Category Archives: Genome

Gene editing is inexpensive, simple and becoming more widely used inclinical applications.One example is clustered regularly interspaced short palindromic repeats(CRISPR)genome editing, whichis an efficient tool to introduce changes in DNA.Germline editing promises efficiency in eradicating many diseases, but ethical and legal questions persistabout unknown, transgenerational and global consequences.

TheDecember issueof theAMA Journal of Ethics(@JournalofEthics)features numerous perspectives ongoverning human genome editingand gives you an opportunity to earn CME credit.

Articles include:

How Should Physicians Respond When They Learn Patients Are Using Unapproved Gene Editing Interventions?Responding to patients violating U.S.health commerce regulations can be critical when they buy and use unproven interventions.

Using the 4-S Framework to Guide Conversations With Patients About CRISPR.Empathic communication skills help motivate understanding of safety, significance of harms, impact on succeeding generations, and social consequences.

What Should Clinicians Do to Engage the Public About Gene Editing?Clinicians should have a working understanding of gene editing, controversy surrounding its use, and its far-reaching clinical and ethical implications.

How ShouldCRISPRedBabies Be Monitored Over Their Life Course to Promote Health Equity?Transnational monitoring efforts should focus on safety, defining standard of care, and promoting just access to innovation.

In the journalsDecemberpodcast,AMA Senior Policy AnalystSean McConnell,PhDwhose work focuses on genomics and precision medicinediscussesgene editing and CRISPR technology.

ScottJ.Schweikartisa senior research associate for the AMA Council on Ethical and Judicial Affairs and legal editor for theAMA Journal of Ethics. On the podcast, hediscusses what prudent governance requires.

Listen toprevious episodesof the podcast, Ethics Talk, or subscribe iniTunesor other services.

TheAMA Journal of EthicsCME module, Prioritizing Women's Health in Germline EditingResearch,isdesignated by the AMA for a maximum of1AMA PRA Category 1 Credit.

The module is part of theAMA EdHub, anonline platformthat brings togetherhigh-qualityCME, maintenance of certification,and educational contentinone placewithrelevant learningactivities,automated credit tracking and reporting forsome states and specialty boards.

Learn more aboutAMA CME accreditation.

The journals editorial focus is on commentaries and articles that offer practical advice and insights for medical students and physicians.Submit a manuscriptfor publication. The journal alsoinvitesoriginal photographs, graphics, cartoons, drawings and paintings that explore the ethical dimensions of health or health care.

Upcoming issues of theAMA Journal of Ethicswill focus onculture,context andepidemic containment, and onglobal burden of cancer inequality.Sign upto receive email alerts when new issues are published.

Originally posted here:
Human genome editing is here. How should it be governed? - American Medical Association

Psychology has been heavily criticized lately for its research practices. Most commonly discussed is the so-called replication crisis,whereby efforts to replicate classic and non-classic studies alike have often failed. Psychology has become transfixed on this issue, and at times even paralyzed. But there are clear signs that things are changing for the better.

Researchers, journals, and organizations are pushing for greater transparency, cooperation, data sharing, and pre-registration of research hypotheses, methods, and data analytic strategies. This must all surely be good for the science of psychology.

It is clear that psychology bears the brunt of the criticism about replication. Truth be told, however, many (if not most) fields of science have difficulties replicating their findings. John Ioannidis wrote a very highly read and cited paper on this problem called "Why Most Published Research Findings Are False" that has shaken science deeply. Most people concentrate on psychology, and psychologists certainly like pointing their fingers at themselves, but the deeper we dig, the more we find that this is not a problem limited to psychology, but rather is common in other sciences, including medicine and chemistry.

Psychology certainly has its faults. But psychology is also at the forefront of addressing concerns about research methods, inferential statistics, and best practice recommendations.

Replication failures happen for many reasons, including low statistical power and small samples (that generally fail to generalize to the wider world). One of the problems with trying to reproduce psychological findings concerns the sheer complexity of the human mind. (As a psychologist, and especially as a social psychologist, Im often envious of researchers in other disciplines who study more simple phenomena, particularly those that dont react to being studied!).

It is also important to keep in mind that psychology generally attempts to explain relatively universal truths about humanity, but in reality, we only look at a very narrow slice of humanity, what researchers call WEIRD (Western, Educated, Industrialized, Rich, Democratic) participants. As Henrich et al. note, Within the field of psychology, 95 percentof psychological samples come from countries with only 12percentof the worlds population (Arnett 2008).

Is psychology the only offender in this regard? Sadly, no. Apparently, studies that map the human genome are similarly focused on a very narrow slice of humanity. As of 2009, about 96percentof genomic data was derived from people of (White) European background.

And things have not improved much since. Devaney (2019) reports that our present understanding of the human genome has been largely derived from samples who are White European (78 percent), with very little from those with African (2 percent) or Hispanic or Latin American (1 percent) ancestry. This is staggeringone would reasonably expect that researchers attempting to map humanitys genomes would sample a broad swathe of humanity.

So what is the problem with understanding the psychology of humanity from observing predominantly White, European people in educated and enriched environments? And what is the problem with only using such people to map the human genome?

The question almost answers itself, doesnt it?

We should be invested in examining the full diversity of humanity if we want to understand the full diversity of humanity. One wouldnt study only penguins if one wished to learn about birds as a general category. The same applies to the study of humans, whether their psychological makeup or their genetics.

Failure to examine the diversity of a species is fraught with problems and possible dangers when trying to make claims about the nature of that species. After all, wed risk concluding that birds cant fly if we spent our research energies only in the Antarctic.

Originally posted here:
Variety Is the Spice of Life (In Research Too) - Psychology Today

CRISPR, kick-starting the revolution in drug discovery or A year after the first CRISPR babies, stricter regulations are now in place. read some of the recent headlines. CRISPR, a new gene editing technology, is making waves around the world and Israel is no exception. The Israeli startup eggXTt is preparing to use CRISPR-tech to mark chicken eggs by gender in an effort to reduce waste in the poultry industry, and research labs at institutes around the country regularly make use of CRISPR-tech to make groundbreaking discoveries in the biological sciences.

But how does CRISPR actually work, and what are the limitations of this new technology? CRISPR is often touted by scientists and science journalists as a pair of molecular scissors allowing us to edit our genomes at will in a point-and-click fashion. Although it is tempting to believe these buzzwords, they are not particularly accurate, and can be misleading for the public and policymakers considering the potential impacts of this new technology. After all, our DNA is not a tiny Microsoft Word document that can be altered however we see fit. In this article we will dive into exactly what CRISPR is, what it can and cannot do, and why we might not be seeing designer CRISPR babies for a few more decades (or centuries).

First of all, CRISPR is not a pair of molecular scissors. It is a system of proteins that evolved in bacteria to protect them against viruses. Proteins can take all shapes and sizes, and CRISPR proteins look something like the wire cleaning scrubbers you can find in many kitchens. The oft-mentioned analogy that CRISPR are molecular scissors is doubly misleading, because scissors imply that someone (ie: scientists) are somehow wielding them in a precise manner to cut and paste DNA as they please. This gives the false impression that scientists are the sole possessors of CRISPR knowledge, bestowing upon them the power to alter our genomes at will.

In reality, CRISPR proteins slide along DNA strands, recognizing specific areas by their unique feel. More specifically, the proteins move along the DNA until they find a spot on the DNA that matches perfectly with their recognition site, and then they squeeze down and cause the DNA to break at that point. This is similar to how your handprint fits well into its imprint in the sand. When you think about the wide variety of proteins in the human body (over 100,000) it makes sense that few other proteins would make the same match (a rubber duck or iron nail would not fit well into your handprint either). When the CRISPR proteins move along the DNA, they are only able to make the DNA break at these specific points. Scientists are able to take advantage of this tendency of CRISPR proteins, and can manipulate them to make breaks in DNA at the area they want removed or altered in their experiments. The CRISPR system also consists of a few other components, including a set of guide RNAs that help the CRISPR proteins match up with the DNA of their choice.

Unfortunately, CRISPR proteins are not perfect, and DNA is a very long and repetitive molecule, so it is possible for mistakes to occur. Other areas of DNA may look the same to the CRISPR proteins due to similar or identical sequences, causing the CRISPR proteins to break the DNA at undesired places. Recent research has noted that CRISPR can have a high frequency of off-target DNA breaks, up to 50% in many model systems. These issues mean that once CRISPR is released into a living organism it is sometimes hard to predict where these off target effects will occur. The challenge of off-target effects is one of the reasons CRISPR babies are likely a long way off. As a result a number of institutions and many scientists, including the World Health Organization, have called for a comprehensive ban on genetic modifications to reproductive or germline tissues. Despite this, a team of researchers in China recently managed to create a set of genetically altered twins, resulting in significant controversy. The ethical questions surrounding CRISPR in humans are another compelling reason to wait, particularly because edits of germline tissues like eggs and sperm could result in permanent changes to the human genome.

Another issue with the CRISPR system is that it needs to be inserted into living cells using a viral vector. This means the CRISPR system has to be translated into DNA, coded into a type of non-deadly virus, and injected into cells, which then produce the CRISPR proteins themselves. These viral systems are never 100% successful, and sometimes only enter 15-20% of all cells, which is not ideal for medical-grade treatments.

Despite these barriers there are several medical treatments in development using CRISPR-tech to address difficult-to-treat diseases. One of the most advanced is a CRISPR-based treatment for Duchenne Muscular Dystrophy (DMD), a rare and incurable muscle degenerative disease predominantly affecting children. DMD is caused by mutations in the dystrophin gene and is always fatal with an average patient lifespan of 26 years. Recent studies in mouse models and human heart cells in petri dishes have shown that CRISPR can cause reduction in muscular degeneration symptoms, which are the hallmark of this disease. Because DMD is caused by mutations in one specific region in the genome, scientists and clinicians can take advantage of CRISPRs targeted DNA-breakage effects to chop the affected section out of the genome by targeting two RNA guide probes, one to each side of the mutant piece of DNA. In most cases simply excising the mutant piece of DNA is not sufficient to remove symptoms of a disease. However, in this rare case removing the mutant DNA section allows for a partial improvement in some muscle cells, which is why this treatment has shown promise for clinical applications.

Many of the future CRISPR-based treatments will need to insert a new, healthy piece of DNA in addition to removing the mutant DNA. This is obviously many times more difficult as in addition to mitigating risk from off-target CRISPR effects, it will also be necessary to reduce the risk of the new piece of DNA inserting into the wrong portion of the genome and causing undesirable effects. Nevertheless, trials are now underway to translate this treatment method to the clinic in studies investigating the use of CRISPR for Sickle-Cell Anemia, Cystic Fibrosis and non-Hodgkins Lymphoma.

Although the major benefits of CRISPR-tech are likely decades away, CRISPR is already having significant impacts in the scientific, medical and biotech spheres. As long as this technology is used responsibly, we have much to gain from a world where we could one day become the masters of our own genomes.

This is an article in the series Science & Technology in the Holy Land, a regular column on innovations in science, tech, start-ups and futurism by Jamie Magrill, an MSc, Biomedical Sciences Candidate at the Hebrew University of Jerusalem.

Jamie Magrill is a scientist-scholar and world-traveler with an interest in entrepreneurship and startups, particularly in the biomedical and philanthropic fields, an MSc in Biomedical Sciences Candidate at the Hebrew University of Jerusalem, and a Masa Israel Journey alum.

Link:
CRISPR: Are we the Masters of our Own Genomes? - The Times of Israel

This article, written byMichael Mackley, Dalhousie University, originally appeared on The Conversation and is republished here with permission:

Youve likely heard about direct-to-consumer DNA testing kits. In the past few years, at-home genetic testing has been featured in the lyrics of chart-topping songs, and has helped police solve decades-old cold cases, including identifying the Golden State Killer in California.

Even if you dont find a DNA testing kit under your own Christmas tree, theres a good chance someone you know will.

Whether youre motivated to learn about your health or where your ancestors came from, it is important to understand how these tests work before you spit in the tube.

While exciting, there are things that these genetic testing kits cannot tell users and important personal implications that consumers should consider.

Health, traits and ancestry kits

My main area of research is around clinical genome sequencing, where we look through all of a persons DNA to help diagnose diseases. With a PhD in genetics, I often get questions from friends and family about which direct-to-consumer genetic test they should buy, or requests to discuss results. Most questions are about two types of products: ancestry and health kits.

The most popular ancestry kit is from AncestryDNA. These kits are aimed at giving users insight into where their ancestors might be from. They can also connect users with family members who have used the service and have opted into having their information shared. Another option is Living DNA, which has a smaller dataset but provides more precise information on the U.K. and Ireland.

The most popular health kit is from 23andMe. Depending on the users preference, results include information on predispositions for diseases such as diabetes and Alzheimers, as well as on the likelihood of having certain traits such as hair colour and taste. This company also offers ancestry analysis, as well as ancestry and trait-only kits that dont provide health information. The kit offered by the newer MyHeritage DNA also provides a combined ancestry and health option.

There are other kits out there claiming to evaluate everything from athletic potential to relationship compatibility. But gift-buyers beware: for most of these, in contrast to those above, the evidence is seriously lacking.

How these tests work

For all of these tests, customers receive a kit in the mail. The kits contain instructions for collecting a saliva sample, which you mail back to the company for analysis.

During this analysis, these popular tests do not look at the entire genome. Instead, they employ single nucleotide polymorphism (SNP) genotyping. As humans we all share 99.9 per cent of our DNA. SNPs are essentially what is left: all of the points at which we can differ from our neighbour, making us unique. SNP genotyping looks at a subset of these sites to survey the users genome.

These SNPs are then compared to reference datasets of individuals with known conditions or ancestry. Most results are based on the SNPs shared with a given group. For example, if your results say that you are 42 per cent Southeast Asian, its because 42 per cent of your SNPs were most likely to have come from a group in the reference dataset labelled Southeast Asian. The same goes for traits and health conditions.

How they differ from clinical tests

Direct-to-consumer genetic tests are not a substitute for clinical assessment. The methods used differ dramatically from what is done to diagnose genetic diseases.

In a clinical setting, when suspicion of a genetic condition is high, entire genes are often analyzed. These are genes where we understand how changes in the DNA cause cellular changes that can cause the disease. Furthermore, clinical assessment includes genetic counselling that is often key to understanding results.

In contrast, findings from direct-to-consumer genetic tests are often just statistical links; there is commonly no direct disease-causing effect from the SNPs.

Users may interpret a result as positive, when the risk increase is only minimal, or entirely false. These tests can also give false reassurance because they do not sequence genes in their entirety and can miss potentially harmful variants.

Before you spit in a tube, stop and think

These tests are exciting: they introduce new audiences to genetics and get people thinking about their health. Theyre also helping to build vast genetic databases from which medical research will be conducted.

But for individual users, there are important caveats to consider. Recent reports have questioned the accuracy of these tests: identical twins can receive different results. Furthermore, a lack of diversity in the reference data has caused particular concern regarding accuracy of results for ethnic minorities.

There are also concerns about the way these tests emphasize racial categories that science considers to be social constructs and biologically meaningless.

A recent paper in the British Medical Journal suggests four helpful questions for users to consider. First, users should ask themselves why they want the test. If it is to answer a medical question, then they should speak with their doctor. Users should also think about how they might feel when they receive results containing information they would rather not know.

Users should also consider issues around security and privacy. It is important to read the fine print of the service youre using, and determine whether youre comfortable sharing personal information, now and in the future.

In Canada, policies around genetics have not always kept up with the science. At present, direct-to-consumer genetic testing is unregulated. And, although Canadians have legislative protections against genetic discrimination, those laws are being challenged in the courts, and could change.

Finally, it may also be worth discussing DNA testing with relatives. We share half of our genome with our immediate family members, and smaller fractions with more distant relatives. Genetic results not only affect us, but our family.

Bottom line: Its all for fun

Some users may feel they learn more about themselves. For others, results may bring people closer together not a bad outcome for the holiday season.

At the end of the day, these genetic testing kits are for entertainment: they should not be used to assess health risk in any meaningful way.

If you have any questions related to your health or a genetic disease, discuss these with your family doctor or a suitable health-care professional.

Michael Mackley, Junior Fellow, MacEachen Institute for Public Policy and Governance; Medical Student, Dalhousie University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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BEYOND LOCAL: DNA tests might be a fun holiday gift, but beware of the hype - ThoroldNews.com

BRISBANE, Calif.--(BUSINESS WIRE)--Sangamo Therapeutics, Inc. (Nasdaq: SGMO), a genomic medicine company, is hosting an R&D Day today beginning at 8am Eastern Time. During the event, Sangamo executives and scientists plan to provide updates across the Companys clinical and preclinical pipeline, as well as an overview of manufacturing capabilities to support clinical and commercial supply. A live webcast link will be available on the Events and Presentations page of the Sangamo website

The talent, R&D capabilities, manufacturing expertise, and operations infrastructure we have brought to Sangamo have enabled us to advance a genomic medicine pipeline that spans multiple therapeutic areas and now also extends into late-stage development, said Sandy Macrae, CEO of Sangamo. As we make progress in clinical development, we gain insights into the use of our technology and are applying those insights as we advance new programs, such as the gene therapy for PKU and the genome regulation candidates for CNS diseases we are announcing today.

Macrae continued: We will continue to pursue a dual approach of retaining certain programs for our proprietary pipeline while also establishing pharmaceutical partnerships to gain access to therapeutic area expertise and financial, operational, and commercial resources. Strategic collaborations will be a particularly important consideration as we advance programs for diseases affecting large patient populations.

R&D Day updates on clinical and preclinical pipeline programs:

Gene therapy product candidates for hemophilia A, Fabry disease, and PKU

SB-525 is a gene therapy product candidate for hemophilia A being developed by Sangamo and Pfizer under a global development and commercialization collaboration agreement. The transfer of the SB-525 IND to Pfizer is substantially completed. Pfizer is advancing SB-525 into a Phase 3 registrational study in 2020 and has recently begun enrolling patients into a Phase 3 lead-in study.

At R&D Day, Sangamo executives are presenting data from the SB-525 program which were recently announced at the American Society of Hematology (ASH) annual meeting.

The cassette engineering, AAV engineering and manufacturing expertise which Sangamo used in the development of SB-525 are also being applied to the ST-920 Fabry disease program, which is being evaluated in a Phase 1/2 clinical trial, as well as to the newly announced ST-101 gene therapy program for PKU, which is being evaluated in preclinical studies with a planned IND submission in 2021.

Engineered ex vivo cell therapy candidates for beta thalassemia, kidney transplantation, and preclinical research in multiple sclerosis (MS)

Sangamo is providing an overview of the Companys diversified cell therapy pipeline this morning. Cell therapy incorporates Sangamos experience and core strengths, including cell culture and engineering, gene editing, and AAV manufacturing. At R&D Day, Sangamo scientists today are reviewing the early data presented this month at ASH from the ST-400 beta thalassemia ex vivo gene-edited cell therapy program, which is being developed in partnership with Sanofi.

Sangamo is also providing updates on the companys CAR-TREG clinical and preclinical programs. CAR-TREGS are regulatory T cells equipped with a chimeric antigen receptor. Sangamo is the pioneer in CAR-TREGS, which may have the potential to treat inflammatory and autoimmune diseases. TX200 is being evaluated in the STEADFAST study, the first ever clinical trial evaluating a CAR-TREG cell therapy. Tx200 is being developed for the prevention of immune-mediated organ rejection in patients who have received a kidney transplant, a significant unmet medical need. Results from this trial will provide data on safety and proof of mechanism, building a critical understanding of CAR-TREGS in patients, and may provide a gateway to autoimmune indications such as Crohns disease and multiple sclerosis (MS). Sangamo is also presenting preclinical murine data demonstrating that CAR-TREGS accumulate and proliferate in the CNS and reduce a marker of MS.

In vivo genome editing optimization

Clinical data presented earlier this year provided evidence that Sangamo had successfully edited the genome of patients with mucopolysaccharidosis type II (MPS II) but also suggested that the zinc finger nuclease in vivo gene editing reagents were under-dosed using first-generation technology. Sangamo has identified potential improvements that may enhance the potency of in vivo genome editing, including increasing total AAV vector dose, co-packaging both ZFNs in one AAV vector, and engineering second-generation AAVs, ZFNs, and donor transgenes.

Genome regulation pipeline candidates targeting neurodegenerative diseases including Alzheimers and Parkinsons

Sangamo scientists today are presenting data demonstrating that the companys engineered zinc finger protein transcription factors (ZFP-TFs) specifically and powerfully repress key genes involved in brain diseases including Alzheimers, Parkinsons, Huntingtons, ALS, and Prion diseases. Sangamo is advancing its first two genome regulation programs toward clinical development:

Sangamo scientists are also presenting data demonstrating progress in the development of new AAV serotypes for use in CNS diseases.

Manufacturing capabilities and strategy

Sangamo is nearing completion of its buildout of a GMP manufacturing facility at the new Company headquarters in Brisbane, CA. This facility is expected to become operational in 2020 and to provide clinical and commercial scale manufacturing capacity for cell and gene therapy programs. The Company has also initiated the buildout of a cell therapy manufacturing facility in Valbonne, France. Sangamos manufacturing strategy includes in-house capabilities as well as the use of contract manufacturing organizations, including a long-established relationship with Thermo Fisher Scientific for clinical and large-scale commercial AAV manufacturing capacity.

R&D Day webcast

A live webcast of the R&D Day, including audio and slides, will be available on the Events and Presentations page of the Sangamo website today at 8am Eastern Time. A replay of the event will be archived on the website.

About Sangamo Therapeutics

Sangamo Therapeutics is committed to translating ground-breaking science into genomic medicines with the potential to transform patients lives using gene therapy, ex vivo gene-edited cell therapy, and in vivo genome editing and gene regulation. For more information about Sangamo, visit http://www.sangamo.com.

Sangamo Forward Looking Statements

This press release contains forward-looking statements within the meaning of the "safe harbor" provisions of United States securities law. These forward-looking statements include, but are not limited to, the therapeutic potential of Sangamos product candidates; the design of clinical trials and expected timing for milestones, such as enrollment and presentation of data, the expected timing of release of additional data, plans to initiate additional studies for product candidates and timing and design of these studies; the expected benefits of Sangamos collaborations; the anticipated capabilities of Sangamos technologies; the research and development of novel gene-based therapies and the application of Sangamos ZFP technology platform to specific human diseases; successful manufacturing of Sangamos product candidates; the potential of Sangamos genome editing technology to safely treat genetic diseases; the potential for ZFNs to be effectively designed to treat diseases through genome editing; the potential for cell therapies to effectively treat diseases; and other statements that are not historical fact. These statements are based upon Sangamos current expectations and speak only as of the date hereof. Sangamos actual results may differ materially and adversely from those expressed in any forward-looking statements. Factors that could cause actual results to differ include, but are not limited to, risks and uncertainties related to dependence on the success of clinical trials; the uncertain regulatory approval process; the costly research and development process, including the uncertain timing of clinical trials; whether interim, preliminary or initial data from ongoing clinical trials will be representative of the final results from such clinical trials; whether the final results from ongoing clinical trials will validate and support the safety and efficacy of product candidates; the risk that clinical trial data are subject to differing interpretations by regulatory authorities; Sangamos limited experience in conducting later stage clinical trials and the potential inability of Sangamo and its partners to advance product candidates into registrational studies; Sangamos reliance on itself, partners and other third-parties to meet clinical and manufacturing obligations; Sangamos ability to maintain strategic partnerships; competing drugs and product candidates that may be superior to Sangamos product candidates; and the potential for technological developments by Sangamo's competitors that will obviate Sangamo's gene therapy technology. Actual results may differ from those projected in forward-looking statements due to risks and uncertainties that exist in Sangamos operations. This presentation concerns investigational drugs that are under preclinical and/or clinical investigation and which have not yet been approved for marketing by any regulatory agency. They are currently limited to investigational use, and no representations are made as to their safety or effectiveness for the purposes for which they are being investigated. Any discussions of safety or efficacy are only in reference to the specific results presented here and may not be indicative of an ultimate finding of safety or efficacy by regulatory agencies. These risks and uncertainties are described more fully in Sangamo's Annual Report on Form 10-K for the year ended December 31, 2018 as filed with the Securities and Exchange Commission on March 1, 2019 and Sangamo's Quarterly Report on Form 10-Q for the quarter ended September 30, 2019 that it filed on or about November 6, 2019. Except as required by law, we assume no obligation, and we disclaim any intent, to update these statements to reflect actual results.

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Sangamo Highlights Advancements in Genomic Medicine Pipeline and Expanded R&D and Manufacturing Capabilities at R&D Day - Business Wire

The building housing the Ministry of Health, Labor and Welfare is seen in Tokyo's Chiyoda Ward. (Mainichi/Kimi Takeuchi)

TOKYO -- Japan will perform full-genome analysis on medical samples from as many as 93,000 people under an action plan revealed by the country's health ministry.

The blood, cancer cells and other samples are held at hospital and research institute biobanks around the country, and will be prioritized for analysis for a number of years. Special priority will be placed on samples from some 22,000 people expected to be useful for research in hopes of discovering details of cancer and intractable diseases and drugs for their treatment.

Analyzing a person's entire genome could allow researchers to identify genetic causes or trigger mechanisms for certain diseases that may not be apparent from looking at just one part of the patient's genes. There are also hopes that building a database combining results of the full-genome analysis of cancer patients with clinical information will help Japan formulate broader cancer-fighting measures.

According to the action plan, cancer patient samples make up some 65,000 of the total set for full genome analysis, while about 28,000 are from people with other intractable conditions. For the analysis, a sample genome needs to be compared with data such as a healthy blood sample and the genetic makeup of the patient's parents. That being the case, the plan will in fact require full analysis of some 168,000 genomes. Furthermore, new samples from the patients will also be obtained for analysis.

In the coming years, blood and cancer cell samples from the 22,000 people stored at biobanks in the country will be given priority for analysis, with the subjects' consent. These initial studies will seek the genetic causes of cancers with low 5-year survival rates, rare and hereditary cancers as well as intractable illnesses that could not be identified through partial genome analysis.

However, there remain many unanswered questions about whether and to what degree information from full-genome breakdowns will lead to new and effective diagnostic, treatment, and drug options. The Ministry of Health, Labor and Welfare will examine the results from studies using the priority samples, and clarify a target number of specimens needed for analysis in cases where the development of diagnostic and treatment methods can be expected.

Full-genome analysis medical research projects are proceeding apace under government-backed programs in other countries. Britain, for example, began full-genome analysis for 100,000 people with cancer or rare diseases in 2018. The U.K. government is aiming to analyze the genomes of a million people by 2023.

(Japanese original by Sooryeon Kim, Lifestyle and Medical News Department)

Link:
Japan gov't plans full-genome analysis on 93000 people to boost medical research - The Mainichi

This Carolina parakeet was collected sometime in the late 1800s.

Not very long ago, wild parrots lived in the forests of New York. The brightly-colored birds squawked among the treetops of old-growth riverine forests and swamps from Florida to New York and as far east as Colorado, gathering in flocks of hundreds at a time. Today, the great vociferous flocks are gone, and the bright green, red, and yellow plumage can be seen only in museums.

The last known Carolina parakeet was born sometime around 1883 and died in the Cincinnati Zoo in 1918, in the same ill-fated cage where the worlds last passenger pigeon had died in 1914. Inca, the last Carolina parakeet, had outlived his mate, Lady Jane, by around a year and as far as anyone knew, the pair had outlived their wild relatives by nearly a decade. No one had reported a credible sighting of a wild Carolina parakeet since 1910.

The Carolina parakeet has been extinct for roughly a century, and a new genetic study pins the blame squarely on humans.

The Last Stand Of Americas Parrots

As European settlers and their descendants pushed westward in the 1700s and 1800s, they cleared many of the forests the Carolina parakeet had once called home. They also shot the birds in droves to keep them away from grain fields and to collect their bright feathers for ladies hats. The Carolina parakeet made an easy target; flocking instinct would bring large numbers of birds back to the scene of a fresh kill, giving hunters another shot at them.

By the mid-1800s, Carolina parakeets were rare outside the swamps of Florida, and by 1900, they couldnt be found anywhere else. But even in their last bastion of habitat, Carolina parakeets seemed to be doing pretty well, under the circumstances. Farmers had stopped hunting them, because they turned out to be useful for keeping cockleburs in check (the Carolina parakeet was one of the only animals who could survive eating the poisonous plant, although the toxic glucoside accumulated in the birds flesh and made them deadly prey. Cats who ate Carolina parakeets usually died soon after). And naturalists described large flocks, with plenty of young birds and good access to nesting sites.

And then, abruptly, the Carolina parakeet simply vanished. A century later, ecologists still dont understand what happened. Maybe, some say, the species wasnt faring as well as it looked from the outside; population decline and habitat loss could have left them with a limited gene pool, doomed to fade away before too long. But maybe, others argue, the Carolina parakeet would have been just fine if they hadnt been exposed, in their last refuge, to deadly poultry diseases like Newcastle Disease from nearby farms.

If this is true, the very fact that the Carolina parakeet was finally tolerated to roam in the vicinity of human settlements proved its undoing, wrote the Audobon Society a few years ago. Theres no actual evidence to support the poultry disease hypothesis: no eyewitness report of sick parrots with symptoms of something like Newcastle Disease, and no smoking gun in the form of pathogen samples from a preserved parrot corpse. But a new study, published in the journal Current Biology, sequenced the Carolina parakeet genome for the first time and searched for signs of inbreeding or population decline and found none. That means the species wasnt doomed long before its disappearance, which means something must have tipped the balance.

Solving A Cold Case

Evolutionary biologist Carlez Laluzela-Fox and colleagues sampled nuclear DNA from the tibia (shin bone) and toe pads of a Carolina parakeet, killed and stuffed in the late 1800s and now owned by a private collector in Spain. They used the genome of the extinct species closest living relative, a South American parrot called the sun parakeet, as a reference to help them map the genome and understand what the sequences of adenine, thymine, guanine, and cytosine meant for the birds actual physiology.

Demographic declines leave specific signals in the genomes of the species, explained Laluzela-Fox in a statement to the press. If members of a species have spent several generations breeding with close genetic relatives, or if the overall breeding population was too small, geneticists can spot the signs in an organisms genome.

But the Carolina parakeet genome had none of those warning signs so its sudden extinction wasnt the end of a much longer decline. Something new had happened and the odds are good that it was our fault. That lends some support to the poultry disease idea, although its a long way from actually proving that sick chickens, and not some other problem, actually killed off the Carolina parakeets.

Meanwhile, Laluzela-Fox and colleagues say that the same process they used to look for signs of population decline in the Carolina parakeet genome could also help screen living species for warning signs and maybe solve more extinction cold cases, too.

The genomic study also solved another century-old mystery: how did the Carolina parakeet live on poisonous cockleburs, when their toxins even made the birds flesh too poisonous to eat? In the Carolina parakeets genome, Laluzela-Fox and colleagues found two proteins that interact with the toxic glucoside in cockleburs. They suggest that those proteins allowed the bird to safely enjoy its toxic treats.

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Scientists Sequenced The Genome Of The Carolina Parakeet, Americas Extinct Native Parrot - Forbes

In centuries past, large flocks of noisy, brightly colored parrots squawked their way across the United Statesfrom New England, to Florida, to eastern Colorado. The Carolina parakeet, or Conuropsis carolinensis, was the only parrot native to the eastern part of the country. But by the beginning of the 20th century, it had disappeared.

Experts believe that humans played a prominent role in the species extinction. The clearing of forests to make way for agricultural land destroyed the birds habitat and may have contributed to their loss. They were hunted for their vibrant feathers of green, yellow and red, which made a popular addition to ladies hats. Farmers considered them pests and killed them in large numbers; the parrots were easy targets, due to their unfortunate tendency to congregate around wounded flockmates.

But as Liz Langley reports for National Geographic, some experts have speculated that causes not directly driven by humanslike diseases spread by poultry and natural disasters that fragmented the Carolina parakeets habitatmay have contributed to the species decline. Hoping to shed new light on the issue, a team of researchers sequenced the Carolina parakeets genomeand found that human causes were likely the sole driver of the birds abrupt extinction.

To conduct their analysis, the team looked at the tibia bone and toe pads of a preserved parakeet specimen held in a private collection in Spain. Because its DNA was fragmented, the researchers also sequenced the genome of the Carolina parakeets closest living relative, the sun parakeet, which gave them a more complete picture of the extinct birds genetic profile.

The researchers were specifically looking for signs of a drawn-out decline that might have started before humans began hunting the birds extensivelysigns like inbreeding. They found that after the Last Glacial Period around 110,000 years ago, Carolina parakeets began experiencing a population decline that continued until recent timesbut the still-extant sun parakeets decline was stronger, according to the study.

Crucially, the researchers didnt discover evidence of inbreeding that you might expect to see in a species that has been endangered for some time, which suggests the parakeet suffered a very quick extinction process that left no traces in the genomes of the last specimens, the researchers write in Current Biology. And when extinction happens at a rapid pace, human action is common, study co-author Carles Lalueza tells Ryan F. Mandelbaum of Gizmodo.

Whats more, the study authors did not find a significant presence of bird viruses in the Carolina parakeets DNA, though they acknowledge that further research is needed to rule out poultry disease as a driver of the birds extinction. For now, however, they conclude that the parakeets extinction was an abrupt process and thus likely solely attributable to human causes.

Earlier this month, a separate team of researchers came to the same conclusion about the disappearance of the great auk, a large, flightless bird that appears to have been wiped out by rapacious hunters. These cases offer sobering insight into how quickly humans are capable of decimating a species; the Carolina parakeet, Lalueza tells Mandelbaum, likely went extinct within the order of [a] few decades.

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The Extinction of This U.S. Parrot Was Quick and Driven by Humans - Smithsonian.com

University of WisconsinMadison researchers have developed a computational tool that can accurately predict the three-dimensional interactions between regions of human chromosomes.

The predictive tool is a boon for researchers studying how cells control the activity of genes. The fine-tuned interaction between regulatory signals and the three-dimensional architecture of chromosomes helps explain how cells achieve their key functions, and how they go haywire, as happens in diseases such as cancer.

The experimental technique to measure these three-dimensional interactions, Hi-C, is expensive, which has limited high-quality data to just a few types of cells. In contrast, the new tool can predict these interactions using much more easily measurable and commonly available data. This could help biologists perform across many cell types more detailed research into tissue development, cancer and other diseases that are affected by this type of distant gene regulation.

Roy

Zhang

UWMadison researcher Sushmita Roy and her graduate studentShilu Zhang led the work, which was published Dec. 6 in Nature Communications. The researchers have made the tool freely available to other scientists and continue to improve the predictive power of the tool, which they named HiC-Reg after the resource-intensive experiments.

We can very cheaply predict the output of Hi-C experiments, which can help us prioritize other regions of the genome to follow up with more fine-tuned experiments, says Roy, a professor in the Wisconsin Institute for Discovery and the UWMadison Department of Biostatistics and Medical Informatics. This can be used as a resource to interpret regulatory variation in the genome.

The human genome consists of 23 pairs of chromosomes. A new study from UWMadisons Sushmita Roy describes a computational tool for researchers to better predict the three-dimensional interactions between chromosomes. Wikimedia Commons

A far cry from the neat, straight lines of DNA pictured in textbooks, real chromosomes fold, twist and bend to fit several linear feet of DNA into a tiny cell nucleus. These loops also bring distant regions of a chromosome together. Some of these regions carry regulatory information that can promote or repress the expression of distant genes. This intricate gene expression magnifies the complexity of traits that organisms exhibit.

Roy and other researchers have previously developed models that could predict whether or not two distant regions of a chromosome would interact. HiC-Reg builds on that model and not only predicts whether two regions will interact but also how strong that interaction might be. It provides a more complex and realistic model of how chromosomal regions interact and potentially regulate gene expression.

The packing of chromosomes into a nucleus allows distant regions of a chromosome to interact and affect one another. Consistently interacting regions are known as topologically associated domains, or TADs. This kind of fine-tuned gene regulation produces more complexity in the traits that organisms express. Navneet Matharu and Nadav Ahituv

To create HiC-Reg, Roys team fed a series of commonly available genomic data, such as the presence of proteins and chemical modifications that activate or repress gene expression, into a machine learning algorithm. It also included Hi-C data from the few cell lines for which it is available. The tool then learned relationships that enabled it to predict the Hi-C measurements for a new pair of genomic regions.

Lets try to use the data thats easy to measure to predict the information thats harder to gather, says Roy. The research was supported by the National Institutes of Health Big Data to Knowledge program, which allowed the team to mine this freely available but underutilized data. Were trying to leverage publicly available datasets as much as possible.

HiC-Reg correctly predicted between 40 percent and 80 percent of regional associations. The tool is more accurate than estimating the strength of interactions based on chromosomal distance alone or just mapping the interactions from a pair of regions in one cell line to the same pair of regions in another cell line. But the interactions were harder to predict in some cell types than in others, a limitation the researchers are now working to overcome.

The computationally intensive work relied on UWMadisons Center for High Throughput Computing, the UW Center for Predictive Computational Phenotyping and the Core Computational Technology research group at the Wisconsin Institute for Discovery.

Other researchers can now use HiC-Reg as-is to predict these three-dimensional interactions in their favorite cell line. Or, they can elect to re-train the program using their own datasets to improve its accuracy for their work.

Roy says that free access is consistent with the question that motivated this research: How can we help biologists gather this data?

This work was supported by the National Institutes of Health (BD2K grant U54 AI117924 and grant R01-HG010045-01).

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New tool predicts three-dimensional organization of human chromosomes - University of Wisconsin-Madison

Global Genome Editing Market: Overview

Also known as genome editing with engineered nucleases (GEEN), genome editing is a method of altering DNA within a cell in a safe manner. The technique is also used for removing, adding, or modifying DNA in the genome. By thus editing the genome, it is possible to change the primary characteristic features of an organism or a cell.

The global genome editing market can be segmented on the basis of delivery method, technology, application, and geography. By technology, the global genome editing market can be segmented into Flp-In, CRISPR, PiggyBac, and ZFN. Based on delivery method, in vivo and ex vivo can be the two broad segments of the global genome editing market. By application, the global genome editing market can be categorized into medicine, academic research, and biotechnology.

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Global Genome Editing Market: Key Trends

Since genome editing is gaining rising adoption in the domain of scientific research for attaining a better understanding of biological aspects of organisms and how they work, the global genome editing market is likely to promise considerable growth over the forthcoming years. More importantly, genome editing is being used by medical technologies, where it can be used for modifying human blood cells which can then be placed back in the body for treating conditions such as AIDS and leukemia. The technology can also be potentially utilized to combat infections such as MRSA as well as simple genetic disorders including hemophilia and muscular dystrophy.

Global Genome Editing Market: Market Potential

As more easy-to-use and flexible genome technologies are being developed, greater potential of genome editing is being recognized across bioprocessing and treatment modalities. For instance, in May 2017, MilliporeSigma announced that it successfully developed a novel genome editing tool which can make the CRISPR system more productive, specific, and flexible. The researchers thus have a more number of experimental options along with faster results.

All this can lead to a growing rate of drug development, enabling access to more advanced therapies. Proxy-CRISPR, the new technique, makes access to earlier inaccessible aspects of the genome possible. As most of the existing CRISPR systems cannot manage without re-engineering of human cells, the new method is expected to gain more popularity by virtue of the elimination of the need for re-engineering, simplifying the procedures.

Several other market players are focusing on clinical studies with a view to produce effective treatments for different health conditions. For example, another major genome editing firm, Editas Medicine, Inc. announced the results of its pre-clinical study displaying the success of the CEP290 gene present in the retina of primates in the same month. With the positive results of the study, the companys belief in the vast potential of its candidate in the treatment of a genetically inherited retinal degenerative disease, Leber congenital amaurosis type 10, affecting childrens eyesight has been reinforced.

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Global Genome Editing Market: Regional Outlook

By geography, the global genome editing market can be segmented into Latin America, Europe, Asia Pacific, the Middle East and Africa, and North America. North America registered the highest growth in the past, and has been claiming the largest portion of the global genome editing market presently. The extraordinary growth of this region can be attributed to greater adoption of cutting edge technologies across several research organizations. The U.S., being the hub of research activities, is expected to emerge as the leading contributor. Asia Pacific is also likely to witness tremendous demand for genome editing over the forthcoming period, assisting the expansion of the global genome editing market.

Global Genome Editing Market: Competitive Analysis

CRISPR THERAPEUTICS, Caribou Biosciences, Inc., Sigma Aldrich Corporation, Sangamo, Intellia Therapeutics, Inc., Editas Medicine, Thermo Fisher Scientific, Inc., and Recombinetics, Inc are some of the key firms operating in the global genome editing market.

The study presents reliable qualitative and quantitative insights into:

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Genome Editing Market Exclusive insight on Transformation 2025 - Techi Labs