WuXi NextCODE expanding Illumina sequencing capabilities

WuXi NextCODE Launches New State-of-the-art Genetic Analysis Laboratory in U.S. with Illumina's New TruSight 500™ Assay

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.

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Demand for genetically-modified mice skyrocketing in China

China's Selling Genetically-Modified Mice for $17,000 a Pair

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.

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Classic sex chromosome evolution

Sex chromosome evolution of Wallace's birds-of-paradise

Qi Zhou

Ecology & Evolution

“Two groups of birds, Darwin’s finches and Birds-of-Paradise are historically and respectively associated with the discoverers of the rules of natural selection:Charles Darwin and Alfred Wallace. These two groups of species are also among the best demonstration of natural selection and sexual selection. We reconstructed the history of sex chromosome evolution of bird-of-paradise, and also other songbirds in this work.”

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Tasmanian devils adapting to transmissible cancers

Tasmanian devils 'adapting to coexist with cancer'

There's fresh hope for the survival of endangered Tasmanian devils after large numbers were killed off by facial tumours.

The world's largest carnivorous marsupials have been battling Devil Facial Tumour Disease (DFTD) for over 20 years.

But researchers have found the animals' immune system to be modifying to combat the assault.

And according to an international team of scientists from Australia, UK, US and France, the future for the devils is now looking brighter.

"In the past, we were managing devil populations to avoid extinction. Now, we are progressively moving to an adaptive management strategy, enhancing those selective adaptations for the evolution of devil/DFTD coexistence," explains Dr Rodrigo Hamede, from the University of Tasmania.

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Snake venom genomics provides important insights

New insights into chromosome evolution, venom regulation in snakes

How do snake genomes direct the production of deadly venom toxins and other key extreme features of snakes?

Snake genomes encode the secrets to their unique and often extreme adaptations, but genome resources for snakes and other reptiles have lagged behind their mammal and bird counterparts.

In a new paper, a team of biologists led by Todd Castoe, associate professor of biology at The University of Texas at Arlington, addressed these questions by generating and analyzing the first most complete chromosome-level genome for a snake – the prairie rattlesnake (Crotalus viridis). Their work, “The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes,” is published in the April issue of Genome Research, the scientific journal published by Cold Spring Harbor Laboratory.

Clinical application of tumor evolution analysis

Translating insights into tumor evolution to clinical practice: promises and challenges

Matthew W. Fittall and Peter Van Loo

Genome Medicine (Review Article)

Abstract—Accelerating technological advances have allowed the widespread genomic profiling of tumors. As yet, however, the vast catalogues of mutations that have been identified have made only a modest impact on clinical medicine. Massively parallel sequencing has informed our understanding of the genetic evolution and heterogeneity of cancers, allowing us to place these mutational catalogues into a meaningful context. Here, we review the methods used to measure tumor evolution and heterogeneity, and the potential and challenges for translating the insights gained to achieve clinical impact for cancer therapy, monitoring, early detection, risk stratification, and prevention. We discuss how tumor evolution can guide cancer therapy by targeting clonal and subclonal mutations both individually and in combination…

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Next Generation Sequencing Assay for Blood Cancers

Researchers Develop Targeted Next Generation Sequencing Assay for Myeloid Neoplasms

via GIPHY

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.

Lowering the barrier to stem cell therapies

Team develops iPS cells with less chance of being rejected

Researchers developed a way to produce induced pluripotent stem (iPS) cells with a lower risk of rejection, overcoming a major obstacle to the clinical application of regenerative medicine.

A team headed by Akitsu Hotta, a junior associate professor at Kyoto University’s Center for iPS Cell Research and Application (CiRA), used genome editing technology to change the structure of genes to create safer iPS cells. The findings were published in the U.S. scientific journal Cell Stem Cell on March 8.

Although using donor blood of third-party individuals results in cheaper and faster iPS cell production, the procedure poses a higher risk of immune rejection after transplantation.

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Genotyping Market Overview

Genotyping Market to Undergo Very High CAGR Growth by 2024 | A report by Illumina, Thermo Fisher Scientific, Agilent Technologies, Bioline, Qiagen, Danaher, F. Hoffmann-La Roche and other

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.

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Deep sequencing of Adult Gliomas has promising results

Prospective Clinical Sequencing of Adult Glioma

Siyuan Zheng, Kristin Alfaro-Munoz, Wei Wei, Xiaojing Wang, Fang Wang, Agda Karina Eterovic, Kenna R Mills Shaw, Funda Meric-Bernstam, Gregory N Fuller, Ken Chen, Roel G. Verhaak, Gordon B. Mills, W.K. Alfred Yung, Shiao-Pei Weathers and John F. de Groot

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.

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CRISPR cut slows aging

Recently Developed Gene Therapy Assists To Slow Down Aging Process

Aging is a key risk factor for numerous debilitating conditions. It includes cancer, heart disease, and Alzheimer’s disease. This situation triggers the anti-aging treatments all the more critical. Recently, the researchers at Salk Institute proclaimed that they have developed a novel gene therapy to assist decelerate this aging process.

The findings of this research can be accessed in the journal Nature Medicine. The study highlights a new CRISPR/Cas9 genome-editing therapy. It holds an ability to curb the accelerated aging observed in mice suffering from Hutchinson-Gilford progeria syndrome. This is an uncommon genetic disorder that is found to be afflicting humans as well. The latest treatment offers key insight into the molecular pathways engaged in accelerated aging. It also highlights how to minimize toxic proteins using gene therapy. Juan Carlos Izpisua Belmonte, Professor, Gene Expression Laboratory, Salk, is the senior author of this study. He proclaimed that aging is a complicated process in which cells begin losing their functionality.

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Or read the original article HERE …

RNA-based method for killing cancer cells

Scientists may have found a way to kill cancer cells without chemotherapy

• Researchers at Northwestern have discovered a genetic "kill code" that might enable the destruction of cancer cells.

• This novel new therapy "downstream" of chemo might destroy cancer cells without affecting the body's immune system.

• While no animal trials have been conducted, this potential therapy could signal the demise of chemotherapy.

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Cockroaches thrive with extra-large genomes

American cockroaches thrive in cities, thanks to their incredibly long genomes

“Few insects have a reputation for grossing people out as thoroughly as the American cockroach. The so-called water bugs, which thrive indoors on fermenting and rotting foods, are rich sources of disease-causing bacteria. Now, researchers have sequenced their genome for the first time—and have uncovered some of the secrets to their uncanny ability to survive in our urban jungles.

Compared with other insects, the genome of the American cockroach (Periplaneta americana) is the second largest sequenced to date after the locust. Like the locust, much of the cockroach genome, some 60%, is made of repetitive elements—sequences of DNA that occur over and over. And compared with three other species in its family—the German cockroach and two termite species—it is actually more closely related to the termites.“

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6mer seed toxicity in tumor suppressive microRNAs

6mer seed toxicity in tumor suppressive microRNAs

Quan Q. Gao, William E. Putzbach, Andrea E. Murmann, Siquan Chen, Aishe A. Sarshad, Johannes M. Peter, Elizabeth T. Bartom, Markus Hafner, & Marcus E. Peter

Nature Communications (Research Article)

Abstract—Many small-interfering (si)RNAs are toxic to cancer cells through a 6mer seed sequence (positions 2–7 of the guide strand). Here we performed an siRNA screen with all 4096 6mer seeds revealing a preference for guanine in positions 1 and 2 and a high overall G or C content in the seed of the most toxic siRNAs for four tested human and mouse cell lines. Toxicity of these siRNAs stems from targeting survival genes with C-rich 3′UTRs. The master tumor suppressor miRNA miR-34a-5p is toxic through such a G-rich 6mer seed and is upregulated in cells subjected to genotoxic stress. An analysis of all mature miRNAs suggests that during evolution most miRNAs evolved to avoid guanine at the 5′ end of the 6mer seed sequence of the guide strand. In contrast, for certain tumor-suppressive miRNAs the guide strand contains a G-rich toxic 6mer seed, presumably to eliminate cancer cells.

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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.

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High-resolution, single-cell DNA domain analysis in vivo, identify domain structures that change with cell identity

Visualizing DNA folding and RNA in embryos at single-cell resolution

Leslie J. Mateo, Sedona E. Murphy, Antonina Hafner, Isaac S. Cinquini, Carly A. Walker & Alistair N. Boettiger Nature (Research Article)

Abstract

The establishment of cell types during development requires precise interactions between genes and distal regulatory sequences. We have a limited understanding of how these interactions look in three dimensions, vary across cell types in complex tissue, and relate to transcription. Here we describe optical reconstruction of chromatin architecture (ORCA), a method that can trace the DNA path in single cells with nanoscale accuracy and genomic resolution reaching two kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila embryos and labelled around 30 RNA species in parallel. We identified cell-type-specific physical borders between active and Polycomb-repressed DNA, and unexpected Polycomb-independent borders. Deletion of Polycomb-independent borders led to ectopic enhancer–promoter contacts, aberrant gene expression, and developmental defects. Together, these results illustrate an approach for high-resolution, single-cell DNA domain analysis in vivo, identify domain structures that change with cell identity, and show that border elements contribute to the formation of physical domains in Drosophila.

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Check out the GenomeWeb summary HERE …

‘Jumping genes’ drive many cancers

‘Jumping genes’ drive many cancers

Mistakes in DNA are known to drive cancer growth. But a new study, from Washington University School of Medicine in St. Louis, heavily implicates a genetic phenomenon commonly known as “jumping genes” in the growth of tumors.

The study is published March 29 in the journal Nature Genetics.

Since jumping genes aren’t mutations — mistakes in the letters of the DNA sequence — they can’t be identified by traditional cancer genome sequencing. As such, this study opens up new lines of research for future cancer therapies that might target such genes.

Jumping genes, which scientists call transposable elements, are short sections of the DNA sequence that have been incorporated randomly into the genome over the long course of human evolution. The evolutionary histories of jumping genes are the subject of much current research, but viral infection is thought to play an important role in their origins.

Researchers led by Ting Wang, PhD, the Sanford C. and Karen P. Loewentheil Distinguished Professor of Medicine, have plumbed genomic databases, looking specifically for tumors whose jumping genes are driving cancer growth.

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Specificity helps with cancer outcome prediction, therapies

Acute Erythroleukemia Genomic Subtypes Help Predict Outcomes, Suggest Therapies

NEW YORK (GenomeWeb) – A new genomic analysis of acute erythroid leukemia (AEL) has uncovered recurrent tumor gene mutation and expression profiles, including genomic features that appear to coincide with outcomes for patients affected by the rare, difficult-to-treat form of acute myeloid leukemia (AML).

"These results mark a new era in understanding and treatment of AEL, an aggressive leukemia that has been plagued by diagnostic controversy and poor outcomes," senior author Charles Mullighan, a pathology researcher and co-leader of the St. Jude Children's Research Hospital's hematological malignancies program, said in a statement. 

As they reported online today in Nature Genetics, Mullighan and colleagues performed whole-genome, exome, targeted, and transcriptome sequencing on samples from 159 pediatric or adult AEL patients treated at sites around the world, comparing the somatic mutations and gene expression patterns they found to those in samples from more than 1,900 individuals with non-AEL conditions — from other forms of AML to myelodysplastic syndrome.

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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.

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Origins and Evolution of Mental Health Genetic Variants

Illumina and the Lundbeck Foundation GeoGenetics Centre Collaborate to Generate One of the Largest Ancient Genome Datasets to Decode the Genetic Origins and Evolution of Mental Health Issues

SAN DIEGO--(BUSINESS WIRE)--Illumina (NASDAQ:ILMN) and the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen, Denmark partner to explore the relationship between the evolutionary history of select mental and neurological disorders and infectious pathogens. One of the first projects of its kind worldwide, the endeavor aims to acquire new knowledge in terms of the medical and biological understanding of special factors underlying the development of human neuropsychiatric diseases through the ages. Ultimately, the project may provide a new approach to the development of medicines and other therapeutic treatments for mental and neurological conditions.

Where do brain disorders come from? In an effort to shed light on the role of microbes in the pathogenesis of neuropsychiatric illnesses, such as Alzheimer’s disease and schizophrenia, Professor Eske Willerslev and his team will build one of the largest genomic datasets of its kind, by complete DNA mapping of thousands of ancient Eurasian human remains. The data will be obtained from bones and teeth, the oldest remains dating back 10,000 years.

The international, multi-disciplinary team of scientists, which includes specialists in ancient genomics, neuro-genetics, population genetics, archaeology, linguistics, and experts in brain health, among others, will focus on creating two unique subsets of genomic data. The first panel is a 5,000 ancient human genomes panel. The second panel will consist of ancient pathogen DNA that is associated with human diseases. Both panels, which will be made publicly available, will together advance our understanding of the evolution of disease variance and its interaction with the human genome and pathogen pressure. The project will generate and analyze one of the largest sets of ancient human and pathogen genome panels ever created.

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Read additional coverage HERE…