Tag Archives: NextCODE Health

Bringing Together Core Technologies Unlocks Genomic Data to Improve Healthcare

Posted on by
genome analysis technologies

Within the “3-legged stool” of genomics-enabling technologies, lower-cost genome sequencing has reached a point of strong commercial viability, and the remaining two legs—genomic analysis tools database storage—are rapidly evolving to support the use of genomic information in medical care.

The adoption of genome sequencing technology is rapidly expanding as medical centers around the world embrace its utility in informing healthcare decisions—an emerging reality of personalized medicine.

There are three important areas of technology that are driving the use of genomic data in healthcare:  genome sequencing, genomic analysis tools, and database storage.

The first of these—genome sequencing—has advanced to the point that it is more widely accessible, with the cost of sequencing at nearly $1,000 or less. This lower cost of genome sequencing has reached a critical milestone to enable the use of sequencing as a mass-market product for medical care.

The second and third core genomic technologies—genomic analysis tools and database storage—are in the midst of evolution. Their progress and integration are critical for the next stage of adoption of genomic data into health care.

The rapidly evolving legs of the “3-legged stool” of genomics technology are genomic analysis tools and database storage.

  • Genomic Analysis Tools: Since the human genome was first sequenced more than a decade ago, an increasingly robust body of research has showcased the links between mutations identified in the genome and disease risk. Informatics tools have been developed by medical centers and genomics companies to apply to whole-genome samples. Increasingly, these genome analysis tools will need to adapt to the steady pace of new genomic linkages to disease and to operate at a level approaching “big data.”
  • Database Storage for Human Genomes: There are a growing number of robust databases of human genomes, including data for healthy people or those with certain diseases. When properly analyzed, these databases offer the potential to provide the medical community with a reference library against which to compare genetic data. Large-scale, high-quality databases are an essential element to cross-reference a patient genome to guide more informed medical decisions.

Recently, two leading genomics companies—WuXi and NextCODE Health—have combined their technology capabilities in these two areas. WuXi has industry-leading capabilities to analyze, store, and manage the vast amounts of genomic data. NextCODE Health brings a leading-edge system for sequence-based clinical diagnostic applications and genome analysis.

The combination of WuXi’s foundational genomic database storage and management and NextCODE’s sophisticated genome analysis tools will integrated the key components that are most rapidly evolving to apply genomics to medical care.

Initiatives like these advance the state-of-the-art in genomic analysis and database storage, bringing us to the heart of helping the world to fully harness personalized medicine and providing tools directly to doctors to provide better diagnostics and treatments to patients.

The progress to date has been amazing. Yet the opportunities ahead are even more extraordinary to improve the speed, accuracy, and accessibility of genomic information to improve human health.

Share on Tumblr
0
email

A New Era, New Vision for WuXi and NextCODE Health

Posted on by
WuXi-NextCODE

WuXi PharmaTech has acquired NextCODE Health to create WuXi NextCODE Genomics, a global leader in genomic medicine. Pairing WuXi’s technology and existing reach with NextCODE’s leading analytics and database promises to advance the pace of genomics research today.

In the fast-paced genomics community, we continually look for new opportunities and strategies to enhance the value of genomics and use the increasingly robust body of genomic data for the advancement of clinical medicine.

We’re excited to announce a new, ambitious vision to do just that, with WuXi’s acquisition of NextCODE Health. NextCODE will be merged with WuXi’s existing Genome Center in wholly-owned subsidiary called WuXi NextCODE Genomics, with unique, comprehensive and global capabilities for using genomic data to deliver better medicine and improve healthcare.

WuXi, a Shanghai-based genomic laboratory service partner for companies in the pharma and biotech community, has already been collaborating with NextCODE to provide analysis services to customers of the WuXi Genome Center. Now, with the in-house capability to analyze, store, and manage the vast amount of genomic data, NextCODE’s industry-leading genome sequence analysis platform will expand WuXi’s core next-generation sequencing benefits and services.

Pairing WuXi’s technology and existing reach with NextCODE’s leading analytics and database promises to advance the pace of genomics research today. More importantly, however, this new era for NextCODE brings exciting opportunities to maximize the most advanced tools available today and contribute to major advances in genomic medicine.

Global Projects Move Genomic Medicine to the Next Level

Posted on by
nextcode-genomics-england-hannes-smarason

NextCODE takes top marks in Genomics England analysis and interpretation “bake-off:” NextCODE’s proven population-scale platform delivered the best results in rare disease and cancer clinical interpretation, as well as secondary analysis and variant refinement.

New genomics-based technologies and tools are making their way into a range of exciting research programs and clinical studies around the world. Leading-edge organizations are quickly adopting hardware for sequencing and systems for collecting genomic data. Now, the focus has turned to analysis and interpretation – the critical component necessary to gain the insights from the sequence data that will transform medicine.

Earlier this year, Genomics England announced investments for broad sequencing and analysis of 100,000 human genomes. At the time, Genomics England had selected Illumina as its sequencing partner and was coordinating resources and centers to support the effort, including resourcing for analysis and interpretation. [See blog post here]. Other initiatives, such as the Qatar genomics program and the initiatives by Longevity and Regeneron also represent the accelerated progress in seeking medical advancements from genomic data insights. [See blog post here.]

This week, Genomics England announced a select group of companies with advanced capabilities to move to the next stage of evaluation to provide clinical interpretation for the 100K Genomes Project. At the tip top was NextCODE, which received top marks by Genomics England for its analytical capabilities across all the categories evaluated: rare disease interpretation, secondary pipeline analysis and cancer interpretation. [See press release here.] The company’s advanced Genomically-Ordered Relational database, or GOR, combined with its clinical and discovery interfaces offer the most advanced and reliable capabilities to support the ambitious tasks undertaken by Genomics England, and are already proven at population scale. [Read more on the GOR database here.]

The coming months will be a very exciting time for genomic medicine, with interpretation taking the spotlight as we take leaps toward the next stage of personalized medicine.

Population-Scale Research Efforts Enabled by Progress in Sequencing

Posted on by
population-scale genomics

Significant insights gained from population-scale genomic studies, based on the knowledge of genetic variation and disease causation, will help to enable a new reality of personalized medicine and treatment.

The ability to sequence whole genomes quickly and economically is driving interest in population-scale sequencing efforts that can reveal meaningful insights on a much more systematic basis than previous approaches. A range of large initiatives announced recently are prime examples of the trend in population sequencing, including industry programs by Regeneron and Human Longevity, and the 100,000 Genomes Project by Genomics England. Perhaps better than any other effort since the founding of deCODE in Iceland, the establishment of a high-throughput Genomics Center at Sidra Medical and Research Center in Qatar embodies the movement toward these types of population studies. The eventual goal of the project is to sequence the entire Qatari population of some 300,000 people. But from the beginning, the Sidra facility will help advance genetic mapping projects, including the creation of Arab consensus genome to obtain a better understanding of genetic variants that influence health across Arab populations and, indeed, beyond. In addition to these efforts, the center will focus on uncovering the causes of rare genetic diseases. The significant insights that can be gained from population-scale studies, based on the knowledge of genetic variation and disease causation, will help to enable a new reality of personalized medicine and treatment. And this is where efficient, powerful and industrial-scale analysis will become critical. NextCODE’s analytics and interpretation systems have already been tested at such scale, as they are based on the world’s first and largest population genomics effort—that of deCODE. [see blog post] Our systems will be useful tools to efficiently deliver insights based on the vast amount of data that will be generated by these major population-based efforts to improve the state of global healthcare.

Genome Data Interpretation: How to Ease the Bottleneck

Posted on by
Bloomberg NextCODE Hannes Smarason

Bloomberg BNA Business’ “Diagnostic Testing & Emerging Technologies,” highlights how NextCODE is providing a qualitatively different way to store and analyze genomic information to meet growing opportunities in personalized medicine.

With advances in sequencing technology and reduced costs, more and more data are generated every day on the genetic basis of disease. The challenge has become how to derive meaningful information from these mountains of data.

While various systems have been established in recent years to store the large amounts of genomic data from patients’ DNA, a remaining obstacle is to “break the bottleneck” so that researchers can process the vast data in multiple human genomes in order to identify and isolate a small, useful piece of information about disease. Conventional databases and algorithms have not been able to efficiently and reliably identify subset information among the millions of genetic markers in order to inform clinical decisions. This has become a major data management roadblock.

The key is to find new approaches for databases and algorithms that accommodate the unique ways that genomic information is analyzed and interpreted. As discussed in Bloomberg BNA, Diagnostic Testing & Emerging Technologies, NextCODE is already easing this bottleneck by providing a qualitatively different way to store and analyze genomic information and apply it to meet the growing opportunities for personalized medicine.

NextCODE’s Genomically Ordered Relational (or GOR) database infrastructure is a truly different way of storing this huge amount of data. The principle is very simple: rather than store sequence and reference data in vast unwieldy files, it ties data directly to its specific genomic position. As a result, the algorithms are vastly more efficient compared to a traditional relational database because they can isolate by location in the genome. That makes analysis faster, more powerful, and radically more efficient, both in terms of clinicians’ and researchers’ time, as well as computer infrastructure, I/O, and CPU usage.

This holistic approach applies broadly to the priorities of genome scientists around the world, helping them eliminate the data management bottleneck to identify more culprits to many inherited diseases, more quickly and cost effectively.

Read more about NextCODE’s work here.

Trends in Sequencing and Analysis Today Leading to Tomorrow’s Clinical Advances

Posted on by
The insights we’re gaining from sequencing and analysis techniques are delivering new advances in healthcare with ever greater speed and precision.

The challenge for programs seeking to accelerate their research discoveries with genomic data is how to analyze the wealth of information—to make it clinically relevant and rapidly deliver reliable insights to better inform patient care.

The insights we’re gaining from sequencing and analysis techniques are delivering new advances in healthcare with ever greater speed and precision. It’s a particularly exciting time to be a part of this evolving industry, with continual opportunities for new clinical applications of these technologies and platforms.

Companies like Illumina and others who are delivering next-generation sequencing technologies are gaining global exposure. New partnerships and programs are placing these advanced techniques into the hands of the world’s leading clinicians and researchers, who are then applying them to some of today’s greatest medical challenges.  Recently, plans to integrate sequencing technologies have been announced by world renowned organizations like the Baylor College of Medicine in the U.S., Genomics England, and Sidra Medical and Research Center in Qatar.

The challenge for these and other programs seeking to accelerate their research discoveries with genomic data is how to analyze this wealth of information – to make it clinically relevant and rapidly deliver reliable insights to better inform patient care.

NextCODE Health is working to advance this piece of the puzzle with its Genomically Ordered Relational (GOR) database and its clinical and discovery interfaces (the Clinical Sequence Analyzer​™ and Sequence Miner™).  Combining next-generation sequencing techniques with increasingly robust analysis tools, NextCODE Health is helping to accelerate global research progress today to deliver unprecedented advances in patient care in the years just ahead.

Genomics-Based Medicine Coming Into View

Posted on by
NextCODE Health

NextCODE Health has quickly gained recognition for its unique capabilities to address unmet needs in the genomics space through a massive genomics database that interprets DNA samples to identify relevant disease markers.

The practice and adoption of genomic medicine is accelerating as technologies improve, costs fall and new insights drive better patient care. While many companies are supporting this emerging field, a select few are providing the unique perspectives and capabilities to advance progress even faster.

NextCODE Health made headlines less than a year ago with the announcement of its launch and funding by major investors in healthcare and biotechnology. The company quickly gained recognition for its unique capabilities to address unmet needs in the genomics space through a massive genomics database that interprets DNA samples to identify relevant disease markers. (See the features in Xconomy, Bio-IT World and PLOS Blog.) The company was later mentioned in Nature Biotechnology News for its potential contributions to genome studies by leveraging key reference data from deCODE’s Icelandic work in Iceland.

Its rapid trajectory since launch and the utility of its genomic analysis technology was featured in BioCentury in May, featuring testimonials from clinicians using NextCODE capabilities to diagnose patients at Boston Children’s Hospital, the Baylor College of Medicine, and the Sanford School of Medicine. In June, it was featured in a major interview with Bio-IT World and the company continues to expand. Since then, NextCODE has announced several programs through which global pioneers in clinical genomics research are applying its interpretation and analysis technology to support research and diagnosis in rare diseases, including:

As more organizations employ genomics in major research initiatives, NextCODE’s interpretation technology will be an increasingly important asset in delivering meaningful insights from the wealth of genomic data being produced. Visit NextCode for the latest on how the future of genomics-based medicine continues to evolve.

Pioneering Genome Sequencing Effort in England Aims to Shape the Future of Global Medicine

Posted on by

£300 million in new investments for Genomics England

Genomics England 100,000 Genomes Project

Genomics England was set up by the UK Department of Health to deliver the 100,000 Genomes Project. Initially the focus will be on rare disease, cancer, and infectious disease. The project is currently in its pilot phase and will be completed by the end of 2017.

These are exciting times for large-scale sequencing projects. Last week, U.K. Prime Minister David Cameron announced over £300 million ($509.4 million) in new investments for Genomics England, which aims to sequence, analyze, and store the genomes of 100,000 UK National Health Service (NHS) patients by 2017. The investments include about £162 million ($275.1 million) from Illumina Inc. (NASDAQ:ILMN), the partner for the sequencing element of the project. In turn, Genomics England will pay Illumina about £78 million ($132.4 million) for its services.

At the same time, the Wellcome Trust will put £27 million ($45.8 million) into a new sequencing hub at its genome campus in Cambridge; the Medical Research Council, or MRC, is investing £24 million ($40.7 million) to support data analysis and interpretation, and the NHS will make £20 million ($34 million) available for the establishment of patient sequencing centers.

This is a prime example of how the implementation of sequencing technologies promises to drive a revolution in the structure of medical research. These new projects aim to capture more data on human DNA than ever before, with the goal of advancing care and solving healthcare challenges.

The 100,000 Genomes Project, developed by the NHS, has the potential to significantly influence the global community through its plans to integrate sequencing data into standard medical practice.

Genomics England plans to generate 100,000 whole genome sequences from NHS patients with cancer, rare diseases, and other conditions, and to share the resulting data for research and development purposes. In the early phases, the program will also seek to develop standards for consent, sample storage, data generation and variant analysis that may be useful for many other organizations conducting large-scale projects within public health systems.

The project is enlisting the help of organizations from around the world to undertake this significant effort. In fact, it recently selected Illumina to conduct the sequencing efforts and is evaluating technologies for storing, annotating, and interpreting the data so that it can be used  for both clinical diagnostics and drug discovery, development, and delivery to the right patients.

The challenges of analyzing data on such a large scale are formidable, but the end result carries great potential to address some of the significant unmet medical needs. NextCODE’s technology has already accomplished analytics on this scale based on its work with the Icelandic population through deCODE genetics. It’s an exciting prospect for advancing the future of genomics-driven medicine and one to watch.

Early Adopters of Sequencing in the Clinic

Posted on by
early adopters of sequencing in the clinic

Leaders in the medical community are actively enhancing their facilities with DNA sequencers and supercomputers—steps toward the routine sequencing of patient genomes that will inform the full spectrum of care decisions.

It is increasingly evident that sequencing and analyzing genomic information can contribute to more informed healthcare decisions, and major research institutions and medical centers around the world seem to agree.

Leaders in the medical community are actively enhancing their facilities with DNA sequencers and supercomputers, recognizing the efficiencies of having this advanced technology at their disposal for innovative research programs. And as they look to the future, they are taking steps toward the routine sequencing of patient genomes that will inform the full spectrum of care decisions, from defining risk, to diagnosing disease, to defining the ideal course of treatment for the best possible outcome.

Just a few examples of the major advances in the use of sequencing technologies that have been announced recently…

From medical centers:

  • Mount Sinai Medical Center in New York initiated a program in which 24,000 patients participate in a biobank to include their DNA sequence and research over their lifetimes. The program, called BioMe™, is among the largest in the United States.
  • Memorial Sloan-Kettering Cancer Center researchers are active in a range of collaborations that seek to understand the molecular changes that characterize cancer, the largest of which is The Cancer Genome Atlas (TCGA), a project jointly funded by the NCI and the National Human Genome Research Institute. MSK currently houses one of TCGA’s Genome Data Analysis Centers.
  • Phoenix Children’s Hospital launched a new molecular and personalized medicine research institute that will “bring genomics research to the forefront of pediatrics.” The infrastructure will include a range of capabilities, such as a biospecimen repository, DNA sequencing and analysis, and a CLIA lab for genomic profiling.

And research institutions:

  • The Wellcome Trust Sanger Institute is dramatically upgrading its storage and data management capacity.  The Institute already operates 30 DNA sequencers, each of which generates roughly a terabyte of data every day. New upgrades will double their capacity and improve data management and organization software.
  • Harvard Medical School’s Center for Biomedical Informatics, conducts informatics research with a strong emphasis on translational science informed by innovative computational strategies; the research staff use mathematical modeling to predict when genetic information could lead to more effective treatment.

By members of industry:

  • Google is jumping into the genomics industry with the launch of “Calico,” a new company that will focus on genomic sequencing and advanced analytics to identify solutions for some of the most challenging diseases today.
  • “N-of-One” is a company offering personalized cancer treatment strategies as a new employee benefit tool for innovative, health-minded employers. Through the service, the company provides interpretation of molecular profiling to employees, their family members fighting cancer and their physicians to help inform treatment decisions.

And even the U.S. government:

  • The National Institutes of Health is one of the greatest proponents of genomic sequencing for research purposes. In fact, a recently initiated program is funding research teams to examine whether sequencing newborn genomes or exomes may provide useful information beyond what is currently captured in newborn screening programs.
  • Further, in the fight against infectious diseases and “super-bugs,” the National Institute of Allergy and Infectious Diseases established the Genomic Sequencing Centers for Infectious Diseases (GSCID) to sequencing priority pathogens, microorganisms responsible for emerging and re-emerging infectious diseases and related organisms.

With such a broad array of innovative research underway within the halls of the world’s leading institutions, there is no doubt sequencing is on the verge of delivering exciting breakthroughs in medicine. In fact, we’re seeing evidence of this with NextCODE, which has engaged with several “early adopter” organizations around the globe.  Check it out here.

Prime Targets for Whole Genome Sequencing: Cancer and Rare Diseases

Posted on by
genome sequencing cancer and rare genetic diseases

There’s a huge opportunity ahead for genome sequencing to impact human health, beginning with cancer and rare genetic diseases.

There is a documented history of conditions classified as “diseases of unknown origin”—in these cases, the biological mechanisms that led to the disease are simply unknown or have not yet been discovered. Yet as we learn more every day, certain diseases have clear links to underlying genetic mutations. As such, analyzing the genome sequence of a patient diagnosed with one of these diseases might help lead to a better understanding of the disease etiology and potential treatment strategies, particularly in the areas of cancer and rare genetic disorders.

Preventing cancer

While cancers have a range of causes and correlations, many have a set of genetic mutations that drive malignant growth. Recent advances have already introduced sequencing to the cancer category, as cancer patients are benefiting from genetic tests that reveal their personal risk for certain tumors (such as BRCA for breast cancer).  Recently, evidence has suggested that certain genetic mutations could be responsible for the development of a wide range of tumor types (see the recent study in Nature, for example). These findings support the idea of using genomic analysis to predict an individual’s cancer risk, by comparing their genome with databases of confirmed genetic mutations linked to disease.

Treating Cancer

In addition, genomic sequencing and analysis may help better understand the genetics of the tumor itself, and can provide explanations for how tumors evolve over time. Tests are increasingly available today that can help predict a tumor’s response to a specific type of treatment. With a genomic-based approach to cancer care, researchers expect that treatment will evolve to be more tailored to an individual tumor’s mutations and, eventually, through drugs that can attack several targeted gene mutations at once. Already we’ve seen evidence of this in certain areas, such as breast cancer drugs intended for use only in patients who test positive for the HER2 gene.

 Identifying Rare Diseases

Rare diseases are another area of significant opportunity for improved diagnosis and treatment through the use of genomics.  Every year there are new cases of children with “unknown” diseases, many of which are likely related to a hereditary genetic disorder. These children and their families often spend years undergoing testing and experimental treatments for a wide range of diseases to attempt to properly diagnose and treat them, usually accompanied by a very high financial and emotional burden.

There is a hope that by offering whole genome sequencing to patients with a suspected rare genetic disease, mutations that might be causing the disease may be identified, and thus correct treatment can be employed much earlier to eliminate the burden of a long-term diagnostic and treatment odyssey.

Cancer and rare genetic diseases are just the start.  There’s a huge opportunity ahead for genome sequencing to impact human health, and personalized medicine may be just on the horizon.  In fact, we are focusing on just these areas with NextCODE, the newly launched company I’ve founded. The improvements brought about by the genomics industry, with the help of the technologies and services offered at NextCODE, will provide enormous value to patients, doctors, and the health care system as a whole.