“Polygenic Adaptation”
“CRISPR-Cas9 is a method for quickly and accurately editing the genome of virtually any living thing… “
Article by Adam Bluestein / Illustration by Jamie Cullen
NEW YORK (GenomeWeb) — Swedish startup Cartana has signed an agreement to integrate its in situ RNA sequencing (ISS) technology with Lunaphore Technologies' microfluidic tissue processor technology.
Cartana's technology, which was originally developed in the lab of Stockholm University's Mats Nilsson, is based on using barcoded padlock probes to target genes of interest. The probes target cDNA and are amplified in situ using rolling circle amplification, followed by sequencing-by-ligation, also directly on the tissue.
Under the terms of the deal, the companies will work with Nilsson to join the technology with Lunaphore's Fast Fluidic Exchange rapid immunohistochemistry platform in order to develop hardware for automated sequencing and imaging cycles.
Want remarkably clear insights into genetics and public health with a bare minimum of reading? Well, some corners of Twitter have recently become an incredible resource if you’re interested in learning something about predictive statistics, epidemiology, genomics, and population genetics. There are no better examples of this than the tweetorials that Dr. Cecile Janssen posts. Dr. Janssen is a professor of translational epidemiology in the department of Epidemiology of the Rollins School of Public Health, Emory University, and her website, like her posts, contains insightful guides for thinking critically about DNA sequence data, heritability and health.
If you would like some key insights into predicting complex traits from DNA in a handful of tweets, follow this link: Why it is so hard to predict complex diseases and traits from DNA?
For a slightly longer read, here’s her article from WIRED on how DNA is best applied: DNA tells great stories -- about the past, not future
And a more advanced read, still aimed at a fairly general audience: Designing babies through gene editing: science or science fiction?
Tempus, a health technology building massive data sets of cancer-related information, knowledge-bases, has acquired an additional $200 million in funding. This injection of cash brings the Chicago based startup’s valuation to $3.1 billion and is reportedly intended to permit increased growth and the investigation of additional pathologies, such as diabetes and depression. With moves like this, Tempus seems like it’s worth watching. Read More at Forbes
A subsidiary of the Chinese sequencing giant BGI is filing a patent infringement suit agains the US sequencing giant. The BGI subsidiary, Complete Genomics, filed its complaint in the the District Court of Deleware, claiming infringement on a patent for “methods and compositions for efficient base calling in sequencing reactions,” which is all pretty central to high throughput sequencing. This appears to be a response to Illumina filing a complaint earlier this month against BGI Europe and Latvia MGI Tech, another BGI subsidiaries, earlier this year. These are probably just the early stages of what is likely to be a long series of antagonistic maneuvers between giants. It is unlikely that this Coke-versus-Pepsi style competition will do much to reduce the dominance of these groups, but one can hope that as this battle plays out some of the smaller sequencing players will grow and insert a little more competition into the market.
All the links in this post are from Genome-Web, another excellent genome news source.
“Each passing year, the success of cell and gene therapy (CGT) becomes clearer, more widely covered in the media, and is increasingly the focus of a rapidly growing society of researchers. Making sense of this extensive ecosystem is no small feat, but by using a data-driven approach, we can get closer to determining what the future holds for CGT.
CGT has emerged as one of the most exciting areas of biotechnology. Its buzz can be attributed to the hope these therapies hold for patients with rare and often deadly inherited diseases; the scientific promise and intrigue of gene editing; and the business opportunity that these revolutionary therapies with lucrative price tags hold.
But what do we really know about cell and gene therapy? What proverbial gold will be found at the end of this rainbow?“
Biotech entrepreneur Darrin Disley, ex-CEO and co-founder of the successful Cambridge gene editing biotech Horizon Discovery, has a new quest — creating the perfect cell therapy. He spoke to me about his position as CEO of new biotech Mogrify and why he thinks now is a good time to get into cell therapy.
Following the meteoric rise of Horizon Discovery from a small startup in 2007 to a company of 500 people and a market cap of more than €445M, Disley decided to step down as CEO of the gene editing company in February 2018. After taking a year off to travel and “get fit and healthy” he is now back in Cambridge and firmly back on the biotech scene to head up a new cell therapy biotech.
Mogrify, which has recently raised a seed round of €3.3M to kick start its technology development, specializes in transforming one type of cell into another. The key difference from other cell transformation methods is that the company can find the chemical recipe needed to flip one adult cell into another adult cell type, without transforming it into a stem cell first.
“If you could take a cell from one part of the body and turn it into any other cell at any other stage of development for another part of the body, you effectively have the Holy Grail of regenerative medicine,” enthused Disley.
Stifel Financial Corp boosted its holdings in Invesco Dynamic Biotechnology & Genome ETF (NYSEARCA:PBE) by 34.4% during the 4th quarter, according to its most recent disclosure with the Securities & Exchange Commission. The institutional investor owned 21,776 shares of the company’s stock after buying an additional 5,578 shares during the quarter. Stifel Financial Corp owned approximately 0.40% of Invesco Dynamic Biotechnology & Genome ETF worth $1,025,000 at the end of the most recent reporting period.
A number of other large investors have also added to or reduced their stakes in PBE. SG Americas Securities LLC acquired a new position in shares of Invesco Dynamic Biotechnology & Genome ETF in the third quarter worth about $452,000. Morgan Stanley boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 6.5% in the third quarter. Morgan Stanley now owns 153,962 shares of the company’s stock worth $9,153,000 after buying an additional 9,391 shares during the period. Carnegie Capital Asset Management LLC boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 10.7% in the third quarter. Carnegie Capital Asset Management LLC now owns 5,330 shares of the company’s stock worth $271,000 after buying an additional 515 shares during the period. B. Riley Financial Inc. boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 14.4% in the third quarter. B. Riley Financial Inc. now owns 6,982 shares of the company’s stock worth $415,000 after buying an additional 880 shares during the period. Finally, YHB Investment Advisors Inc. boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 19.0% in the fourth quarter. YHB Investment Advisors Inc. now owns 25,395 shares of the company’s stock worth $1,195,000 after buying an additional 4,050 shares during the period.
Julia Karow, GenomeWeb
SEATTLE (GenomeWeb) – A study led by researchers at Invitae has found that 23andMe's direct-to-consumer BRCA test, which tests for three common variants in the BRCA1 and BRCA2 genes and is authorized by the US Food and Drug Administration, misses almost 90 percent of BRCA mutation carriers, both in those with and those without a personal or family history of cancer.
In addition, it misses almost 20 percent of BRCA mutations in those of self-reported Ashkenazi Jewish descent because it doesn't test for them.
The results of the study, which looked at data from almost 125,000 de-identified individuals who had been referred to Invitae for diagnostic testing with one of the firm's cancer risk tests, was presented yesterday at the American College of Medical Genetics and Genomics annual meeting by Edward Esplin,Dian a clinical geneticist at Invitae.
Esplin told GenomeWeb that the study, which did not mention 23andMe by name, was meant to criticize a screening strategy with an FDA-authorized DTC test that appears to have limited clinical utility rather than to criticize 23andMe for offering the test.
In his presentation, he pointed out that the FDA's authorization for the test last year "sounds more like a warning than an approval." FDA cautioned that the test, which examines three founder mutations in the BRCA genes that are common in the Ashkenazi Jewish population, does not assess more than 1,000 other known BRCA mutations, so a negative result does not rule out someone is a mutation carrier. It also advises that positive test results should not be used to determine any treatments without confirmatory testing and genetic counseling.
BOULDER, Colo.--(BUSINESS WIRE)--Inscripta, a leading gene editing technology company, today announced that it has increased its previously announced Series C financing with an additional $20 million from existing investors. The new funding adds to the $85.5 million financing Inscripta announced in 2018, bringing the total raised for the round to $105.5 million.
A plethora of technologies are currently required to assess different genomic and epigenomic alterations; however, the associated costs and long turnaround times combined with extensive infrastructure and training requirements have, to date, hindered their implementation1 . To address these challenges, Dr. Philippe Euskirchen and co-workers at the ICM Brain and Spine Institute, France, assessed the potential of nanopore sequencing technology to deliver comprehensive and cost-effective characterisation of genetic alterations in brain cancer samples — including analysis of copy number (CN) alterations, epigenetic base modifications, and single nucleotide variations (SNVs)1,2. Furthermore, all nanopore sequencing workflows were designed to go from sample to result within a single day.
Single Cell Genomics is a rapidly growing market due to the new emerging methodologies in which the genomic technologies are applied at the single cell level, rather to all the cells collectively. The single cell genomic technologies are opening new boundaries by separating the contributions of single cells to the diversity of ecosystem and organisms. The single cell genomics is also creating new insight into multifaceted biological systems that range from the microbial ecosystem diversity to the human cancer genomics. To mention an example, the single cell genomics can probably be used to identify as well as assemble the genomes of the microorganisms which cannot be cultured, single cell genomics also evaluates the part genetic mosaic plays in the normal physiology and also determines the role of intra tumor genetic variation responsible for cancer development or treatment. However, the single cell genomics has the ability to evaluate a single DNA molecule from single isolated cells, but the process is technically challenging.
On Tuesday, DNA testing startup Helix launched a new test that looks at your risk of diseases like breast cancer, colon cancer, and high cholesterol.
You can buy the test online for $260, but it must be approved by a physician.
Helix partnered with clinical diagnostics company PerkinElmer to create the test, which includes genetics counseling.
The test also uses a type of sequencing that some experts say all DNA-based health tests should use.
READ MORE … and HERE …
ATLANTA--(BUSINESS WIRE)--Apr 1, 2019--OncoCell MDx, a company developing novel noninvasive diagnostic and prognostic tests, will present results from a feasibility study of a new prostate cancer prognostic assay in a late-breaking poster session at the American Association of Cancer Research (AACR) Annual Meeting tomorrow. The study demonstrates that the blood-based immunogenomics RNA expression assay provides a prognostic summary comparable to that of prostate biopsy.
OncoCell’s Subtraction-Normalized Expression of Phagocytes (SNEP) based platform, invented by Professor Amin Kassis, while at Harvard Medical School, uses a proprietary algorithm to interrogate changes in gene expression of two immune cell types consequent to prostate cancer including phagocytic (CD14) and non-phagocytic (CD2) cells, filters out intrinsic genomic variation not related to the disease, and identifies and validates prostate cancer-specific signatures. A study of blood samples from 713 prostate cancer patients showed the platform provides a prognostic summary including tumor Gleason grade distribution, size/volume and heterogeneity that is comparable to prostate biopsy information, and that it stratifies patients with aggressive disease that need life-saving treatment from those with indolent disease.
SEATTLE--(BUSINESS WIRE)--Apr 1, 2019--Fabric Genomics will launch a new solution this week for variant interpretation and clinical reporting, allowing clinical laboratories to dramatically accelerate turnaround times. This new software solution, called Fabric Hereditary Panels with ACE (AI Classification Engine), will debut at the American College of Medical Genetics and Genomics (ACMG) annual meeting in Seattle, Washington. It incorporates an extensively validated, automated ACMG classification engine, enabling laboratories to speed up accurate variant classification and clinical reporting.
CAMBRIDGE, Mass. and SHANGHAI, March 30, 2019 /PRNewswire/ -- WuXi NextCODE, a global genomic data and insights company, is expanding its laboratory footprint into the U.S. with the opening of a state-of-the-art, CLIA-certified and CAP-accredited genetic analysis laboratory in Woburn, Massachusetts. The new laboratory is geographically close to WuXi NextCODE's U.S. office in Cambridge, Massachusetts.
"This new laboratory helps us provide our customers with the access to next generation sequencing for clinical trials around the world, under the roof of one single, highly respected organization," says Rob Brainin, Chief Executive Officer of WuXi NextCODE. "Our global lab footprint also ensures a seamless unified workflow with a single chain of custody, from sample management, standard operating procedures, rigorous implementation of quality systems, to analytics and standardized reporting, in the U.S., Asia and the E.U."
As the first CAP/CLIA/ISO 15189 certified laboratory in China, the company's Shanghai laboratory already offers comprehensive next generation sequencing (NGS) clinical and discovery research services. WuXi NextCODE has also recently acquired a large scale NGS laboratory in Dublin, Ireland, which is already CAP-accredited and anticipated to be CLIA-certified in the third quarter of 2019.
Sacks of pungent animal feed cram the corridors of a Cyagen Biosciences Inc. center for laboratory mice in southern China, maximizing space for rodents that sell for as much as $17,000 a pair.
Demand is skyrocketing in China for animals that mimic the diseases of humans. President Xi Jinping’s drive to turn the country into a biomedical powerhouse by 2025 has pushed the country deeper into drug discovery and to the forefront of genetics. That’s helping fuel a global market for gene-altered mice predicted to expand 7.5 percent a year to top $1.59 billion by 2022.
Researchers from South Korea said they have developed a next-generation sequencing (NGS) assay to detect somatic mutations, translocations, and germline mutations in a single assay for the purpose of supplementing or replacing conventional tests in patients with myeloid neoplasms.
Writing in a recent issue of PLoS One, the researchers said were able to discover a high frequency of germline mutations in cancer predisposition genes. Patients with these mutations exhibited different clinical characteristics, suggesting that germline predisposition has significant clinical implications.
Production, consumption, revenue, gross margin, cost, gross, market share, CAGR, and genotyping market influencing factors are outlined in this report. This report includes all company profiles for top players and brands as well as a synopsis of market definition, classifications and trends in the market. The genotyping market’s drivers and limitations were derived from a well-known SWOT analysis method. Regional market segmentation included North America, Europe, Asia-Pacific, Latin America, the Middle East and Africa’s historical and forecast mandates. We took up their company profiles in order to truly understand these key players and brands. The genotyping report provides a far-reaching analysis of the genotyping market by type, application, player, and region. The Global genotyping Market Report has published all business profiles of leading players and brands. This report focuses on genotyping global, regional and business volume and value.
Molecular Cancer Therapeutics (Research Article)
Abstract—Malignant gliomas are a group of intracranial cancers associated with disproportionately high mortality and morbidity. Here we report ultradeep targeted sequencing of a prospective cohort of 237 tumors from 234 patients consisting of both glioblastoma (GBM) and lower-grade glioma (LGG) using our customized gene panels. We identified 2485 somatic mutations including single nucleotide substitutions and small indels using a validated in-house protocol. Sixty one percent of the mutations were contributed by 12 hypermutators. The hypermutators were enriched for recurrent tumors, had comparable outcome, and most were associated with temozolomide exposure. TP53 was the most frequently mutated gene in our cohort, followed by IDH1 and EGFR. We detected at least one EGFR mutation in 23% of LGGs, which was significantly higher than 6% seen in TCGA, a pattern that can be partially explained by the different patient composition and sequencing depth. IDH hotspot mutations were found with higher frequencies in LGG (83%) and secondary GBM (77%) than primary GBM (9%). Multivariate analyses controlling for age, histology, and tumor grade confirm the prognostic value of IDH mutation. We predicted 1p/19q status using the panel sequencing data, and received only modest performance by benchmarking the prediction to Fluorescent In Situ Hybridization (FISH) results of 50 tumors. Targeted therapy based on the sequencing data resulted in three responders out of 14 participants. In conclusion, our study suggests ultradeep targeted sequencing can recapitulate previous findings and can be a useful approach in the clinical setting.
