Daily Archives: September 2, 2022

This week the National Human Genome Research Institute is holding a meeting to discuss progress and identify solutions to genomic medicine implementation challenges. Participants from academic medical centers are presenting examples of how genomic learning healthcare systems apply cycles of genomic medicine implementation, evaluation, adjustment, and updated implementation practices across their delivery systems.

One of the speakers was Travis Osterman, D.O., M.S., a medical oncologist, informatician, clinical director in the Office of the Chief Health Information Officer at Vanderbilt University Medical Center (VUMC), and director of Cancer Clinical Informatics in the Vanderbilt-Ingram Cancer Center. His talk focused on progress made integrating clinical genomic results into the electronic health record and some of the downstream benefits Vanderbilt is seeing from that.

Osterman gave the audience an update on some recommendations in a 2015 National Academy of Medicine report on this topic. The first was establishing data standards and common ways of representing outcomes that would facilitate the scalability and translation of genomic information into clinical care. The second was integrating genomic data into the clinic through clinical decision support, so the guidance is scalable and interoperable.

He praised the HL7 clinical genomics working group for its work on an evolving data standard for transmitting clinical genomics information that includes pharmacogenomics, somatic and germline information. The standard for trial use was initially published in November of 2018. Today Vanderbilt is one of 29 healthcare systems that are utilizing this data transmission standard to connect to reference laboratories and receive structured information, Osterman said.

Our tagline at Vanderbilt is making healthcare personal and re-examining our efforts in precision medicine led to a clinical genomics workstream, which I help to lead, Osterman said. Many of these efforts were already ongoing, and it was bringing them together so we could leverage scale, understand what each of what we jokingly call silos of excellence were doing and make that work across our enterprise.

In terms of clinical decision support, Osterman said, most health systems are either recommending genomic testing or personalizing care for an individual patient. That is what we did from 2010 through 2020, and we have a robust pharmacogenomics program. We started that program in 2010, and currently have almost 20 drug-gene interactions that we track. We're both recommending that test in our electronic health record, and then able to integrate those results to help make sure that the right patients are getting the right drugs the right time, he explained. This is not necessarily a new phenomenon, but we're trying to expand those same principles into other spaces.

Osterman spoke about working with Kevin Ess, M.D., Ph.D., who is a pediatric neurologist at Vanderbilt. Ess shared that about 40 percent of pediatric seizure disorders are due to genetic factors. The ones that aren't potentially have an anatomic cause and therefore can go to surgery and potentially have a really good outcome.

Informaticists worked with Ess to identify which specific patients may actually need testing to identify a genetic cause of their seizure disorder, and they developed a clinical work flow to make it happen.

This is live in our system, and is one of the ways that we're trying to push forward into spaces that are outside of pharmacogenomics, Osterman said. We've had several other examples. Routinely, for the last many years, we've been doing both recommended genomic testing and personalized care for individual patients, but I think we need to do more. We need to think not just about individual patients; we need to think about how we do this is for patient populations. We need to think about how we recommend genetic testing or genomic testing to patient populations. Then how do we care for and deliver care to the entire population to personalize their care.

To do this, Osterman said, we need to get the data out of PDFs. We want to receive all of those discrete final results, just like any other internal lab that we would order. We want to flow downstream into the electronic health record, and then ultimately both provide patient care and then support our research enterprise, he added. We don't want to give up all of those raw unprocessed files, whether that's from our internal genomics lab or whether that's from an external partner. Those are going to go into operational data storage and still may help provide patient care, because we have an internal lab that may leverage those upstream files. Those are going to go into a research repository.

Vanderbilt went live on Epic's genomics module, which allows health systems to receive those structured results from third-party reference laboratories, in July of 2021. The real value isn't me receiving those genetic results in my in-basket in our electronic health record, Osterman said. The real value is how this benefits all of our downstream processes. The order goes out and the variant data come back into Epics database, which is called Chronicles, and it's immediately available to patients. We've talked about putting patients at the center of this. If I have a test that I ordered on one of my patients, that patient can then take that test and show it to another provider, regardless of what electronic health record they're using, because they'll have those data on their phone, he said.

We're now able to leverage some of the tools within our electronic health record to do queries that we would otherwise need to do with one of our business intelligence tools. For instance, our electronic health record has the ability to do some kind of rudimentary data visualizations through a tool called Slicer Dicer. And because these are structured data, those work right out of the box, and all of my colleagues can access those data as well, he said. Because these are structured data flowing through all of our database systems, they also flow downstream to our research system, called the Research Derivative, which is a copy of our electronic health record use for research. And then that is de-identified in something called the Synthetic Derivative, which then is linked up to our biobank Bioview. By putting these data in structured form, not only are we improving patient care, but these data flow all the way downstream.

Here is another example of process improvement: Before we implemented the structured data, when a new first-class drug became approved for cancer treatments, we had data scientists that would query multiple vendor systems; they would take that query, and they would look against our electronic health record system to see which of those patients were still living and who their oncologists were, Osterman explained. Then they would give us a report on which patients would potentially benefit from these new treatments after their FDA approval. This process took about one to two weeks, but we thought it was high value, and so we absolutely supported that. I treat primarily lung cancers, and we have 22 approved drugs with targeted variants, and that number continues to grow every year. Now, since we moved to receiving structured data, this process is much, much shorter. When we know that there's a new first-class drug approved, the clinical team can do these queries directly within Epic.

So how does Osterman think the progress on a genomics learning health system is going overall? Well, as far as establishing data standards, through the work of HL7, I think we've made tremendous progress, he said. And second, integrating clinical decision support, I think we're pushing the envelope. I think there are opportunities to do this even at the population level today.

What are the next challenges? One is providing a standard way for patients to provide and transfer genetic and genomic information, he said. I think that's certainly going to be key going forward. I'll take it one step further and say that patients are going to be consenting for large consortium studies and healthcare systems are going to then be asked to share those data with that research consortium, and we need to figure out ways to do that. Finally, I think education is going to be key for both physicians and nurses. This has been a huge effort in our organization.

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Vanderbilt Sees Downstream Benefits From Integrating Genomic Results Into EHR - Healthcare Innovation

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.

(Brand Connect Initiative)

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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