Category Archives: Genetics

Childrens Hospital of Philadelphia is growing its footprint on the east side of the Schuylkill, adding a second high rise next to the 20-story Roberts Center for Pediatric Research.

At 14 stories, the new Schuylkill Avenue Research Building will provide a complement to the existing tower by offering a distinct form of research space. CHOP is searching for a sponsor to christen the structure, as the Roberts family of Comcast fame did for its neighbor.

The new building will add 250,000 square feet of wet lab space, a term for laboratories used to research biological or chemical subjects. Across its real estate holdings, CHOP already provides 800,000 square feet of wet lab space, but the Roberts Center is focused on administrative and meeting space as well as dry labs that are more focused on patient trials and computational or policy work.

At this campus we will be looking at opportunities for new cell and gene therapies and ways to develop vaccines or target the immune system to promote health, said Sue Furth, CHOPs chief scientific officer. Itll be a next-generation research campus totally dedicated to improving the health of children. Philadelphia is really up and coming in this area, just after Boston.

The building comes as Philadelphia is making big bets on the life sciences, an employment sector that has proven more resilient to the growing trend of work-from-home than traditional office space during the pandemic. Biomedical and pharmaceutical work cannot be done from home, and the market has been growing in University City, the Navy Yard, King of Prussia, and even downtown.

READ MORE: Philadelphias glass skyline is killing birds. A new Fairmount Park building has a solution. | Inga Saffron

CHOP believes this new work setup will continue to result in fewer workers in its buildings at any given time, as evidenced by the fact that the Schuylkill Avenue Research Building will not include any new parking. There are already 404 parking spaces on site and that is believed to be sufficient even after the new structure is completed. CHOP did not offer the precise number of workers it expects to be based out of the new building.

The density of research is not the same as an administrative building, said Donald Moore, CHOPs senior vice president for real estate, facilities and operations. It will be less intense than what we have at the Roberts Center right now [in terms of the number of people coming to the building].

The building will include 33,000 square feet of office space and 6,500 square feet of retail space, with an eatery or cafe planned with an entrance near the South Street Bridge. The Roberts building currently hosts an establishment called the Waterfront Cafe that is open to the public, but CHOP acknowledges that its existence is little known to those who dont work for the institution.

They hope the new cafe, which will be visible from the street, will prove a boon to the public, add more amenities to the surrounding residential area, and provide a space for collaboration for CHOP workers.

If you consider the dearth of food service amenities in this particular community, and the amount of foot traffic that goes past our site on a daily basis, it should be a very attractive offering for someone, said Moore.

The plan for the new structure was created by the international architecture firm Cannon Design and it won plaudits when presented to Philadelphias Civic Design Review board, a municipally appointed team of architects and planners who review large real estate developments.

The Schuylkill Avenue Research Building will look similar to the Roberts Center, but with darker materials and lighting. The designers drew from lessons learned from the previous building about the toll that glassy skyscrapers can take on avian life. Ornithologists believe that between 350 million and a billion birds die each year in the United States because the reflective glass confuses them, and they fly into the buildings at top speed.

READ MORE: From 2020: Up to 1,500 birds flew into some of Phillys tallest skyscrapers one day last week. The slaughter shook bird-watchers.

Weve taken a lot of time and effort to try and address the fact that many of the high rises along the Schuylkill River migratory bird path are magnets for migrating birds, said John Roach, office engineering leader with Cannon Design. In our cladding choices and brick patterns, weve tried to take proven measures to help reduce the incidence of bird strikes here.

Hurricane Ida also offered a lesson to CHOP, as last years flooding created elevator and parking issues at the Roberts Center. Although Moore couldnt provide immediate details, he said the institution will be convening an expert panel this week to discuss how to protect the new building from 100-year flood events that are expected to be ever more frequent.

The general plan for further construction on the site has been anticipated for some time. The foundation of the Schuylkill Avenue Research Building is already in place, which community groups cited as an example of CHOPs neighborliness construction is expected to be less disruptive because the site was prepared for a new building years in advance.

Unusually, for a building of this size next to a residential area, it has enjoyed a rapturous reception by near neighbors and community groups.

If the first one was a salt shaker, the latest is like a pepper shaker, they go so well together, said Murray Spencer, zoning chair for the South of South Neighborhood Association.

Read the rest here:
CHOPs new bird-proofed skyscraper will focus on vaccine and genetics research - The Philadelphia Inquirer

Clinicians agree that evidence supports testing benefits for all

SAN FRANCISCO, Sept. 15, 2022 /PRNewswire/ -- Invitae (NYSE: NVTA), a leading medical genetics company, joined other clinical experts in releasing a new commentary in Journal of Clinical Oncology Precision Oncology, underscoring the importance of universal germline testing for all patients with cancer (solid tumors). The paper reports a meta-analysis of multiple clinical publications supporting universal testing, independent of age, stage, family history or type of cancer. It reports that for cancer types such as pancreatic and ovarian where universal genetic testing is already recommended, 13% and 20% of patients (respectively) have identifiable actionable heritable gene mutations,2. In comparison, the actionable inherited gene mutation rate for patients with other cancer types is similar: breast 11%, endometrial 13%, prostate 14%, kidney 13%, bladder 14%, testicular 13%, colorectal 13%, liver 14%, and stomach 14%.

Furthermore, it reports that between 5-13% of patients with cancer with heritable gene mutations are missed by current restrictive testing guidelines and are unable to benefit from associated precision treatment and clinical trial benefits. First, allowing all patients to receive germline testing, without restrictive guidelines, affords patients access to precision therapies, clinical trials and other risk reducing interventions that can improve outcomes, and even extend overall patient survival1. Second, genetic testing informs surveillance and risk reduction for future cancers in patients already affected by cancer. Third, cascade testing helps alert their family members of an increased risk for cancer, so they too can then take advantage of monitoring and risk reducing interventions. Consistent with the Cancer Moonshot 2.0and the President's Cancer Panel report 2022, the expert consensus concludes that current evidence supports the implementation of universal germline genetic testing for all patients with cancer (solid tumors).

"This consensus from nationally recognized, cancer genetics clinical experts reinforces the current guidelines that universal genetic testing be offered in all patients with ovarian and pancreatic cancer and either be offered or considered in all patients with colorectal," said Ed Esplin, MD, PhD, FACMG, FACP, clinical geneticist at Invitae. "More importantly, this is a call to all guidelines committees, insurer medical policy makers and the President's Cancer Moonshot Cabinetto make universal genetic testing available to potentially reduce mortality and improve the lives of all patients with cancer."

The collaborative commentary included experts from the Carolina Urologic Research Center, City of Hope, Dana-Farber Cancer Institute, Mayo Clinicand Invitae.

"The PROCLAIM studydemonstratesthe clinical utility of universal germline genetic testing in patients with prostate cancer. Current NCCN guidelines precludesome prostate cancer patients from receiving germline testing, thus depriving these patients of the potential to receive precision-based therapies and specificclinical trial eligibility, whileperpetuating healthcare disparities among historically underrepresented populations. The PROCLAIM data supports universal genetic testing for prostate cancer patients. We should expeditiously eliminate barriers to gene-based precision therapies to optimize patient outcomes and accelerate equitable access to care," said Neal Shore, MD, urologist and medical director, Carolina Urologic Research Center.

Cancer is a leading cause of death worldwide, accounting for nearly 10 million deaths in 2020.

Worldwide, there were an estimated 18.1 million new cases of cancer in 2018, with one in four men and one in five women developing the disease. In addition, there were 43.8 million persons living with cancer in 2018 who were diagnosed within the last five years.

"The INTERCEPT study has shown the prevalence and clinical utility of germline genetic testing is virtually the same across 14 cancer types, even those cancers not traditionally considered hereditary. This data supports universal genetic testing not only for colorectal cancer, but patients with all cancer types, to potentially improve their treatment and future cancer prevention for them and their family members," said Jewel Samadder, MD, enterprise co-leader precision/individualized cancer medicine, Mayo Clinic Comprehensive Cancer Center.

Restrictive guidelines can lead to disparities in cancer care. Offering germline genetic testing to all patients with cancer at diagnosis may help reduce inequities in cancer care by expanding access for all patients to precision therapy or clinical treatment trials.

"The prevalence of pathogenic variants in cancer susceptibility genes for which there are management guidelines is similar among patients with all types of solid tumors, therefore, it does not makes sense that current guidelines only recommend germline genetic testing for all patients with ovarian, pancreatic, and recently, colorectal cancers. This information has the potential to affect the treatment of these individuals' current cancers. In addition, it has the potential to allow for the prevention or early detection of future cancers in both these patients and their family members," said Heather Hampel, MS, CGC, professor, Department of Medical Oncology & Therapeutics Research, City of Hope.

About InvitaeInvitae Corporation (NYSE: NVTA) is a leading medical genetics company, whose mission is to bring comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. Invitae's goal is to aggregate the world's genetic tests into a single service with higher quality, faster turnaround time and lower prices. For more information, visit the company's website at invitae.com.

Safe Harbor StatementThis press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including statements relating to the potential benefits of universal genetic testing for all patients with cancer; and that restrictive guidelines can lead to disparities in cancer care. Forward-looking statements are subject to risks and uncertainties that could cause actual results to differ materially and reported results should not be considered as an indication of future performance. These risks and uncertainties include, but are not limited to: the company's history of losses; the company's ability to compete; the company's failure to manage growth effectively; the company's need to scale its infrastructure in advance of demand for its tests and to increase demand for its tests; the company's ability to use rapidly changing genetic data to interpret test results accurately and consistently; security breaches, loss of data and other disruptions; laws and regulations applicable to the company's business; and the other risks set forth in the company's filings with the Securities and Exchange Commission, including the risks set forth in the company's Quarterly Report on Form 10-Q for the quarter ended June 30, 2022. These forward-looking statements speak only as of the date hereof, and Invitae Corporation disclaims any obligation to update these forward-looking statements.

Contact:Renee Kelley[emailprotected](628) 213-3283

SOURCE Invitae Corporation

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Leading Clinical Experts Across the U.S. Unite to Support Universal Genetic Testing for all Patients with Cancer - PR Newswire

Wilmington, Delaware, United States, Transparency Market Research Inc. The preimplantation genetic testing is an increasingly go-to option for identifying genetic birth effects in children. The technique relies on the use of vitro fertilization before pregnancy. The technique is highly recommended in clinical practices especially in cases wherein both parents have a genetic defect. The tests are performed on an embryo to determine various genetic associations or factors. The PGD or preimplantation genetic diagnosis is the medium to avail this test.

Read Report Overview - https://www.transparencymarketresearch.com/preimplantation-genetic-testing-market.html

On the other hand, PGS or presumed genetic screening refers to techniques are applied for the screening of genetically sound parents. The technique is used to screen aneuploidy. The growing demand for genetically testing and rising knowledge of genetics, thanks to big data and AI technology is a promising driver for growth of the preimplantation genetic testing market.

Preimplantation Genetic Testing Market: Notable Developments

In 2018, twin girls in China were conceived using embryos that were specifically designed with the method of gene altering. In 2019, a 74 year Indian women gave birth to first-time twins. It is estimated that nearly 12% of the overall couples are infertile.

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Additionally, thanks to rising financial stress, and compatibility issues, women tend to conceive a far later in lifecycle. The growth of couples opting for reproductive technologies in Denmark stands at near 7% of all couples. The new technologies made available due to preimplantation genetic testing is expected to witness robust future as economies of scale drive down costs.

HelpCureHD, an organization has helped 24 families with Huntingtons disease to conceive healthy. The family-supported organization paid for the treatment of 24 families who were diagnosed with huntingtons disease. This is important to take note of as reproduction remains a key family concern and is likely to drive growth from charities. However, the costs of preimplantation genetic testing remain high and pose a major barrier to growth.

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Preimplantation Genetic Testing Market: Drivers and Restraints

The rising advent of medical knowledge and growth of technologically advanced genetic devices are expected to result in considerable growth for the preimplantation genetic testing market. Additionally, positive response from several regulatory authorities to genetic testing and possible opportunities for conceving healthier children are expected to be major opportunities. Additionally, more tech companies are also expected to invest in testing.

Recently, Facebook announced its desire to pay women more to conceive later as many women opted out of their jobs to take care of their families. The growing need for women to seek a balance between family and career, and growing tendency towards opting for family are expected to drive investment from the tech sector wherein salaries are extremely high and replacing labor can be far more costly.

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Preimplantation Genetic Testing Market: Geographical Analysis

The preimplantation genetic testing market is expected to witness major growth in North America region. The growing choice of women towards conceiving later, growing reliance on technology to identify pre-birth conditions, and expected cutting down costs due to scales of economy are expected to drive major growth in region.

Additionally, the preimplantation genetic testing market is expected to drive considerable growth in Asia Pacific region. The region is home to a rising disposable income, and growing access to healthcare. Additionally, large investment in big data and Artificial Intelligence technology by countries like Japan and China are expected to remain major drivers for growth.

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Preimplantation Genetic Testing Market: Growing Demand for Genetically Testing and Rising Knowledge of Genetics to Drive the Market - BioSpace

People who have been diagnosed with myalgic encephalomyelitis (ME) are being invited to take part in the worlds largest genetic study of the disease.

The study, named DecodeME and led by researchers at Edinburgh Universitys MRC Human Genetics Unit, aims to reveal the tiny differences in a persons DNA that can increase their risk of developing ME, also known as chronic fatigue syndrome (CFS).

It is estimated that more than 250,000 people in the UK are affected by the condition, with symptoms including pain, brain fog and extreme exhaustion that cannot be improved with rest.

The causes of the disease are still unknown, and there is no diagnostic test or effective treatments thus far.

Testing DNA in the saliva of 20,000 donated samples will allow for analysis on whether the disease is partly genetic, and if so, research into its cause and effective treatments.

The study has also been expanded to include analysis on the DNA of a further 5,000 people who have been diagnosed with ME or CFS after having Covid-19.

We believe the results should help identify genes, biological molecules and types of cells that may play a part in causing ME/CFS

Professor Chris Ponting

Along with the DNA research, an anonymous survey will provide an insight into the experience of those with the condition.

The research team is being led by Professor Chris Ponting.

He said: This is the first sizable DNA study of ME/CFS, and any differences we find compared to control samples will serve as important biological clues.

Specifically, we believe the results should help identify genes, biological molecules and types of cells that may play a part in causing ME/CFS.

The university is working alongside charity Action for ME, the Forward ME alliance of UK charities, and people with lived experience of the condition.

Chief executive of Action for ME Sonya Chowdhury said: People with lived experience of ME/CFS are at the very heart of the DecodeME project and our Patient and Participant Involvement group has worked closely with researchers on all aspects of the study.

Their profound involvement has been so transformational that we firmly believe it sets a new standard for health research in this country.

Individuals with ME or CFS who are aged 16 and over and based in the UK are invited to take part from home by signing up on the DecodeME website from 12pm on Monday.

See the rest here:
People with ME invited to take part in major genetic study - The Independent

So argued Glen Illing, a partner at AquaWoo, who gave a talk on the species at the recent Global Shrimp Forum in Utrecht.

According to Illing, the reasons for the current stagnation of the giant river prawn sector include the comparatively low profitability of the species compared to monodon and vannamei shrimp.

The species is grown at relatively low stocking densities, often as a secondary crop and quite frankly the second choice for cultivation, favoured in the main by small subsistence farmers. If profitability can be improved, farming freshwater shrimp will increase and this is where genetics can play a part, he reflected.

Genetic improvement is synonymous with efficiency, profitability and resilience to diseases, he added. But it baffles me why its so poorly applied to a species with as much potential as the giant freshwater prawn and yet its been applied to other species such as vannamei, where there have been massive jumps and improvements since the year 2000.

There are woefully few breeding programmes that are actually applying genomics to giant freshwater prawns.

This is even more surprising as, according to Illing, researchers have laid some of the vital groundwork.

There have been some notable [breeding] programmes and also some great research projects, but they havent been integrated into mainstream giant freshwater prawn production, he observed.

There are woefully few breeding programmes that are actually applying genomics to giant freshwater prawns, he added.

Although there have been a handful of successful breeding programmes in countries including Indonesia, China, Vietnam, Thailand and India, Illing noted that the generation-on-generation benefits have since slowed down, largely due to issues caused by inbreeding.

One development that Illing sees as having great potential is the use of genomics to produce all-male and all-female stocks the former are grown to large sizes over long cycles in order to compete with the lobster market, while the latter can produce three cycles a year.

Both gender-focused programmes increase profitability over a mixed sex cultivation, and both can be used in polyculture with vannamei or with fish like tilapia, he said.

Relatively large proportions of freshwater prawn farmers are beginning to cultivate all-males, particularly in Thailand on the other hand the all-female revolution is taking longer to reach wide-scale production, this technology is currently patent protected and being developed exclusively by one company [Enzootic], he explained.

Most recently, Illing argues, the rise of gene editing can bypass most of the backbreaking quantitative genetics work and will come much quicker than people imagine. And he pointed to a number of breakthrough technologies, including one at Ben Gurion University that developed platforms that have been geared up specifically to have the ability to edit freshwater prawns.

Operating at an economic density is key too high and the management challenges are insurmountable, too low the yields would not economically justify the costs.

Illing then focused on the all-female giant river prawn production work being done by Enzootic. While the company is based in Israel, they have recently built a compact, vertical RAS hatchery, with the capacity to produce 450 million giant river prawns per year, near Bangkok one of the main giant freshwater prawn production areas. Here theyre grown to juvenile size before being shipped to farmers.

The crux of all-female production is the ability to increase the stocking rates in ponds or tanks to economic densities and yet obtain a desirable market size within four months to enable three cycles per year and maximise the farmers yields. Operating at an economic density is key too high and the management challenges are insurmountable, too low the yields would not economically justify the costs, Illing observed.

Trials undertaken by the company are set to establish the best stocking densities in commercial farms shortly. But Illing also pointed to the results of a tank-based trial undertaken by the Asian Institute of Technology (AIT) found that optimum yields were around 24 giant river prawns per square metre, whereas the fastest growth rate occurred at 8 prawns per square metre up from the 4 per square metre favoured in traditional farms.

Gregg Yan

The next question Illing would like to see answered is whether the results of these tank-based trials are substantiated in commercial pond production of all-female production.

And, in order to speed up the process and encourage buy-in from farmers, Enzootic has established a large-scale commercial farm to the east of Bangkok, consisting of 55 earthen ponds across 100 ha. The first harvest from these is due soon, he noted.

The company is now also going further down the vertical integration route by developing a branded product which is being tested in the high end retail market in Canada.

Rob Fletcher has been writing about aquaculture since 2007, as editor of Fish Farmer, Fish Farming Expert and The Fish Site. He has an MA in history from the University of Edinburgh and an MSc in sustainable aquaculture from the University of St Andrews. He currently lives and works in Scotland.

Read more:
Can genetics breathe new life into giant river prawn production? - The Fish Site

Legendary US rancher Lee Leachman has said Stabiliser cattle should become the standard suckler cow in the UK to help farmers with future challenges.

Mr Leachman, who is CEO of Leachman Cattle of Colorado, one of the five largest seedstock breeders in the US, made the remarks this week while on a tour of farms in Scotland and Northern England.

He described Stabiliser as the best kept secret in temperate regions, adding that hybrid genetics suited the UK extremely well.

Britain has particular requirements, he said. Running cows on grass, over wintering them inside, feeding them low quality forage and still trying to produce shapely cattle.

"The best way to do that is by producing hybrid cows. Stabilisers thrive here. They produce well over a 95% calving rate so anything that does that must thrive.

The shoe fits. Everyone breeds cows for different reasons, but if youre looking at data and trying to make money, then hybrid genetics are the way forward. We dont have many people stop using them once they start.

Mr Leacham added that for the first time, society was demanding that cattle are productive, while at the same time delivering for sustainability and the environment.

Generally, cattle change slowly, but we are seeing rapid, managed change, he said. Hybrid genetics are a game-changer and our breeders are continually moving to optimise production.

"This means moderately sized cows, better fertility, longevity, and better calves, which feed into everything, from lower carbon emissions to ease of care, eating quality and dollar profit.

Hybrid production is normal in crop production, swine, and poultry. Were using systems aligned with that in beef and I dont think UK cattle farmers have any other source of feed efficiency tested, genomically evaluated composite genetics.

Stabiliser cattle were created in the 1970s at the USDA Meat Animal Research Centre in Nebraska when investigating the benefits of composite breeding on cattle efficiencies, particularly in relation to heterosis, or hybrid vigour.

Three hybrids were created in the initial breeding programme and one that proved most profitable in both cow/calf and feed yard performance was a 25% composition of Hereford, Angus, Simmental, and Gelbvieh, which became the basis for the modern Stabiliser.

The breed was refined and improved by Mr Leachman, first as part of the Leachman Cattle Company in Billings, Montana, and latterly as part of Leachman Cattle of Colorado, which now markets more than 2,000 bulls each year.

Stabiliser cattle were first introduced to the UK in the late 1990s when a group of Yorkshire beef farmers, led by industry innovator Richard Fuller, started searching for a more efficient alternative to the dairy crosses they were producing at the time.

A total of 52 embryos were imported from the Leachman Cattle Company in 1999 which formed the basis of the UK herd.

Mr Leachman sits on the board of the Stabiliser Cattle Company, based in Southburn, East Yorkshire, which is responsible for improving and promoting the breed in the UK.

He said his visit to the country had been focussed on helping the Stabiliser Cattle Company direct their genetic improvements programme, as well as assessing the quality of the UK herd.

He said: These visits are a great opportunity to see how cattle here are progressing and ask what UK breeders want to focus on for improvement.

It is also fantastic to see people enjoying Stabiliser. Theyre the UK's ultimate suckler cow with highly fertile, docility, calving ease, and efficiency.

"Raising beef is hard work, but raising Stabilisers is more fun and more profitable.

Excerpt from:
Hybrid genetics is the future of UK beef, legendary US rancher says - FarmingUK

Editors Note

Spectrums house style is to lowercase autistic, but we have made an exception in this instance at the authors request.

Wrigley Kline

Graduate student, Northeastern University

In October, the researchers behind the U.K. genetics study Spectrum 10k had to pause and reorganize their project after some in the Autistic community questioned the teams aims and methods.

This derailment exemplifies the growing tensions between genetics researchers and portions of the Autistic community and reflects the fact that some in the community are increasingly hesitant to share their genetic material with researchers. One of their primary concerns is that some geneticists are working to cure autism or prevent it via prenatal testing. They see that the availability of reliable noninvasive prenatal testing has contributed to the plummeting prevalence of Down syndrome in Europe, which is an example of modern eugenics, and fear that genetics research could lead to similar outcomes for Autistic people.

To be sure, Spectrum 10k explicitly states that it is not trying to cure or eradicate autism. Still, some Autistic people find it easier to avoid participating in any genetics research rather than trying to avoid projects that may obfuscate their aims with abstract descriptions, lack data security or reshare stored genetic information indiscriminately.

I understand why some members of the Autistic community feel this way: I am an Autistic person, and I study white supremacist violence, including eugenics. Listening to some researchers discuss their visions for the future of autism research often provokes emotions similar to reading about what neo-Nazis want to do with people like me.

As a researcher, I understand the value of good datasets, and as an Autistic person, I know that genetics research into the health problems that accompany autism is important. This intersection of my personal and academic experience enables me to value the goals of Autistic people and scientists at the same time and to work toward a collaborative solution.

I have what I think could be several effective, noncontroversial suggestions that could begin to address the concerns of Autistic people, and in turn increase the likelihood of their participation in genetics research. My recommendations arent meant to prevent researchers from accessing data; instead, they can foster a collaborative relationship between researchers and the Autistic community, resulting in an increase in the availability of genetic data.

Francis Galton, who coined the term eugenics in 1883, described his research as an attempt to improve theracial qualities of future generations either physically ormentally through science. Attempting to cure autism or prevent Autistic people from being born clearly fits this definition.

Though many genetics researchers dont want to cure autism, their research can inadvertently benefit scientists who do and who believe that severely disabled autistic people cannot enjoy a good quality of life. That view ignores a substantial body of research that explores strategies to increase happiness for severely disabled people. People who work to eliminate severely disabled people under the pretext that they are sparing those people from suffering are misguided. The aim of curing or eliminating severely disabled people also violates human rights and UNESCOs 1997 Universal Declaration on the Human Genome and Human Rights.

Autistic people hesitate to share their genetic material because it frequently ends up in large databases that are readily available to qualified researchers at universities, private companies or medical institutions who apply for access. Once a database hands over genetic information, the information could rapidly change hands and be used for purposes that are anathema to an Autistic study participant.

Most of these large-scale databases fail to meet the privacy standards laid out in UNESCOs declaration to protect identifiable genetic data, because researchers are getting better at re-identifying certain types of genetic data. An example of such privacy failures is MSSNG, a database of genetic material created by Autism Speaks and Google that currently hosts more than 11,300 whole-genome sequences on a cloud-based system. MSSNG shares datasets with academic institutions internationally. Such cloud-hosted databases, however, are routinely hacked.

Additionally, MSSNG does not specify which countries it shares its data with. Human rights groups and academic publishers have criticized China, for example, for conducting unethical genetics research, such as human CRISPR-Cas9 experimentation and attempting surveillance via the short tandem repeats that occur on the Y chromosome. Researchers in countries with low ethical standards could access MSSNGs data, either through an application or through hacking.

Large-scale databases also struggle to comply with the intellectual honesty requirements in UNESCOs declaration, which states that genetics research participants should be required to give informed consent for each project that analyzes their data. Most databases grant access to their datasets once the datasets owner approves an application, but the people who contributed their genetic material do not have the opportunity to refuse to consent to the new research.

Some organizations are even less clear about how they share data. Spectrum 10k, which is revising its approach after backlash from the Autistic community, says it plans to share its data with researchers whose aims are in line with our efforts to improve the well-being of autistic people. But well-being is abstract, and Spectrum 10k doesnt define the term in this context, giving the project plenty of legal leeway to share data with whomever they want.

Such ambiguity highlights another reason that Autistic people distrust autism geneticists. As recently as 2016, Autism Speaks openly said it was looking at the genetic origins of autism to create a cure. Now it publicly denounces that goal and says its work will lead to treatments for autisms associated health problems, but most of its research looks the same. Article 17 of UNESCOs declaration encourages solidarity between researchers and participants; opaque statements about research outcomes contradict this goal.

Failing to make informed consent accessible to intellectually disabled people who are their own legal guardians also breaks that solidarity. Severely disabled Autistic people care about the impact genetics research could have on their lives. Some projects create non-binding documents that summarize informed consent, but these documents tend to be created internally and paint research in the most favorable light. Instead, a neutral third party, such as a disability rights law firm, should draft these accessible informed-consent documents. Putting the usual accessible and traditional informed-consent documents side by side readily shows how the former often leaves out important information for intellectually disabled people.

Having good intentions doesnt prevent research from doing harm, and geneticists are not always best positioned to see the long-term implications of their work. Social scientists, particularly disabled social scientists, could play a valuable role in both fostering solidarity and enforcing research ethics in the autism field. Article 16 of the UNESCO declaration recommends the establishment of multidisciplinary ethics committees to consider the implications of genetics research projects. This isnt occurring publicly, yet this type of oversight is uniquely important, given the history of eugenics against Autistic people and the ongoing suspicion many in the Autistic community harbor toward geneticists.

Ultimately, to gain greater participation from the Autistic community, geneticists should come into compliance with UNESCOs 1997 Universal Declaration on the Human Genome and Human Rights: They must secure their databases to the degree they would identifiable genetic data, require database participants to sign an informed consent for each project their data is used for, provide third-party accessible informed consents, and involve disabled social scientists in the development of research.

Cite this article: https://doi.org/10.53053/XZSI8371

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How geneticists can gain greater buy-in from the autistic community - Spectrum

Preventing serious negative effects

The research team then examined the ancient stool samples gathered from various locations and compared them with contemporary samples received from people with whipworms from around the world. This provided them an insight into the evolution of the worm over ten-thousands of years.

"Unsurprisingly, we can see that the whipworm appears to have spread from Africa to the rest of the world along with humans about 55,000 years ago, following the so-called 'out of Africa' hypothesis on human migration," stated Kapel.

As mentioned above, a whipworm infection can have a beneficial impact on a healthy host. When it comes to severe infections, on the other hand, it can lead to dysentery, anemia, and rectal prolapse, and in children, it can impede healthy growth.

The researchers believe that this new research could help develop new ways to prevent such effects.

The findings have been published in the journal Nature Communications.

Abstract:

The neglected tropical disease trichuriasis is caused by the whipworm Trichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today, T. trichiura infects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.

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Ancient Viking poop helped scientists map the genetics of a 5000-year-old parasite - Interesting Engineering

A clinical trial involving University of Utah Health and NYU Langone Health in New York is seeking to identify patients who qualify for genetic risk assessment using a clinical decision support algorithm to automatically evaluate family history of cancer. The BRIDGE Trial also is testing the use of a chatbot for patient outreach.

At last weeks National Human Genome Research Institute meeting on genomic learning healthcare systems, Guilherme Del Fiol, M.D., Ph.D., associate professor and vice-chair of research in the University of Utahs Department of Biomedical Informatics, described the BRIDGE (Broadening the Reach, Impact, and Delivery of Genetic Services) Trial.

This randomized controlled trial has been funded by two grants from the National Cancer Institute, one of them focused on a software platform for population-level, genomic clinical decision support, and the other one is a randomized multi-site trial using this platform for a specific use case.

Kimberly Kaphingst, ScD,a professor in the Department of Communication and the director of Cancer Communication Research at the Huntsman Cancer Institute (HCI) at the University of Utah, is the principal investigator on the project.

The original motivation for this project was the finding that about 13 percent of individuals are at elevated risk for familial breast and colorectal cancer, and that most of these individuals are unaware of their risk, Del Fiol said, and at the same time, there are evidence-based guidelines recommending genetic testing based on their family history.

The goals of the project were essentially to enable a population health management platform that allows clinicians to use computable logic to identify patients who meet evidence-based criteria for genetic testing, and then to use a registry-based approach with patient outreach tools to manage the risk, he explained.

We leverage family history that's available in the EHR, and we do not try to collect or improve the collection of family history, Del Fiol stressed. Another essential part of the strategy is that in order to minimize primary care effort, primary care providers are kept into the loop of this whole process, but they are not asked to do anything extra.

Part of the innovation is to try to use automated chatbots for the patient outreach process, which includes patient education, in offering genetic testing. The BRIDGE Trial is about to finish enrollment at University of Utah Health and New York University Langone Health.

From the project website, here is information on the BRIDGE Trials goals:

The researchers hypothesize that uptake of genetic counseling and genetic testing will be equivalent between the chatbot and the genetic services delivery models. They also plan to explore how race, ethnicity, and geographic location modify the effects of the cancer genetics services delivery models on the outcomes.

Del Fiol said the project involves use of the OpenCDS platform. OpenCDS is a multi-institutional, collaborative effort to develop open-source, standards-based clinical decision support (CDS) tools and resources that can be widely adopted to enable CDS at scale.

Del Fiol explained how the system works: The population coordinator system identifies a screening population, which in this case is basically everyone who meets a certain age range and has been seen in a primary care at University of Utah or NYU-Langone. The population coordinator retrieves data from these patients and transforms everything into FHIR from the EHR. Next, FHIR data is transmitted to OpenCDS in bulk. OpenCDS has an interface based on the CDS Hooks standard, which is a clinical decision support services standard that allows an independent service to receive a request to analyze patients according to certain logic, and then respond with the results of those analyses all in a standard format. CDS Hooks uses FHIR as the data standard both for requests and responses.

The results are then exported back into the EHR. In our case, for Epic, it uses Epics population registry solution, Del Fiol said. We load patients who meet criteria into the registry, and then the genetic counseling assistants uses that registry functionality to manage the population and conduct patient outreach activities.

This platform is supporting the BRIDGE trial, which is comparing two approaches for patient education and outreach, with the goal of offering genetic testing for patients who meet family history-based criteria. There are two arms of the study, Del Fiol explained. One is our usual care, which basically involves genetic counselors making phone calls to those patients, one by one, providing some education over the phone, in trying to schedule a genetic counseling appointment. The alternative approach in the second arm of the study is using an automated chatbot, which provides education about genetics and then at the very end of a chatbot conversation, it offers the option to receive genetic testing. If they decide to do testing, they receive a kit in the mail, collect the sample at home, mail the sample back to the lab, and an outreach note is written back into Epic with the patient's decision and the transcript of that conversation.

For patients who test positive, they get a genetic counseling appointment, and are basically back to the usual care workflow. But most patients test negative and are managed in an automated fashion using the chatbot. In both cases, a note is written into the EHR, with clinical recommendations. For patients who test negative that's an automated note, and for patients whose test positive, the note is written by a genetic counselor.

So far, more than 3,000 patients have received outreach in one of the two study arms. I'm not going to make comparisons here because the trial hasn't been completed yet, he said, but so far, 23 percent of the people who received an offer to use the chatbot or receive the phone call for genetic counseling completed the entire process they either completed the chatbot interaction, or they scheduled a genetic counseling appointment and had that appointment completed.

Del Fiol described some early lessons learned in this process. We found that using chatbots does seem to be a scalable approach for patient outreach and engagement. It minimizes the genetic counseling efforts, he said.

Overall, family history data is incomplete in the EHR. But when you have a family history assertion in the EHR, we found that it's largely correct, and rarely leads to false positive patient identification, he added.

Regarding clinical workflow, they tested interoperability using two EHR systems at three institutions, two on Epic and one on Cerner. At Intermountain Healthcare, we demonstrated that this works with a Cerner system, but we found there are significant disparities in family history documentation across different patient populations," he added. In addition, one problem with the chatbot is that it really relies on smartphone technology, and higher percentages of the people in low-SES and rural populations don't have a smartphone.

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Project Uses OpenCDS, Chatbots to Broaden Genetic Testing's Reach - Healthcare Innovation

How can the biology of a crop be manipulated for greater profits in this fast-growing market through breeding?

Since early farmers began collecting seeds for propagation, they focused on varieties that performed best in unpredictable field conditions, not in highly controlled environments. Specifically, crop plants exude up to 40% photosynthate into the soil to "feed" beneficial microbes and allocate additional resources to produce secondary products to protect against pests and diseases.

Unlocking the full potential of seed for precisely controlled environments, where every day is a good day, will allow breeders to focus on plant characteristics that improve when grown indoors and downplay problems that would be of great concern for outdoor production. As we control the environment more, we can engineer crops with traits to delight the consumer and improve the supply chain.

Marc Oshima, co-founder of AeroFarms, says, "For vertical farms, breeders can focus on qualities of primary importance to consumers: flavor, aroma, texture, and other quality-related attributes. It's also important to have plants that are architecturally efficient so that they can be easily maintained and harvested in our unique environment."

The biggest breeding goals for field-grown fruits and vegetables are disease resistance. Breeders are spinning on a treadmill to stay ahead of the next disease in the field. It's not simply a matter of swapping disease-resistant genes for genes that confer good flavor, but CEA allows breeders to stay ahead of the next potentially devastating disease outdoors. Some diseases, such as powdery mildew, are possible indoors but can often be controlled by management practices.

Source: http://www.bioeconomia.info.

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The power of genetics to unleash the potential of indoor farming - Vertical Farm Daily