Category Archives: Genetics

So maybe its time to take a peek at what scientists around the world are striving to achieve, where developments in the science of genetic development is concerned.

Lets start with the world of plants. There are three main crops responsible for delivering all of the plant-based energy and protein required in the world today. These consumed directly by mankind or fed to livestock in order to produce animal protein.

The crops in question are: wheat, maize (corn) and soya bean. Given Northern Irelands temperate climate, wheat is the one which farmers and consumers will be most familiar with.

So here comes the shocking fact: A first-of-its-kind analysis of the untapped genetic potential of wheat shows global yields are only half of what they could be!

The team of international experts, led from the UKs Rothamsted Research, says this genetic yield gap could be closed by developing wheat varieties tailored to each region.

In other words, by utilising the vast genetic variation available in global and historical wheat gene banks with modern techniques such as speed breeding and gene editing.

Dr Mikhail Semenov and Dr Nimai Senapati, who co-led this study, define a crops genetic yield potential as the highest yield achievable by an idealised variety.

A plant with an optimal genome allows it to capture water, sunlight and nutrients more efficiently than any other.

Dr Semenov said: Current wheat cultivars are, on average, only at the half-way point with respect to the yields they could produce given the mismatches between their genetics and local wheat growing conditions.

Global wheat production could be doubled by the genetic improvement of local wheat cultivars - without increasing global wheat area.

Using existing data on the contribution of different genes to individual plant traits such as size, shape, metabolism and growth, the researchers ranmillions of computer simulations to design perfect wheat plantsthat were tailored to their local environments.

When compared to the performance of locally adapted cultivars, in all cases they found current wheat varieties were underperforming for grain yield, with an obvious genetic yield gap between reality and possibility.

According to Dr Senapati, closing the genetic yield gap would go a long way to feeding the growing world population and would reduce pressure to convert wild habitats to farmland.

Using a state-of-the-art wheat model, called Sirius, the team first calculated the potential yield from a total of 28 commonly used wheat varieties grown at a number of sites around the world, assuming the best possible cultivation conditions for each one.

This gave harvests of less than four tons in Australia and Kazakhstan - compared with 14 tons of wheat produced per hectare in New Zealand.

Next, they designed idealized local varieties within their model, which optimised several plant traits that contribute to yield and whose underlying genetics will allow them to be improved by plant breeders.

Simulations were based on extensive data on the natural genetic variation underpinning the traits.

These included tolerance and response to drought and heat stresses, the size and orientation of the light-capturing upper leaves, and the timing of key life cycle events.

The results showed that by optimizing these key traits, genetic yield gaps could be anywhere from 30-70% across different countries, with a global average genetic yield gap of 51%. Therefore, global wheat production could be doubled by exploiting this existing genetic yield gap towards achieving global food security in a sustainable way.

Not unsurprisingly, the countries with the lowest current yields could gain the most from closing their genetic yield gaps, said Dr Senapati.

That said, even improvements in those countries with a medium genetic yield gap of 40 to 50%, but with a large proportion of the global wheat harvest, would have a substantial effect on global wheat production due to the larger wheat cultivation areas involved.

Meanwhile, here in Ireland, sheep production has been a key focus of genetic research for many years.

In fact, the myriad sources of data now available to Sheep Ireland is allowing the organisation to achieve the role it was created to fulfil on its establishment back in 2009.

This was the core message delivered by Sheep Irelands manager, Kevin McDermott, courtesy of his presentation to the recent EasyCare open evening. The event was held on the Co Antrim farm of Campbell Tweed.

Our aim is to secure balanced breeding goals for the Irish sheep industry, he stressed.

The good news is that the facts expanding network of data sources and real time information available to us is making this possible.

For example, genetic evaluations can be updated on a weekly basis. Making this possible is the fact that Sheep Ireland is a centralised data source for the entire Irish sheep industry.

McDermott particularly highlighted the role that genomics is now playing within Irelands sheep breeding sectors.

He further explained:Being able to genotype sheep brings with it many benefits. At a very fundamental level, it allows us to verify the parentage of pedigree breeding stock.

This is significant, given that up to 8% of pedigree ewes and lambs born in Ireland have been attributed the wrong ancestry, up to this point.

However, genomics opens up a host of new opportunities, when it comes to delivering improved performance at farm level.

McDermott continued:But none of this would be possible without the increasing buy-in of both pedigree and commercial sheep farmers throughout Ireland.

A total of 8 pedigree sheep societies are now using the Sheep Ireland IT system to administer their flockbooks: Belclare, Beltex, Charollais, Galway, Irish Suffolk Sheep Society, Rouge de lOuest, Texel and Vendeen.

The Sheep Ireland representative also confirmed the benefits that will be accrued by farmers using the organisations new phone app.

Essentially, it allows flockowners associated withSheep Irelandto record information about their animals, such as lambing, and growth rates on an almost real-time basis.

Kevin McDermott again: The new app allows farmers to record and submit information reliably and accurately while they are actually out in the field or in sheds.

Gone are the days when recordings are initially written down on paper and then uploaded into the Sheep Ireland once the farmer gets back to his or her office computer. As a result, the margin for error is greatly reduced.

The impact of the continuing progress made by Sheep Ireland over recent years has been significant.

The organisation was designated the responsibility of increasing the rate of genetic gain within the Irish sheep sector by identifying and promoting the use of rams with more profitable and sustainable genetics.

This has been achieved by gathering performance data from the top rams in the country and accessing their strengths and weaknesses using a genetic evaluation which is updated weekly to include any new data.

The results of these genetic evaluations are then displayed in sales catalogues and online in a simple one to five star rating system, allowing sheep farmers to make a more informed breeding decision when selecting their next stock ram.

Looking to the future, Sheep Ireland sees its role as being part of the response from Irish agriculture to the challenge of global warming.

Specifically, the organisation is currently seeking to develop an Estimated Breeding Value (EBV) for sheep, linked to their methane emissions.

Kevin McDermott again: Again, genomics can play a role in this context.

He concluded: All of the work carried out by Sheep Ireland is independently validated. This approach gives sheep producers a very high level of confidence in the performance-related data that we make available.

Dairy is the largest sector within local agriculture at the present time.

There is a growing recognition of the role that improved genetics will play in delivering future sustainability for the milk sector in Northern Ireland.

Technologies including the use of sexed semen and embryo transfer are already making a significant difference in this regard.

Ai Services Breeding Services Manager Ivan Minford takes up the story: Committing to AI has always represented a very small investment relative to the overall costs incurred within any dairy farming business. Feed, fertiliser and energy prices continue to increase at an exponential rate.

Whats more, the development of effective breeding policies has always been the cornerstone of improved herd performance that will continue to deliver for many generations.

In money terms, the size of the initial investment required to make all of this happen is inconsequential, relative to the scale of the benefits accrued.

He continued; And this remains the case. Ai Services has developed a strong working relationship with the worlds premier breeding companies to secure elite dairy genetics at prices that represent unbeatable value for money for local milk producers.

According to the Ai Services representative, an investment in improved genetics will deliver at two fundamental levels for dairy farmers: improved efficiency and improved profitably.

He further explained: Genetics impacts on every impact of cow performance: improved milk production, enhanced milk quality, extended longevity within a milking group and improved health traits to name but a few.

Significantly, all of these factors combine to deliver a smaller carbon footprint and improved sustainability for all dairy farming operations.

Cow size has also been identified as a key factor in determining the carbon footprint of all milk production business.

There is scope to reduce cow size while still maintaining overall animal performance, Minford concluded.

So how does all this fit into the future development of agriculture in Northern Ireland.

Farm Minister Edwin Poots has set out his vision for the future of farm support in Northern Ireland.

Speaking at the Irish National Ploughing Championships in Co Laois, he confirmed that the post-Brexit farm support measures will focus on a number of key themes: recognising the role of active farmers in adopting sustainable production practices, creating the conditions that will provide encouragement for young people coming into the industry and driving up efficiency levels across the industry.

Where beef is concerned, the minister referred to a revolution taking place within the sector, similar to that which has already been effected within the pig and poultry sectors.

He added:The use of improved genetics and the introduction of management systems that drive performance and reduce environmental impacts, particularly greenhouse gas emissions, are priorities for the beef industry.

Edwin Poots concluded:All future support measures will be underpinned by a measurable improvement in farm economic and environmental performance.

So there you have it: improving genetics will play a critically important role as farming in Northern Ireland looks to the future.

And no doubt, this is something that we can all look forward to.

But developing new genotypes and bloodlines is one thing: managing them effectively is another days work entirely!

Read the rest here:
The real power ofimproved genetics - Farming Life

As a rapidly advancing climate emergency turns the planet ever hotter, the Dallas-based biotechnology company Colossal Biosciences has a vision: To see the Woolly Mammoth thunder upon the tundra once again. Founders George Church and Ben Lamm have already racked up an impressive list of high-profile funders and investors, including Peter Thiel, Tony Robbins, Paris Hilton, Winklevoss Capital and, according to the public portfolio its venture capital arm released this month, the CIA.

Colossal says it hopes to use advanced genetic sequencing to resurrect two extinct mammals not just the giant, ice age mammoth, but also a mid-sized marsupial known as the thylacine, or Tasmanian tiger, that died out less than a century ago. On its website, the company vows: Combining the science of genetics with the business of discovery, we endeavor to jumpstart natures ancestral heartbeat.

In-Q-Tel, its new investor, is registered as a nonprofit venture capital firm funded by the CIA. On its surface, the group funds technology startups with the potential to safeguard national security. In addition to its long-standing pursuit of intelligence and weapons technologies, the CIA outfit has lately displayed an increased interest in biotechnology and particularly DNA sequencing.

Why the interest in a company like Colossal, which was founded with a mission to de-extinct the wooly mammoth and other species? reads an In-Q-Tel blog post published on September 22. Strategically, its less about the mammoths and more about the capability.

Biotechnology and the broader bioeconomy are critical for humanity to further develop. It is important for all facets of our government to develop them and have an understanding of what is possible, Colossal co-founder Ben Lammwrote in an email to The Intercept. (A spokesperson for Lamm stressed that while Thiel provided Church with$100,000 in funding to launchthe woolly mammoth project that became Colossal, he is not a stakeholderlike Robbins, Hilton, Winklevoss Capital, and In-Q-Tel.)

Colossal uses CRISPR gene editing, a method of genetic engineering based on a naturally occurring type of DNA sequence. CRISPR sequences present on their own in some bacterial cells and act as an immune defense system, allowing the cellto detect and excise viral material thattries to invade. The eponymous gene editing technique was developed to function the same way, allowing users to snip unwanted genes and program a more ideal version of the genetic code.

CRISPR is the use of genetic scissors, Robert Klitzman, a bioethicist at Columbia University and a prominent voice of caution on genetic engineering, told The Intercept. Youre going into DNA, which is a 3-billion-molecule-long chain, and clipping some of it out and replacing it. You can clip out bad mutations and put in good genes, but these editing scissors can also take out too much.

The embrace of this technology, according to In-Q-Tels blog post, will help allow U.S. government agencies to read, write, and edit genetic material, and, importantly, tosteerglobal biological phenomena that impact nation-to-nation competition whileenabling the United States to help set the ethical, as well as the technological, standards for its use.

In-Q-Tel did not respond to The Intercepts requests for comment.

In recent years, the venture firms portfolio has expanded to include Ginkgo Bioworks, a bioengineering startup focused on manufacturing bacteria for biofuel and other industrial uses; Claremont BioSolutions, a firm that produces DNA sequencing hardware; Biomatrica and T2 Biosystems, two manufacturers for DNA testing components; and Metabiota, an infectious disease mapping and risk analysis database powered by artificial intelligence. As The Intercept reported in 2016, In-Q-Tel also invested in Clearista, a skincare brand that removes a thin outer epidermal layer to reveal a fresher face beneath it and allow DNA collection from the skin cells scraped off.

President Joe Bidens administration signaled its prioritization of related advances earlier this month, when Biden signed an executive order on biotechnology and biomanufacturing. The order includes directives to spur public-private collaboration, bolster biological risk management, expand bioenergy-based products, and engage the international community to enhance biotechnology R&D cooperation in a way that is consistent with United States principles and values.

The governments penchant for controversial biotechnology long predates the Biden administration. In 2001, a New York Times investigation found that American defense agencies under Presidents George W. Bush and Bill Clinton had continued to experiment with biological weapons, despite a 1972 international treaty prohibiting them. In 2011, The Guardian revealed that the CIA under President Barack Obama organized a fake Hepatitis B vaccine drive in Pakistan that sought to locate family members of Osama bin Laden through nonconsensual DNA collection, leading the agency to eventually promise a cessation of falseimmunization campaigns.

CIA Labs, a 2020 initiative overseen by Donald Trumps CIA director, Gina Haspel infamous for running a torture laboratory in Thailand follows a model similar to In-Q-Tels. The program created a research network to incubate top talent and technology for use across U.S. defense agencies, while simultaneously allowing participating CIA officers to personally profit off their research and patents.

In-Q-Tel board members are allowed to sit on the boards of companies in which the firm invests, raising ethics concerns over howthe non-profit selects companies to back with government dollars. A 2016 Wall Street Journal investigation found that almost half of In-Q-Tel board members were connected to the companies where it had invested.

The size of In-Q-Tels stake in Colossal wont be known until the nonprofit releases its financial statements next year, but the investment may provide a boon on reputation alone: In-Q-Tel has claimed that every dollar it invests in a business attracts 15 more from other investors.

Colossals co-founders, Lamm and Church, represent the ventures business and science minds, respectively. Lamm, a self-proclaimed serial technology entrepreneur, founded his first company as a senior in college, then pivoted to mobile apps and artificial intelligence before helping to start Colossal.

Church a Harvard geneticist, genome-based dating app visionary, and former Jeffrey Epstein funding recipient has proposed the revival of extinct species before. Speaking to Der Spiegel in 2013, Church suggested the resurrection of the Neanderthal an idea met with controversy because it would require technology capable of human cloning.

We can clone all kinds of mammals, so its very likely that we could clone a human, Church said. Why shouldnt we be able to do so? When the interviewer reminded him of a ban on human cloning, Church said, And laws can change, by the way.

Even when the methods used for de-extinction are legal, many scientists are skeptical of its promise. In a 2017 paper for Nature Ecology & Evolution, a group of biologists from Canada, Australia, and New Zealand found that [s]pending limited resources on de-extinction could lead to net biodiversity loss.

De-extinction is a fairytale science, Jeremy Austin, a University of Adelaide professor and director of the Australian Center for Ancient DNA,toldthe Sydney Morning Herald over the summer, when Colossal pledged to sink $10 million into the University of Melbourne for its Tasmanian tiger project. Its pretty clear to people like me that thylacine or mammoth de-extinction is more about media attention for the scientists and less about doing serious science.

Critics who say de-extinction of genes to create proxy species is impossible are critics who are simply not fully informed and do not know the science. We have been clear from day one that on the path to de-extinction we will be developing technologies which we hope to be beneficial to both human healthcare as well as conservation, Lamm wrote to The Intercept. We will conitnue [sic] to share these technologies we develop with the world.

It remains to be seen if Colossal, with In-Q-Tels backing, can make good on its promises. And its unclear what, exactly, the intelligence world might gain from the use of CRISPR. But perhaps the CIA shares the companys altruistic, if vague, motives: To advance the economies of biology and healing through genetics. To make humanity more human. And to reawaken the lost wilds of Earth. So we, and our planet, can breathe easier.

Update: September 28, 2022, 1:00 p.m. ETThis story has been updated with a statement from Colossal co-founder Ben Lamm.

Here is the original post:
CIA Just Invested In Woolly Mammoth Resurrection Tech - The Intercept

Monkeypox is a painful and debilitating viral infection. Cases have been rising rapidly since April, causing the World Health Organization to declare the monkeypox outbreak a global health emergency as of July 20221. Thankfully, science is on our side and vaccinia-based vaccines may be the key to stopping another pandemic.

Vaccinia-based vaccines contain inactivated or non-pathological viruses. These types of vaccines are being explored for use against monkeypox as this type of vaccine is behind the eradication of the smallpox outbreak that wiped out millions worldwide2. Recent evidence demonstrates that these vaccines have been effective against the monkeypox virus due to a concept known as cross-reactivity.

Cross-reactivity simply means that there are similarities within each virus which may mean similar targets to develop immunity2. However, the virus responsible for smallpox is genetically different from the virus responsible for monkeypox. Due to this genetic variation, it is unknown whether the vaccinia-based vaccines would be effective2.

To gain further understanding, a group of researchers accessed public databases to compare the genetic code of the vaccinia virus pre-1980s (smallpox) and compared these to the 2022 monkeypox viruses2. The exploration focused on the segments of the viruses that are targeted by the immune system, known as epitopes. Comparing epitopes between the viruses could show how effective the vaccinia-based vaccine may be against the 2022 monkeypox virus2.

The researchers then sought to determine the degree of genetic similarity among the epitopes that are recognized by our T cells. T cells are paramount in fighting pathogens and are responsible for inducing a range of immune responses against different infectious agents1,3. These researchers found similarities among the epitopes recognized by our T cells which means there is a positive association between the vaccinia-based vaccine and the activation and function of our T cells2.

The 2022 monkeypox virus contains mostly similar epitopes to that of the vaccinia virus. This implies that the vaccinia-based vaccine may be the defense needed against this monkeypox virus and its strains2,3.

Despite these encouraging results, additional studies are warranted to discover the specificity of immune responses based on genetic differences, but similarities of epitopes observed between the 2022 monkeypox virus and the vaccinia virus3.

Here is the original post:
Fighting the Monkeypox Virus: Genetics as a Predictor of Vaccinia Vaccine Effectiveness - Medical News Bulletin

Meyer, R. S. & Purugganan, M. D. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840852 (2013).

CAS PubMed Article Google Scholar

Olsen, K. & Wendel, J. Crop plants as models for understanding plant adaptation and diversification. Front. Plant. Sci. 4, 290 (2013).

PubMed PubMed Central Article Google Scholar

Bevan, M. W. et al. Genomic innovation for crop improvement. Nature 543, 346354 (2017).

CAS PubMed Article Google Scholar

Yuan, Y., Bayer, P. E., Batley, J. & Edwards, D. Improvements in genomic technologies: application to crop genomics. Trends Biotechnol. 35, 547558 (2017).

CAS PubMed Article Google Scholar

Edwards, D., Batley, J. & Snowdon, R. J. Accessing complex crop genomes with next-generation sequencing. Theor. Appl. Genet. 126, 111 (2013).

CAS PubMed Article Google Scholar

Jiao, Y. et al. Improved maize reference genome with single-molecule technologies. Nature 546, 524527 (2017).

CAS PubMed PubMed Central Article Google Scholar

Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408414 (2015).

CAS PubMed Article Google Scholar

Varshney, R. K. et al. Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits. Nat. Genet. 49, 10821088 (2017).

CAS PubMed Article Google Scholar

Wang, W. S. et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 4349 (2018).

CAS PubMed PubMed Central Article Google Scholar

Wei, T. et al. Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce. Nat. Genet. 53, 752760 (2021).

CAS PubMed Article Google Scholar

Wu, J. et al. Resequencing of 683 common bean genotypes identifies yield component trait associations across a northsouth cline. Nat. Genet. 52, 118125 (2020).

CAS PubMed Article Google Scholar

Feuk, L., Marshall, C. R., Wintle, R. F. & Scherer, S. W. Structural variants: changing the landscape of chromosomes and design of disease studies. Hum. Mol. Genet. 15, R57R66 (2006).

CAS PubMed Article Google Scholar

Wang, Y. et al. Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat. Genet. 47, 944948 (2015).

CAS PubMed Article Google Scholar

Alonge, M. et al. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell 182, 145161 (2020).

CAS PubMed PubMed Central Article Google Scholar

Kou, Y. et al. Evolutionary genomics of structural variation in asian rice (Oryza sativa) domestication. Mol. Biol. Evol. 37, 35073524 (2020).

CAS PubMed PubMed Central Article Google Scholar

Liu, Y. et al. Pan-genome of wild and cultivated soybeans. Cell 182, 162176 (2020).

CAS PubMed Article Google Scholar

Zhou, Y. et al. The population genetics of structural variants in grapevine domestication. Nat. Plants 5, 965979 (2019).

PubMed Article Google Scholar

Khan, A. W. et al. Super-pangenome by integrating the wild side of a species for accelerated crop improvement. Trends Plant Sci. 25, 148158 (2020).

CAS PubMed PubMed Central Article Google Scholar

Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome. Proc. Natl Acad. Sci. USA 102, 1395013955 (2005).

CAS PubMed PubMed Central Article Google Scholar

Golicz, A. A., Batley, J. & Edwards, D. Towards plant pangenomics. Plant Biotechnol. J. 14, 10991105 (2016).

PubMed Article Google Scholar

Golicz, A. A., Bayer, P. E., Bhalla, P. L., Batley, J. & Edwards, D. Pangenomics comes of age: from bacteria to plant and animal applications. Trends Plant Sci. 36, 132145 (2020).

CAS Google Scholar

Gao, L. et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 51, 10441051 (2019).

CAS PubMed Article Google Scholar

Dolezel, J. & Greilhuber, J. Nuclear genome size: are we getting closer? Cytometry A 77, 635642 (2010).

PubMed Article CAS Google Scholar

Smkal, P. et al. Pea (Pisum sativum L.) in the genomic era. Agronomy 2, 74115 (2012).

Article Google Scholar

Tayeh, N. et al. Genomic tools in pea breeding programs: status and perspectives. Front. Plant Sci. 6, 1037 (2015).

PubMed PubMed Central Google Scholar

Guillon, F. & Champ, M. M. Carbohydrate fractions of legumes: uses in human nutrition and potential for health. Br. J. Nutr. 88, S293S306 (2002).

CAS PubMed Article Google Scholar

Dahl, W. J., Foster, L. M. & Tyler, R. T. Review of the health benefits of peas (Pisum sativum L.). Br. J. Nutr. 108, S3S10 (2012).

CAS PubMed Article Google Scholar

MacWilliam, S., Wismer, M. & Kulshreshtha, S. Life cycle and economic assessment of Western Canadian pulse systems: the inclusion of pulses in crop rotations. Agr. Syst. 123, 4353 (2014).

Article Google Scholar

Ellis, T. H., Hofer, J. M., Timmerman-Vaughan, G. M., Coyne, C. J. & Hellens, R. P. Mendel, 150 years on. Trends Plant Sci. 16, 590596 (2011).

CAS PubMed Article Google Scholar

Reid, J. B. & Ross, J. J. Mendels genes: toward a full molecular characterization. Genetics 189, 310 (2011).

CAS PubMed PubMed Central Article Google Scholar

Zohary, D. & Hopf, M. Domestication of pulses in the Old World: legumes were companions of wheat and barley when agriculture began in the Near East. Science 182, 887894 (1973).

CAS PubMed Article Google Scholar

Smkal, P. et al. Phylogeny, phylogeography and genetic diversity of the Pisum genus. Plant Genet. Resour. 9, 418 (2010).

Article Google Scholar

Smkal, P. et al. Legume crops phylogeny and genetic diversity for science and breeding. Crit. Rev. Plant Sci. 34, 43104 (2015).

Article Google Scholar

Kreplak, J. et al. A reference genome for pea provides insight into legume genome evolution. Nat. Genet. 51, 14111422 (2019).

CAS PubMed Article Google Scholar

Roberts, R. J., Carneiro, M. O. & Schatz, M. C. The advantages of SMRT sequencing. Genome Biol. 14, 405 (2013).

PubMed PubMed Central Article Google Scholar

Chaisson, M. J. P. et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 517, 608611 (2015).

CAS PubMed Article Google Scholar

Sun, X. et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat. Genet. 52, 14231432 (2020).

CAS PubMed PubMed Central Article Google Scholar

Tayeh, N. et al. Development of two major resources for pea genomics: the GenoPea 13.2K SNP array and a high-density, high-resolution consensus genetic map. Plant J. 84, 12571273 (2015).

CAS PubMed Article Google Scholar

Hufford, M. B. et al. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808811 (2012).

CAS PubMed PubMed Central Article Google Scholar

Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393402 (2010).

CAS PubMed PubMed Central Article Google Scholar

Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C. & Martin, C. The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60, 115122 (1990).

CAS PubMed Article Google Scholar

Martin, D. N., Proebsting, W. M. & Hedden, P. Mendels dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins. Proc. Natl Acad. Sci. USA 94, 89078911 (1997).

CAS PubMed PubMed Central Article Google Scholar

Powers, S. E. & Thavarajah, D. Checking agricultures pulse: field pea (Pisum sativum L.), sustainability, and phosphorus use efficiency. Front. Plant Sci. 10, 1489 (2019).

PubMed PubMed Central Article Google Scholar

Coyne, C. J. et al. Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement. Legume Sci. 2, e36 (2020).

Article Google Scholar

Smkal, P. et al. From Mendels discovery on pea to todays plant genetics and breeding. Theor. Appl. Genet. 129, 22672280 (2016).

PubMed Article CAS Google Scholar

Ye, C. Y. & Fan, L. Orphan crops and their wild relatives in the genomic era. Mol. Plant 14, 2739 (2021).

CAS PubMed Article Google Scholar

Morrell, P. L., Buckler, E. S. & Ross-Ibarra, J. Crop genomics: advances and applications. Nat. Rev. Genet. 13, 8596 (2012).

CAS Article Google Scholar

Pandey, A. K. et al. Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.). Theor. Appl. Genet. 134, 755776 (2021).

PubMed Article Google Scholar

Zong, X. X. et al. Analysis of a diverse global Pisum sp collection and comparison to a Chinese local P. sativum collection with microsatellite markers. Theor. Appl. Genet. 118, 193204 (2009).

CAS PubMed Article Google Scholar

Liu, R. et al. Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers. J. Syst. Evol. 60, 85100 (2022).

Article Google Scholar

Read more from the original source:
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics - Nature.com

Highlights include: a memorandum of understanding with Memorial Sloan Kettering Cancer Center and a novel new partnership with Boundless Bio, a next-generation precision oncology company

SOPHiA GENETICS next-generation solution CarePath, fueled by current real world observational data, was previewed for attendees

BOSTON and GENEVA, Switzerland, Sept. 21, 2022 (GLOBE NEWSWIRE) -- SOPHiA GENETICS (Nasdaq: SOPH), a cloud-native software company in the healthcare space, hosted its first-ever Investor Day on Tuesday, September 20, 2022, in New York City.

The event, hosted by the CEO and Co-Founder Dr. Jurgi Camblong and members of the executive leadership team, provided a roadmap of the Companys long-term vision and highlighted new commercial opportunities and partnerships. One takeaway from the event was SOPHiA GENETICS acceleration into the Biopharma space, which opens the door for new opportunities for market growth. The audience also heard how the Companys strategic business model allows for it to continue to provide robust depth in the clinical space.

A key theme throughout the day was how we innovate; how SOPHiA GENETICS, from its inception, has identified opportunities in the healthcare industry for innovation and acceleration of data sharing to advance medicine, research and patient care, said Jurgi Camblong, CEO and Co-Founder, SOPHiA GENETICS. Our vision is made possible by the strong foundation our company has been built on, as well as the strategic relationships we have formed to further our mission of democratizing data-driven medicine.

New Collaboration with One of the Top-Ranked Cancer Centers in the United StatesSOPHiA GENETICS recently announced a memorandum of understanding to enter into a collaboration with Memorial Sloan Kettering Cancer Center (MSK). Once executed, the collaboration agreements will blend the power of SOPHiA GENETICS large, global network and deep expertise in predictive algorithms with MSKs clinical expertise in cancer genomics. The collaboration agreements will also allow SOPHiA GENETICS global network of healthcare providers access to MSKs proprietary tumor sequencing tests such as MSK-IMPACT, for analyzing tumors. Additionally, the collaboration agreements will combine MSKs rich precision oncology data with the SOPHiA CarePathmodule to enable the acceleration of actionable insights from data to improve patient outcomes.

Our vision is to expand access to world-class data, including to our current network, which contributes to the collective intelligence of the SOPHiA GENETICS platform, said Philippe Menu, M.D.-Ph.D., Chief Medical Officer, SOPHiA GENETICS.

Enabling Biotech Developing Novel Cancer Therapies Targeting Oncogene AmplificationSOPHiA GENETICS announced a partnership with Boundless Bio, a next-generation precision oncology company developing innovative therapeutics directed against extrachromosomal DNA (ecDNA) in oncogene amplified cancers.

It has been well established that patients with oncogene amplification generally do not benefit from standard of care cancer treatments, and unlike other forms of oncogenic gene alterations, oncogene amplification frequently occurs on ecDNA. ecDNA are circular units of nuclear DNA that are distinct from normal chromosomes and are the primary site for high copy number amplification in cancer. Boundless Bio is developing the first ecDNA-directed therapies (ecDTx) along with a precision diagnostic method called ECHO (ecDNA Harboring Oncogenes) to detect ecDNA from a patients routine tumor sequencing data.

The partnership between Boundless Bio and SOPHiA GENETICS will further develop ECHO for use in ecDTx clinical trials.

SOPHiA GENETICS unique ability to harmonize data derived from diverse genomic instruments and deploy as a robust, standardized solution enables a new model for clinical trial testing. This decentralized, global genomic solution combined with Boundless Bios ecDTx drug development capabilities aims to unlock value by breaking the barriers inherent to the traditional central lab approach; optimizing patient selection and clinical trial design; and enabling a global collective network of major hospitals and academic centers to effectively deliver new treatment options to patients with oncogene amplified cancers.

We are pleased to partner with SOPHiA GENETICS for the development of Boundless Bios ecDNA detection algorithm, ECHO, into a clinical trial device, said Peter Krein, Ph.D., Vice President of Precision Medicine at Boundless Bio. The ability to identify patients with ecDNA driven tumors is critical to our mission in addressing this area of high unmet medical need. SOPHiA GENETICS unique expertise in developing cloud based IVD NGS software algorithms makes them an ideal partner to develop ECHO into an investigational device.

DEEP-Lung-IV Multimodal Clinical Study Fuels New SOPHiA Carepath PlatformIn late 2021, SOPHiA GENETICS launched a DEEP-Lung-IV Multimodal Clinical Study with the goal of aggregating real-world multimodal (genomic, clinical, biological and radiomic) data for patients with metastatic non-small cell lung cancer. The study has garnered interest from top-tier centers globally, with a strong patient recruitment trend; to-date, nearly 900 patients across 23 sites have been enrolled in the study. As patients have been followed along the patient journey, data sets have been collected and analyzed by SOPHiA GENETICS machine learning algorithm to predict how the patients will respond to immunotherapy and why.

These robust and growing patient data will inform SOPHiA GENETICS artificial intelligence and machine learning that will fuel the forthcoming SOPHiA CarePathmodule, a new product that will be launched on the SOPHiA DDM Platform and aims to be the vehicle healthcare practitioners can use to leverage the real-world, real-time insights obtained from this study. The SOPHiA CarePathmodule will provide the following benefits:

Alongside these announcements, a full recording of the event is available on theInvestor Relationspage of the companys website.

About SOPHiA GENETICSSOPHiA GENETICS (Nasdaq: SOPH) is a software company dedicated to establishing the practice of data-driven medicine as the standard of care and for life sciences research. It is the creator of the SOPHiA DDM Platform, a cloud-native platform capable of analyzing data and generating insights from complex multimodal data sets and different diagnostic modalities. The SOPHiA DDM Platform and related solutions, products and services are currently used by a broad network of hospital, laboratory, and biopharma institutions globally. For more information, visitSOPHiAGENETICS.COM, or connect onTwitter,LinkedIn, Facebook, andInstagram.Where others see data, we see answers

SOPHiA GENETICS products are for Research Use Only and not for use in diagnostic procedures, unless specified otherwise. The information in this press release is about products that may or may not be available in different countries and, if applicable, may or may not have received approval or market clearance by a governmental regulatory body for different indications for use. Please contact support@sophiagenetics.com to obtain the appropriate product information for your country of residence.

SOPHiA GENETICS Forward-Looking Statements:This press release contains statements that constitute forward-looking statements. All statements other than statements of historical facts contained in this press release, including statements regarding our future results of operations and financial position, business strategy, products and technology, as well as plans and objectives of management for future operations, are forward-looking statements. Forward-looking statements are based on our managements beliefs and assumptions and on information currently available to our management. Such statements are subject to risks and uncertainties, and actual results may differ materially from those expressed or implied in the forward-looking statements due to various factors, including those described in our filings with the U.S. Securities and Exchange Commission. No assurance can be given that such future results will be achieved. Such forward-looking statements contained in this press release speak only as of the date hereof. We expressly disclaim any obligation or undertaking to update these forward-looking statements contained in this press release to reflect any change in our expectations or any change in events, conditions, or circumstances on which such statements are based, unless required to do so by applicable law. No representations or warranties (expressed or implied) are made about the accuracy of any such forward-looking statements.

Media Contact:Kelly KatapodisSenior Manager, Media & Communicationsmedia@sophiagenetics.com

Investor Contact:Jennifer PottageHead of Investor Relationsir@sophiagenetics.com

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SOPHiA GENETICS Unveils Strategy to Drive Health Care Innovations at Inaugural Investor Day Event - GlobeNewswire

September 19, 2022

Contact:Thonnia Lee, Office of Communications, Public Relations and Marketing

Researchers at Tuskegee University have discovered specific genetic variants found in prostate tumors of men of African descent were associated with African ancestry, according to two studies led by Dr. Clayton Yates, professor of biology and director of the university's multidisciplinary Center for Biomedical Research and graduate student Isra Elhussin.

Both studies supported by the United States Department of Defense and the National Cancer Institute of the National Institutes of Health highlight the contributions of African ancestry to prostate cancer genetics and provide a resource for addressing cancer health disparities. The studies were presented during the 15th AACR Conference on the Science of Cancer Health Disparities in Racial and Ethnic Minorities and the Medically Underserved held in Philadelphia, Pennsylvania.

Inherited Genetic Factors

"In the United States, Black men have the highest rate of prostate cancer-related mortality. Most studies examining disparities focus on race, typically self-reported and defined by skin color and social and cultural traits," said Dr. Yates, who also serves as the senior author on both studies, and chair of the AACR Minorities in Cancer Research Council.

Dr. Yates said addressing health disparities requires understanding genetic ancestry's contributions to tumor biology. Insights into genetic ancestry could aid precision medicine efforts by uncovering potential therapeutic targets specific to patients with African ancestry.

In the first study, Isra Elhussin, an AACR NextGen Star, examined the impact of African ancestry on the expression of immune inflammation gene signatures associated with higher immunogenicity and aggressive prostate cancers in men of African descent. Elhussin and other project colleagues reported that prostate tumors from African American men had a twofold greater activation of inflammatory signaling, which may contribute to the more aggressive disease typically observed in these patients.

"Cancer is one of the primary leading causes of death in the Black community. Access to healthcare, socioeconomic status, and genetic ancestry are directly correlated to survival disparities," said Elhussin. "The underrepresentation of Black patients in genomic studies and clinical trials precisely impacts their benefits of personalized medicine."

" Our research highlights the need for diversity in cancer research, filling the gap and building trust with our Black community," said Elhussin. "We are focusing on strategies that could help with disease prevention and therapeutic intervention by linking cancer genes back to their Ancestral origin and stratifying Ancestry-specific markers that affect patients' outcomes and their response to targeted therapy."

Investigating the possibilityElhussin and colleagues sequenced prostate tumors from 72 patients in the United States who had not undergone cancer treatment to determine the role of African ancestry in prostate cancer. Using reference databases, Elhussin determined that most of the patients who identified as African American had genetic markers consistent with men of African descent.

"We are the first to demonstrate that African genetic ancestry is associated with SPOP mutation, which leads to higher immunogenicity, upregulation of an immune inflammation signature, and higher tumor infiltration of immune cells expressing exhaustion markers, providing a potential mechanism for the higher prostate cancer-related mortality among men with African ancestry," said Elhussin. "These findings have implications for treating prostate cancers and could lead to new therapeutic strategies using anti-inflammatory drugs and immune modulators to decrease the disease burden among men of African descent."

"This is an exciting discovery that may help identify patients who would benefit from immunotherapy, which is particularly important given that African Americans are often underrepresented in clinical trials evaluating such therapies," noted Yates.

The second study was published in the American Association for Cancer Research (AACR) in the journal Cancer Research Communities; Yates, alongside colleague Jason White, MS, compared DNA sequences from Nigerian, African American, and European American prostate tumor patients. The study was completed in collaboration with the Prostate Cancer Transatlantic Consortium (CaPTC).

"Our goal was to understand the genomic contributions to prostate cancer among Nigerian men, something that had never been studied before," said Dr. Yates. "We performed sequencing to determine if there were unique mutations associated with the Nigerian population that was distinct from those in tumors from African Americans or European Americans, as well as to identify any similarities across these populations."

The research found that genetic variants were similar between the Nigerian and African American prostate tumors, with specific variants in particular genes.

2022 Tuskegee University

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TU Researchers connect genetic ancestry with prostate tumors - Tuskegee University

Adema CM, Bayne CJ, Bridger JM, Knight M, Loker ES, Yoshino TP, et al. Will all scientists working on snails and the diseases they transmit please stand up? PLoS Negl Trop Dis. 2012;6:56.

Article Google Scholar

Brown DS, Shaw KM. Freshwater snails of the Bulinus truncatus/tropicus complex in Kenya: tetraploid species. J Molluscan Stud. 1989;55:50932.

Article Google Scholar

Jorgensen A, Madsen H, Nalugwa A, Nyakaana S, Rollinson D, Stothard JR, et al. A molecular phylogenetic analysis of Bulinus (Gastropoda: Planorbidae) with conserved nuclear genes. Zool Scr. 2011;40:12636.

Article Google Scholar

Jrgensen A, Jrgensen LVG, Kristensen TK, Madsen H, Stothard JR. Molecular phylogenetic investigations of Bulinus (Gastropoda: Planorbidae) in Lake Malawi with comments on the topological incongruence between DNA loci. Zool Scr. 2007;36:57785.

Article Google Scholar

Brown D. Freshwater snails of Africa and their medical importance. Boca Raton: Taylor & Francis; 1994.

Book Google Scholar

Cowie RH, Dillon RT, Robinson DG, Smith JW. Alien non-marine snails and slugs of priority quarantine importance in the United States: a preliminary risk assessment. Am Malacol Bull. 2009;27:11332.

Article Google Scholar

Maes T, Hammoud C, Volckaert FAM, Huyse T. A call for standardised snail ecological studies to support schistosomiasis risk assessment and snail control efforts. Hydrobiologia. 2021;848:177393.

Article Google Scholar

Najarian HH. Biological studies on the snail, Bulinus truncatus, in central Iraq. Bull World Health Organ. 1961;25:43546.

CAS PubMed PubMed Central Google Scholar

Watson JM. Ecology and distribution of Bulinus truncatus in the Middle East; with comments on the effect of some human activities in their relationship to the snail host on the incidence of Bilharziasis haematobia in the Middle East and Africa. Bull World Health Organ. 1958;18:83394.

CAS PubMed PubMed Central Google Scholar

Picquet M, Ernould JC, Vercruysse J, Southgate VR, Mbaye A, Sambou B, et al. The epidemiology of human schistosomiasis in the Senegal river basin. Trans R Soc Trop Med Hyg. 1990;90:3406.

Article Google Scholar

Abdel-Wahab MF, Yosery A, Narooz S, Esmat G, El Hak S, Nasif S, et al. Is Schistosoma mansoni replacing Schistosoma haematobium in the Fayoum? Am J Trop Med Hyg. 1993;49:697700.

CAS PubMed Article Google Scholar

Barakat R, El Morshedy H, Farghaly A. Human schistosomiasis in the Middle East and North Africa region. In: Mary AM, Sima R, editors. Neglected tropical diseasesMiddle East and North Africa. Neglected tropical diseases series. Vienna: Springer; 2014. p. 2357.

Hotez PJ, Savioli L, Fenwick A. Neglected tropical diseases of the Middle East and North Africa: review of their prevalence, distribution, and opportunities for control. PLoS Negl Trop Dis. 2012;6:1475.

Article Google Scholar

Stensgaard AS, Vounatsou P, Sengupta ME, Utzinger J. Schistosomes, snails and climate change: current trends and future expectations. Acta Trop. 2019;190:25768.

PubMed Article Google Scholar

Boissier J, Grech-Angelini S, Webster BL, Allienne J-F, Huyse T, Mas-Coma S, et al. Outbreak of urogenital schistosomiasis in Corsica (France): an epidemiological case study. Lancet Infect Dis. 2016;16:9719.

PubMed Article Google Scholar

Githeko A, Lindsay S, Confalonieri U, Patz J. Climate change and vector-borne diseases: a regional analysis. Bull World Health Organ. 2000;78:113647.

CAS PubMed PubMed Central Google Scholar

Berry A, Mon H, Iriart X, Mouahid G, Aboo O, Boissier J, et al. Schistosomiasis haematobium, Corsica. Fr Emerg Infect Dis. 2014;20:15957.

Article Google Scholar

Martnez-Ort A, Vilavella D, Bargues MD, Mas-Coma S. Risk map of transmission of urogenital schistosomiasis by Bulinus truncatus (Audouin, 1827) (Mollusca Gastropoda, Bulinidae) in Spain and Portugal. Anim Biodivers Conserv. 2019;42:25766.

Article Google Scholar

Mulero S, Rey O, Arancibia N, Mas-Coma S, Boissier J. Persistent establishment of a tropical disease in Europe: the preadaptation of schistosomes to overwinter. Parasit Vectors. 2019;12:379.

PubMed PubMed Central Article Google Scholar

Stensgaard A-S, Booth M, Nikulin G, McCreesh N. Combining process-based and correlative models improves predictions of climate change effects on Schistosoma mansoni transmission in eastern Africa. Geospat Health. 2016;11:406.

PubMed Article Google Scholar

Coustau C, Gourbal B, Duval D, Yoshino TP, Adema CM, Mitta G. Advances in gastropod immunity from the study of the interaction between the snail Biomphalaria glabrata and its parasites: a review of research progress over the last decade. Fish Shellfish Immunol. 2015;46:516.

CAS Article Google Scholar

Rollinson D, Webster JP, Webster B, Nyakaana S, Jrgensen A, Stothard JR. Genetic diversity of schistosomes and snails: implications for control. Parasitology. 2009;136:180111.

CAS PubMed Article Google Scholar

Gow JL, Noble LR, Rollinson D, Tchuent LAT, Jones CS. Contrasting temporal dynamics and spatial patterns of population genetic structure correlate with differences in demography and habitat between two closely-related African freshwater snails. Biol J Linn Soc. 2007;90:74760.

Article Google Scholar

Gow JL, Noble LR, Rollinson D, Mimpfoundi R, Jones CS. Breeding system and demography shape population genetic structure across ecological and climatic zones in the African freshwater snail, Bulinus forskalii (Gastropoda, Pulmonata), intermediate host for schistosomes. Mol Ecol. 2004;13:356173.

CAS PubMed Article Google Scholar

Jarne P, Thron A. Genetic structure in natural populations of flukes and snails: a practical approach and review. Parasitology. 2001;123:2740.

Article Google Scholar

Adema CM, Hillier LDW, Jones CS, Loker ES, Knight M, Minx P, et al. Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Nat Commun. 2017;8:112.

Article CAS Google Scholar

Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE. 2011;6:110.

Article CAS Google Scholar

Hebert PDN, Cywinska A, Ball SL, DeWaard JR. Biological identifications through DNA barcodes. Proc R Soc B Biol Sci. 2003;270:31321.

CAS Article Google Scholar

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 1994;3:2949.

CAS PubMed Google Scholar

Kane RA, Stothard JR, Emery AM, Rollinson D. Molecular characterization of freshwater snails in the genus Bulinus: a role for barcodes? Parasit Vectors. 2008;1:15.

PubMed PubMed Central Article CAS Google Scholar

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28:16479.

PubMed PubMed Central Article Google Scholar

Sonet G, Jordaens K, Nagy ZT, Breman FC, De Meyer M, Backeljau T, et al. Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification. Zookeys. 2013;365:32935.

Article Google Scholar

Meier R, Shiyang K, Vaidya G, Ng PKL. DNA barcoding and taxonomy in diptera: a tale of high intraspecific variability and low identification success. Syst Biol. 2006;55:71528.

PubMed Article Google Scholar

Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:11120.

CAS PubMed Article Google Scholar

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:27259.

CAS PubMed PubMed Central Article Google Scholar

Boon NAM, Mbow M, Paredis L, Moris P, Sy I, Maes T, et al. No barrier breakdown between human and cattle schistosome species in the Senegal River Basin in the face of hybridisation. Int J Parasitol. 2019;49:103948.

CAS PubMed Article Google Scholar

Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. Stacks: building and genotyping loci de novo from short-read sequences. G3 Genes Genomes Genet. 2011;1:17182.

CAS Google Scholar

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27:21568.

CAS PubMed PubMed Central Article Google Scholar

Keenan K, McGinnity P, Cross TF, Crozier WW. Diversity: an R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol Evol. 2013;4:7828.

Article Google Scholar

Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under linux and windows. Mol Ecol Resour. 2010;10:5647.

PubMed Article Google Scholar

Guo SW, Thompson EA. Performing the exact test of HardyWeinberg proportion for multiple alleles. Biometrics. 1992;48:361.

CAS PubMed Article Google Scholar

Wright S. Coefficients of inbreeding and relationship. Am Nat. 1922;56:3308.

Article Google Scholar

Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38:135870.

CAS PubMed Google Scholar

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289300.

Google Scholar

Jombart T, Devillard S, Dufour A-B, Pontier D. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity. 2008;101:92103.

CAS PubMed Article Google Scholar

Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:94559.

CAS PubMed PubMed Central Article Google Scholar

Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol. 2005;14:261120.

CAS PubMed Article Google Scholar

Earl DA, VonHoldt BM. Structure harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Resour. 2012;4:35961.

Article Google Scholar

Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007;23:18016.

CAS PubMed Article Google Scholar

Rosenberg NA. Distruct a program for the graphical display of population structure. Mol Ecol Notes. 2004;4:1378.

Article Google Scholar

Smouse PE, Peakall R. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity. 1999;82:56173.

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Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia) -...

Direct-to-consumer home genetic kits allowed startups like 23andMe to offer health and ancestry insights at an affordable cost. Now, similar tech is coming to pets.

Itll help vets, breeders and pet parents to verify parentage and breed, diagnose diseases and plan for future health risks.

Everything we have seen happening in humans, in terms of predictive and personalised medicine and genetics-based diagnostics, has migrated into the pet space, says Sergey Jakimov, founding partner of LongeVC, a European VC fund that focuses on early-stage biotech and longevity. This is super exciting because pets, as living beings, have equalised themselves in importance in terms of how much money and attention is spent on their longevity, and in disease diagnostics and prevention.

Its not the first time human health innovation has come to the animal world US-based Signal Pet, for example, provides artificial intelligence-based radiology but animal genetics could be big business.

Animal genetics market revenue is predicted to exceed $6.4bn by 2027, up from $99m in 2020. Sifted dug into the sector and found the startups to watch and the VCs watching them.

Feragen, an Austria-based pet genetics startup, sees the vet sector as a growth engine for its business. It wants to move from diagnostics, where such tools are common, into disease prevention.

Puppies are more like family members

We want to push the prevention angle. What can we learn from genetics to create a life plan for a dog? says Anja Geretschlger, founder and CEO. Pet parents are becoming more interested in understanding the risk of diseases that might come when the pet is five or six, so they are more prepared when the symptoms show up.

Michael Geretschlger, Anjas husband and collaborator, says preventive health is getting more [attention] as puppies are more like family members. Anja Geretschlger adds that genetic insights are valuable for breeders in the era of designer dogs.

This is because cross-breeding can lead to health complications, such as labradoodles developing skin problems due to different fur structures between labradors and poodles.

Another European player is Germany-based Generatio, which provides genetic testing for animal owners, vets and breeders.

Theres also UK-based AffinityDNA, acquired in May by Australian diagnostics company Genetic Technologies, which provides animal testing for allergies and intolerances, paternity testing and direct-to-consumer (DTC) genetic tests from companies like Embark, Wisdom Panel and BasePaws.

Genetic Technologies portfolio includes General Genetics Corporation and associated brand EasyDNA, which offers UK pet owners breed composition tests, disease susceptibility tests for dogs, and feline and equine offerings.

European VCs are also interested in startups across the pond. Garri Zmudze, a Latvian biotech angel investor and founder of Switzerland-based LongeVC, investedin Basepaws, the American cat genetics company recently acquired by Zoetis, an animal medicines and vaccinations company.

Basepaws plans to expand into the veterinary portfolio of genetic, oral and microbiome screening tools for disease risk, screening 64 feline health markers and over 210 canine health markers.

For some, the pet genetics space is not just a play on the pet market but could inform human health and longevity science. Some diseases are rare in humans but are common in certain breeds of pets, who are useful for studies into genetic disease origins.

There is a tight connection between humans and animals and we can learn from both, says Anja Geretschlger.

Zmudzes investment in Basepaws, for instance, was not a pet consumer market bet at all. Instead it was aligned with his interest in human longevity, given the genetic overlaps between animals and humans in diseases like cancer and some neurodegenerative conditions.

There is a tight connection between humans and animals and we can learn from both

These overlaps are the reason we have animal models in clinical trials, because the metabolic processes are translatable, says Jakimov. There are tonnes of matches.

Matt Kaeberlein, professor of laboratory medicine and pathology at the University of Washington School of Medicine and head of the dog ageing project, a world-leading biological study of ageing in dogs, sits on the LongeVC advisory board, alongside executives from European pharmaceutical giants Roche and Novartis. And Zmudze was also an investor in Insilico Medicine, an AI drug discovery unicorn.

As home to many of the worlds top pharmaceutical companies, Europe could be a major player in longevity research. Switzerland is developing a Longevity Valley initiative, Bristol Myers Squibb and Merck are major investors in cancer immunotherapies and the pharma industry is investing in early stage longevity companies like senescent cells companies, through initiatives like Mercks early stage venture arm.

Pharmaceutical companies live in the future, they live in 10 to 20 year cycles, says Jakimov. They are super focused on the longevity sector.

This article first appeared in our monthly Unleashed pet tech newsletter, a collaboration with Purina Accelerator Lab. All content is editorially independent.Sign upto our newsletter here to keep up to date with the latest goings on in the European pet tech industry.

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Purrsonalised health: The startups and VCs betting on pet genetics - Sifted

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Mental illness is a growing public health problem. In 2019, an estimated 1 in 8 people around the world were affected by mental disorders like depression, schizophrenia or bipolar disorder.

While scientists have long known that many of these disorders run in families, their genetic basis isnt entirely clear. One reason why is that the majority of existing genetic data used in research is overwhelmingly from white people.

In 2003, the Human Genome Project generated the first reference genome of human DNA from a combination of samples donated by upstate New Yorkers, all of whom were of European ancestry.

Researchers across many biomedical fields still use this reference genome in their work. But it doesnt provide a complete picture of human genetics. Someone with a different genetic ancestry will have a number of variations in their DNA that arent captured by the reference sequence.

When most of the worlds ancestries are not represented in genomic data sets, studies wont be able to provide a true representation of how diseases manifest across all of humanity.

Despite this, ancestral diversity in genetic analyses hasnt improved in the two decades since the Human Genome Project announced its first results. As of June 2021, over 80 per centof genetic studies have been conducted on people of European descent. Less than two per cent have included people of African descent, even though these individuals have the most genetic variation of all human populations.

To uncover the genetic factors driving mental illness, I, Sinad Chapman and our colleagues at the Broad Institute of MIT and Harvard have partnered with collaborators around the world to launch Stanley Global, an initiative that seeks to collect a more diverse range of genetic samples from beyond the US and Northern Europe and train the next generation of researchers around the world.

Not only does the genetic data lack diversity, but so do the tools and techniques scientists use to sequence and analyse human genomes. So we are implementing a new sequencing technology that addresses the inadequacies of previous approaches that dont account for the genetic diversity of global populations.

To study the genetics of psychiatric conditions, researchers use data from genome-wide association studies that compare the genetic variations between people with and without a particular disease.

However, these data sets are mostly based on people of European ancestry, largely because research infrastructure and funding for large-scale genetics studies, and the scientists conducting these studies, have historically been concentrated in Europe and the United States.

One way to close this gap is to sequence genetic data from diverse populations. My colleagues and I are working in close partnership with geneticists, statisticians and epidemiologists in 14 countries across four continents to study the DNA of tens of thousands of people of African, Asian and Latino ancestries who are affected by mental illness.

We work together to recruit participants and collect DNA samples that are sequenced at the Broad Institute in Massachusetts and shared with all partners for analysis.

Prioritising the voices and priorities of local communities and scientists is foundational to our work. All partners have joint ownership of the project, including decision-making and sample and data ownership and control.

To do this, we build relationships and trust with the local communities we are studying and the local university leaders and scientists with whom we are partnering. We work to understand local cultures and practices, and adapt our collection methods to ensure study participants are comfortable.

For example, because there are different cultural sensitivities around providing saliva and blood samples, we have adapted our practices by location to ensure study participants are comfortable.

We also freely share knowledge and materials with our partners. There is a two-way exchange of information between the Broad Institute and local teams on study progress and results, enabling continual learning, teaching and unity between teams.

We strive to meet each other where we are by exchanging practices and training scientists to support the development of locally grown and locally led research programmes.

Our collaboration with African research groups provides a prime example of our model. For example, our African research colleagues are co-leaders on the grants that fund the lab equipment, scientists and other staff for projects based at their study sites. And we help to support the next generation of African geneticists and bioinformaticians through a dedicated training programme.

Analysing variation

Collecting samples from more diverse populations is only half of the challenge.

Existing genomic sequencing and analysis technologies do not adequately capture genetic variation across populations from around the world. Thats because these technologies were designed to detect genetic variations based on reference DNA from people of European ancestry, and they reduce accuracy when analysing sequences that arent derived from the reference genome.

When these tools are applied to genetic data from other populations, they fail to detect much of the rich variation in their genomes. This can lead researchers to miss out on important biomedical discoveries.

To address this issue, we developed an approach to genome sequencing that can detect more genetic variation from populations around the world. It works by sequencing the exome the less thantwo per cent of the genome that codes for proteins in high detail, as well as sequencing the 98 per cent of the genome that does not code for proteins in less detail.

This combined approach reduces the trade-offs geneticists often have to make in sequencing projects. High-depth whole genome sequencing, which reads through the entire genome multiple times to get detailed data, is too costly to do on a large number of DNA samples.

While low-coverage sequencing reduces costs by reading smaller segments of the genome, it may miss some important genetic variation. With our new technology, geneticists can get the best of both worlds: sequencing the exome in depth maximises the likelihood of pinpointing specific genes that play a role in mental illness, while sequencing the whole genome less in depth allows researchers to process large numbers of whole genomes more cost-effectively.

Personalising medicine

Our hope is that this new technology will allow researchers to sequence large sample sizes from a diverse range of ancestries to capture the full breadth of genetic variation. With a better understanding of the genetics of mental illness, clinicians and researchers will be better equipped to develop new treatments that work for everyone.

Genomic sequencing opened a new era of personalised medicine, which promises to deliver treatments tailored to each individual person. This can be done only if the genetic variations of all ancestries are represented in the data sets that researchers use to make new discoveries about disease and develop treatments.

Hailiang Huang, Assistant Professor of Medicine, Harvard University

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

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Uncovering the genetic basis of mental illness requires data and tools that aren't just based on white people - Down To Earth Magazine

At 44, Janet Waterhouse should have been the picture of health; a former Division I soccer player, she taught yoga, enjoyed running, and didnt drink alcohol. Despite her healthy and active lifestyle, over a span of decades she experienced a number of unexplained symptoms.

Her symptoms continued to worsen into her 20s when she began to sporadically lose function of her hands and experience severe bouts of vertigo. Most doctors attributed her symptoms to stress and anxiety. During this time, Waterhouse was seeing a pain management specialist, who was concerned enough about her worsening symptoms to run a blood test, where he found irregularly shaped blood cells, called acanthocytes.

A series of serendipitous referrals led Waterhouse to Ali Hamedani, an assistant professor of neurology and ophthalmology in the Perelman School of Medicine. Based on her symptoms and exam, he suspected a genetic condition called chronic progressive external ophthalmoplegia (CPEO) and referred her to Laynie Dratch, a certified genetic counselor in the Penn Neurogenetics Therapy Center, for genetic testing.

In May of 2022, Dratch gave Waterhouse what she had been chasing for decades: a diagnosis. When the genetic counselor told me they found the genetic mutation they were looking for, I cried for a solid five minutes out of relief, Waterhouse says.

Waterhouses case of CPEO was found to be caused by a variation on her RRM2B gene, which affects the mitochondria in her cells. While the condition is very rare and can sometimes take years to locate and diagnose, Hamedanis hunch about the gene mutation led them right to it.

Because little is known about CPEO, treatment options are limited. Most people would be discouraged by the uncertainty, she says, but it thrills me to get to be the blueprint. I get to show people how to live with this.

Launched in March 2020, the Penn Neurogenetics Therapy Center has a team of clinicians, nurses, genetic counselors, and clinical research staff who are devoted to the care of patients with inherited neurological disorders and to participating in clinical trials of novel gene and molecular therapies.

The programs mission is twofold: first, they utilize the expertise of clinicians and researchers throughout the department of Neurology and across Penn Medicine to achieve a genetic diagnosis for as many patients like Waterhouse as possible, creating a database of eligible patients for new treatments and clinical trials. Second, they work to establish clinical trials using novel gene and molecular therapies for patients with genetically-based neurological disorders.

Our genetics counselors are some of the best in the country, and are incredibly effective at diagnosing patients and matching them with effective treatments and clinical trials, says Steven Scherer, a professor of neurology and director of the Neurogenetics Therapy Center. Now we can utilize this expertise to design tomorrows therapies.

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Solving medical mysteries with genetics: The Penn Neurogenetics Therapy Center | Penn Today - Penn Today