Illumina retaliates against BGI

Illumina Files Patent Infringement Suit Against BGI in Germany

SAN DIEGO--(BUSINESS WIRE)--Mar 29, 2019--Illumina, Inc. (NASDAQ: ILMN) today announced that it has filed a patent infringement suit against BGI Group’s subsidiary, Latvia MGI Tech SIA, in the Düsseldorf Regional Court in Germany. The complaint alleges that BGI’s sequencing products, including the BGISeq-500, MGISeq-2000, and related chemistry reagents, infringe EP 1 530 578 B1. This patent covers Illumina’s proprietary sequencing-by-synthesis chemistry.

“Illumina will not tolerate the unauthorized, infringing use of its patented technology. Illumina filed this suit to defend the substantial investments we have made in our industry leading sequencing technology, as validated in our global intellectual property portfolio. We will continue to monitor the field and file patent suits where appropriate when our patents are infringed,” said Charles Dadswell, Senior Vice President and General Counsel for Illumina.

READ MORE …

Canopy Biosciences aims to capitalize on Sequencing Error-Correction

Canopy Biosciences Aims to Improve Rare Variant Detection With Error-Correction Sequencing Service

NEW YORK (GenomeWeb) – After receiving an exclusive license from the Washington University in St. Louis for its error-correction sequencing technology, startup Canopy Biosciences now plans to develop the bioinformatic tool further to identify and monitor ultra-rare gene variants in patient blood samples.

With the new license, Canopy will build upon its gene expression analysis portfolio by offering a streamlined research-use-only service for next-generating sequencing applications.

READ MORE …

A high-quality raspberry genome assembly is on its way

BerryWorld Plus wins KeyGene’s genome-for-free contest

KeyGene is pleased to announce that BerryWorld Plus has won the genome-for-free contest, organised on the occasion of the Genome Insights meetup on 21 March 2019 in Wageningen. The raspberry breeders at BerryWorld Plus will receive a high-quality genome assembly of a genotype of their choice.  BerryWorld Plus was selected because they are a leader in considering state-of-the-art technology to accelerate the development of premium, healthy raspberries. With this high-quality genomic resource, raspberry breeding can now fully benefit from KeyGene’s ample experience and state of the art technologies.

READ MORE …

The Banana Genome Browser is Online

This may not be particularly useful for most readers, but you should check it out simply because it is the Banana Genome Hub.

Check it out …

Promise of cheap and fast CRISPR-based diagnostics

Handheld CRISPR device to enable faster diagnosis of genetic disease

A team of researchers in the US has developed a handheld device that diagnoses genetic diseases at point-of-care. Called CRISPR-Chip, the device combines a deactivated clustered regularly interspaced short palindromic repeats (CRISPR) Cas9 protein with electronic transistors to identify genetic mutations in DNA samples without the need for amplification or replication of the DNA segment using the polymerase chain reaction (PCR).

Avoiding the time-consuming PCR step is expected to enable the use of CRISPR-Chip for genetic testing in a doctor’s office or field work setting, rather than sending samples to a laboratory.

The method can also be used to assess the accuracy of gene-editing techniques.

The researchers included scientists from the University of California, Berkeley (UC Berkeley) and the Keck Graduate Institute (KGI) of The Claremont Colleges.

READ MORE HERE …

And HERE …

And watch the promo video HERE …

NGS-heavy investigation of Neuropsychiatric Disease

Illumina, University of Copenhagen to Study Genetic Evolution of Neuropsychiatric Disease

NEW YORK (GenomeWeb) – Illumina said today that it is working with the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen to study how infectious pathogens influenced the evolutionary history of certain mental and neurological disorders.

An international, multi-disciplinary team including specialists in ancient genomics, neurogenetics, population genetics, archaeology, linguistics, and brain health will create two subsets of genomics data: one consisting of 5,000 ancient human genomes, and another consisting of ancient pathogen DNA associated with human diseases. Both datasets will be made publicly available.

The research team will use Illumina's NovaSeq 6000 system with S4 flow cells to sequence up to 20 billion ancient DNA fragments every two days, Illumina said.

READ MORE …

Liquid Biopsies help with Lung Cancer Diagnostics

Illumina-Sponsored Study Finds Liquid Biopsy Complements Tissue-Based Genotyping in Lung Cancer

NEW YORK (GenomeWeb) – The Illumina-sponsored Actionable Genome Consortium reported this week that cell-free DNA-based tumor genotyping for non-small cell lung cancer patients is concordant with tissue tumor-based genotyping most of the time and could be particularly useful in cases where acquiring a tissue biopsy is not feasible.

The group, which includes researchers from Memorial Sloan Kettering Cancer Center, Dan-Farber Cancer Center, MD Anderson Cancer Center, Grail, and Illumina, published its study this week in Annals of Oncology.

READ MORE …

Abbot gets clearance for Alinity Molecular Diagnostics

Abbott Receives CE Mark for Alinity Molecular Diagnostics System, Assays

“NEW YORK (GenomeWeb) – Abbott announced today that it has received CE marking for its Alinity molecular diagnostics system and assays, which are now available in countries that recognize the designation.

The firm said that its molecular system will help clinicians who are struggling to keep up with demand for infectious disease testing.

The MDx platform offers a number of initial assays, including virology testing for human immunodeficiency virus type 1, hepatitis B virus, and hepatitis C virus; sexual health-related testing for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, and Mycoplasma genitalium, or a CT/NG/TV/MG panel; and high-risk human papillomavirus testing.“

READ MORE …

Walnut genome to be sequenced by UC Davis and USDA

Deciphering the Walnut Genome

“In a new study, a team of scientists at the University of California, Davis, and USDA’s Agricultural Research Service (ARS) used a unique approach to sequence the genomes of the English walnut and its wild North American relative by tapping into the capabilities of two state-of-the-art technologies: long-read DNA sequencing and optical genome mapping. The resulting genome sequences are believed to be of the highest quality ever assembled of any woody perennial.”

READ MORE …

Genome sequencing has been getting cheaper, but library preps haven't--until now

IDT lowers genomic barriers with targeted sequencing system

“Itegrated DNA Technologies (IDT) has introduced its rhAmpSeq targeted sequencing system, providing researchers with highly accurate, cost-effective and easy-to-use amplicon sequencing on Illumina next-generation sequencing (NGS) platforms. The rhAmpSeq chemistry enables multiplexing at impressive levels with high on-target rates and uniform coverage, delivering accurate results and accelerating projects. The system has wide-ranging applications, including human disease research and sample tracking and analysis, CRISPR genome editing analysis and agricultural biotechnology.”

READ MORE …

Motley-Fool's monthly speculation on cancer treatment stocks

3 Cancer Treatment Stocks to Buy in March

There has been tremendous progress in the battle against cancer, but it remains the second leading cause of death in the U.S., behind heart disease. That means there is plenty of work left to be done.

So which cancer-focused companies are worth watching? We asked three Motley Fool healthcare contributors to weigh in, and they called out Blueprint Medicines(NASDAQ:BPMC), Halozyme Therapeutics (NASDAQ:HALO), and Merck (NYSE:MRK). 

READ MORE …

Interesting Indian Genomics Advertorial

Genes2Me- Bringing New Healthcare Paradigm with Genomics

Genes2Me, India’s first diagnostic chain to bridge clinical diagnostics with genomics has reinvigorated the preventive healthcare sector in the country. Genes2Me has evolved as a game changer in the field of molecular testing by yielding health statistics of today and suitable lifestyle guidance for a healthy tomorrow. 

Read more …

Fisher makes big move buying Brammer Bio

Thermo Fisher to acquire Brammer Bio in $1.7 billion deal

(Reuters) - Thermo Fisher Scientific Inc, the world’s largest maker of scientific instruments, said on Sunday it has agreed to buy Brammer Bio in a roughly $1.7 billion cash deal.

Brammer Bio, a viral vector manufacturer for gene and cell therapies, is expected to post $250 million in revenue for 2019, Thermo Fisher said in a statement.

READ MORE …

Strata Oncology using NGS for advanced cancer

Strata Oncology Launches Expanded StrataNGS for Patients with Advanced Cancer

ANN ARBOR, Mich., March 19, 2019 /PRNewswire/ -- Strata OncologyTM, a leading precision oncology company, today announced the launch of version 3.0 of StrataNGSTM, its pan-cancer assay for solid tumors. The updated 500-gene assay utilizes DNA and RNA from tumor samples to detect all clinically actionable biomarkers — including microsatellite instability (MSI), tumor mutational burden (TMB), and PD-L1 — recommended by leading guidelines, in a single test. Test results are provided in a streamlined report that facilitates rapid, confident interpretation and identification of potential treatment options and clinical trials.

READ MORE …

New CRISPR Diagnostics Firm

Broad, Wyss Institute Researchers Launch CRISPR Dx Firm Sherlock Biosciences

NEW YORK (GenomeWeb) – Engineering biology startup Sherlock Biosciences announced today that it has launched with initial financing of $35 million and licenses to foundational CRISPR and synthetic biology technology from the Broad Institute and Harvard's Office of Technology Development…

Sherlock will use engineering biology tools, including CRISPR and synthetic biology, to develop a new generation of molecular diagnostics that can rapidly deliver accurate results for a vast range of needs in virtually any setting and at low cost, the company said.

The financing includes a $17.5 million non-dilutive grant and an investment from the Open Philanthropy Project, as well as funds from additional undisclosed investors.

READ MORE …

Setback for myeloma therapy Venclexta

Roche, AbbVie forced to slam brakes on myeloma studies of star drug Venclexta after researchers flag higher risk of death

“Two heavyweight pharma players today said they’ve been forced to stop recruiting patients for all ongoing studies involving Venclexta (venetoclax) for multiple myeloma. Roche and AbbVie say the drug arm has been linked to a higher rate of death than the control group, prompting the FDA to issue a partial hold ordering them to suspend any new patient recruitment for the blood cancer trials until they can sort out what is happening.“

READ MORE …

Distinguishing amplification artifacts from biologically derived somatic mutations in single-cell sequencing data

Linked-read analysis identifies mutations in single-cell DNA-sequencing data

Craig L. Bohrson, Alison R. Barton, Michael A. Lodato, Rachel E. Rodin, Lovelace J. Luquette, Vinay V. Viswanadham, Doga C. Gulhan, Isidro Cortés-Ciriano, Maxwell A. Sherman, Minseok Kwon,  Michael E. Coulter, Alon Galor, Christopher A. Walsh & Peter J. Park

Nature Genetics (Research Article)

Whole-genome sequencing of DNA from single cells has the potential to reshape our understanding of mutational heterogeneity in normal and diseased tissues. However, a major difficulty is distinguishing amplification artifacts from biologically derived somatic mutations. Here, we describe linked-read analysis (LiRA), a method that accurately identifies somatic single-nucleotide variants (sSNVs) by using read-level phasing with nearby germline heterozygous polymorphisms, thereby enabling the characterization of mutational signatures and estimation of somatic mutation rates in single cells.

Google AI variant caller goes deep on rice genomes

Analyzing 3024 rice genomes characterized by DeepVariant

“Rice is an ideal candidate for study in genomics, not only because it’s one of the world’s most important food crops, but also because centuries of agricultural cross-breeding have created unique, geographically-induced differences. With the potential for global population growth and climate change to impact crop yields, the study of this genome has important social considerations.

This post explores how to identify and analyze different rice genome mutations with a tool called DeepVariant. To do this, we performed a re-analysis of the Rice 3Kdataset and have made the data publicly available as part of the Google Cloud Public Dataset Program pre-publication and under the terms of the Toronto Statement.

We aim to show how AI can improve food security by accelerating genetic enhancement to increase rice crop yield. According to the Food and Agriculture Organization of the United Nations, crop improvements will reduce the negative impact of climate change and loss of arable land on rice yields, as well as support an estimated 25% increase in rice demand by 2030.”

READ MORE …

ALS Awards for target discovery and therapy development

TARGET ALS AWARDS SIX INNOVATIVE RESEARCH TEAMS WITH ADDITIONAL TARGET DISCOVERY FUNDS

New York City – Target ALS is pleased to announce that it has awarded target discovery and development funding to six research consortia that are working toward the development of ground-breaking therapeutic approaches to treating ALS.

In 2016 – 2017, Target ALS provided multi-year grants to a number of unique research consortia to encourage ALS research ideation and active involvement from both the pharma/biotech industry as well as the most talented new investigators in the field. In a historic first, either a pharma/biotech researcher or a new investigator led each team. These teams were awarded funding for a range of novel projects from early stage target discovery to the development of new therapeutic approaches.

A wave of creative thinking and collaboration followed. Indeed, many projects have led to the development of new, ground-breaking therapeutic approaches while others are advancing our understanding of pathophysiology of ALS.  In response to this growing momentum, the Target ALS Independent Review Committee (IRC) granted six of the most promising collaborative projects an additional year of funding.

READ MORE …

Personalis introduces new universal cancer immunogenomics platform, ImmunoID NeXT™

Personalis, Inc. to Present at ICI-IO Combinations Summit 2019

MENLO PARK, Calif.--(BUSINESS WIRE)--Personalis Inc., a leader in advanced genomics for precision oncology, today announced that they are scheduled to present at ICI-IO Combinations Summit 2019 in Boston on Wednesday, March 20, 2019 at 2:30 PM, EDT.

The presentation, entitled “Challenges and Solutions: Enabling multidimensional tumor immunogenomics for advancing biomarker discovery,” will introduce Personalis’ new universal cancer immunogenomics platform, ImmunoID NeXT™. In addition to an overview, the presentation will also highlight how this platform can be used to overcome the challenges facing immuno-oncology translational and clinical researchers. By deriving new insights through our industry leading NGS analysis platform, ImmunoID NeXT provides solutions to enable the development of safer, more effective precision oncology therapeutics and combinations.

READ MORE …