Work on world’s first CRISPR gene-edited babies declared illegal by China

Chinese authorities have declared the work of He Jiankui, who shocked the scientific community by claiming he successfully created the world’s first gene-edited babies, an illegal decision in pursuit of “personal fame and gain.” Investigators have completed preliminary steps in a probe that began in November following He’s claims and say they will “seriously” punish the researcher […]

Chinese authorities have declared the work of He Jiankui, who shocked the scientific community by claiming he successfully created the world’s first gene-edited babies, an illegal decision in pursuit of “personal fame and gain.” Investigators have completed preliminary steps in a probe that began in November following He’s claims and say they will “seriously” punish the researcher for violations of the law, China’s official news agency Xinhua reported on Monday.

He, who taught at Shenzhen’s Southern University of Science and Technology, had led a team to research the gene-editing technique CRISPR since mid-2016 in attempts to treat cancers and other diseases. The incident drew significant attention to the professor’s own biotech startups that are backed by local and overseas investors.

The official probe shows that He fabricated ethics approvals which he used to recruit eight couples to participate in clinical procedures between March 2017 and November 2018. The attempt led to two pregnancies, including one that resulted in the birth of twins and the other embryo yet to be born. Five couples failed to achieve fertilization and one pair dropped out of the experiment.

He’s project has sparked a wave of criticism among scientists across the world. CRISPR is still dangerously unethical at this point for it may cause serious genetic damage. Some researchers have proposed a moratorium on CRISPR until more guidelines become clear while others call for developing safer and more ethical methods to propel the technology forward. Many countries, including the United States and China, prohibit gene-editing of human embryos for reproductive purposes.

Curious 23andMe twin results show why you should take DNA testing with a grain of salt

If you’ve ever enthusiastically sent your spit off in the mail, you were probably anxious for whatever unexpected insights the current crop of DNA testing companies would send back. Did your ancestors hang out on the Iberian peninsula? What version of your particular family lore does the science support? Most people who participate in mail-order […]

If you’ve ever enthusiastically sent your spit off in the mail, you were probably anxious for whatever unexpected insights the current crop of DNA testing companies would send back. Did your ancestors hang out on the Iberian peninsula? What version of your particular family lore does the science support?

Most people who participate in mail-order DNA testing don’t think to question the science behind the results — it’s science after all. But because DNA testing companies lack aggressive oversight and play their algorithms close to the chest, the gems of genealogical insight users hope to glean can be more impressionistic than most of these companies let on.

To that point, Charlsie Agro, host of CBC’s Marketplace, and her twin sister sent for DNA test kits from five companies: 23andMe, AncestryDNA, MyHeritage, FamilyTreeDNA and Living DNA.

As CBC reports, “Despite having virtually identical DNA, the twins did not receive matching results from any of the companies.” That bit shouldn’t come as a surprise. Each company uses its own special sauce to analyze DNA so it’s natural that there would be differences. For example one company, FamilyTreeDNA, attributed 14% of the twins’ DNA to the Middle East, unlike the other four sets of results.

Beyond that, most results were pretty predictable — but things got a bit weird with the 23andMe data.

As CBC reports:

“According to 23andMe’s findings, Charlsie has nearly 10 per cent less “broadly European” ancestry than Carly. She also has French and German ancestry (2.6 per cent) that her sister doesn’t share.

The identical twins also apparently have different degrees of Eastern European heritage — 28 per cent for Charlsie compared to 24.7 per cent for Carly. And while Carly’s Eastern European ancestry was linked to Poland, the country was listed as “not detected” in Charlsie’s results.”

The twins shared their DNA with a computational biology group at Yale which verified that the DNA they sent off was statistically pretty much identical. When questioned for the story, 23andMe noted that its analyses are “statistical estimates” — a phrase that customers should bear in mind.

It’s worth remembering that the study isn’t proper science. With no control group and an n (sample size) of one set of twins, nothing definitive can be gleaned here. But it certainly raises some interesting questions.

Twin studies have played a vital role in scientific research for ages. Often, twin studies allow researchers to explore the effects of biology against those of the environment across any number of traits — addiction, mental illness, heart disease, and so on. In the case of companies like 23andMe, twin studies could shed a bit of light on the secret algorithms that drive user insights and revenue.

Beyond analyzing the cold hard facts of your DNA, companies like 23andMe attract users with promises of “reports” on everything from genetic health risks to obscure geographic corners of a family tree. Most users don’t care about the raw data — they’re after the fluffier, qualitative stuff. The qualitative reporting is where companies can riff a bit, providing a DNA-based “personal wellness coach” or advice about whether you’re meant to be a morning person or a night owl.

Given the way these DNA services work, their ancestry results are surprisingly malleable over time. As 23andMe notes, “because these results reflect the ancestries of individuals currently in our reference database, expect to see your results change over time as that database grows.” As many non-white DNA testing customers have found, many results aren’t nearly as dialed in for anyone with most of their roots beyond Europe. Over time, as more people of color participate, the pool of relevant DNA grows.

Again, the CBC’s casual experiment is by no means definitive science — but neither are DNA testing services. For anyone waiting with bated breath for their test results, remember that there’s still a lot we don’t know about how these companies come to their conclusions. Given the considerable privacy trade-off in handing your genetic material over to big pharma through a for-profit intermediary, it’s just some food for thought.

Driving down the cost of preserving genetic material, Acorn Biolabs raises $3.3 million

Acorn Biolabs wants consumers to pay them to store genetic material in a bet that the increasing advances in targeted genetic therapies will yield better healthcare results down the line. The company’s pitch is to “Save young cells today, live a longer, better, tomorrow.” It’s a gamble on the frontiers of healthcare technology that has managed […]

Acorn Biolabs wants consumers to pay them to store genetic material in a bet that the increasing advances in targeted genetic therapies will yield better healthcare results down the line.

The company’s pitch is to “Save young cells today, live a longer, better, tomorrow.” It’s a gamble on the frontiers of healthcare technology that has managed to net the company $3.3 million in seed financing from some of Canada’s busiest investors.

For the Toronto-based company, the pitch isn’t just around banking genetic material — a practice that’s been around for years — it’s about making that process cheaper and easier.

Acorn has come up with a way to collect and preserve the genetic material contained in hair follicles, giving its customers a way to collect full-genome information at home rather than having to come in to a facility and getting bone marrow drawn (the practice at one of its competitors, Forever Labs) .

“We have developed a proprietary media that cells are submerged in that maintains the viability of those cells as they’re being transported to our labs for processing,” says Acorn Biolabs chief executive Dr. Drew Taylor.

“Rapid advancements in the therapeutic use of cells, including the ability to grow human tissue sections, cartilage, artificial skin and stem cells, are already being delivered. Entire heart, liver and kidneys are really just around the corner. The urgency around collecting, preserving and banking youthful cells for future use is real and freezing the clock on your cells will ensure you can leverage them later when you need them,” Taylor said in a statement.

Typically, the cost of banking a full genome test is roughly $2,000 to $3,000 and Acorn says they can drop that cost to less than $1,000. Beyond the cost of taking the sample and storing it, Acorn says it will reduce the fees to store such genetic materials to roughly $100 a year.

It’s important to note that Healthcare doesn’t cover any of this. It’s a voluntary service for those neurotic enough or concerned enough about the future of healthcare and their potential health. 

There’s also no services that Acorn will provide on the back end of the storage… yet.

What people do need to realize is that there is power with that data that can improve healthcare. Down the road we will be able to use that data to help people collect that data and power studies,” says Taylor. 

The $3.3 million that the company raised came from Real Ventures, Globalive Technology, Pool Global Partners and Epic Capital Management and other undisclosed investors.

“Until now, any live cell collection solutions have been highly expensive, invasive and often painful, as well as being geographically limited to specialized clinics,” said Anthony Lacavera, Founder and Chairman at Globalive.  “Acorn is an industry-leading example of how technology can bring real innovation to enable future healthcare solutions that will have meaningful impact on people’s wellbeing and longevity, while at the same time – make it easy, affordable and frictionless for everyone.”

 

Up to $818 million deal between J&J and Locus Biosciences points to a new path for CRISPR therapies

The up to $818 million deal between Locus Biosciences and Janssen Pharmaceuticals (a division of Johnson & Johnson) that was announced yesterday points toward a new path for CRISPR gene editing technologies and (potentially) the whole field of microbiome-targeted therapies. Based in Research Triangle Park, N.C., Locus is commercializing research initially developed by scientists at […]

The up to $818 million deal between Locus Biosciences and Janssen Pharmaceuticals (a division of Johnson & Johnson) that was announced yesterday points toward a new path for CRISPR gene editing technologies and (potentially) the whole field of microbiome-targeted therapies.

Based in Research Triangle Park, N.C., Locus is commercializing research initially developed by scientists at North Carolina State University that focused on Cas3 proteins, which devour DNA Pac-Man-style, rather than edit it like the more well-known Cas9-based CRISPR technologies being used by companies like Caribou Biosciences, Editas Medicine, Synthego, Intellia Therapeutics, CRISPR Therapeutics and Beam Therapeutics.

While the Cas9 CRISPR technologies can edit targeted DNA — either deleting specific genetic material or replacing it with different genetic code — Cas3 simply removes DNA strains. “Its purpose is the destruction of invading DNA,” says Locus chief executive, Paul Garofolo.

The exclusive deal between Janssen Pharmaceuticals and Locus gives Janssen the exclusive license to develop, manufacture and commercialize CRISPR-Cas3-enhanced products targeting bacterial pathogens for the potential treatment of respiratory and other organ infections.

Under the terms of the deal, Locus is getting $20 million in upfront payments and could receive up to $798 million in potential future development and commercial milestone payments and any royalties on potential product sales.

A former executive at Valiant Pharmaceuticals and Paytheon, Garofolo was first introduced to the technology that would form the core of Locus as an executive in residence at North Carolina State University. It was there that he met Dr. Chase Beisel and Rodolphe Barrangou, whose research into Cas3 proteins would eventually be productized by Locus.

The company spun out of NC State in 2015 and raised its first cash from the North Carolina Biotech Center a year later.

Locus is already commercializing a version of its technology with bacteriophages designed to target e coli bacteria to treat urinary tract infections. The company is on target to begin its first clinical trials in the third quarter of the year.

The focus on bacterial infection and removing harmful bacteria while ensuring that the rest of a patient’s microbiome is intact is a huge step forward for treating diseases that scientists believe could be linked to bacterial health in a body, according to Garofolo.

“Most microbiome companies are about adding probiotics to your body,” says Garofolo, representing a thesis that introducing “good” bacteria to the body can offset any harmful pathogens that have infected it.

“Things you’re exposed to are creating the groundwork for an infection or disease, or exacerbating an existing disease,” says Garofolo. And while he believes that the microbiome is the next big field for scientific discovery, the approach of adding probiotics to a system seems less targeted and effective to him.

Already, Garofolo has managed to convince investors of his approach. In addition to the initial outside investment from the North Carolina Biotech Center, Locus has attracted $25 million in financing from investors, including Artis Ventures and the venture capital arm of the Chinese internet giant, Tencent.

Meanwhile, investors have spent millions backing alternative approaches to improving human health through the manipulation of the microbiome.

Companies like Second Genome, Viome and Ubiome are all using approaches that identify bacteria in the human body and try to regulate the production of that bacteria through diet and probiotic pills. It’s an approach that allows these companies to skirt the more stringent requirements the Food and Drug Administration has put in place for drugs.

That doesn’t mean that extensive amounts of research haven’t gone into the development of these probiotics. Seed, a Los Angeles-based startup that launched last year, has recruited as its chief scientist George Reid, the leading scientist on microbial health and the microbiome.

Founded by Raja Dhir, a graduate from the University of Southern California and a leading researcher on microbiotics in his own right, and Ara Katz, the former chief marketing officer of BeachMint and an MIT Media Lab fellow, Seed focuses on developing probiotic treatments using well-established research.

“Foundational to our approach is that it’s not which microbes are present in your gut… It’s based on looking at what specific microbes can do to a healthy individual to improve that status of health independent of what is already present,” Dhir said in an interview around the company’s launch last June. “It’s a little bit less exciting from a tech perspective, but it’s hardcore grounded in basic science… The question is, does this have changes and effects in validated bio-makers in a controlled and placebo setting?”

Dhir said that a basic understanding of how different bacteria can influence health is necessary before getting into the benefits of personalization.

These things can dance between drugs and nutrition,” Dhir said. “Probacteria are an additional lever that people should pull… like diet and exercise and cessation of smoking… In every correspondence we always have been and need to be clear that this should never be seen as a replacement of therapies.”

By contrast, the tools that Locus is developing are very much therapies with potentially far-reaching implications for illnesses, from irritable bowel syndrome to gastrointestinal cancers and even neurological disorders.

“The science [around the microbiome] is early, but it is very well-known that a potentially deadly pathogen should be removed from your body,” Garofolo said.

Up to $818 million deal between J&J and Locus Biosciences points to a new path for CRISPR therapies

The up to $818 million deal between Locus Biosciences and Janssen Pharmaceuticals (a division of Johnson & Johnson) that was announced yesterday points toward a new path for CRISPR gene editing technologies and (potentially) the whole field of microbiome-targeted therapies. Based in Research Triangle Park, N.C., Locus is commercializing research initially developed by scientists at […]

The up to $818 million deal between Locus Biosciences and Janssen Pharmaceuticals (a division of Johnson & Johnson) that was announced yesterday points toward a new path for CRISPR gene editing technologies and (potentially) the whole field of microbiome-targeted therapies.

Based in Research Triangle Park, N.C., Locus is commercializing research initially developed by scientists at North Carolina State University that focused on Cas3 proteins, which devour DNA Pac-Man-style, rather than edit it like the more well-known Cas9-based CRISPR technologies being used by companies like Caribou Biosciences, Editas Medicine, Synthego, Intellia Therapeutics, CRISPR Therapeutics and Beam Therapeutics.

While the Cas9 CRISPR technologies can edit targeted DNA — either deleting specific genetic material or replacing it with different genetic code — Cas3 simply removes DNA strains. “Its purpose is the destruction of invading DNA,” says Locus chief executive, Paul Garofolo.

The exclusive deal between Janssen Pharmaceuticals and Locus gives Janssen the exclusive license to develop, manufacture and commercialize CRISPR-Cas3-enhanced products targeting bacterial pathogens for the potential treatment of respiratory and other organ infections.

Under the terms of the deal, Locus is getting $20 million in upfront payments and could receive up to $798 million in potential future development and commercial milestone payments and any royalties on potential product sales.

A former executive at Valiant Pharmaceuticals and Paytheon, Garofolo was first introduced to the technology that would form the core of Locus as an executive in residence at North Carolina State University. It was there that he met Dr. Chase Beisel and Rodolphe Barrangou, whose research into Cas3 proteins would eventually be productized by Locus.

The company spun out of NC State in 2015 and raised its first cash from the North Carolina Biotech Center a year later.

Locus is already commercializing a version of its technology with bacteriophages designed to target e coli bacteria to treat urinary tract infections. The company is on target to begin its first clinical trials in the third quarter of the year.

The focus on bacterial infection and removing harmful bacteria while ensuring that the rest of a patient’s microbiome is intact is a huge step forward for treating diseases that scientists believe could be linked to bacterial health in a body, according to Garofolo.

“Most microbiome companies are about adding probiotics to your body,” says Garofolo, representing a thesis that introducing “good” bacteria to the body can offset any harmful pathogens that have infected it.

“Things you’re exposed to are creating the groundwork for an infection or disease, or exacerbating an existing disease,” says Garofolo. And while he believes that the microbiome is the next big field for scientific discovery, the approach of adding probiotics to a system seems less targeted and effective to him.

Already, Garofolo has managed to convince investors of his approach. In addition to the initial outside investment from the North Carolina Biotech Center, Locus has attracted $25 million in financing from investors, including Artis Ventures and the venture capital arm of the Chinese internet giant, Tencent.

Meanwhile, investors have spent millions backing alternative approaches to improving human health through the manipulation of the microbiome.

Companies like Second Genome, Viome and Ubiome are all using approaches that identify bacteria in the human body and try to regulate the production of that bacteria through diet and probiotic pills. It’s an approach that allows these companies to skirt the more stringent requirements the Food and Drug Administration has put in place for drugs.

That doesn’t mean that extensive amounts of research haven’t gone into the development of these probiotics. Seed, a Los Angeles-based startup that launched last year, has recruited as its chief scientist George Reid, the leading scientist on microbial health and the microbiome.

Founded by Raja Dhir, a graduate from the University of Southern California and a leading researcher on microbiotics in his own right, and Ara Katz, the former chief marketing officer of BeachMint and an MIT Media Lab fellow, Seed focuses on developing probiotic treatments using well-established research.

“Foundational to our approach is that it’s not which microbes are present in your gut… It’s based on looking at what specific microbes can do to a healthy individual to improve that status of health independent of what is already present,” Dhir said in an interview around the company’s launch last June. “It’s a little bit less exciting from a tech perspective, but it’s hardcore grounded in basic science… The question is, does this have changes and effects in validated bio-makers in a controlled and placebo setting?”

Dhir said that a basic understanding of how different bacteria can influence health is necessary before getting into the benefits of personalization.

These things can dance between drugs and nutrition,” Dhir said. “Probacteria are an additional lever that people should pull… like diet and exercise and cessation of smoking… In every correspondence we always have been and need to be clear that this should never be seen as a replacement of therapies.”

By contrast, the tools that Locus is developing are very much therapies with potentially far-reaching implications for illnesses, from irritable bowel syndrome to gastrointestinal cancers and even neurological disorders.

“The science [around the microbiome] is early, but it is very well-known that a potentially deadly pathogen should be removed from your body,” Garofolo said.

Sophia Genetics bags $77M Series E, with 850+ hospitals signed up to its “data-driven medicine”

Another sizeable cash injection for big data biotech: Sophia Genetics has announced a $77M Series E funding round, bringing its total raised to $140M since the business was founded back in 2011. The company, which applies AI to DNA sequencing to enable what it dubs “data-driven medicine”, last closed a $30M Series D in fall 2017. […]

Another sizeable cash injection for big data biotech: Sophia Genetics has announced a $77M Series E funding round, bringing its total raised to $140M since the business was founded back in 2011.

The company, which applies AI to DNA sequencing to enable what it dubs “data-driven medicine”, last closed a $30M Series D in fall 2017.

The Series E was led by Generation Investment Management . Also investing: European private equity firm, Idinvest Partners. Existing investors, including Balderton Capital and Alychlo, also participated in the round.

When we last spoke to Sophia Genetics it had around 350 hospitals linked via its SaaS platform, and was then adding around 10 new hospitals per month.

Now it says its Sophia AI platform is being used by more than 850 hospitals across 77 countries, and it claims to have supported the diagnosis of more than 300,000 patients.

The basic idea is to improve diagnoses by enabling closer collaboration and knowledge sharing between hospitals via the Sophia AI platform, with an initial focus on oncology, hereditary cancer, metabolic disorders, pediatrics and cardiology. 

Expert (human) insights across the network of hospital users are used to collectively enhance genomic diagnostics, and push towards predictive analysis, by feeding and training AI algorithms intended to enhance the reading and analysis of DNA sequencing data.

Sophia Genetics describes its approach as the “democratization” of DNA sequencing expertise.

Commenting on the Series E in a statement, Lilly Wollman, co-head of Generation’s growth equity team said: “We believe that leveraging genetic sequencing and advanced digital analysis will enable a more sustainable healthcare system. Sophia Genetics is a leader in the preventive and personalized medicine revolution, enabling the development of targeted therapeutics, thereby vastly improving health outcomes. We admire Sophia Genetics not just for its differentiated analytics capability across genomic and radiomic data, but also for its exceptional team and culture”.

The new funding will be put towards further expanding the number of hospitals using Sophia Genetics’ technology, and also on growing its headcount with a plan to ramp up hiring in the US especially.

The Swiss-founded firm is now co-based in Lausanne and Boston, US.

In another recent development the company added radiomics capabilities to its platform last year, allowing for what it describes as “a prediction of the evolution of a tumour”, which it suggests can help inform a physician’s choice of treatment for the patient.

Companies tracking mutations in cancer cells can provide a key to unlocking better therapies

Investors and entrepreneurs are beginning to bring new diagnostic tools to market that promise better results for cancer patients through the identification of mutations in cancer cells that can create more targeted therapies. Earlier this month, research using technology developed by the startup Mission Bio helped identify cellular mutations in acute myeloid leukemia cancer cells that could […]

Investors and entrepreneurs are beginning to bring new diagnostic tools to market that promise better results for cancer patients through the identification of mutations in cancer cells that can create more targeted therapies.

Earlier this month, research using technology developed by the startup Mission Bio helped identify cellular mutations in acute myeloid leukemia cancer cells that could be indicators of potential relapse or recurrence of the cancer after therapy.

In the study, which was presented at the American Society for Hematology’s recent conference, a team from the MD Anderson cancer research institute in Texas, including Dr. Koishi Takahashi, sequenced more than 500,000 cells across 70 patients using Mission Bio’s “Tapestri” platform.

“These results demonstrate the power of analyzing heterogeneity for the study and treatment of cancer patients,” said Dr. Takahashi, in a statement. “Tapestri’s ability to precisely identify cancer subclones throughout treatment and disease progression brings us closer to delivering on the promise of precision medicine.”

Increasingly, researchers are coming to the conclusion that genetic mutations of individual cancer cells can lead to the persistence of minimal residual disease and therapy resistance. Other leading cancer centers at  universities including the University of California, San Francisco, University of Pennsylvania, and Stanford University have also released papers on the viability of Mission Bio’s approach.

That research may help explain why Mission Bio was able to land $30 million in new funding from a slew of investors including Agilent Technologies, Cota Capital, LabCorp, LAM Capital, and Mayfield.

The company said it will use the cash to increase the work it’s doing in blood cancer research while expanding its business into the analysis of CRISPR applications and potential mutations that can occur through the use of that gene editing technology.

“Cancer will kill 10 million people this year alone. We can beat cancer with more effective, dynamic therapies, but we first need to precisely understand its biology, starting with the varying genetic composition of each and every cancerous cell,” explained Charlie Silver, CEO of Mission Bio. “Minimal residual disease is a major cause of cancer relapse; overlooking even one cell could put a life at risk. With the Tapestri Platform, we can track every cell, every mutation, to better guide treatments and save patient lives.”

That mutation tracking is also what brought Agilent on board as the company takes its initial steps into monitoring the intended and unintended consequences of using CRISPR technology to edit genes.

“The Tapestri platform’s unique quality control capabilities are strenghtening our CRISPR R&D programs,” remarked Darlene Solomon, Senior Vice President and Chief Technology Officer of Agilent Technologies. “Agilent’s commitment to innovation and precision medicine are well matched with Mission Bio’s Tapestri platform as it has the potential to improve patient outcomes in the fight against cancer — and that’s the most meaningful benchmark of all.”

Mission Bio isn’t the only company making strides when it comes to cancer treatments and new targeted monitoring technologies.

Cambridge Cancer Genomics is another startup company working on bringing new technologies to blood sample analysis that can better identify cancer and target personalized therapies for the disease.

The company has raised $4.5 million to build what it’s calling one of the largest datasets of longitudinal cancer in the world

Like Mission Bio, CCG is hoping that its data can help map the ways cancer cells evolve in response to treatments and suggest new therapies to doctors.

Financing the companies rollout are investors including AME Cloud Ventures, Refactor Capital, Romulus Capital and Y Combinator. Additional capital has come from the company’s early partner, the Comprehensive Blood and Cancer Center in Bakersfield, Calif. who invested not only cash but provided 4,000 clinical samples for CCG to analyze and develop their monitoring and predictive solution.

Both companies are trying to tackle the “one-size-fits-all” approach to cancer therapy that exists for most patients around the world.

First line cancer treatment fails two-thirds of all patients and the realization that treatments aren’t working can take up to six months to recognize. Like Mission Bio, CCG is also working to identify whether a patient is at risk of relapse — something the company claims it can do 7 months earlier than standard practices.

“When you drill down into the DNA changes behind cancer, you quickly find that no two tumors are the same. To apply cancer therapies more successfully to any given tumor, we need a deeper understanding of what exactly has gone wrong in each case at a molecular level,” says Dr. Harry Clifford, a co-founder and chief technology officer at Cambridge Cancer Genomics. “This starts with effective tools to capture that information. The approaches we’re developing at CCG will have widespread applications, from identifying targets for new therapy development, to deciding which personalized approach is best for a given patient.”

That echoes the thinking of companies like Mission Bio, and like Mission Bio, CCG has published results from recent trials of its technology.

The company applied its predictive technology to the outcome of different therapies in over 2,500 breast cancer patients and used its machine learning technology to identify the same kind of variants that Mission Bio is working to call out in an attempt to understand when and how relapses can occur.

 

1) Interlacing Personal and Reference Genomes for Machine Learning Disease-Variant Detection 

https://arxiv.org/abs/1811.11674

Summary: Differences in our DNA underlie many aspects of human health; from rare genetic diseases to cancer. In this paper, we build a new class of software for detecting DNA variants. Based on the same principles behind facial recognition, our technique can identify cancer variants with unparalleled accuracy. We hope that releasing this software for non-commercial use will lead to more successful targeted therapy and personalized cancer medicine. 

DeepMind claims early progress in AI-based predictive protein modelling

Google -owned AI specialist, DeepMind, has claimed a “significant milestone” in being able to demonstrate the usefulness of artificial intelligence to help with the complex task of predicting 3D structures of proteins based solely on their genetic sequence. Understanding protein structures is important in disease diagnosis and treatment, and could improve scientists’ understanding of the human […]

Google -owned AI specialist, DeepMind, has claimed a “significant milestone” in being able to demonstrate the usefulness of artificial intelligence to help with the complex task of predicting 3D structures of proteins based solely on their genetic sequence.

Understanding protein structures is important in disease diagnosis and treatment, and could improve scientists’ understanding of the human body — as well as potentially helping to support protein design and bioengineering.

Writing in a blog post about the project to use AI to predict how proteins fold — now two years in — it writes: “The 3D models of proteins that AlphaFold [DeepMind’s AI] generates are far more accurate than any that have come before — making significant progress on one of the core challenges in biology.”

There are various scientific methods for predicting the native 3D state of protein molecules (i.e. how the protein chain folds to arrive at the native state) from residual amino acids in DNA.

But modelling the 3D structure is a highly complex task, given how many permutations there can be on account of protein folding being dependent on factors such as interactions between amino acids.

There’s even a crowdsourced game (FoldIt) that tries to leverage human intuition to predict workable protein forms.

DeepMind says its approach rests upon years of prior research in using big data to try to predict protein structures.

Specifically it’s applying deep learning approaches to genomic data.

“Fortunately, the field of genomics is quite rich in data thanks to the rapid reduction in the cost of genetic sequencing. As a result, deep learning approaches to the prediction problem that rely on genomic data have become increasingly popular in the last few years. DeepMind’s work on this problem resulted in AlphaFold, which we submitted to CASP [Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction] this year,” it writes in the blog post.

“We’re proud to be part of what the CASP organisers have called “unprecedented progress in the ability of computational methods to predict protein structure,” placing first in rankings among the teams that entered (our entry is A7D).”

“Our team focused specifically on the hard problem of modelling target shapes from scratch, without using previously solved proteins as templates. We achieved a high degree of accuracy when predicting the physical properties of a protein structure, and then used two distinct methods to construct predictions of full protein structures,” it adds.

DeepMind says the two methods it used relied on using deep neural networks trained to predict protein properties from its genetic sequence.

“The properties our networks predict are: (a) the distances between pairs of amino acids and (b) the angles between chemical bonds that connect those amino acids. The first development is an advance on commonly used techniques that estimate whether pairs of amino acids are near each other,” it explains.

“We trained a neural network to predict a separate distribution of distances between every pair of residues in a protein. These probabilities were then combined into a score that estimates how accurate a proposed protein structure is. We also trained a separate neural network that uses all distances in aggregate to estimate how close the proposed structure is to the right answer.”

It then used new methods to try to construct predictions of protein structures, searching known structures that matched its predictions.

“Our first method built on techniques commonly used in structural biology, and repeatedly replaced pieces of a protein structure with new protein fragments. We trained a generative neural network to invent new fragments, which were used to continually improve the score of the proposed protein structure,” it writes.

“The second method optimised scores through gradient descent — a mathematical technique commonly used in machine learning for making small, incremental improvements — which resulted in highly accurate structures. This technique was applied to entire protein chains rather than to pieces that must be folded separately before being assembled, reducing the complexity of the prediction process.”

DeepMind describes the results achieved thus far as “early signs of progress in protein folding” using computational methods — claiming they demonstrate “the utility of AI for scientific discovery”.

Though it also emphasizes it’s still early days for the deep learning approach having any kind of “quantifiable impact”.

“Even though there’s a lot more work to do before we’re able to have a quantifiable impact on treating diseases, managing the environment, and more, we know the potential is enormous,” it writes. “With a dedicated team focused on delving into how machine learning can advance the world of science, we’re looking forward to seeing the many ways our technology can make a difference.”

CRISPR scientist in China claims his team’s research has resulted in the world’s first gene-edited babies

In a dramatic development for CRISPR research, a Chinese scientist from a university in Shenzhen claims he has succeeded in helping create the world’s first genetically-edited babies. Dr. Jiankui He told the Associated Press that twin girls were born earlier this month after he edited their embryos using CRISPR technology to remove the CCR5 gene, […]

In a dramatic development for CRISPR research, a Chinese scientist from a university in Shenzhen claims he has succeeded in helping create the world’s first genetically-edited babies. Dr. Jiankui He told the Associated Press that twin girls were born earlier this month after he edited their embryos using CRISPR technology to remove the CCR5 gene, which plays a critical role in enabling many forms of the HIV virus to infect cells.

The AP’s interview comes after the MIT Technology Review reported earlier today that He’s team at the Southern University of Science and Technology is using CRISPR technology to eliminate the CCR5 gene and create children with resistance to HIV. The news also comes right before the Second International Summit on Human Genome Editing is set to begin in Hong Kong tomorrow.

According to the Technology Review, the summit’s organizers were apparently not notified of He’s plans for the study, though the AP reports that He informed them today.

During his interview with the AP, He, who studied at Rice and Stanford before returning to China, said he felt “a strong responsibility that it’s not just to make a first, but also make it an example” and that “society will decide what to do next.”

(It is important to note that there is still no independent confirmation of He’s claim and that it has not been published in a peer-reviewed journal.)

According to documents linked by the Technology Review, the study was approved by the Medical Ethics Committee of Shenzhen HOME Women’s and Children’s Hospital. The summary on the Chinese Clinical Trial Registry also says the study’s execution time is between March 7, 2017 to March 7, 2019, and that was seeking married couples living in China who meet its health and age requirements and are willing to undergo IVF therapy. The research team wrote that their goal is to “obtain healthy children to avoid HIV providing new insights for the future elimination of major genetic diseases in early human embryos.”

A table attached to the trial’s listing on the Chinese Clinical Trial Registry said genetic tests have already been carried out on fetuses of 12, 19, and 24 weeks of gestational age, though it is unclear if those pregnancies included the one that resulted in the birth of the twin girls, whose parents wish to remain anonymous.

“I believe this is going to help the families and their children,” He told the AP, adding that if the study causes harm, “I would feel the same pain as they do and it’s going to be my own responsibility.”

Chinese scientists at Sun Yat-sen University in Guangzhou first edited the genes of a human embryo using CRISPR technology (the acronym stands for Clustered Regularly Interspaced Short Palindromic Repeats), which enables the removal of specific genes by acting as a very precise pair of “genetic scissors,” in 2015. Though other scientists, including in the United States, have conducted similar research since then, the Southern University of Science and Technology’s study is considered especially radical because many scientists are wary of the ethical implications of CRISPR, which they fear may be used to perpetuate eugenics or create “designer babies” if carried out on embryos meant to be carried to term.

As in the United States and many European countries, using a genetically-engineered embryo in a pregnancy is already prohibited in China, though the Technology Review points out that this guideline, which was issued to IVF clinics in 2003, may not carry the weight of the law.

In 2015, shortly after the Sun Yat-sen University experiment (which was conducted on embryos that were unviable because of chromosomal effects) became known, a meeting called by several groups, including the National Academy of Sciences of the United States, the Institute of Medicine, the Chinese Academy of Sciences and the Royal Society of London, called for a moratorium on making inheritable changes to the human genome.

In addition to ethical concerns, Fyodor Urnov, a gene-editing scientist and associate director of the Altius Institute for Biomedical Sciences, a nonprofit in Seattle, told the technology Review that He’s study is cause for “regret and concern” because it may also overshadow progress in gene-editing research currently being carried out on adults with HIV.

TechCrunch has contacted He for comment at his university email.

Synthego raises $110 million to make gene editing technologies more accessible

Paul Dabrowski, the chief executive officer of Synthego, which provides genetically engineered cells to scientists and researchers, worries about a future where access to the genetic technologies that will reshape the world are only available to the few who can afford them. To hear him tell it, that’s why Dabrowski began working on Synthego in […]

Paul Dabrowski, the chief executive officer of Synthego, which provides genetically engineered cells to scientists and researchers, worries about a future where access to the genetic technologies that will reshape the world are only available to the few who can afford them.

To hear him tell it, that’s why Dabrowski began working on Synthego in the first place — to democratize access to the new technologies that will give scientists, researchers, and consumers new ways to rewrite the code that has defined human existence.

“People talk about access to the tools, but the question is access to the therapies,” Dabrowski said. “We’re talking about the basis of what does it mean to be human not right now, but in the next 100 years.”

Now, the company has a fresh $110 million in cash from new investors at Founders Fund and the company’s previous backers — 8VC and Menlo Ventures — to try and drive costs down.

“This new funding allows us to expand our reach and build out of our full stack platform capabilities at a perfect time,” said Dabrowski, co-founder and CEO, Synthego, in a statement. “Biological medicines are on the cusp of a revolution with the coming curative cell and gene therapies, and we are proud to support this industry.”

While Dabrowski said the financing will be used for further research and development — and bringing new services to market — in the near term the funding will be used to expand two main areas of interest for the company. One is the creation of CRISPR kits that can create different genetic lines based on the requests from researchers and scientists, and the other is creating materials that are “clinical-grade”, which means that they can be used in clinical trials on animal (and potentially human) subjects.

“In general the demand for these products is quite high. Building capacity and building out the informatics models for the predictability on the CRISPR research side. 

In all, the Redwood City, Calif.-based company has raised $166 million in funding to develop its technology that makes research and development using the gene editing tool known as CRISPR more economical and faster for researchers. Synthego claims that  by offering researchers one-click access to engineered cells with guaranteed edits in their desired target, the company can slash the time it takes to conduct experiments by months, enabling predictable and rapid outcomes in cell and gene therapy research and development. 

As we’d written previously, Synthego launched its first CRISPR offerings to the market earlier this year.

There are two basic functions that people use CRISPR for, said Dabrowski. The first is to remove a gene or function and the second is adding a function to genetic material.

Both of those processes involve three (very complicated) steps. First scientists have to identify the gene that they want to target and then understand what genetic material within that gene they want to target for removal. Then a research team would need to identify and procure the reagents and components they need to edit a gene. Finally, the team would need to figure out whether the edit was made successfully and watch for results when the edited genetic material is cultivated.

Synthego’s first set of products were designed to simplify the process for identifying and designing genetic material for experimentation. This next set of tools are supposed to help scientists by providing them with the material they want to observe or experiment with.

“Our vision is a future where cell and gene therapies are ultimately as accessible as vaccines, so that everyone can benefit from next-generation cures,” said Dabrowski in a statement. “Synthego will continue to innovate to help researchers redefine the boundaries of transformative medicines.”