even how they reproduce) is still largely a mystery. The genome sequence can provide important insight.
In terms of their genes, we found the giant squid look a lot like other animals. This means we can study these truly bizarre animals to learn more about ourselves, says Albertin, who in 2015 led the team that sequenced the first genome of a cephalopod (the group that includes squid, octopus, cuttlefish, and nautilus).
Led by Rute da Fonseca at University of Copenhagen, the team discovered that the giant squid genome is big: with an estimated 2.7 billion DNA base pairs, its about 90 percent the size of the human genome.
Albertin analyzed several ancient, well-known gene families in the giant squid, drawing comparisons with the four other cephalopod species that have been sequenced and with the human genome.
She found that important developmental genes in almost all animals (Hox and Wnt) were present in single copies only in the giant squid genome. That means this gigantic, invertebrate creature long a source of sea-monster lore did NOT get so big through whole-genome duplication, a strategy that evolution took long ago to increase the size of vertebrates.
So, knowing how this squid species got so giant awaits further probing of its genome.
A genome is a first step for answering a lot of questions about the biology of these very weird animals, Albertin said, such as how they acquired the largest brain among the invertebrates, their sophisticated behaviors and agility, and their incredible skill at instantaneous camouflage.
While cephalopods have many complex and elaborate features, they are thought to have evolved independently of the vertebrates. By comparing their genomes we can ask, Are cephalopods and vertebrates built the same way or are they built differently?' Albertin says.
Albertin also identified more than 100 genes in the protocadherin family typically not found in abundance in invertebrates in the giant squid genome.
Protocadherins are thought to be important in wiring up a complicated brain correctly, she says. They were thought they were a vertebrate innovation, so we were really surprised when we found more than 100 of them in the octopus genome (in 2015). That seemed like a smoking gun to how you make a complicated brain. And we have found a similar expansion of protocadherins in the giant squid, as well.
Lastly, she analyzed a gene family that (so far) is unique to cephalopods, called reflectins. Reflectins encode a protein that is involved in making iridescence. Color is an important part of camouflage, so we are trying to understand what this gene family is doing and how it works, Albertin says.
Having this giant squid genome is an important node in helping us understand what makes a cephalopod a cephalopod. And it also can help us understand how new and novel genes arise in evolution and development.
Marine Biological Laboratory. Original written by Diana Kenney. .
Posted: at 10:13 am
The success of the genomics industry has led to generation of huge amounts of sequence data. If put to good use, this information has the potential to revolutionize medicine, but the expense of the high-powered computers needed to achieve this is making full exploitation of the data difficult. Could cloud computing be the answer?
Over the last decade, genomics has become the backbone of drug discovery. It has allowed scientists to develop more targeted therapies, boosting the chances of successful clinical trials. In 2018 alone, over 40% of FDA-approved drugs had the capacity for being personalized to patients, largely based on genomics data. As the percentage has doubled over the past four years, this trend is unlikely to slow down anytime soon.
The ever-increasing use of genomics in the realm of drug discovery and personalized treatments can be traced back to two significant developments over the past decade: plunging sequencing costs and, consequently, an explosion of data.
As sequencing technologies are constantly evolving and being optimized, the cost of sequencing a genome has plummeted. The first sequenced genome, part of the Human Genome Project, cost 2.4B and took around 13 years to complete. Fast forward to today, and you can get your genome sequenced in less than a day for under 900.
According to the Global Alliance for Genomics and Health, more than 100 million genomes will have been sequenced in a healthcare setting by 2025. Most of these genomes will be sequenced as part of large-scale genomic projects stemming from both big pharma and national population genomics initiatives. These efforts are already garnering immense quantities of data that are only likely to increase over time. With the right analysis and interpretation, this information could push precision medicine into a new golden age.
Are we ready to deal with enormous quantities of data?
Genomics is now considered a legitimate big data field just one whole human genome sequence produces approximately 200 gigabytes of raw data. If we manage to sequence 100M genomes by 2025 we will have accumulated over 20B gigabytes of raw data. The massive amount of data can partially be managed through data compression technologies, with companies such as Petagene, but that doesnt solve the whole problem.
Whats more, sequencing is futile unless each genome is thoroughly analyzed to achieve meaningful scientific insights. Genomics data analysis normally generates an additional 100 gigabytes of data per genome for downstream analysis, and requires massive computing power supported by large computer clusters a feat that is economically unfeasible for the majority of companies and institutions.
Researchers working with large genomics datasets have been searching for other solutions, because relying solely on such high-performance computers (HPC) for data analysis is economically out of the question for many. Large servers require exorbitant amounts of capital upfront and incur significant maintenance overheads. Not to mention, specialized and high-level hardware, such as graphics processing units, require constant upgrades to remain performant.
Furthermore, as most HPCs have different configurations, ranging from technical specs to required software, the reproducibility of genomics analyses across different infrastructures is not a trivial feat.
Cloud computing: a data solution for small companies
Cloud computing has emerged as a viable way to analyze large datasets fast without having to worry about maintaining and upgrading servers. Simply put, Cloud computing is a pay-as-you-go model allowing you to rent computational power and storage. and its pervasive across many different sectors.
According to Univa the industrial leader in workload scheduling in the cloud and HPC more than 90% of organizations requiring high performance computing capacity have moved, or are looking into moving to the cloud. Although this is not specific for companies in the life sciences, Gary Tyreman Univas CEO suggests that pharmaceutical companies are ahead of the market in terms of adoption.
The cloud offers flexibility, an alluring characteristic for small life science companies that may not have the capital on-hand to commit to large upfront expenses for IT infrastructure: HPC costs can make or break any company. As a consequence, many opt to test their product in the cloud first, and if numbers look profitable, they can then invest in an in-house HPC solution.
The inherent elasticity of cloud resources enables companies to scale their computational resources in relation to the amount of genomic data that they need to analyze. Unlike with in-house HPCs, this means that there is no risk money will be wasted on idle computational resources.
Elasticity also extends to storage: data can be downloaded directly to the cloud and removed once the analyses are finished, with many protocols and best practices in place to ensure data protection. Cloud resources are allocated in virtualized slices called instances. Each instance hardware and software is pre-configured according to the users demand, ensuring reproducibility.
Will Jones, CTO of Sano Genetics, a startup based in Cambridge, UK, offering consumer genetic tests with support for study recruitment, believes the cloud is the future of drug discovery. The company carries out large data analyses for researchers using its services in the cloud.
In a partnership between Sano Genetics and another Cambridge-based biotech, Joness team used the cloud to complete the study at a tenth of the cost and in a fraction of the time it would have taken with alternative solutions.
Besides economic efficiency, Jones says that moving operations to the cloud has provided Sano Genetics with an additional security layer, as the leading cloud providers have developed best practices and tools to ensure data protection.
Why isnt cloud computing more mainstream in genomics?
Despite all of the positives of cloud computing, we havent seen a global adoption of the cloud in the genomics sector yet.
Medley Genomics a US-based startup using genomics to improve diagnosis and treatment of complex heterogeneous diseases, such as cancer moved all company operations to the cloud in 2019 in a partnership with London-based Lifebit.
Having spent more than 25 years at the interface between genomics and medicine, Patrice Milos, CEO and co-founder of Medley Genomics, recognized that cloud uptake has been slow in the field of drug discovery, as the cloud has several limitations that are preventing its widespread adoption.
For starters, long-term cloud storage is more expensive than the HPC counterpart: cloud solutions charge per month per gigabyte, whereas with HPC, once youve upgraded your storage disk, you have no additional costs. The same goes for computing costs: while the cloud offers elasticity, Univas CEO Tyreman says that the computation cost of a single analysis is five times more expensive compared to an HPC solution in many scenarios. However, as cloud technologies continue to progress and the market becomes increasingly more competitive among providers, the ongoing cloud war will likely bring prices down.
Furthermore, in the world of drug discovery, privacy and data safety are paramount. While cloud providers have developed protocols to ensure the data is safe, some risks still exist, for example, when moving the data. Therefore, large pharmaceutical companies prefer internal solutions to minimize these risks.
According to Milos, privacy remains the main obstacle for pharmaceutical companies to fully embrace the cloud, while the cost to move operations away from HPCs is no longer a barrier. While risks will always exist to a certain extent, Milos highlighted that the cloud allows seamless collaboration and reproducibility, both of which are essential for research and drug discovery.
Current players in the cloud genomics space
Cloud computing is a booming business and 86% of cloud customers rely on three main providers: AWS (Amazon), Azure (Microsoft) and Google Cloud. Although the three giants currently control the market, many other providers exist, offering more specialized commercial and academic services.
Emerging companies are now leveraging the technology offered by cloud providers to offer bioinformatics solutions in the cloud, such as London-based Lifebit, whose technology allows users to run any bioinformatics analyses through any cloud provider with a user-friendly interface effectively democratizing bioinformatics for all researchers, regardless of skill set.
Federation is a concept from computing now used in the field of genomics. It allows separate computers in different networks to work together to perform secure analysis without having to expose private data to others, effectively removing any potential security issues.
The amount of data organizations are now dealing with has become absolutely unmanageable with traditional technologies, and is too big to even think about moving, explained Maria Chatzou Dunford, Lifebits CEO and co-founder.
When data is moved, you increase the chances of having it be intercepted by third-parties, essentially putting it at significant risk. Data federation is the only way around this unnecessary data storage and duplication costs, and painstakingly slow data transfers become a thing of the past.
Getting ready for the genomics revolution
Its no secret that genomics is key to enabling personalized medicine and advancing drug discovery. We are now seeing a genomics revolution where we have an unprecedented amount of data ready to be analyzed.
The challenge now is: are we ready for it? To be analyzed, big data requires massive computation power, effectively becoming an entry barrier for most small organizations. Cloud computing provides an alternative to scale analyses, while at the same time, facilitating reproducibility and collaboration
While the cost and security limitations of cloud computing are preventing companies from fully embracing the cloud, these drawbacks are technical and are expected to be resolved within the next few years.
Many believe that the benefits of the cloud heavily outweigh its limitations. With major tech giants competing to offer the best cloud solutions a market valued at $340 billion by 2024 we might be able to expect a drastic reduction in costs. While some privacy concerns may still exist, leading genomics organizations are developing new tools and technologies to protect genomic data.
Taken as a whole, it is likely that the cloud will be increasingly important in accelerating drug discovery and personalized medicine. According to Univas Tyreman, it will take around 1015 years to see the accelerated transition from HPC to cloud, as large organizations are often conservative in embracing novel approaches.
Distributed big data is the number one overwhelming challenge for life sciences today, the major obstacle impeding progress for precision medicine, Chatzou Dunford concluded.
The cloud and associated technologies are already powering intelligent data-driven insights, accelerating research, discovery and novel therapies. I have no doubt we are on the cusp of a genomics revolution.
Filippo Abbondanza is a PhD candidate in Human Genomics at the University of St Andrews in the UK. While doing his PhD, he is doing an internship at Lifebit and is working as marketing assistant at Global Biotech Revolution, a not-for-profit company growing the next generation of biotech leaders. When not working, he posts news on LinkedIn and Twitter.
Images via E. Resko, Lifebit and Shutterstock
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Is Cloud Computing the Answer to Genomics Big Data... - Labiotech.eu
Will the sequencing of the Indian cobra genome help in discovering broad-based antivenoms? – The Hindu
Posted: at 10:13 am
The story so far: A consortium of scientists, which includes several of them from India, has mapped the genome of the Indian cobra considered to be among the most poisonous. Few snakes have had their genomes sequenced in detail and less so for a species of India. The Indian cobra genome sequencing is reportedly the most detailed blueprint of a snakes genes.
The Indian cobra, common cobra, spectacled cobra are names for the same species, Naja naja, and is part of the so called Big 4: the Indian cobra, the common krait (Bungarus caeruleus), Russells viper, and the saw-scaled viper. The quartet has long been considered responsible for most snake bites on the Indian subcontinent. The king cobra (Ophiophagus hannah), another poisonous snake, had its genome sequenced in 2013 by a research team in the U.K. (along with an international team). The foray into the Indian cobra genome involved making a map of its 38 chromosomes. Chromosomes are where DNA is tightly packed and the reptiles gene map unveiled in the latest issue of the scientific journal, Nature Genetics revealed over 12,000 genes. The human genome, in comparison, has 23 chromosomes and the estimated number of protein coding genes in the 20,000-25,000 range.
Knowing the sequence of genes could aid in understanding the chemical constituents of the venom and contribute to development of new antivenom therapies, which have remained practically unchanged for over a century.
According to the World Health Organisation, though the exact number of snake bites is unknown, an estimated 5.4 million people are bitten each year with up to 2.7 million envenomings. Around 81,000 to 1,38000 people die each year because of snake bites, and around three times as many amputations and other permanent disabilities are caused by snakebites annually. Somasekar Seshagiri of the SciGenome Research Foundation, Bengaluru (and the Molecular Biology Department, Genentech, Inc., South San Francisco, CA, U.S.), who is one of the authors of the study, used the genome and gene expression data from 14 different cobra tissues. Among the genes mapped are 139 toxin genes, or those that produce biological products specific to toxins. Nineteen of them are venom-specific, and expressed only in the venom gland. These are the constituents of venom that cause paralysis, internal bleeding and death associated with snakebite. Knowing these genes, the scientists argue in their paper, can help scientists design new antivenom using recombinant protein technologies. If genomes of more snakes are sequenced, there is a bigger possibility of genes commonly associated with venom production (across snake species) are identified and more broad-spectrum antivenoms are made.
Sequencing a genome is an important step to making antivenom but will not on its own solve the problem of making and supplying enough of the product to address the huge volume and variety of snakebites in India. A study in December by Kartik Sunagar, Assistant Professor at the Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, said that though bites from 60 of 270 species of Indian snakes are known to kill or maim, the antivenom now available is effective only against the Big 4. The study is titled Beyond the big four: Venom profiling of the medically important yet neglected Indian snakes reveals disturbing antivenom deficiencies, published in the journal, PLOS Neglected Tropical Disease. For instance, the monocled cobra (Naja kaouthia), found in east and north-east India, is not among the Big 4, but its venom, tested in mice, is more potent than that of the Indian cobra. But the commercial antivenom is not effective against the monocled cobra. Sunagars research also shows that the antivenom is effective against the common krait in south India but is not against the same species in Punjab. His study also notes that while various medically important species of cobras (N. sagittifera, N. oxiana, N. kaouthia), kraits (B. andamanensis, B. fasciatus, B. niger, B. sindanus), vipers (Hypnale hypnale, Ovophis monticola, E.c. sochureki, Macrovipera labetina), coral snakes (Calliophis nigrescens, Sinomicrurus macclellandi), sea snakes (Pelamis platurus, Enhydrina schistose, Hydrophis cyanocinctus) and sea kraits (Laticauda colubrina), etc., are capable of delivering clinically significant and, even, fatal bites, specific antivenoms do not exist. This is because snake venom is surprisingly varied and comes in a staggering variety that has not been completely understood by scientists.
Antivenom is made by extracting venom from the snake and injecting small amounts into rabbits or horses. In the case of the polyvalent antivenom available in India, it is made by injecting it into horses. The antibodies that form are then collected from the domestic animals blood, purified and isolated. The first antivenom for snakes was actually made for the Indian cobra by Lon Charles Albert Calmette, a French scientist of the Pasteur Institute, in 1894. The process is considered laborious, expensive and time consuming. Using recombinant technology, the genetic sequence for each toxin can be pasted into a yeast or E. coli bacterium, and have them multiply. Then they can be compared to libraries of human antibodies to check which ones stick best and make stable antivenom.
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Will the sequencing of the Indian cobra genome help in discovering broad-based antivenoms? - The Hindu
Emendo Biotherapeutics Raises $61 Million to Advance Next Generation Genome Editing Therapeutics – Business Wire
Posted: at 10:13 am
NEW YORK--(BUSINESS WIRE)--Emendo Biotherapeutics, a leader in next-generation gene editing using synthetic biology to address untreatable diseases, today announced a Series B investment totaling $61 million led by AnGes, Inc., a Japan-based biopharma, reflecting its strategic interest in partnering with Emendo on the development of specific indications.
This financing provides a strong foundation from which we can accelerate our proprietary OMNI gene editing platform towards a broad clinical pipeline for addressing devastating untreatable diseases, said Dr. David Baram, President & CEO, Emendo Biotherapeutics. We are grateful for such strong support from so many high-quality investors and strategic partners including AnGes, OrbiMed Advisors, OrbiMed Israel Partners and Takeda Ventures who share our vision to translate this powerful science into transformative medicines.
Emendo Biotherapeutics is pioneering OMNI, a next-generation allele-specific gene editing platform that uses synthetic biology to expand what is possible in genome-editing. In 2019, Emendo granted an option to Takeda to use the OMNI nuclease gene editing program for two research and development targets. Emendo received an undisclosed investment from Takeda Ventures that was converted in the Series B.
Emendos OMNI technology enables precision gene editing while maintaining high efficiencies, uniquely addressing dominant indications such as Severe Congenital Neutropenia (SCN), caused by mutations in the neutrophil elastase gene ELANE. Dominant indications represent the vast majority of genetic diseases which until now have been untreatable.
AnGes is a Tokyo and Osaka, Japan-based biopharmaceutical company focused on the development and commercialization of gene-based medicines including gene therapy and oligonucleotide molecules. AnGes lead product HGF plasmid, which received conditional approval in Japan in 2019, is a DNA plasmid which encodes the human Hepatocyte Growth Factor (HGF) gene, an angiogenic (new blood vessel growth) factor for critical limb ischemia (CLI). The company is also developing NF-kB Decoy oligonucleotide for the treatment of inflammatory diseases. For more information please visit http://www.anges.co.jp.
Emendo Biotherapeutics is transforming the landscape of genome-editing based medicine through its use of novel CRISPR nucleases, advanced cutting-edge protein engineering platforms, diverse pipeline of clinical programs and extensive intellectual property portfolio. For more information please visit us at http://www.emendobio.com.