Monthly Archives: July 2020

By Allison Proffitt

July 21, 2020 |It seems like a very long time ago, now, that Illumina and Pacific Biosciences dissolved their merger agreement, but in fact their announcement is just about six months old. Since then, PacBio has been busy reestablishing itself as an independent business and looking ahead, their sights set on the human genome sequencing market.

The dissolution of the Illumina mergercalled off due to the lengthy regulatory approval process and continued uncertaintydid require some back-pedaling. We were actively moving as much as we could without the full regulatory review having completed, Luke Hickey, Senior Director of Strategic Marketing, told Bio-IT World. But Hickey is optimistic about PacBios future.

There was a fairly large breakup fee that ended up giving us significant operating capital, Hickey said of the $98 million termination fee. We have a healthy balance sheet and wereif anythingmore energized to continue as an independent company within the long read space.

As for competitive exposure, Aaron Wenger, Principal Scientist at PacBio, is not worried.

I know that there was some sharing of information, but PacBio has been developing SMRT sequencing for, I think, 20 years, Wenger said. I think there are ways to protect the technology through patents that Illumina can't legally copy, and then also I think many trade secrets that they did not have access to. An added strength, Wenger noted: the many people who could actually execute that on the day to day basis here are still employed at PacBio.

Hickey agreed. We feel like were in an incredibly strong position with the patent portfolio andto Aarons pointhow many years its taken to develop a robust and reliable system for doing the sequencing.

The PacBio sequencing system announced an overhaul itself in 2019. About a year ago, the company launched its Sequel II platform. PacBio shipped 104 Sequel II platforms to customers between June and December 2019, Hickey said, highlighting a healthy mix of existing and new customers. While PacBios historical customers may have focused on microbial or plant and animal sequencing, We have seen just great adoption from the human biomedical market, he emphasized. He name-dropped a few groups to adopt the new platform: the NIHs All of Us program, Mercy Childrens Hospital in Kansas City, Ira Halls group at Washington University in St. Louis, and Evan Eichler at the University of Washington.

The Sequel II system takes advantage of a new read typeHiFi readsthat the company announced in January 2019. The corresponding paper was published in Nature Biotechnologyin August 2019; Wenger is first author (DOI: 10.1038/s41587-019-0217-9). The team optimized circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5kilobases (kb).

What we were able to do, was significantly increase the efficiency of being able to get multiple observations of the DNA molecule, Wenger explained, through repetitive or circular sequencing of the same DNA. That first time through you detect with 87% accuracy. Then you go around the turn and go back in the other direction and now you get another read thats 87% accurate. But its an independent read from the first one. Now you have two things, each of which are 87% accurate, but you make different mistakes in the two times through. By making multiple observations in series of the same physical DNA molecule, you can generatein softwarea consensus of those passes, he said. If you do 5 passes, you can get 99% accuracy; if you get 8 passes, you get 99.9% accuracy.

The result is highly accurate reads that are opening up new applications.

Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants, Wenger and his co-authors wrote in August 2019 paper. De novogenome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.

The Sequel II platform enabled researchers to generate the new read type at greater scales than before. By April 2019, at least five early adopter institutions were using Sequel II platforms, and Luke Tallon from the University of Maryland Institute for Genome Services reported seeing, comparable data quality with yields 8-9 times higher than that of the Sequel.

The new platform and read types have been included in several publications including a paper from the PacBio team with scientists from the University of Washington describing improved assembly and variant detection of a haploid human genome published in the Annals of Human Genetics(DOI: 10.1111/ahg.12364). Two additional papers are in review and published on bioRxiv.

Already there have been some interesting trends emerging, Wenger said: some things you would have predicted, and some things we didnt.

Sequencing has labored under a general wisdom, Wenger said, that short, very accurate reads are critical to calling small variants like single nucleotide variants, while do novoassembly required long reads, even with less accuracy. But the HiFi reads, Wenger says, have struck a middle ground. They are accurate and longer (though not as long as longest PacBio reads): about 15,000-20,000 base pairs at greater than 99% accurate.

The question is, how does do these HiFi reads perform compared to either the short or long reads we are used to? Whats interesting is actually seeing thatat least for human genomesthese highly accurate, pretty long reads just significantly outperform even reads that are 100,000 or 150,000 bases long, Wenger says.

A HiFi read that is 20,000 base pairs long and 99% accurate is superior to a 60,000 base pair read that is 85% accurate, Wenger argues. When you call something in the genome a repeat, theyre never 100% identical, he said. If two things are 98% identical in the genome, but your reads are 99% accurate, then you can tell those two things apart. This accuracy lets you resolve more repeats than having long reads.

Wenger says this balance between read length and accuracy is not only scientifically interesting, but also somewhat surprising. At this current point [with the Sequel II], what the platform can deliver is likely enough to completely assemble human genomes from telomere to telomere, he says.

New Applications

There is a group working on that. The Telomere to Telomere Consortiumis an open, community-based effort headed by Adam Phillippy of NIH/NHGRI and Karen Miga of UC Santa Cruz. Their goal is to sequence human chromosomes from end to endincluding tricky centromeresfilling hundreds of gaps across the genome including segmental duplications, ribosomal rRNA gene arrays, and satellite arrays.

We aim to finish these remaining regions and generate the first truly complete assembly of a human genome, the group writes on their website. The ultimate goal of this effort is to drive technology to dramatically increase the throughput of complete, high quality telomere-to-telomere assemblies from diploid human genomes.

At AGBT in 2019 (Feb 27-March 2), Phillippy presented the sequence of the full human X chromosome which was assembled, then iteratively polished with a combination of technologies from Oxford Nanopore, PacBio (both the continuous long reads and the HiFi reads), 10x Genomics/Illumina, and Bionano Genomics. Since then, Wenger says, HiFi has been used to sequence through more centromeres. Now with the HiFi reads, a number of groups have been able to assemble centromeres. Now, I think, theyve assembled nearly half the human centromeres using 15,000 to 20,000 base pairs and 99% accuracy rate, he said. (The sequenced X chromosome was published July 14 in Nature, DOI: 10.1038/s41586-020-2547-7.)

The Human Pangenome Reference Sequence Project is another project making use of the combination of long reads plus accuracy, Hickey added. That project includes researchers from the University of Washington, Washington University and the University of California, Santa Cruz. The two sequencing centersUniversity of Washington and Washington Universityare using the PacBio HiFi reads as the primary sequencing technology for assembly, Hickey said. The group will also use Oxford Nanopore for scaffolding work. The group has done 30 human reference genomes this year, Wenger addeda huge increase from output in the past.

Sweet Spot

The Sequel II and HiFi reads mark a shift in PacBios technical focus moving forward. Wenger says that 20,000 bases is, likely sufficient for anything youd want to do in a human genome, so pushing for longer read lengths isnt a priority. There are still a few centromeres that have to be finished, so maybe youll need 30,000 for those. But Im kind of skeptical. I think that 20,000 is going to be plenty and that its just continued algorithmic improvements that will take it the rest of the way, he said.

He also pointed out a practical reason that 20,000 base pairs is an ideal read length. We found that the 20,000 base-pair-range is the comfortable range where people can collect samples, consistently process them, and generate good libraries at that read length. When you try to push to more extreme read lengths, there become a lot more limitations on sample collection and libraries fail a lot more. Thats not a problem with the sequencing technology, thats a problem with the upstream DNA handling.

Hickey agreed. The next step for us is not necessarily to drive up read lengths, because we think that is sufficient, but to drive down the cost. Thats our roadmap for 2020 We are trying to get to one human genome, on one SMRT cell, in one day. For just over $1,000 in consumable costs, Hickey points out, and could give you, all of the answers you want.

Hickey sees clinical utility in the platforms future. The NIH-funded research has an eye toward eventual clinical applications and he mentions a HudsonAlpha group exploring the Sequel II for diagnostics.

As those studies get published, that will really set us up for maybe more of push into the clinical market for using the whole genome sequencing with HiFi in a more routine way, Hickey said. But certainly for the next few years, well be in this basic human genetics research, and then all of this translational, clinical, exploratory research realm to demonstrate utility.

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PacBio's Focus on Human Genomics And Read Length Sweet Spot - Bio-IT World

DetailsCategory: AntibodiesPublished on Tuesday, 21 July 2020 11:10Hits: 150

Clinical trajectory initiated towards development of novel treatment for dyslipidaemia

NIJMEGEN, The Netherlands I July 21, 2020 I Staten Biotechnology B.V. announced today the initiation of dosing of the Companys lead asset, STT-5058, in a First-in-Human clinical study.

STT-5058 is a monoclonal antibody that targets the lipoprotein ApoC3 and is being developed in collaboration with Novo Nordisk. Staten Biotechnology and Novo Nordisk entered a collaboration and exclusive option agreement in December 2018 to develop novel therapeutics for the treatment of dyslipidaemia. Novo Nordisk is providing funding and support to Staten for the development of STT-5058 in this indication.

Hilde Steineger, CEO of Staten Biotechnology, said: Staten Biotechnology, with great support from Novo Nordisk, has been able to rapidly progress from research to product manufacturing to a clinical trial for our lead drug candidate. We are very excited to dose the first healthy volunteer.

Professor John Kastelein, Chief Medical Officer of Staten Biotechnology, added: The commencement of the FIH trial is an important milestone for the Company. We believe STT-5058, based on its favourable safety profile and novel mechanism targeting ApoC3, which is supported by human genetics, has the potential to address an unmet medical need in patients with mixed dyslipidaemia and high cardiovascular risk.

About Staten Staten Biotechnology B.V. aims to develop novel and innovative strategies for the treatment of dyslipidaemia, with a focus on hypertriglyceridemia treatment. BioGeneration Ventures (BGV) provided the companys seed financing in 2014 and Forbion led the Series A round, as the sole new investor. Staten is a prime example of Forbions and BGVs company building activities, growing great scientific ideas into promising companies. For further information: http://www.statenbiotech.com

About STT-5058 STT-5058 is a humanized, monoclonal antibody targeting novel and unique epitopes on apoC3. This recycling antibody with extended half-life has the potential to lower triglyceride levels and increase clearance of ApoC3-containing atherogenic particles. Multiple studies have identified ApoC3 levels to be inversely associated with a favourable lipid profile and insulin resistance, both key components in managing residual cardiovascular risk. This antibody was licensed from Statens research collaboration partner argenx and is developed in collaboration with Novo Nordisk.

About ApoC3 ApoC3 is a small apolipoprotein that inhibits the uptake of lipoprotein particles by the liver and inhibits the activity of lipoprotein lipase leading to high levels of lipoproteins and triglycerides. It is secreted from the liver and small intestine and circulates on both triglyceride-rich lipoproteins such as very-low-density-lipoproteins (VLDL), chylomicrons in addition to high-density lipoproteins. Population groups with loss-of-function mutations in apoC3 have reduced incidence of vascular and heart diseases. High levels of apoC3 correlates with higher amounts of triglycerides and increased incidence of vascular and heart disease. This supports the potential of the anti-apoC3 antibody to act as key molecule in dyslipidemia management.

SOURCE: Staten Biotechnology

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Staten Biotechnology, in collaboration with Novo Nordisk, starts dosing of anti-apoC3 antibody SST-5058 in First-in-Human Trial | Antibodies | News...

Wrapping up the month of July, there are three PDUFA dates on the U.S. Food and Drug Administration (FDA) calendar, although one of the drugs has already been approved and another company is in the process of refiling their application. Heres a look.

Jazz Pharmaceuticals Drug for Cataplexy

Jazz Pharmaceuticals has a target action date of July 21 for its New Drug Application (NDA) for JZP-258 for cataplexy or excessive daytime sleepiness (EDS) in patients seven years of age and older with narcolepsy. The drug is a novel oxybate product with a unique composition of cations resulting in 92% less sodium than Jazzs Xyrem (sodium oxybate).

At this time, Xyrem is the only product approved to treat both cataplexya sudden loss of muscle tone with retained consciousnessand EDS in patients with narcolepsy ages seven years and older.

We developed JZP-258 to be a safer and long-term treatment option for patients, said Robert Iannone, executive vice president, research and development of Jazz, back in March when the FDA accepted the NDA application. JZP-258 represents between 1,000 and 1,500 milligrams daily reduction of sodium for patients currently treated with Xyrem, depending on the dose. Given the broad scientific consensus that reducing daily sodium consumption is associated with clinically meaningful reductions in blood pressure and cardiovascular disease risk, we believe that JZP-258 has the potential to be an important treatment option for patients living with the life-long condition of narcolepsy. Narcolepsy patients are known to be at increased risk of comorbidities, including obesity, hypertension, diabetes and dyslipidemia.

ANI Pharmaceuticals Purified Cortrophin Gel Prior Approval Supplement

ANI Pharmaceuticals had a target action date of July 23, 2020, for its supplemental new drug application (sNDA) for Purified Cortrophin Gel (Repository Corticotropin Injection USP). In an announcement in March, when it submitted the sNDA, the company noted the current annual market for the drug is about $950 million and there is only one competitor.

Cortrophin Gel was originally approved by the FDA in 1954 and halted use in the 1980s. The drug has more than 54 indications in its previously approved label, including acute exacerbations of multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus and ulcerative colitis. The company acquired the NDA from Merck in January of 2016 and spent more than four years and over $100 million to re-establish and validate the commercial corticotropin active pharmaceutical ingredient and the drugs manufacturing processes. This included rebuilding a U.S.-based supply chain.

On April 28, the FDA issued a Refusal to File (RTF) letter regarding the sNDA. The FDA said on preliminary review, certain portions of the Chemistry, Manufacturing and Controls section were not sufficiently complete to permit a substantive review. On June 1, ANI provided an update and indicated it plans to refile the sNDA when it completes the review process.

Ultragenyx Pharmaceuticals UX007 for Long-chain Fatty Acid Oxidation Disorders

Ultragenyx Pharmaceuticals has a target action date of July 31 for UX-007 for long-chain fatty acid oxidation disorders (LC-FAOD). On June 30, the FDA approved UX007 (triheptanoin) under the trade name Dojolvi.

LC-FAOD are a group of rare, lifelong and life-threatening genetic disorders. In them, the body cannot convert long-chain fatty acids into energy. Dojolvi is a highly purified, synthetic, 7-carbon fatty acid triglyceride designed to provide medium-chain, odd-carbon fatty acids as an energy source and metabolite replacement for LC-FAOD patients. When people are born in the U.S. and certain European countries, LC-FAOD is included in newborn screening panels because of the risk for serious health issues, including early death. The current treatments include avoiding fasting, low-fat/high-carbohydrates diets, carnitine and even-carbon medium-chain triglyceride (MCT) oil, a medical food product. These diseases affect about 2,000 to 3,5000 children and adults in the U.S.

FDA approval of Dojolvi for the treatment of long-chain fatty acid oxidation disorders is a huge milestone for patients and their families, as it is the first such medication, said Jerry Vockley, Professor of Human Genetics and chief of Medical Genetics at Childrens Hospital of Pittsburgh of UPMC. While we have been able to identify these disorders at birth for many years, treatment options have been limited. Dojolvi brings hope as a new tool now available to clinicians taking care of these patients.

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FDA Action Alert: Jazz, ANI and Ultragenyx - BioSpace

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Gaucher Disease Treatment Market Global Advance Stimulators, Market Size Composition and Market Subdivision Over the Prediction Period - 3rd Watch...

TMR Research speaks on the core issues and characteristics of the global humanized mouse model market, along with its nuances and opportunities of growth over the coming years, in Humanized Mouse Model Market Global Industry Analysis, Size, Share, Trends, Analysis, Growth, and Forecast 2017 2025.

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Some of the prominent players holding a substantial stake in the global humanized mouse models market are The Jackson Laboratory, Harbour Antibodies BV, HuMurine Technologies, Inc., Ingenious Targeting Laboratory, Axenis S.A.S, GenOway S.A., and Horizon Discovery Group PLC.

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Humanized Mouse Model Market Key Players are Aggressively Investing on Research and Development - BioSpace

People wear face masks as they attend the live broadcast of Pope Francis' Sunday Angelus prayer at Saint Peter's Square in Vatican City, March 8, 2020. Antonio Masiello/Getty Images

Experts continue to throw out conflicting ideas about whether the coronavirus has changed. Some Italian doctors say it's gotten weaker over time. A group of researchers has suggested the opposite: that a mutated version of the virus became dominant worldwide because it's more transmissible than the original.

All viruses, including the coronavirus, change over time by accumulating mutations as they replicate. But according to Emma Hodcroft, a geneticist at the Nextstrain project, there's still no evidence this virus changed in any significant way not to become less deadly, and not to be more contagious.

The Nextstrain project has been tracking changes in the coronavirus for months. So far, Hodcroft's team has collected and sequenced the genome of thousands of virus samples collected around the world since December 2019.

Geneticists differentiate these samples into five clades the term for groups of virus samples that have descended from a common ancestor characterized by mutations that have accumulated over time in one or more of a dozen genes.

But none of those mutations have meaningfully changed how lethal or infectious the coronavirus is, Hodcroft said.

It's easy to think that humanity's attempts to control the coronavirus's spread via social distancing, mask wearing, and lockdowns may have applied evolutionary pressure on the virus. Given impediments to its spread, this line of logic suggests, perhaps the virus might evolve to improve how it passes between people.

But according to Hodcroft, the virus has no significant impetus to change right now.

"The virus is very successful at what it's doing most people who get infected don't die. They pass along the virus to a new host and recover," Hodcroft said. "It's current strategy has helped it cover the whole world in months."

People wearing masks wait on a crowded subway platform on May 30, 2020, in New York City. Alexi Rosenfeld/Getty Images

If the original strain of the coronavirus killed its host within a few days, then perhaps it might have mutated over time to not kill as quickly, she added that would give it more opportunities to jump to new hosts. But on average, people die of COVID-19 18 to 19 days after symptoms start, according to a study from Wuhan, China.

Alternatively, if social distancing were having an effect, Hodcroft said, the coronavirus might mutate to become more infectious "to overcome barriers we put in its way."

Research has in fact shown that a mutated coronavirus strain became dominant worldwide one that appears to be more transmissible between human cells than the original virus. But Hodcroft said the strain might simply have gotten lucky, since it ended up being the version that spread to countries in Europe and North America. Many of those countries did not enact lockdowns for weeks after their first cases appeared, which allowed that version of the virus to proliferate.

Plus, scientists still aren't sure whether observations at the cellular level apply to real people.

"We don't know how things we see in a lab scale up to a size of a full human. Transmissibility in cells and people are completely different ballgames," Hodcroft said.

An artists's rendering of the coronavirus. Corona Borealis Studio/Shutterstock

She added that such mutations, though possible, "happen over decades or centuries."

In a June op-ed, 10 Italian doctors suggested that the coronavirus was weakening and had changed to be less lethal.

The "virus from the clinical point of view no longer exists" in Italy, they wrote, citing a marked reduction in symptomatic coronavirus cases and hospitalizations. The op-ed also noted that viral loads how much of the virus is present in swabs from many Italian patients were so negligible that patients were not even contagious.

"The concentration of viral RNA on the swab is so small that it does not infect anything," Giuseppe Remuzzi, one of the op-ed co-authors, told Politico last week.

A hospital employee wearing protective gear shows a cotton swab for taking a coronavirus sample. Miguel Medina/AFP via Getty

But Hodcroft said"there isn't any validity to those claims."

In fact, she added, it's "misleading for Italian doctors to say this when they're looking at only Italian patients."

Michael Ryan, the executive director of WHO's Health Emergencies Program, similarly warned in June: "We need to be exceptionally careful not to create a sense that all of sudden the virus, by its own volition, has now decided to be less pathogenic. This is still a killer virus."

Nurses transport a COVID-19 patient in a biological containment stretcher in the Da Procida Hospital in Salerno, Italy, in April. Ivan Romano/Getty Images

The more likely explanation for the trend the Italian doctors have observed, Hodcroft said, is that in March, Italy's healthcare system was strained, so most patients admitted to the hospital had very severe cases. At that time, about 6,500 new cases were being reported per day in Italy. But by the end of May, the number had dropped to about 300. That may have enabled more Italians with milder cases to get care, which could explain the lower viral loads in swab tests.

Indeed, two studies found that people who develop more severe respiratory issues linked to COVID-19 have higher viral loads when admitted to the hospital relative to people with mild cases.

"As the pandemic slows down, more of the general population is getting tested, so you'll probably pick up more people with mild symptoms," Hodcroft said. "If you don't account for that, that could lead you to believe the virus has become less severe."

Adam Payne contributed reporting to this story.

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Coronavirus is not mutating to be weaker over time, genetics show - Business Insider - Business Insider