SAINT LOUIS, MO, United States
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SAN FRANCISCO--(BUSINESS WIRE)--Cofactor Genomics, developer of a leading platform for RNA sequencing and expression analysis, today announced $18M in financing led by Menlo Ventures with major participation from existing investor Data Collective (DCVC) and new investor Ascension Ventures, and participation from existing and new investors iSelect, Y Combinator, Wilson Sonsini Goodrich & Rosati, and Stanford. The company welcomes Mark Siegel (Menlo Ventures), Matt Ocko (DCVC), and John Kuelper (Ascension Ventures) to its board of directors. “This financing—which includes leading investors who have grown hugely successful companies spanning the data science, biotech, and healthcare verticals—is enormous validation of the platform that we’ve built and reflects excitement for Cofactor’s next phase of growth where we intend to package this expertise in discrete applications that can be easily adopted by research labs and clinical practices throughout the nation,” said Dr. Jarret Glasscock, CEO of Cofactor. “I, as well as many on my team, have lost family members to cancer, so being able to see Cofactor’s technology improve oncologists’ ability to select therapy and impact patient outcomes is of great importance to my talented and tenacious team.” The investment comes on the heels of Cofactor securing CAP/CLIA accreditation of its platform in order to process clinical-grade formalin-fixed paraffin embedded (FFPE) patient samples, as well as the validation and launch of two initial products: Pinnacle and Paragon. Pinnacle examines nearly 600 RNA biomarkers known to be associated with response to targeted therapeutics, while Paragon is an RNA-based immunophenotyping assay with broad applications to the field of Immuno-Oncology and beyond. Mark Siegel, Managing Director of Menlo Ventures, commented; “RNA is the unwritten chapter in the book of personalized oncology care. We at Menlo are happy to be supporting the growth of Cofactor and their team with decades of genomics experience as they leverage their powerful technology to write this new chapter.” While most attention has been paid to applications of DNA analysis for precision medicine, Cofactor’s team of past Human Genome Project scientists have spent the last four years optimizing its platform specifically for the analysis of RNA, a rich source of information on the molecular mechanisms involved in complex and heterogeneous diseases such as cancer that cannot be uncovered through DNA alone. “RNA messages are the human body’s analog of Internet data packets, constantly emitted by every cell and organ, and containing very specific information about processes at their point of origin. DCVC seed financed the brilliant computational biologists at Cofactor because they created technology to read these RNA data packets and translate their information into disease insight. We are now increasing our commitment and involvement with team Cofactor through this funding round because this technology has clearly shown the potential to save lives,” said Matt Ocko, co-Managing Partner of DCVC. “Targeted therapeutics have advanced so rapidly that today it’s impossible to follow oncology best practices without embracing precision medicine,” said John Kuelper, Investment Director at Ascension Ventures (AV). “While NGS has already revolutionized clinical DNA analysis, the practical and computational challenges of multiplexed clinical RNA analysis have relegated this technology to research settings. Cofactor is uniquely positioned to bring this technology out of academia and into the clinic, expanding the reach of precision medicine to a broader class of molecularly targeted drugs whose efficacy can’t be assessed with DNA alone. As AV’s 13 health system partners—who collectively represent nearly 500 hospitals and nearly $90 billion in annual patient care—adapt to new models of precision medicine, the need for diagnostic platforms that combine high accuracy and consistency with broad applicability and cost-effectiveness has become apparent.” Cofactor Genomics uses RNA to help researchers and clinicians understand, diagnose, and predict drug response for the 95% of disease that can’t be assessed by DNA alone. Founded by three former Human Genome Project scientists, Cofactor has built a proprietary platform capable of overcoming the chemical and computational challenges of performing complex RNA fingerprint analysis on clinical-grade human samples. Cofactor has contracts to provide RNA sequencing and analysis services to the research arms of eight of the world’s largest pharma and biotech companies, and is in the process of commercializing a suite of clinical diagnostic assays targeting oncologic, immunologic, and neurodegenerative diseases. Find out more about Cofactor Genomics at cofactorgenomics.com.


News Article | February 16, 2017
Site: www.businesswire.com

SAN FRANCISCO & ST. LOUIS--(BUSINESS WIRE)--Cofactor Genomics, a software-driven biotechnology company developing unique molecular diagnostics centered on RNA, has launched a clinically-validated oncology assay which provides unique insight into a patient’s cancer profile. The assay, named Cofactor Pinnacle, utilizes the company’s proprietary software technology to compare each patient’s cancer expression profile to Cofactor’s database of thousands of expression profiles from the same cancer type. The assay reports on both aberrant oncology-relevant gene expression and known cancer gene fusions detected in the tumor sample. In 2016, after multi-year efforts to standardize and certify Cofactor’s foundational molecular protocols for clinical use, Cofactor became one of the first laboratories to receive CAP-accreditation for RNA-seq. Pinnacle is built on the foundation of these protocols; the assay is currently approved for use with Formalin-Fixed, Paraffin-Embedded (FFPE) tumor tissue. Cofactor has secured early-access partnerships for the assay within two key groups: drug developers and academic medical centers. Within the drug development pipeline, Pinnacle is being used to identify new patient populations and explain phenotypic responses in trials. In the clinic, Cofactor Pinnacle is providing potential treatment targets for patients who have not responded to first or second line chemotherapy. “Clinical oncology has relied so heavily on the development of DNA assays, but there’s still a biological gap to be addressed. Recognizing RNA’s ability to identify relevant targets in cancer drug development, as well as more accurately predict the correct treatment for cancer patients, are the key reasons we have built a company committed to developing technologies to interpret the complex data represented by RNA. Cofactor’s Pinnacle adds valuable biological context that’s needed and currently missing from oncology assays,” noted Cofactor CEO, Dr. Jarret Glasscock. Pinnacle is offered as a laboratory-developed test exclusively through Cofactor’s CAP-accredited laboratories. Pinnacle will be featured at CHI’s 24th International Molecular Med TRI-CON 2017. Jon Armstrong, Cofactor’s CSO will present "Reaching the Pinnacle: A Unique Cancer Diagnostic Tool that Harnesses the Power of RNA" on Tuesday, February 21 at 11:45 am - 12:15 pm in the Molecular Diagnostics track. Cofactor Genomics uses RNA to diagnose disease. Y Combinator backed Cofactor is founded by three former Human Genome Project molecular and data scientists who are developing key technologies to enable RNA’s use in understanding and diagnosing disease in the 95 percent of disease that can’t be diagnosed with DNA alone. Cofactor has contracts with eight of the world’s largest pharma and biotech companies, providing pre-clinical RNA sequencing and analysis, custom assay development, and clinical RNA sequencing. With the acquisition of Narus Biotechnologies in 2015 and a fully-funded Phase II SBIR grant, Cofactor has expanded into the molecular diagnostics arena, centered on oncology and neurodegenerative diseases. Find out more about Cofactor Genomics at cofactorgenomics.com.


PubMed | Indiana University and Cofactor Genomics, Llc
Type: Journal Article | Journal: British journal of cancer | Year: 2016

Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing.The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used.Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. A substantial differentiator was a large microRNA cluster on chr19q13.42 that was significantly overexpressed in all A and AB tumours and whose expression was virtually absent in the other thymomas and normal tissues. Overexpression of this microRNA cluster activates the PI3K/AKT/mTOR pathway. Treatment of a thymoma AB cell line with a panel of PI3K/AKT/mTOR inhibitors resulted in marked reduction of cell viability.A large microRNA cluster on chr19q13.42 is a transcriptional hallmark of type A and AB thymomas. Furthermore, this cluster activates the PI3K pathway, suggesting the possible exploration of PI3K inhibitors in patients with these subtypes of tumour. This work has led to the initiation of a phase II clinical trial of PI3K inhibition in relapsed or refractory thymomas (http://clinicaltrials.gov/ct2/show/NCT02220855).


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 161.50K | Year: 2014

DESCRIPTION (provided by applicant): Modified ribonucleic acids (RNA) are important regulators of translation and other cellular pathways. Non- coding RNAs like microRNAs play significant roles in neuronal development, and can serve as biomarkers for psychiatric disorders. Another such modified RNA is circular RNA (circRNA), a non-coding transcript present in the cytoplasm. Since circRNAs are present in lower abundance than other RNA molecules, and share sequence homology with mRNA, they are difficult to isolate from total RNA. To facilitate identification and examination of these molecules, we propose to develop a streamlined approach that uses selective reduction of linear and ribosomal RNAs combined with a novel reverse transcriptase to enrich for circular RNAs. To optimize for robust reduction and amplification, we will test a range of conditions and assess their relative efficiencies using qRT-PCR specific for known circRNAs and synthetic spiked-in linear RNAs. We will use our validated approach to


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase II | Award Amount: 1.41M | Year: 2015

DESCRIPTION provided by applicant Long term objectives Modified ribonucleic acids RNA are important regulators of numerous cellular processes and are increasingly being associated with human diseases For example non coding microRNAs play significant roles in neuronal development and can serve as biomarkers for psychiatric disorders Another such modified RNA is circular RNA circRNA a non coding transcript present in the cytoplasm Since circRNAs are present in lower abundance than other RNA molecules and share sequence homology with mRNA they are difficult to isolate from total RNA Our long term objective is to further develop and distribute a molecular biology kit which will foster broader research in this nascent field and expand our understanding of the role of circular RNAs in neuronal development substance abuse and psychiatric disorders We have established four Phase II Aims Method optimization Clinical Sample Applicability Optimization Internal Kit Testing Cofactor circRNA Service and External Field Testing Kit Beta Testers Research Design Aim We will utilize universal human brain reference RNA containing a known quantity of circRNA control and our optimized enzyme mix to determine ideal reaction parameters i e primer design temperature and incubation time that will lead to the most robust enrichment of ciRNA species Input titrations will determine the threshold and range of total RNA input for the optimized protocol Success will be measured by qPCR and sequencing metrics on libraries passing our quality control measures Aim We will obtain commercially available biobank samples such as FFPE tissue frozen brain and plasma to test the kit applicability and robustness on clinically relevant samples Quality metrics assayed by Qubit Bioanalyzer Tapestation and Nanodrop will be recorded for the corresponding sequencing libraries to identify kit robustness In addition samples provided by commercial and academic partners will further bolster our metric reports for varying sample types and input amounts Aim Our production scientists will translate the Randamp D SOP into a production service offering with client submitted samples We will continue to collect quality metrics on these samples in the production setting to determine expected yields for library construction and circRNA control enrichment We will use the data generated from both our Randamp D and production setting to develop and optimize our analysis software ActiveSite to incorporate circRNA enrichment reports Aim We have interested commercial and academic partners that have volunteered to test our circRNA kit in their respective laboratories Our partners will collect quality metric scoes about the samples generate circRNA enriched samples and provide these to us for evaluation and sequencing We will utilize feedback from these Beta testers to refine the SOP and our market strategy PUBLIC HEALTH RELEVANCE Circular RNAs are a recently discovered non canonical form of RNA that have been shown to interact with microRNAs molecules which are important in multiple neurological disorders We are developing a user friendly kit that will enable a broad range of biomedical researchers to access and study these important molecules in order to further our understanding of their role in biology and human health


As part of Y Combinator’s push into computational biology and bioinformatics, the early-stage firm is backing a team that used to work on the Human Genome Project and is now experimenting with RNA testing through a startup called Cofactor Genomics. They argue RNA, which is the intermediate step between a person’s DNA and the proteins their bodies make, is a much more accurate and real-time way of diagnosing disease. DNA, on the other hand, is predictive. It can tell you your risks of contracting a disease later in life. But for many conditions, it can’t definitively tell you if you have them at the moment. RNA also dynamically changes over time in response to what you eat and what kind of environment you’re living in. “We believe that RNA is a better barometer of health. It changes dynamically and we think it’s a much more accurate and much earlier way to diagnose disease,” said Jarret Glasscock, the company’s CEO. “DNA is pre-symptomatic. But with RNA, we think we’ll be able to see a molecular signature sooner.” Since being founded six years ago, the St. Louis, Missouri-based company has signed contracts with nine of the country’s largest pharmaceutical companies. They couldn’t disclose who, however. They also have about $1.5 million in grant funding from the National Institutes of Health. They expect to work in diagnostics for cancer, heart disease and Alzheimer’s first, and their tests use blood samples. They don’t have an expected price range for their tests, but they hope to start making diagnostics available next year. Even though they’ve been around for six years, co-founders Glasscock, Dave Messina and Jon Armstrong felt that a connection to the Valley through Y Combinator would help their business, which is in the Midwest. “They don’t necessarily have the domain knowledge, but they make these connections in the Valley that for us are extremely important,” Glasscock said. While Cofactor focuses on RNA, there is a whole wave of DNA diagnostic companies that have been funded in Silicon Valley in recent years, including Color Genomics, which tests for breast cancer risk genes BRCA1 and BRCA2, and Counsyl, which does carrier screening to test whether parents might pass on single gene recessive disorders to their future children.


News Article | August 19, 2015
Site: techcrunch.com

Smart mattress covers, RNA diagnostics, and photosynthetic grow lights were among the big ideas that shone brightest on stage at Demo Day 1 for Y Combinator’s Summer 2015 batch. Fifty startups presented on the record, including a massive influx of hardware companies and biotech firms. You can read about all of them here. And learn about Y Combinator getting hardcore about hardware here. Click through to see TechCrunch’s picks for the top 9 startups from the day. To select our picks, we asked for the opinion of some of Silicon Valley’s top venture capitalists, as well as founders in this YC class. Then, fellow TechCrunchers Matthew Lynley, Kim-Mai Cutler, and I combined these suggestions with our own favorites and debated the merits of the candidates. Continue to see our selections, in no particular order.


ST. LOUIS--(BUSINESS WIRE)--Cofactor Genomics has been awarded a $1.5 million Phase II Small Business Innovation Research (SBIR) grant by the National Institute on Drug Abuse (NIDA) at the National Institutes of Health. This award follows a successful phase I showing the performance of Cofactor’s technology in enriching for circular RNAs (circRNAs) from multiple sample types. This product proved critical in identifying circular RNAs and will advance studies where circRNAs have been implicated, including coronary artery disease, Parkinson’s, psychiatric disorders, and cancer. Cofactor is continuing to sign up beta users to access the technology under their early access program. Learn more at https://cofactorgenomics.com/circRNA/. “Our team is aggressively continuing the development of our novel circRNA enrichment technology and are honored to be recognized by this award,” said Cofactor’s CSO, Jon Armstrong. “With recent publications implicating circular RNAs in dozens of diseases as well as interesting results coming out of our early access program, we recognize that both resistance to degradation and implications as a biomarker in disease provides a perfect opportunity for a new class of disease diagnostics,” he added. CircRNA, a non-coding transcript present in the cytoplasm, has been identified as a potential biomarker for a wide variety of common diseases such as coronary artery disease, Parkinson’s, psychiatric disorders, and various forms of cancer. Since circRNAs are present in lower abundance than other RNA molecules, and share sequence homology with mRNA, they are difficult to isolate from total RNA. Cofactor’s technology, which enriches circRNAs, paired with a way to bioinformatically identify these molecules will be a powerful tool for the future study and diagnosis of disease. Research reported in this release was supported by the National Institute on Drug Abuse (NIDA) at the National Institutes of Health under grant number R44DA038993. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Cofactor Genomics is a privately held biotechnology company founded in 2008 after the completion of the Human Genome project by Technology Development Scientists from Washington University’s Genome Center in Saint Louis, MO. Cofactor is committed to translating next-generation sequencing based technologies into stable and complete end-to-end product solutions through R&D developments that combine molecular, sequencing, and bioinformatics. Cofactor Genomics is the market leader in RNA based products and services in the rapidly expanding functional genomics market. Find out more about Cofactor Genomics at cofactorgenomics.com.


News Article | June 18, 2014
Site: recode.net

Revive & Restore has attracted worldwide attention for its ambitious plans to use genetic engineering to bring back extinct species, including the passenger pigeon and — perhaps, someday — the Woolly Mammoth. But Executive Director Ryan Phelan provided a reminder on Tuesday that the San Francisco research organization is working to preserve endangered animals as well. Onstage at the Techonomy Bio conference at the Computer History Museum in Silicon Valley, Phelan said the group wants to help the black-footed ferret through a crowdsourced project that will kick off next month. In a follow-up interview, she said they believe it’s the first “citizen science” project designed to aid endangered animals. The species was thought to be extinct until a colony of 18 was discovered in 1981 near Meeteetse, Wyo. Captive breeding, conservation and release programs have helped bolster the animal’s numbers during the last three decades, including efforts at the Smithsonian National Zoological Park. But Phelan noted that possible signs of inbreeding have emerged, specifically fertility issues that could get progressively worse in subsequent generations. Revive & Restore, co-founded by Phelan’s husband Stewart Brand of Whole Earth Catalog fame, has been working with Cofactor Genomics to sequence the DNA of several living ferrets as well as older specimens from the “Frozen Zoo” in San Diego (which I wrote about earlier this year). On July 15, they plan to launch a public website with clear descriptions of the challenges as well as the genomic datasets. They want to invite “citizen scientists” and professionals to help analyze the information and potentially pinpoint the genomic differences implicated in loss of fertility, low sperm count and other issues. “The idea is ultimately to help find out what areas of the genome have been compromised over time through this population bottleneck,” she said. What happens next, if anything, will be determined by the U.S. Fish and Wildlife Service, which oversees endangered animal programs. They could use the information to selectively breed those animals most likely to produce healthy offspring, perhaps through artificial insemination. “The idea would be to provide this knowledge to see if there’s anything that would help make more informed choices,” Phelan said. But long-term, whether with this species or others, there’s also the possibility of using genetic engineering to help along struggling animal populations. Researchers could potentially reproduce the healthy strands of the genome using DNA synthesis technology, splice it into stem cells and inject into a living species’ eggs — the same basic technique Revive & Restore is exploring for de-extinction. Elizabeth Kolbert, the New Yorker writer and author of the “Sixth Extinction,” said of the latter subject: “I’m pretty down on the idea. I think it’s basically being done for people, not for other species or for the planet. It’s being done because we think it’s cool or it assuages our guilt.” But the audience at the conference seemed nothing if not receptive, with one member, a science fiction writer, eagerly asking about the “ship date” for the passenger pigeon. The last one died in 1914. Phelan said they hope to produce the first birds within the next five years — and that flocks could once again fill the sky by 2025. “We don’t consider a one-off a success,” she said. “We consider the restoration of the species a success.”

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