Tag: DNA

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Nanopath is looking to drastically change medical diagnostics

For co-founders Amogha Tadimety and Alison Burklund, the idea of starting Nanopath, a women-focused molecular diagnostic company, came from a need to create a company focused on women’s health diagnoses based on their own experiences. They said they wanted to make sure women can get proper diagnoses because scientifically, there’s no reason they shouldn’t.

“We understand the disease biology, we just don’t have the appropriate tools to characterize the bugs that are causing these problems,” Burklund told TechCrunch in an interview. “You don’t just want to know, is there an infection? You want to know what bug is causing the infection. Is it susceptible to antibiotics? What is the relative concentration of that pathogen, those are all necessary criteria for a clinician to make a decision on treatment.”

The company claims to identify DNA and RNA without the use of any nucleic acid amplification technology (NAAT) to screen potential disease, and get results within 15 minutes, compared to up to two hours for a generic PCR test. NAATs are typically used to diagnose diseases today, and oftentimes allow untrained staff in a controlled setting to use — though, there are concerns for use in decentralized settings. 

Currently, however, Nanopath’s technology is only able to identify genetic make-ups of human papillomavirus (HPV) and urinary tract infections.

According to a report done by Medscape, the usual time a doctor estimated they spent with a patient is between 13 to 16 minutes. 

The goal for Burklund and Tadimety is to have their technology across medical offices in the country so women can get a diagnosis within 15 minutes, the standard duration of the average appointment. 

“It’s crucial that there’s a place where [patients] can get a point of care result, and that treatment within that single office visit,” Burklund said. “Eventually there might be a reimbursement model that supports that, but we just want to make sure that our business model is really holistically serving the needs of all patients.”

Nanopath just raised a $10 million Series A funding round co-led by Norwest Venture Partners and the Medtech Convergence Fund with participation from Gingerbread Capital and Green D Ventures. 

This round’s funds will go towards building out the startup’s technical teams and potentially moving their product mainstream — once they conduct pilot studies and apply for FDA approval.

Even assuming the product clears those hurdles and makes it to market, the idea that they will come to set a new direction for diagnostic testing is ambitious. Despite their claims on being able to provide faster and precise diagnosis, they are still going up against the mainstream testing companies used nationally. 

But for the founders, the idea of trying to reinvent the space is a challenge worth tackling.

“[Patients, now] have to wait a few days for the local lab to get the answer, and then the doctor has to track down the patient and maybe change their treatment,” Tadimety sadid. “And so this is critically important when we think about the number of patients that are lost to follow up, or that are hard to reach or that are being given the wrong treatment, because we just don’t have a tool that can identify what they need during that visit.”

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Volta Labs grabs $20 million to address a growing genomics bottleneck

Twenty years ago, getting a human genome sequenced was a billion-dollar, international project. Today, you can get your dog’s genome sequenced by the end of the month for a few bucks. It speaks to the speed with which genetics has permeated our lives, but despite massive improvements to the technology, the process can still be a bit clunky in the lab.

Before you can even start to disentangle someone’s genetic code, you have to start with a sample. And that sample has to get prepped the right way. It’s a relatively boring process that is often sidelined in favor of flashier applications of genome sequencing (read: reviving mammoths). But it’s a place where Volta Labs is aiming to bring a new focus.

Founded in 2018, Volta Labs is a startup spun out of MIT’s media lab focusing on creating a programmable approach to DNA sample prep. The team is in the process of creating a desktop-sized instrument that can automate the processes used to get genetic samples ready.

“The entire world could not sequence a single human genome 20 years ago, and today, I as a non biologist can sequence a human genome in a day or two on a bench. But if you look at the steps for sample prep, it’s still lagging by a large margin. It’s almost been neglected,” CEO and co-founder Udayan Umapathi told TechCrunch.

The origin story of Volta’s instrument goes back to 2015, when Umapathi was working on his graduate thesis at MIT. “What I noticed was that the existing technologies for moving, mixing and heating fluids were archaic,” he said. “I realized if we have to do biology at scale, automation for biology has to be built from the ground up.”

The DNA sample prep process starts with a biological sample, like blood, saliva or even plant tissue. From there, a series of enzymatic and chemical reactions are performed that draw out DNA molecules. Then they need to be manipulated so they can then be “read” by a sequencer. Those reactions are performed by liquid manipulating robots, or in some cases by hand.

Volta automates this process with what Umapathi called “digital fluidics” — a form of electrowetting. This uses an array of electrodes organized on a grid, each of which can be charged or discharged, creating something like a maze that can precisely position drops of liquid.

Volta’s digital fluidics array. Image Credits: Volta Labs

With the right programming, Umapathi is confident his platform allows liquids to be manipulated in even more complex ways, like using magnetic fields to draw certain molecules out of samples for further analysis.

Despite these capabilities, the instrument is supposed to be small: Umapathi’s goal is to keep it the size of a laptop.

Umapathi isn’t the first to see the potential that “digital fluidics” hold for biological applications. In fact, Illumina has been interested in technology of this nature for years.

In 2013, Illumina acquired Advanced Liquid Logic, a company founded in 2004 that had already been working on applying digital microfluidics to prep work for Next Generation DNA sequencing. In 2015, Illumina went on to try to launch its own version of a DNA library sample prep product called NeoPrep, which rolled the four to five day process into one instrument that could accomplish the task in 30 minutes. However, as the authors of a 2020 review paper on the electrowetting industry note, the instrument was “discontinued for undisclosed reasons” in 2017.

Whether the end of NeoPrep in 2017 has bigger implications for Volta’s own commercialization process is hard to say. But, it does seem that Illumina hasn’t put the idea to bed yet.

On Thursday, Volta announced a $20 million Series A round, which was led by Maverick Ventures (Maverick also led a previous seed round), with participation from Khosla Ventures, Casdin Capital and E14 Funds. Participants also include Illumina co-founder John Stuelpnagel, and other big names in the genetics space like Anne Wojcicki, CEO of 23andMe, and Paul McEwan, founder of Kapa Biosystems. McEwan specifically has led sequencing sample prep programs at Roche Sequencing Solutions.

The natural question here is: Does Volta’s instrument actually exist yet? It does, Umapathi said, and it is already in the hands of four partners that are testing it in the field. He declined to name the partners but described them briefly.

One is a company focusing on cancer care and neurological disorders, which has been using Volta’s tech to develop a DNA extraction process. One is a research institution in RNA applications. The third is a “genome center,” he says. The fourth company is a biotech firm interested in synthetic biology.

The company’s goal is to launch a “limited trial edition” at the AGBT Genomics conference in June. During that launch, Umapathi also expects to present data from the trial projects run with the “genome center.” He expects to have a commercial product ready in 2023.

The rapidly accelerating genomics industry may have room for Volta to climb on board. It cost $3 billion to sequence the human genome as part of the Human Genome Project. Today, that same process can be repeated for about $600. McKinsey’s 2020 genetics industry analysis estimated that the cost of genome sequencing could dip below $100 within a decade.

Amidst this background, the sample prep bottleneck seems obvious. The bigger question here is: Why haven’t the giants in genome sequencing already created the solution?

Part of the answer is that they’ve already tried, and some places, like Roche do have instruments that will address each little piece of the sequencing prep puzzle individually, as opposed to the integrated system Umapathi aims to create. But the answer Umapathi prefers is that existing sequencing technology is already complicated enough to be a full-time job.

“The technology we have built today is almost as complex as the sample prep itself. So for a lot of the sequencing tech companies, getting their core technology was already a massive challenge.”

Going forward, Volta has to prove that relatively complex chemistries can be manipulated inside such a compact instrument. It will have to publish far more data than it has right now to truly prove it can fit into this niche. Confidential trials with four customers and unpublished data aren’t enough.

But if it actually works, Volta may join the rise of an industry that’s already booming. With this Series A round, Umapathi plans to outline a manufacturing plan, and start to build out commercialization capacity.

“I think the big chunk of capital is likely going to go into building out a product strategy and commercialization or team as well as we approach commercialization next year,” he said.

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Gingko Bioworks, valued at $15B, begins trading today: Here’s how their business works

Gingko Bioworks, a synthetic biology company now valued at around $15 billion, begins trading on the New York Stock Exchange today.

Gingko’s market debut is one of the largest in biotech history. It’s expected to raise about $1.6 billion for the company. It’s also one of the biggest SPAC deals done to date — Gingko is going public through a merger with Soaring Eagle Acquisition Corp., which was announced in May. 

Shares opened at $11.15 each this morning under the ticker DNA — biotech dieharders will recognize it as the former ticker used by Genentech. 

The exterior of the NYSE is decked out in Gingko décor. The imagery is clearly sporting Jurassic Park themes, as MIT Tech Review’s Antonio Regalado pointed out. It’s probably intentional: Jason Kelly, the CEO of Ginkgo Bioworks, has been re-reading “Jurassic Park” this week, he tells TechCrunch. 

The décor also sports a company motto: “Grow everything.”

Ginkgo was founded in 2009, and now bills itself as a synthetic biology platform. That’s essentially premised on the idea that one day, we’ll use cells to “grow everything,” and Gingko’s plan is to be that platform used to do that growing. 

Kelly, who often uses language borrowed from computing to describe his company, likens DNA to code. Gingko, he says, aims to “program cells like you can program computers.” Ultimately, those cells can be used to make stuff: like fragrances, flavors, materials, drugs or food products. 

The biggest lingering question over Gingko, ever since the SPAC deal was announced, has centered on its massively high valuation. When Moderna, now a household name thanks to its COVID-19 vaccines, went public in 2018, the company was valued at $7.5 billion. Gingko’s valuation is double that number. 

“I think that surprises people to be honest,” Kelly says. 

How is Gingko going to make money? 

Ginkgo’s massive valuation seems even starker when you look at its existing revenues. SEC documents show that the company pulled in $77 million in revenue in 2020, which increased to about $88 million in the first six months of 2021 (per an August investor call). The company has also reported losses: including $126.6 million in December 2020 and $119.3 million in 2019. 

Gingko is aiming to increase revenue a significant amount in 2021. SEC documents initially noted that the company aimed to draw about $150 million in revenue in 2021, but the August earning call updated that total for the year to over $175 million. 

Gingko aims to make money in two ways: first it contracts with manufacturers during the research and development phase (i.e. while the company works out how to manufacture a cell that spits out a certain fragrance, bio-based nylon or meatless burger). That process happens in Gingko’s “foundry,” a massive factory for bioengineering projects. 

This source of money is already starting to flow. Gingko reported $59 million in foundry revenue for 2020, and anticipates $100 million in 2021, per the August investor call. 

This revenue, though, isn’t covering the full costs of Gingko’s operations, according to the information shared by the company in SEC documents. It is covering an increasing share, though, and as Gingko scales up its platform, costs will come down. Based on fees alone, Kelly projects Gingko will break even by 2024 or 2025. 

The second type of revenue comes from royalties, milestone payments or, in some cases, equity stakes in the companies that go on to sell products, like fragrances or meatless burgers, made using Gingko’s facilities or know-how. It’s this source of income that will make up the vast majority of the company’s future worth, according to its expectations. 

Once the product is made and marketed by another company, it requires little to no more work on Gingko’s part — all the company does is collect cash. 

The company is often hesitant to incorporate these earnings into projections, because they rely on other companies bringing products to market. That means it’s hard to know for sure when these downstream payments will emerge. “In our models, we are very sensitive that, at the end of the day, they’re not our products. I cannot predict when Roche might bring a drug to market and give me my milestones,” says Kelly. 

Kelly says there’s evidence this model will start to work in the near-term. 

Gingko earned a “bolus” milestone payment of 1.5 million shares of The Cronos Group, a cannabis company, for developing a commercially viable, lab-grown rare cannabinoid called CBG for commercial use (there are seven more in strains development, says Kelly). These milestone payments (in cash or shares) are earned when a company achieves some predetermined goal using Gingko’s platform. 

Gingko has also worked with Aldevron to manufacture an enzyme critical to the production of mRNA vaccines, and plans to collect royalty payments from that relationship — though no foundry fees were collected from this project. 

Finally, Gingko has negotiated an equity stake in Motif Foodworks, a spinout company based on its technology. That company has so far raised about $226 million, and will aim to launch a lab-grown beef product developed at Gingko’s foundry, paying Gingko the aforementioned foundry fees already for this contribution.

“The biggest value driver” of Gingko, according to Kelly

This rich source of cash will depend a lot on the outside contractor’s ability to manufacture and sell products made using Gingko’s platform. This opens the company up to some risk that’s beyond its control. Maybe, for instance, it turns people don’t want bio-manufactured meat as much as many anticipated — that means some types of downstream payments may not materialize. 

Kelly says he’s not particularly worried about this. Even if one particular program fails, he’s planning on having so many programs running that one or two are bound to succeed. 

“I’m just sorta like: some will work, some won’t work. Some will take a year, some will take three years. It doesn’t really matter, as long as everybody is working with us,” he says. “Apple doesn’t stress about what apps are going to be the next big app in the app store,” he continues.  

In an increasingly hot biotech market, protecting IP is key

One key metric to watch for Gingko going forward will be how many new cell programs they’re managing to close. So far, Gingko has added 30 programs this year, says Kelly. Last year, there were 50 programs. 

Remember: Some of the projects are Gingko spinouts, like Motif Foodworks, not customers that come to the platform on their own. And historically, the number of companies Gingko has partnered with has been a point of criticism. Per SEC documents, the majority of revenue came from two large partners in 2020 — though Kelly told Business Insider that this was a pandemic-related downturn. 

The more programs Gingko has, the more it becomes insulated from the success or failure of any one product. Plus it’s a sign that people are at least using the “app store” for biology. 

“The biggest value driver of Gingko is how quickly we add programs,” Kelly says. 

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SoftBank-backed Embark Veterinary valued at $700M after $75M Series B

Now that you have that COVID dog, Embark Veterinary wants to help him or her be in your life for a long time by offering DNA testing with the goal of curbing preventable diseases and increasing the lifespan of dogs by three years within the next decade.

The Boston-based dog genetics company raised $75 million in Series B funding in what the company is calling “the biggest Series B for a pet startup to date.” SoftBank Vision Fund 2 was the lead investor and was joined by existing investors F-Prime Capital, SV Angel, Slow Ventures, Freestyle Capital and Third Kind Venture Capital.

The new round boosts Embark’s total funding to $94.3 million since the company was founded in 2015, according to Crunchbase data. It also gives it a post-money valuation of $700 million, Embark founder and CEO Ryan Boyko told TechCrunch.

Boyko has been a dog lover all his life, and also interested in biology and evolution. Dogs, in particular, are fascinating to him because of their variety: they can be bred to be two pounds or 200 pounds, and come in all shapes and sizes. His interest led him to study dogs in order to understand their evolution.

“I began to think about health problems, and honestly, dogs are a better system for using genetics to better their health than humans,” Boyko said. “You can breed them, so genetics has as much power to cause health problems as it can improve quality and life.”

Embark’s dog DNA test retails for $199 and enables dog owners, breeders and veterinarians to personalize care plans based on a dog’s unique genetic profile. It can test for over 350 breeds and 200 genetic health risks, as well as physical traits. Similar to a 23andMe test, test users can learn characteristics about breed, health and ancestry.

For example, the test could show that a healthy dog may have a gene that predisposes them to slipped discs. If the dog has that, then weight management would be an important factor in their care regime, as would not allowing them to jump off the couch. Another common genetic risk is HUU, or Hyperuricosuria, which is elevated levels of uric acid in urine that could lead to bladder stones due to the way dogs process minerals. By changing the dog’s diet, it could reduce the risk for developing the stones, which are painful and expensive to treat, Boyko said.

The test’s technology revolves around proprietary genotyping technology that analyzes more than 200,000 genetic markers, currently two times more information than any other dog DNA test on the market, Boyko said. This gives Embark the world’s largest database of canine health and biological information, enabling the company to provide insights into certain conditions and make new discoveries about health risks, traits and breeds.

Wagmo raises $12.5M to offer pet insurance (and a lot more)

Embark aims to become the standard of care for dog owners and vets. It grew 235% between 2019 and 2020 and saw five times the sales over the past two years. To support that growth, the company intends to use the new funding to bring on key hires and expand its database. Boyko anticipates adding more than 100 employees between 2021 and 2022.

Boyko said the opportunity in the pet startup space is huge. Indeed, U.S. spending on pets reached nearly $100 billion in 2020, up from $95.7 billion in 2019, according to the American Pet Products Association.

At the same time, venture capital interest in U.S. pet-focused companies, from nutrition to travel to healthcare, grew 29.5% from 2019 and 2020, according to Crunchbase data. In addition to Embark’s funding, 2021 was good to other pet startups as well, including pet insurance company Wagmo, raising $12.5 million, connected pet collar company Fi received $30 million and Rover, which announced plans to go public via SPAC.

Lydia Jett, partner at SoftBank Investment Advisers, told TechCrunch that this was her first pet-based investment, and what Embark is doing brings advances to a category right now where people care about their pets enough that they want to do something that will expand their value of life.

Jett said the management team being dedicated to DNA-based analytics is the future, and Embark is starting this big curve when it comes to pets and the convergence of real emotional ties to pets and the ability to improve their lives.

“This company is a driver of change to happen,” she added. “We are the largest consumer investor in the world, and Embark is very much aligned with what we are seeing across our portfolio that consumers are revisiting priorities and choices. That is a major trend, but still early in the cycle of personalization for their pets.”

Where top VCs are investing in digital health

 

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Maryland and Montana are restricting police access to DNA databases

Maryland and Montana have become the first U.S. states to pass laws that make it tougher for law enforcement to access DNA databases.

The new laws, which aim to safeguard the genetic privacy of millions of Americans, focus on consumer DNA databases, such as 23andMe, Ancestry, GEDmatch and FamilyTreeDNA, all of which let people upload their genetic information and use it to connect with distant relatives and trace their family tree. While popular — 23andMe has more than three million users, and GEDmatch more than one million — many are unaware that some of these platforms share genetic data with third parties, from the pharmaceutical industry and scientists to law enforcement agencies.

When used by law enforcement through a technique known as forensic genetic genealogy searching (FGGS), officers can upload DNA evidence found at a crime scene to make connections on possible suspects, the most famous example being the identification of the Golden State Killer in 2018. This saw investigators upload a DNA sample taken at the time of a 1980 murder linked to the serial killer into GEDmatch and subsequently identify distant relatives of the suspect — a critical breakthrough that led to the arrest of Joseph James DeAngelo.

While law enforcement agencies have seen success in using consumer DNA databases to aid with criminal investigations, privacy advocates have long warned of the dangers of these platforms. Not only can these DNA profiles help trace distant ancestors, but the vast troves of genetic data they hold can divulge a person’s propensity for various diseases, predict addiction and drug response, and even be used by companies to create images of what they think a person looks like.

Ancestry and 23andMe have kept their genetic databases closed to law enforcement without a warrant, GEDmatch (which was acquired by a crime scene DNA company in December 2019) and FamilyTreeDNA have previously shared their database with investigators. 

To ensure the genetic privacy of the accused and their relatives, Maryland will, starting October 1, require law enforcement to get a judge’s sign-off before using genetic genealogy, and will limit its use to serious crimes like murder, kidnapping, and human trafficking. It also says that investigators can only use databases that explicitly tell users that their information could be used to investigate crimes. 

In Montana, where the new rules are somewhat narrower, law enforcement would need a warrant before using a DNA database unless the users waived their rights to privacy.

The laws “demonstrate that people across the political spectrum find law enforcement use of consumer genetic data chilling, concerning and privacy-invasive,” said Natalie Ram, a law professor at the University of Maryland. “I hope to see more states embrace robust regulation of this law enforcement technique in the future.”

The introduction of these laws has also been roundly welcomed by privacy advocates, including the Electronic Frontier Foundation. Jennifer Lynch, surveillance litigation director at the EFF, described the restrictions as a “step in the right direction,” but called for more states — and the federal government — to crack down further on FGGS.

“Our genetic data is too sensitive and important to leave it up to the whims of private companies to protect it and the unbridled discretion of law enforcement to search it,” Lynch said.

“Companies like GEDmatch and FamilyTreeDNA have allowed and even encouraged law enforcement searches. Because of this, law enforcement officers are increasingly accessing these databases in criminal investigations across the country.”

A spokesperson for 23andMe told TechCrunch: “We fully support legislation that provides consumers with stronger privacy protections. In fact we are working on legislation in a number of states to increase consumer genetic privacy protections. Customer privacy and transparency are core principles that guide 23andMe’s approach to responding to legal requests and maintaining customer trust. We closely scrutinize all law enforcement and regulatory requests and we will only comply with court orders, subpoenas, search warrants or other requests that we determine are legally valid. To date we have not released any customer information to law enforcement.”

GEDmatch and FamilyTreeDNA, both of which opt users into law enforcement searches by default, told the New York Times that they have no plans to change their existing policies around user consent in response to the new regulation. 

Ancestry did not immediately comment.

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Ansa Biotechnologies wants to usher in a new era of DNA manufacturing

Daniel Arlow has spent the last eighteen years studying genomics and synthetic biology. The arc of his career has taken the first-time founder of the new startup Ansa Biotechnologies from MIT to the famous Keasling Lab at the University of California at Berkeley and now to the world of startups.

Now, Arlow is ready to tell the world what he’s been working on at Ansa, which is nothing less than the delivery of the next generation of synthetic DNA manufacturing.

His company is bringing to market a new process for making DNA that Arlow said is faster and more accurate than existing technologies.

“DNA read, write, and edit are the core pillars of synthetic biology,” said Seth Bannon, a founding partner at the frontier investment firm Fifty Years, and an investor in Ansa’s recent $7.9 million investment round. “Currently the ability to write DNA is the main bottleneck in the synthetic biology industry. By enabling faster, longer, and higher quality DNA synthesis with their fully enzymatic process, Ansa will help accelerate the entire synthetic biology industry.”

Arlow likens the state of the industry now to the early days of programming. “If it took three weeks to compile your code or recompile your code to make a simple change you could never make any progress in developing software for the computer,” Arlow said. And that’s the state for programmable biology these days.

“It took a really long time to test your idea after it was designed. It forces you to plan things out much more carefully and to be less spontaneous and less agile,” he said. 

Using Ansa, companies can have DNA made based on their specific requirements at a speed and scale that Arlow said other companies in the market can’t match.

Daphne Koller: ‘Digital biology is an incredible place to be right now’

Currently, DNA molecules are made using a thirty year-old chemical method that has limitations on the length of molecules that can be made. By contrast, Ansa’s biologically inspired DNA synthesis method means that the company can make long molecules directly, without the risk of errors that can result from patching pieces of genetic material together.

The company has developed an enzyme that basically adds bases to a DNA molecule. The company basically has a cut and paste function that serves to unblock DNA and then allows another base to be attached.

It’s also important to note that Arlow’s company is doing synthesis as a service rather than selling bioprinters that can enable any researcher to make their own DNA.

“One of the reasons we’re developing our business as a DNA synthesis service… as opposed to making a printer… is because that gives us a much greater ability to vet orders for biosecurity risk before we manufacture them,” Arlow said.

Other companies like DNA Script (from France) and Nuclera (a Cambridge, UK-based company) are going to market with bioprinters that they’re selling directly to research labs, according to Arlow.

All of these businesses are the next iteration of companies like Twist Bioscience, that are manufacturing DNA to power the synthetic biology revolution (something that TechCrunch Disrupt attendees have been hearing a lot about).

CRISPR in the post-COVID Era

Ansa hasn’t shipped any DNA yet, but the company will soon be taking orders to begin competing in a market that Arlow estimates is over $1 billion today and is growing quite rapidly.

“Writing is really the bottleneck,” Arlow said. “The business we’re in is selling to R&D.. the faster we can crank out the DNA the better it is. Part of the reason why we’re still pretty bad at engineering biology is because it takes so long to build a new design. My hope is by building more we’ll get better at designing because we’ll be able to see what works and what doesn’t work.”

 

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Gedmatch confirms data breach after users’ DNA profile data made available to police

Gedmatch, the DNA analysis site that police used to catch the so-called Golden State Killer, was pulled briefly offline on Sunday while its parent company investigated how its users’ DNA profile data apparently became available to law enforcement searches.

The company confirmed Wednesday that the permissions change was caused by a breach.

The site, which lets users upload their DNA profile data to trace their family tree and ancestors, rose to overnight fame in 2018 after law enforcement used the site to match the DNA from a serial murder suspect against the site’s million-plus DNA profiles in the site’s database without first telling the company.

Gedmatch issued a privacy warning to its users and put in new controls to allow users to opt-in for their DNA to be included in police searches.

But users reported Sunday that those settings had changed without their permission, and that their DNA profiles were made available to law enforcement searches.

In a statement on Wednesday, the company told users by email that the cause were two security breaches on July 19 and July 20.

“We became aware of the situation a short time later and immediately took the site down. As a result of the breach, all user permissions were reset, making all profiles visible to all users,” the email read. “This was the case for approximately 3 hours. During this time, users who did not opt-in for law enforcement matching were also available for law enforcement matching, and conversely, all law enforcement profiles were made visible to Gedmatch users.”

The statement said that the second breach caused user’s settings to reset, allowing law enforcement to search profile data for users who had previously opted out.

DNA profiling and analysis companies are increasingly popular with users trying to understand their cultural and ethnic backgrounds by discovering new and ancestral family members. But law enforcement are increasingly pushing for access to genetic databases to try to solve crimes from DNA left at crime scenes.

When reached on Sunday when the incident began, Brett Williams, chief executive of Verogen — which acquired Gedmatch in 2019 — would not say if Verogen or Gedmatch have received any law enforcement requests for user data in the past day, or if either company has responded.

A spokesperson for the company on Wednesday said the company had reported the incident to the authorities.

Gedmatch does not publish how frequently law enforcement seeks access to the company’s data. Its rivals, like 23andMe and Ancestry.com, have already published these so-called transparency reports. Earlier this year Ancestry.com revealed that it rejected an out-of-state police warrant, indicating that police continue are still using DNA profiling and analysis sites for information.

“The acknowledgement of an issue is a start, but if a ‘resolution’ means simply correcting the error, there are many questions that remain,” Elizabeth Joh, a professor of law at University of California, Davis School of Law, told TechCrunch.

“For instance, does Gedmatch know whether any law enforcement agencies accessed these improperly tagged users? Will they disclose any further details of the breach? And of course, this isn’t simply Gedmatch’s problem: a privacy breach in a genetic genealogy database underscores the woefully inadequate regulatory safeguards for the most sensitive of information, in a novel arena for civil liberties,” she said. “It’s a mess.”

Updated on July 22 with confirmation of the security breach. First published on July 19 at 5:38pm ET.

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Emerging from stealth, Octant is bringing the tools of synthetic biology to large scale drug discovery

Octant, a company backed by Andreessen Horowitz just now unveiling itself publicly to the world, is using the tools of synthetic biology to buck the latest trends in drug discovery.

As the pharmaceuticals industry turns its attention to precision medicine — the search for ever more tailored treatments for specific diseases using genetic engineering — Octant is using the same technologies to engage in drug discovery and diagnostics on a mass scale.

The company’s technology genetically engineers DNA to act as an identifier for the most common drug receptors inside the human genome. Basically, it’s creating QR codes that can flag and identify how different protein receptors in cells respond to chemicals. These are the biological sensors which help control everything from immune responses to the senses of sight and smell, the firing of neurons; even the release of hormones and communications between cells in the body are regulated.

“Our discovery platform was designed to map and measure the interconnected relationships between chemicals, multiple drug receptor pathways and diseases, enabling us to engineer multi-targeted drugs in a more rational way, across a wide spectrum of targets,” said Sri Kosuri, Octant’s co-founder and chief executive officer, in a statement.

Octant’s work is based on a technology first developed at the University of California Los Angeles by Kosuri and a team of researchers, which slashed the cost of making genetic sequences to $2 per gene from $50 to $100 per gene.

“Our method gives any lab that wants the power to build its own DNA sequences,” Kosuri said in a 2018 statement. “This is the first time that, without a million dollars, an average lab can make 10,000 genes from scratch.”

Joining Kosuri in launching Octant is Ramsey Homsany, a longtime friend of Kosuri’s, and a former executive at Google and Dropbox . Homsany happened to have a background in molecular biology from school, and when Kosuri would talk about the implications of the technology he developed, the two men knew they needed to for a company.

“We use these new tools to know which bar code is going with which construct or genetic variant or pathway that we’re working with [and] all of that fits into a single well,” said Kosuri. “What you can do on top of that is small molecule screening… we can do that with thousands of different wells at a time. So we can build these maps between chemicals and targets and pathways that are essential to drug development.”

Before coming to UCLA, Kosuri had a long history with companies developing products based on synthetic biology on both the coasts. Through some initial work that he’d done in the early days of the biofuel boom in 2007, Kosuri was connected with Flagship Ventures, and the imminent Harvard-based synthetic biologist George Church . He also served as a scientific advisor to Gen9, a company acquired by the multi-billion dollar synthetic biology powerhouse, Ginkgo Bioworks.

“Some of the most valuable drugs in history work on complex sets of drug targets, which is why Octant’s focus on polypharmacology is so compelling,” said Jason Kelly, the co-founder and CEO of Gingko Bioworks, and a member of the Octant board, in a statement. “Octant is engineering a lot of luck and cost out of the drug discovery equation with its novel platform and unique big data biology insights, which will drive the company’s internal development programs as well as potential partnerships.”

The new technology arrives at a unique moment in the industry where pharmaceutical companies are moving to target treatments for diseases that are tied to specific mutations, rather than look at treatments for more common disease problems, said Homsany.

“People are dropping common disease problems,” he said. “The biggest players are dropping these cases and it seems like that just didn’t make sense to us. So we thought about how would a company take these new technologies and apply them in a way that could solve some of this.”

One reason for the industry’s turn away from the big diseases that affect large swaths of the population is that new therapies are emerging to treat these conditions which don’t rely on drugs. While they wouldn’t get into specifics, Octant co-founders are pursuing treatments for what Kosuri said were conditions “in the metabolic space” and in the “neuropsychiatric space”.

Helping them pursue those targets, since Octant is very much a drug development company, is $20 million in financing from investors led by Andreessen Horowitz .

“Drug discovery remains a process of trial and error. Using its deep expertise in synthetic biology, the Octant team has engineered human cells that provide real-time, precise and complete readouts of the complex interactions and effects that drug molecules have within living cells,” said Jorge Conde, general partner at Andreessen Horowitz, and member of the Octant board of directors. “By querying biology at this unprecedented scale, Octant has the potential to systematically create exhaustive maps of drug targets and corresponding, novel treatments for our most intractable diseases.”

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Oxford scientists develop new coronavirus test that provides results in just 30 minutes

Scientists at the University of Oxford have developed a new coronavirus test that produces results around three times faster than the current fastest testing methods, and that requires only relatively simple technical instrumentation. In addition to these benefits, the researchers behind the test’s development say that it  could even help detect patients affected by coronavirus in earlier stages of infection vs. current methods, and that its results can can “read by the naked eye,” which makes it more accessible to a broader range of healthcare facilities and professionals.

The Oxford-developed test can provide results in only half an hour – the fastest current methods that focus on viral RNA, like this one does, produce results in between 1.5 and 2 hours. The new tests have already been validated using real clinical samples of the virus at the Shenzhen Luohou People’s Hospital in China, and though they’ve so far only been used on 16 samples, evenly split between those positive for the virus and those that contain none, they’ve demonstrated a 100% success rate, which is a very reassuring result.

The biggest impact of this test, should it prove effective at scale, is that it manages to sidestep some of the existing limiting factors that apply to the existing early test methods. Scientists currently have to isolate COVID-19 RNA (the instructions for coding DNA), and then perform a process through which that RNA is actually turned into DNA – followed by testing the DNA in a microbiology laboratory setting by trained technicians using a specialized polymerase chain reaction machine.

The Oxford test, on the other hand, requires only relatively simple equipment for both conducting the test and for interpreting the results, which unlocks the possibility of deploying it in hard to reach areas or in local facilities that lack specialized equipment and personnel. The team that developed it is also working on the possibility of making it even more flexible with an integrated hardware design that could make it possible for it to be “used at clinics, airports or even for home use.”

This is still an early technology that’s coming out of a lab, which means that there are still a number of steps required before it becomes approved for broad use. Still, testing equipment doesn’t face quite as many hurdles as do treatments and antivirals, which can obviously have a much more direct impact on human patients, and given the current situation it’s likely everyone involved will want to expedite the next steps in terms of testing and validation.

Testing, and the ability to so accurately and in large numbers across a population, is a key element of any effort to counter the spread of coronavirus, and to evaluate the efficacy of the measures put in place to do so. Currently, the U.S. is far behind other countries in terms of its testing efforts, for instance, with the White House confirming that only under 60,000 tests had been conducted as of yesterday based on available data.

Testing is also focused on only the most severe and obvious cases, which means that large swaths of potentially asymptomatic carries who feel just fine are going untested. That has a huge impact on any effort to accurately track the transmission of COVID-19, and, as a result, of tracking the impact of measures like isolation, social distancing, and shelter-in-place tactics.

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Karius raises $165 million for its liquid biopsy technology identifying diseases in a drop of blood

“What Karius is good at is identifying those novel microbes before they become an outbreak like coronavirus,” says Mickey Kertesz, a chief executive whose life sciences startup just hauled in $165 million in new funding.

While the new money may have been raised under the looming threat of Covid 19, the company’s technology is already being used to test for infection-causing pathogens in immunocompromised pediatric patients, and for potential causes of complex pneumonia, fungal infections and endocarditis, according to a statement from the company. 

Liquid biopsy technology has been widely embraced in cancer treatments as a way to identify which therapies may work best for patients based on the presence of trace amounts of genetic material in a patient’s bloodstream that are shed by cancer cells.

Karius applies the same principles to the detection of pathogens in the blood — developing hardware and software that applies computer vision and machine learning techniques to identify the genetic material that’s present in a blood sample.

As the company explains, microbes infecting the human body leave traces of their DNA in blood, which are called microbial cell-free DNA (mcfDNA). The company’s test can measure the that cell free DNA of more than 1,000 clinically relevant samples from things like bacteria, DNA viruses, fungi, and parasites. These tests indicate the types of quantities of those pathogens that are likely affecting a patient. 

“We’re through the early stages of adoption and clinical studies show that the technology literally saves lives,” says Kertesz.

Its early successes were enough to attract the attention of SoftBank, which is backing the company through capital raised for its second Vision Fund.

While SoftBank has been roundly criticized for investing too much too soon (or too late) into consumer startups which have not lived up to their promise (notably with implosions at Brandless, Zume, and the potential catastrophe known as WeWork), its life sciences investing team has an impressive track record. “They have the experience and the expertise and the network that’s very relevant to us,” Kertesz said of the decision to take SoftBank’s money. “That’s the team that was on the board of Guardant Health [and] 10X Genomics.”

Both of those companies have proven to be successful in public markets and with validated technology. That’s a feature which Karius shares. The company’s published an analytical and clinical validation of its test in the peer-reviewed journal, Nature Microbiology showing that its test identified the likely pathogens causing an infection when compared to standard methods more quickly and more accurately. 

With initial validation behind it, the company raised its new cash to pursue rapid commercial adoption for its tests and to continue validating applications of its technology while exploring new ones.

Among the primary areas of exploration is the identification of new biomarkers, which could serve as indicators for new diseases (like Covid 19).

“As humanity we haven’t figured out infectious diseases yet,” said Kertesz. “Specifically at the stage where the pathogen is identified.” Karius has the technology to do that — although it doesn’t yet have the capability to screen for RNA viruses (which are types of diseases like SARS and the coronavirus), Kertesz said. “It’s the only type of virus that the platform is unable to detect… [We’re] adding that detection capability.” 

Karius works by digitizing the microbial information in a blood sample and uses machine learning and computer vision to recognize the microbial signatures. The company uses public databases which have records of over 300,000 pathogens. For the ones that the company can’t identify, it creates a identifier for those as well. “One of the biggest challeges we have here is to know what we don’t know,” said Kertesz.

At $2,000 per test, Karius’ biopsies aren’t cheap, but they’re safer and more cost effective than surgeries, according to Kartesz. It’s obviating the need to dig into a patient for a piece of tissue and the technology is already being used in over 100 hospitals and health systems, the company said.

With that kind of reach new investors including General Catalyst and HBM Healthcare Investments were willing to sign on with SoftBank’s Vision Fund and previous investors like Khosla Ventures and LightSpeed Venture Partners to participate in the latest round.

“Infectious diseases are the second leading cause of deaths worldwide. Karius’ innovative mcfDNA technology accurately diagnoses infections that cannot be determined by other existing technologies,” said Deep Nishar, Senior Managing Partner at SoftBank Investment Advisers, in a statement.