Category Archives: Genome

Researchers explore how an organisms genome affects its ability to live in an extreme environment

The Lagunitas pond in the Cuatro Cinegas Basin of Mexico.

February 25, 2020

The Cuatro Cinegas Basin in the Chihuahuan Desert of Mexico was once a shallow sea. Some 43 million years ago, it became separated from the Gulf of Mexico. The basin is nutrient-poor and harbors a "lost world" of aquatic microbes of ancient marine ancestry.

Because of these characteristics, it is an invaluable place for researchers to study and understand how life may have existed on other planets in our solar system.

In a National Science Foundation-funded study published in the journal eLIFE, a team of researchers at Arizona State University conducted experiments in the basin.

Their goal was to shed light on how an organism's genome -- its size, the way it encodes information, and the density of information -- affects its ability to thrive in an extreme environment.

For their experiment, the scientists conducted field monitoring, sampling and routine water chemistry testing for 32 days in a shallow, nutrient-poor pond called Lagunita.

They installed mesocosms, or miniature ecosystems, that served as a control group and remained separate from the rest of the pond. They then added fertilizer that was rich in nitrogen and phosphorus to increase microbial growth in the pond.

At the end of the experiment, the scientists examined how the community in the pond changed in response to the additional nutrients, focusing on the organisms' ability to process biochemical information in their cells.

Ultimately, the researchers found that indeed a nutrient-enriched community became dominated by species that could process biochemical information at a faster rate, whereas the original low-nutrient community harbored species with reduced biochemical information processing.

"We were able to identify and confirm that there are fundamental genome-wide traits associated with systematic microbial responses to ecosystem nutrient status, without regard to the species identity of those microbes," says Jim Elser, an ecologist at ASU and paper co-author.

What this may suggest for life on other planets is that organisms, no matter where they are, need information-processing machinery fine-tuned to the key resources around them.

"This study provides new insights into how microbes adapt to different types of environments, and the tradeoffs they may face in doing so," says Doug Levey, a program director in NSF's Division of Environmental Biology.

Read more:
Rules of life: From a pond to the beyond - National Science Foundation

Life science researchers at Tel Aviv University (TAU) have stumbled upon a non-breathing animal, challenging current understanding of the animal world, according to a study published in the Proceedings of the National Academy of Sciences of the United States of America.The research, led by Prof. Dorothee Huchon of the School of Zoology at TAUs Faculty of Life Sciences and Steinhardt Museum of Natural History, detailed the 10-celled parasite organism called Henneguya salminicola that is found in the muscles of salmon. The research was supported by the US-Israel Binational Science Foundation, and conducted along with Prof. Paulyn Cartwright of the University of Kansas, and Prof. Jerri Bartholomew and Dr. Stephen Atkinson of Oregon State University."The parasites anaerobic nature was an accidental discovery," TAU said in a statement. "While assembling the Henneguya genome, Huchon found that it did not include a mitochondrial genome. The mitochondria are the powerhouse of the cell where oxygen is captured to make energy, so its absence indicated that the animal was not breathing oxygen." The animal itself, a "myxozoan relative" of jellyfish and corals, apparently gave up on breathing and consuming oxygen in order to produce energy, somewhere along its evolutionary track. Aerobic respiration was thought to be ubiquitous in animals, but now we confirmed that this is not the case, Huchon explains. Our discovery shows that evolution can go in strange directions. Aerobic respiration is a major source of energy, and yet we found an animal that gave up this critical pathway.Fungi, amoebas or ciliate lineages living in oxygen-poor environments abandoned the need to consume fresh air quite some time ago, after their evolutionary trajectories followed an anaerobic path. The findings allude to the possibility that the same type of occurrence could happen to an animal if the conditions are right."Its genome was sequenced, along with those of other myxozoan fish parasites," TAU said in a statement. Before the discovery, experts were unsure whether organisms within the animal kingdom could survive without oxygen, given that animals are "multicellular, highly developed organisms, which first appeared on Earth when oxygen levels rose." The findings are important for future evolutionary research.Its not yet clear to us how the parasite generates energy," Huchon said. "It may be drawing it from the surrounding fish cells, or it may have a different type of respiration such as oxygen-free breathing, which typically characterizes anaerobic non-animal organisms. It is generally thought that during evolution, organisms become more and more complex, and that simple single-celled or few-celled organisms are the ancestors of complex organisms.But here, right before us, is an animal whose evolutionary process is the opposite. Living in an oxygen-free environment, it has shed unnecessary genes responsible for aerobic respiration and become an even simpler organism.

Excerpt from:
Tel Aviv University researchers discover a non-breathing living animal - The Jerusalem Post

DUBLIN, Feb. 26, 2020 /PRNewswire/ -- The "Genomics Market Size, Share & Trends Analysis Report by Application and Technology (Functional Genomics, Pathway Analysis), by Deliverables (Products, Services), by End Use, by Region, and Segment Forecasts, 2020 - 2027" report has been added to ResearchAndMarkets.com's offering.

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The global genomics market is expected to reach USD 31.1 billion by 2027, registering a CAGR of 7.7% over the forecast period according to this report. Significant changes in disease management processes along with advancements in genomics and personalized medicine are expected to propel the market.

Increasing pool of market innovators such as 23andMe, Oxford Nanopore Technologies, and Veritas Genetics that have launched breakthrough genomic technologies in recent years are also contributing toward market development. 23andMe has expertise in developing direct-to-consumer genomic tests targeted toward disease prognosis and has recently received FDA approval for its commercialization.

MinION - a trademark sequencing device of Oxford Nanopore Technologies, is witnessing significant traction owing to its ability to sequence any fragment length of DNA in real time. On the other hand, Veritas Genetics offers an affordable solution for a complete readout of the genomic sequence. Earlier procured only by doctors, these tests can now be taken by anyone curious about their DNA and costs approximately USD 1,000. The company has also begun the commercialization of this technique for newborn's genomic sequencing applications in China in 2017.

Further key findings from the report suggest:

Key Topics Covered

Chapter 1 Research Methodology

Chapter 2 Executive Summary2.1 Genomics Market Outlook, 2016-2027

Chapter 3 Industry Outlook3.1 Penetration & Growth Prospects Mapping3.2 Trend Analysis3.2.1 Application Trends3.2.2 Product Trends3.2.3 End-Use Trends3.2.4 Regional Trends3.3 Genomics - Market Dynamics3.3.1 Market Driver Analysis3.3.1.1 Growing Integration of Genomics Data into Clinical Workflows3.3.1.1.1 More Targeted and Personalized Healthcare3.3.1.1.2 Growth of Newborn Genetic Screening Programs3.3.1.1.3 Advancements in Non-invasive Cancer Screening3.3.1.1.4 Military Genomics3.3.1.2 Technological Advances to Facilitate Genomic R&D3.3.1.2.1 Emergence of Advanced Genome Editing Techniques3.3.1.2.2 Integration of New Data Streams3.3.1.2.3 RNA Biology3.3.1.2.4 Single Cell Biology3.3.1.3 Rising Adoption of Direct to Consumer Genomics3.3.1.4 Success of Genetic Tools in Agrigenomics3.3.1.5 Increasing Participation of Different Companies3.3.1.6 Increase in Government Role and Funding in Genomics3.3.2 Market Restraint Analysis3.3.2.1 Issues Regarding Intellectual Property Protection, Data Management, and Public Policies3.3.2.2 Dearth of Skilled Personnel3.4 Opportunity Analysis3.5 Industry Analysis - Porter's3.5.1 Supplier Power - Medium3.5.2 Buyer Power - High3.5.3 Substitution Threat - Low3.5.4 New Entrants Threat - Low3.6 Regulatory Landscape: Genomics - SWOT by PEST Analysis3.6.1 Political Landscape3.6.2 Economic Landscape3.6.3 Social Landscape3.6.4 Technology Landscape3.7 Company Market Share Analysis3.8 Competitive Landscape3.8.1 Strategy Framework3.8.2 Company Categorization3.8.2.1 New Entrants3.8.2.2 Mature Players & Leaders

Chapter 4 Genomics Market Categorization: Deliverable Outlook4.1 Genomics Market Share By Deliverable Outlook, 2016 to 20274.2 Products Market, 2016 to 20274.3 Services Market, 2016 to 2027

Companies Mentioned

Story continues

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Worldwide Genomics Markets, 2020-2027 - Comprehensive Analysis on the $31.1 Billion-Projected Industry - Yahoo Finance

What The Study Found

The largest genomic study of population groups in Asia, generating and analysing whole-genome sequences of 1,739 individuals from 219 groups.

***

On December 5, 2019, scientists from the GenomeAsia 100K project published an article (The GenomeAsia 100K Project enables genetic discoveries across Asia) in the prestigious science journal Nature. It is the largest genomic study of Asian populations, covering 1,739 individuals from 219 different population groups and 64 countries. India has the maximum number of whole-genome sequences at 598. Besides enabling a better understanding of how Asian populations were formed, the resulting work will also make it possible to find out which medicines suit them better, based on genetic data.

The need for a more varied genetic database from populations across the world was highlighted in 2009, when analysis revealed that 96 per cent of participants in genome-wide association studies (GWAS) were of European descent. GWAS studies associate certain diseases with specific variations and the lack of data from different parts of the world meant medicines either couldnt be catered to suit them or were entirely unsuitable to them.

We show that the variant data produced by this project improve variant filtering for the discovery of disease-associated genes of rare diseases. We show that Asia has sizable founder populations and that further studies in these populations may be useful for the discovery of rare-disease-associated genes, the paper says. For example, the researchers found that carbamezepine, an anti-convulsant, may have adverse effects on about 400 million South-East Asians who form part of the Austronesian language group. The paper also mentions that drugs like clopidogrel, peginterferon and warfarin showed the largest variation between populations in predicted adverse drug responses.

Dr Partha P. Majumder, founder of National Institute of Biomedical Genomics, Kalyani, and one of the co-authors, tells Outlook that the differential carbamezepine effect among Austronesians was so striking that we decided to report this quickly. We also report about warfarin, a commonly used blood-thinning drug, used for prevention of blood clots, especially for individuals at high risk for heart attacks.

Using the data, the scientists were able to reveal a DNA variant in a gene (NEUROD1), which is probably responsible for a particular kind of diabetes. Another DNA variant in the haemoglobin gene has been linked to beta-thalassemia found only in South Indians, says Majumder.

The scientists discovered close to 200,000 DNA markers in Asians, which had been previously unreported in existing genetic databases. Majumder explains their significance, saying that the catalogues that are now used for disease-association studies in Asia, including India, are those that have primarily been generated in western populations, hence of limited use in Asia. The scientists also found 23 per cent of previously unreported protein variants. Since alterations of proteins are usually associated with disease, we specifically investigated those DNA variants that alter proteins, says Majumder.

Medicines will become more specific and more useful to us. More importantly, we will not use the medicines that do not work for us, Dr Ch Mohan Rao, distinguished scientist at the Council of Scientific and Industrial Research and former director at the Centre for Cellular & Molecular Biology, tells Outlook. Rao says that the same medicines used in the West are being used without context in Asia, but now studies show that certain mutations (in DNA) are probably benign.

While the fundamental biology discovered by genetic studies at individual sites in the genome are mostly shared across humanity, studies carried out primarily in a single population means we miss low-hanging fruit in other populations, and limit the utility of genomic prediction across other populations, says Vagheesh Narasimhan, fellow at the Reich lab, department of genetics, Harvard Medical School. He adds that scientists are currently able to predict heritable risk of complex diseases several-fold more accurately in European populations than in non-Europeans, putting it down to a lack of similar databases in other countries. Studies such as this one will help close that gap, he adds.

The study also paints a finer picture of how the South Asian populations were formed, while throwing up interesting facets. Close to 4 million years ago, two precursors to modern-day humansthe Neanderthal and the Denisovanevolved. While it was earlier thought that the homo sapien (modern human) wiped out both, our DNA contains a large admixture with them, the degree of mixing varying across Asia. In India, the researchers found that tribal and non-Indo European speakers had more Denisovan DNA than the non-tribals and Indo-European speakers. Elite-caste groups have lesser Denisovan DNA, with Indo-European speakers of Pakistan having the least, he adds.

Majumder says the simplest explanation is that Indo-European-speaking migrants, who came to the subcontinent from the north-west, mixed with an indigenous group ancestral to present-day south Indians; the ancestral group had a high level of Denisovan admixture.

Using an approach from a previous study, the researchers also tried to identify the degree to which populations are inherited as identical by descent (IBD). The researchers found multiple Asian urban populations with IBD scores close to or above the Finnish population. For example, samples from an outpatient hospital in Chennai, a city with a census size of 9 million, had an IBD score that was approximately 1.3 times greater than the score for the Finnish group, the paper says. Majumder explains: It is, therefore, possible that some urban populations may have arisen from a small number of founders and then numerically expanded quickly.

With such large numbers of samples being sequenced, we now have the potential to study population movements and mixtures in much finer detail. Databases like this will also enable better estimates of ancestry and genealogy, says Narasimhan.

When the Human Genome Project began in 1990, India was not part of it. Fortunately, we did not miss out because the whole database was in public. But we did not develop the technology as fast as other countries, says Dr Rao, adding that now things have changed with Indian scientists doing a large part of the work. With India participating in the research our technology and capacity building has increased dramatically. Now we are not second to anyone.

Read more here:
The Genomic Route To Targeted Cures - Outlook India

A nightmarish scene was burnt into my memory nearly two decades ago: Changainjie, Beijings normally chaotic fifth avenue, desolate without a sign of life. Schools shut, subways empty, people terrified to leave their homes. Every night the state TV channels reported new cases and new deaths. All the while, we had to face a chilling truth: the coronavirus, SARS, was so novel that no one understood how it spread or how to effectively treat it. No vaccines were in sight. In the end, it killed nearly 1,000 people.

Its impossible not to draw parallels between SARS and the new coronavirus outbreak, COVID-19, thats been ravaging China and spreading globally. Yet the response to the two epidemics also starkly highlights how far biotech and global collaborations have evolved in the past two decades. Advances in genetic sequencing technologies, synthetic biology, and open science are reshaping how we deal with potential global pandemics. In a way, the two epidemics hold up a mirror to science itself, reflecting both technological progress and a shift in ethos towards collaboration.

Let me be clear: any response to a new infectious disease is a murky mix of science, politics, racism, misinformation, and national egos. Its nave to point to better viral control and say its because of technology alone. Nevertheless, a comparison of the two outbreaks dramatically highlights how the scientific world has changed, for the better, in the last two decades.

A viruss genetic blueprint is the first clue to its origins and traits. The response to COVID-19 was extremely rapid. Within a month of the first identified case in Wuhan, Chinese scientists had deposited the viruss partial genetic blueprint into GenBank, an online, widely-consulted database.

Almost immediately, scientists from all sectorsacademic, biotech, governmentaround the world began ordering parts of the virus genome online to study in their own labs.

The rise of commercial companies that manufacture custom-made DNA molecules, such as Integrated DNA Technology (IDT) and Biobasic, exemplify how much genetic synthesis has changed from 2003 to 2020. Costs for making entire genomes from scratch have dropped dramatically, giving rise to a booming industry of mail-order virus (and other organisms) parts for cheap. Biobasic, for example, offers primers that amplify certain parts of COVID-19 genes at a few bucks apiece. These raw genetic tools, rapidly synthesized and purified to order, form a critical ingredient for scientists to recreate important parts of the virus in their own labs.

Rapid sharing of the viral genome plus easy online ordering make it much easier for scientists to study the bug and test potential vaccines. According to a CBS8 report, Inovio, a biotech company based in San Diego, has already created a potential vaccine for COVID-19 and tested it in mice and guinea pigs. If they gain FDA approval, clinical trials in humans could begin as early as this summer. Sanofi, Moderna, and other pharmaceutical giants are right on Inovios tail. In contrast, a vaccine for SARS took about 20 months to engineer, long after the epidemic had burned out. Although the same fate may await COVID-19, the momentum for vaccine creation is unprecedented.

Going a step further, scientists now also have the ability to recreate COVID-19 from scratch. Partial viral genetic sequences are often sufficient to engineer vaccines. However, only a live, complete version can offer clues to significant questions such as how it spreads, where it came from, and how it jumped from animal to human. For example, by systematically mutating parts of the virus, scientists can decipher critical genes needed for the virus to spread or generate disease, or build more accurate models of its projected spread within the human population.

So far, however, China is the only country with access to the intact virus, which means that other countries need to build the virus directly from its digital DNA code. The technologys been possible for about twenty years, but advances in commercial genetic synthesis are massively simplifying the processes, so much so that the main hurdle is regulatoryfears of lab accidents or bioterrorismrather than technological.

As gene synthesis costs continue to drop and synthetic biology tools become more powerful, lab-made clones of pandemic-level pathogens could become even more prominent to fight off pandemics. As one coronavirus expert said, synthetic viruses are the future in how the medical research community responds to a new threat.

The other distinction between the SARS and COVID-19 responses isnt biotech. Its digital. When SARS broke out in 2003, the internet was only coming online for a majority of users, and email was relatively new. Getting information out from a quarantined region was immensely difficult.

Despite digital challenges, SARS still stood out as a unifying moment where international researchersagainst all odds, rivalry, and internal squabblescame together to share information, specimens, and reagents through personal communications. However, disseminating information to larger audiences relied on government agencies, including the CDC, or academic papers in journals.

In contrast, data exchange for COVID-19 was rapid and abundant. Thanks to the rise of pre-publication servers such as bioRxiv, scientists can now easily circumvent the months-long peer-review process in journal publishing and publish their results directly online.

Open sharing of information is a double-edged sword: because papers on bioRxiv arent peer-reviewed, their quality can be hit or miss. Nevertheless, the resource has rapidly emerged as the online watercooler for scientists studying COVID-19. For example, one team thats building COVID-19 from scratch pulled four different genomic sequences off the server and averaged their results to generate a consensus sequence.

This rapid dissemination of information isnt just helping vaccine development. Its also soothing public fear. A novel, lethal virus is bound to stoke public fear, misinformation, and mistrust, especially if scientists keep mum about early results. BioRxiv provides a way to put preliminary data into the spotlight, where scientists and journalists can examine, build upon, or report solid results to the public.

Pre-publication servers arent perfect; theres a chance of misinformation or misconstrued data, which need to be vetted out. But its clear that bioRxiv is serving a critical role in accelerating viral knowledge, and a testament to the open science movement.

As science becomes more open, its also becoming far more collaborative.

Global collaborations have exploded in numbers since the 2003 SARS outbreak, with international initiatives now a dime a dozen. The scientific communitys response to COVID-19 is a strong example of that shift: in a race against the clock, rather than hogging data for personal fame, lets get everyone to collaborate and accelerate discoveries.

That said, global collaboration is impossible without the ground zero country taking the first step, that is, alerting the world to a new virus outbreak. In 2003, China tried to squash any mention of SARS before it became too big of a problem; in 2019, Chinese officials relatively promptly alerted the World Health Organization to COVID-19 (though not without severe arm-twisting and tragic deaths).

We can marvel at advances in genetic technologies, synthetic biology, or computer modeling for tackling viral epidemics; but fundamentally, preventing a disease outbreak requires early alarm from the country of originembarrassment be damned.

More epidemics will come. Over 30 novel infectious diseases have raged across parts of the globe for the past three decades, and simulations show many viruses in bats and other animal carriers have the potential to directly jump to humans. Scientists have a game plan. Will governments follow?

Image Credit: Novel Coronavirus SARS-CoV-2, NIAID

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How to Battle an Epidemic? Digitize Its DNA and Share It With the World - Singularity Hub

According to research published inNature Communications, comprehensive profiling of tumor samples found that the immunogenomic landscape in osteosarcoma is characterized by genomic complexity and significant heterogeneity.1

Moreover, researchers found that poor infiltration of the tumor by immune cells, low activity from available T-cells, a lack of immune-stimulating neoantigens, and multiple immune-suppressing pathways all combine to dampen responses to immunotherapy in this disease landscape.

This study is important not only because it focuses on a rare cancer, but it sets the groundwork for understanding the multifaceted reasons this cancer doesnt respond to immunotherapy, despite having certain hallmarks that suggest it would, corresponding author Andy Futreal, PhD, chair of Genomic Medicine at MD Anderson Cancer Center, said in a press release.2Understanding those reasons and beginning to pick them apart does begin to give us lines of sight on how to get around the tumors methods of subverting the immune system.

In order to gain insights into the immunogenic potential of this tumor type, researchers conducted whole genome, RNA, and T-cell receptor sequencing, immunohistochemistry and reverse phase protein array profiling (RPPA) on samples from 48 pediatric and adult patients with primary, relapsed, and metastatic osteosarcoma. The majority of the samples were from relapse (23%) and metastatic (51%) cancers.

In the samples, genomic changes were similar to those previously reported and there were few dissimilarities between the sample types. However, in contrast to other disease types, the genomic changes observed in these osteosarcomas did not coincide with an increase in the expression of mutated proteins or neoantigens. Further, the degree of immune cell infiltration into the tumor was found to be generally lower than in other tumor types where immune checkpoint inhibitors are more effective, like lung cancer and melanoma. T-cells in the tumor also displayed a low level of activity, demonstrated by low clonality scores.

These data highlight the need to pursue multiple contributors to immune suppression in [osteosarcoma], the authors wrote. It is unlikely that any single approach will be effective across this patient population.

Gene expression analysis exposed 3 distinct classes within the study samples that corresponded with levels of immune infiltration. Hot tumors were found to have the greatest degree of immune infiltration, however they also had high activity in a number of signaling pathways that suppressed immune activity. Contrastingly, cold tumors had the lowest levels of immune infiltration, reduced expression of human leukocyte antigen (HLA), and a higher number of genes with copy number loss, which signals higher genomic instability.

Notably, researchers also discovered thatPARP2gains and increased expression were correlated with low immune infiltration in cold osteosarcomas, supporting the rationale for studies exploring a combination of PARP inhibitors and immunotherapy. Therefore, ongoing translational studies from patients with osteosarcoma treated with immune checkpoint inhibitors could further inform the next steps in developing immunotherapy trials for this patient population.

By understanding the interplay between tumor genomics and the immune response, we are better equipped to identify osteosarcoma patients who are more likely to benefit from immunotherapy, co-author Andrew Livingston, MD, assistant professor of Sarcoma Medical Oncology and Pediatrics at The University of Texas MD Anderson Cancer Center, said in a press release. These findings lay the groundwork for novel clinical trials combining immunotherapy agents with targeted or cell-based therapies to improve outcomes for our patients.

References:

1. Wu C, Beird HC, Livingston JA, et al. Immuno-genomic landscape of osteosarcoma.Nature Communications. doi:10.1038/s41467-020-14646.

2. Osteosarcoma profiling reveals why immunotherapy remains ineffective [news release]. Houston, Texas. Published February 21, 2020. eurekalert.org/pub_releases/2020-02/uotm-opr022020.php. Accessed February 21, 2020.

Read more from the original source:
Profiling of Osteosarcoma Demonstrates Why Immunotherapy is Ineffective - Cancer Network

The BC Centre for Disease Controls (BCCDC) Public Health Laboratory has announced a newpilot project that will enable researchers to identify and track new cases ofthenovel coronavirus (COVID-19) in British Columbia.

On Feb. 20, Provincial health officer Dr. Bonnie Henry reported thatasixthcase of the novel coronavirus hadbeen diagnosed in B.C.after a woman in her 30s returned to the province this week from travel in Iran. However, she addedthat thewoman's presumptive case is relatively mild anda number of her close contacts have already been put in isolation.

So, while the risk of disease spread in British Columbia remains low at this time, the number of laboratory-confirmed COVID-19 cases worldwide has climbed to over a staggering70,000. As such, the BCCDC has responded by adding, "a critical new dimension to its outbreak response capabilitiesby incorporating genomic analysis into tracking."

Supported by Genome BCs Strategic Initiatives Fund, the$150,000 pilot studywill be able to identify where new cases of the novel coronavirus (COVID-19) in B.C. are coming from and monitor any spread in the community.

Found mostly in animals, coronaviruses are a large family of viruses. In humans, they can cause diseases ranging from the common cold to more severe diseases such as Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS-CoV).

The new coronavirus has been namedSARS-CoV-2, and the disease that it causes is calledCOVID-19. The symptoms ofCOVID-19 are similar to other respiratory illnesses, including the flu and common cold. They include cough, sneezing, fever, sore throat and difficulty breathing.

The BCCDC notes that people can trace their history as a family tree, based on prior knowledge of relationships or the sequence of our DNA the building blocks of all living things. Similarly, the health authority can can place each new strain of a virus on a larger family tree.

"For each new strain, in each new patient, the sequence (of DNA, or related RNA depending on the virus) allows us to place that strain in the larger family tree. If the new strain has a close relative we've seen already in BC, for example, it may be part of a locally-transmitted cluster; if the new strain is more closely related to virus strains recorded in another country, it might be a new introduction to BC. This information enables BCCDC to work with local public health authorities to guide and evaluate interventions. Since this kind of information informs real time decision making, it's essential that this work take full advantage of new rapid, potentially mobile, sequencing technologies," it states.

The new project, "Responding to Emerging Serious Pathogen Outbreaks using Next-gen Data: RESPOND," is designed as a rapid response pilot that will use the fast Oxford Nanopore and other sequencing platforms to simultaneously produce sequence and family tree information.

Leading the team for the pilot project is BCCDC Public Health Laboratory Medical Director Dr. Mel Krajden, one of the investigators from the first team in the world to produce the complete sequence of the SARS virus genome. The team is co-led by UBC faculty Dr. Richard Harrigan, a scientist with decades of experience performing translational HIV studies based on genomics, and Dr. Natalie Prystajecky, a microbiologist overseeing the COVID- 19 test development at the BCCDC.

With SARS, it took the world six months to obtain one virus sequence and BC was first. said Dr. Richard Harrigan. With COVID-19, we are aiming to turn around sequences from each patient in under 24 hours.

This type of project provides an example of the immediate impact Genome BC can have in an emerging public health scenario, like we are seeing for COVID-19, as well as promoting innovative genomic thinking to overcome scientific challenges. This work will improve our ability to respond to this emergency and ultimately benefits public health and the residents of BC, said Prystajecky.

"This experienced team is developing critical tools for response to this and any future outbreaks in BC," said Pascal Spothelfer, President and CEO, Genome BC. "It is a clear demonstration of the power of genomic analysis, and we are proud to be in a position to move it forward quickly."

Prystagjecky adds that it is important for anyone with further questions about the virus to consult the BCCDCCoronavirus(Novel) page. This source gives accurate and up-to-date information about what the virus is, how it is contracted, and what to do to keep yourself safe.

Continue reading here:
B.C. to track the origin and spread of COVID-19 with 'genomic technology' - Vancouver Is Awesome

THE GENE: AN INTIMATE HISTORY

EXECUTIVE PRODUCED BY

KEN BURNS AND DR. SIDDHARTHA MUKHERJEE,

TO PREMIERE ON PBS APRIL 7 & 14, 2020

WASHINGTON, D.C. February 19, 2020 WETA Washington, D.C., the flagship public broadcasting station in the nations capital, announced today thatKEN BURNS PRESENTS THE GENE: AN INTIMATE HISTORY, a two-part, four-hour documentary based on Pulitzer Prize-winning author Dr. Siddhartha Mukherjees book of the same name, will premiere on Tuesdays, April 7 and 14, 2020 from 8-10 pm ET on PBS stations nationwide. The film airs at a critical moment for the scientific community, as geneticists around the world wrestle with the ethical implications of new technologies that offer both promise and peril.THE GENEweaves together science, history and personal stories for a historical biography of the human genome, while also exploring breakthroughs for diagnosis and treatment of genetic diseases and the complex ethical questions they raise.

Groundbreaking treatments will improve the lives of millions of peoplepotentially treating diseases like sickle cellbut there are worries that scientists will take gene-editing technology too far, using it to modify germline DNA in order to enhance certain traits deemed preferable. AsTHE GENEdemonstrates, those fears have already been realized: in November 2018, Chinese researcher He Jiankui stunned and horrified the scientific community with an announcement: he had created the first genetically edited babies, twin girls born in Chinaa medically unnecessary procedure accomplished well before scientists had fully considered the consequences of altering the human genome.

These revolutionary discoveries highlight the awesome responsibility we have to make wise decisions, not just for people alive today, but for generations to come, said Dr. Mukherjee, assistant professor of medicine at the Department of Medicine (Oncology), Columbia University and staff cancer physician at Columbia University Medical Center.At this pivotal moment when scientists find themselves in a new era in which theyre able to control and change the human genome,THE GENEoffers a nuanced understanding of how we arrived at this point and how genetics will continue to influence our fates.

The documentary includes interviews with pioneers in the field including doctors Paul Berg, Francis Collins, Jennifer Doudna, Shirley Tilghman, James Watson, Nancy Wexler and Mukherjee himself. As with Burnss other projects,THE GENEuses a remarkable trove of historical footage, including Rosalind Franklins Photograph 51 from 1952, to track the journey of human genetics. Beginning with the remarkable achievements of the earliest gene hunters and their attempts to understand the nature of heredity, the film traces the history of genetics from Gregor Mendels pea plant studies in the 19thCentury and Watsons and Cricks discovery in 1953 of the structure of DNA to the efforts by Sydney Brenner and Marshall Nirenberg, among others, to understand how the genetic code is translated in human cells. We also witness the massive technological transformation from the 1970s through the 2000s from the sequencing of individual genes by Fred Sanger to the sequencing of the whole human genome. AsTHE GENEintroduces us to the scientists solving these great mysteries, the film also examines the insidious rise of eugenics, which bore horrific results in the United States, Europe and, in particular, in Nazi Germany.

THE GENEjuxtaposes this dynamic history with compelling, emotional stories of contemporary patients and their families who find themselves in a desperate race against time to find cures for their genetic diseases. The film follows the inspiring, heart-wrenching journeys of people such as Audrey Winkelsas, a young scientist born with Spinal Muscular Atrophy researching a treatment for her own condition, and Luke Rosen and Sally Jackson, parents on a tireless quest to raise awareness for their daughters rare degenerative disease. Hopes rise and fall with new discoveries and setbacks, revealing how intimate and profoundly personal this science can be for families affected by genetic diseases.

As it traces groundbreaking developments in genetics that promise to revolutionize life for millions of people,THE GENEalso documents the thorny ethical questions some of these new treatments raise. Today, geneticists find themselves on the brink of curing diseases long thought fatal but given the harrowing history of eugenics, both the scientific community and the public are forced to grapple with the ethical implications of these new technologies. Are there unintended consequences to changing human genomes? Could changes accidentally unleash cancer or some novel new genetic disease? From the prospect of genetic therapies to CRISPR, the film explores the complex web of moral, ethical and scientific questions facing this generation.

The series is directed by Chris Durrance and Jack Youngelson, with award-winning filmmaker Barak Goodman serving as senior producer and Ken Burns as executive producing alongside Dr. Mukherjee.THE GENEhas largely the same production team as CANCER: THE EMPEROR OF ALL MALADIES, which premiered on PBS in 2015 and was the Emmy Award-nominated adaptation of Mukherjees 2010 book,The Emperor of All Maladies: A Biography of Cancer.

THE GENEexplores the ultimate mystery story it unpacks the once-impenetrable science of what makes us who we are, said senior producer Barak Goodman.This is a moment for the general public and the scientific community to engage in a national conversation about the thrilling future of genetics and the ethical challenges posed by new science.

We want people to leave our film feeling both hopeful about these stunning developments and sensitive to the ethical questions facing the field, said directors Chris Durrance and Jack Youngelson.

I was thrilled to reunite with Sid and Barak on this project, said Ken Burns.For me, science, like history, is the exploration of what has come before and the promise of the future.THE GENEuntangles the code of life itself.

THE GENErepresents a groundbreaking opportunity to broaden public understanding of this important subject, and Sid, Ken and Barak are the ideal team to bring the fascinating book to film, noted Sharon Percy Rockefeller, president and CEO of WETA, the producing public media station forTHE GENE.

Integral to the project is an extensive engagement program created by WETA in collaboration with an array of partners, in particular the National Institute of Healths National Human Genome Research Institute, the projects primary Outreach and Education Partner. The project will enable the film to reach an even larger audience, engaging researchers, physicians and patients in the national conversation about the history of genetics and the state of the field today. Partners and funders will host screenings and discussions in cities across the country, working with local public media stations and a wide range of educational, medical and scientific organizations.

In conjunction with the broadcast, WETA is developing an expansive interactive website and social and digital media components, including a multi-media educational initiative designed to engage teachers and students through multiple platforms.including a six-part animated series, that delves into the complexities of genetics. Using mixed illustration styles, each episode will focus on a particular approach to genetics, including How Things Work, When DNA Goes Sideways, The Future of DNA, and more. WETA has also developed a companion teaching guide. The series will be distributed through various digital platforms by the National Institutes of Healths National Human Genome Research Institute, PBS, and member stations.

For more information about KEN BURNS PRESENTS THE GENE: AN INTIMATE HISTORY, visit pbs.org/thegene.

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Written by Seema Chishti | New Delhi | Updated: February 10, 2020 11:15:39 am The project is said to be among the most significant of its kind in the world because of its scale and the diversity it would bring to genetic studies.

LAST WEEK, The Indian Express reported that the government has cleared an ambitious gene-mapping project that is being described by those involved as the first scratching of the surface of the vast genetic diversity of India. A look at the objectives, scale and the diversity of the project, which will be significant not only in India but worldwide:

What is a genome?

Every organisms genetic code is contained in its Deoxyribose Nucleic Acid (DNA), the building blocks of life. The discovery that DNA is structured as a double helix by James Watson and Francis Crick in 1953, for which they won a Nobel Prize in 1962, was the spark in the long, continuing quest for understanding how genes dictate life, its traits, and what causes diseases.

A genome, simply put, is all the genetic matter in an organism. It is defined as an organisms complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism. In humans, a copy of the entire genome more than 3 billion DNA base pairs is contained in all cells that have a nucleus.

Hasnt the human genome been mapped before?

The Human Genome Project (HGP) was an international programme that led to the decoding of the entire human genome. It has been described as one of the great feats of exploration in history. Rather than an outward exploration of the planet or the cosmos, the HGP was an inward voyage of discovery led by an international team of researchers looking to sequence and map all of the genes together known as the genome of members of our species.

Beginning on October 1, 1990 and completed in April 2003, the HGP gave us the ability, for the first time, to read natures complete genetic blueprint for building a human being.

What then is the Genome India Project?

This is being spearheaded by the Centre for Brain Research at Bengaluru-based Indian Institute of Science as the nodal point of about 20 institutions, each doing its bit in collecting samples, doing the computations, and then the research. Its aim is to ultimately build a grid of the Indian reference genome, to understand fully the type and nature of diseases and traits that comprise the diverse Indian population. For example, if the Northeast sees a tendency towards a specific disease, interventions can be made in the region, assisting public health, which make it easier to battle the illness.

Editorial | Genome India Project is extremely promising and should proceed with maximum speed and maximum caution.

The other institutes involved are: AIIMS Jodhpur; Centre for Cellular and Molecular Biology, Hyderabad; Centre for DNA Fingerprinting and Diagnostics; Institute of Genomics and Integrative Biology; Gujarat Biotechnology Research Centre; IIIT Allahabad; IISER (Pune); IIT Madras; IIT Delhi; IIT Jodhpur; Institute of Bioresources And Sustainable Development; Institute of Life Sciences; Mizoram University; National Centre for Biological Sciences; National Institute of Biomedical Genomics; National Institute of Mental Health and Neurosciences; Rajiv Gandhi Centre for Biotechnology; and Sher-e-Kashmir Institute of Medical Sciences.

So, what will the project broadly do?

The mega project hopes to form a grid after collecting 10,000 samples in the first phase from across India, to arrive at a representative Indian genome. This has been found necessary as over 95% of the genome samples available, which are the basis of new, cutting-edge research in medicine and pharmacology, use the white, Caucasian genome as the base. Most genomes have been sourced from urban middle-class persons and are not really seen as representative. The Indian project will aim to vastly add to the available information on the human species and advance the cause, both because of the scale of the Indian population and the diversity here.

Who is an Indian?

The Indian subcontinent has been the site of huge migrations. Scientists associated with the project recognise that while the first migrations were from Africa, later too there were periodic migrations by various populations, making this a very special case of almost all races and types intermingling genetically. This can be seen as horizontal diversity. Moreover, later, there has been endogamy or inter-marriage practised among distinct groups, resulting in some diseases passed on strictly within some groups and some other traits inherited by just some groups. This is what scientists term vertical diversity.

Studying and understanding both diversities would provide the bedrock of personalised healthcare for a very large group of persons on the planet.

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What are the challenges involved?

MEDICAL ETHICS: In a project that aims only to create a database of genetic information, gene modification is not among the stated objectives. It is important to note, however, that this has been a very fraught subject globally. The lure to intervene may be much more if this kind of knowledge is available, without one being fully aware of the attendant risks. The risk of doctors privately running away with the idea of fixing genetic issues came to light most recently after a Shenzen-based scientist, who helped create the worlds first gene-edited babies, was sentenced to three years in prison. He Jiankui stunned the world when he announced in 2018 that twin girls had been born with modified DNA to make them HIV-resistant. He claimed he had managed that using the gene-editing tool CRISPR-Cas9 before their birth.

DATA & STORAGE: After collection of the sample, anonymity of the data and questions of its possible use and misuse would need to be addressed. Keeping the data on a cloud is fraught with problems and would raise questions of ownership of the data. India is yet to pass a Data Privacy Bill with adequate safeguards. Launching a Genome India Project before the privacy question is settled could give rise to another set of problems.

SOCIAL ISSUES: The question of heredity and racial purity has obsessed civilisations, and more scientific studies of genes and classifying them could reinforce stereotypes and allow for politics and history to acquire a racial twist.

In India a lot of politics is now on the lines of who are indigenous people and who are not. A Genome India Project could add a genetic dimension to the cauldron.

Selective breeding has been controversial since time immemorial, and well before the DNA was discovered. But eugenics acquired a dangerous context with the Nazis deliberating on the theme at length and its mention came up in the Nuremberg trials. Post World War-2, it has been a very touchy issue.

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