Monthly Archives: August 2014

Genomics and Rare Diseases: Hope for Solving Unanswered Questions

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genomics and rare diseases

Leading institutions around the world are leveraging the power of advanced sequencing technology to solve some of the greatest unanswered questions in medicine.

As we learn more about disease biology and uncover new insights thanks to the availability of genomic technologies, we are making meaningful progress in identifying means to address many rare diseases for which there is little medical hope today.

With these new genomic tools and insights, a wide range of opportunities has emerged to improve diagnosis and treatment of rare diseases. Over the past few years, DNA sequencing has begun to uncover the causes of rare diseases and, at the heart of each case solved is a patient and a family that has gained new understanding about their condition. With time, these success stories in diagnosis will lead to more successes in treatment.

Now more than ever, there is more hope that identifying the key mutations will lead to better understanding of the biology of disease and then to novel therapies. Better and faster technologies are being promoted by leaders in the field of genomics that are enabling much more rapid analysis and interpretation of a patient’s genome to find answers. The critical first step is to obtain sufficient data to analyze, compare it against a robust database of reference data, and gain an accurate understanding of potential mutations associated with these rare conditions.

As researchers focus on specific areas, new partnerships are extending access to data and accelerating progress with rare diseases around the world. Recently, genomic analysis collaborations were initiated by ACoRD at University College Dublin to implement NextCODE’s proprietary database and analytical tools to mine whole genome data for variants linked to autism spectrum disorders. [See blog post here]. Another genomic analysis program with ANZAC in Australia applies advanced sequencing analysis technology to better understand X-linked Charcot-Marie-Tooth Syndrome, a rare and progressively debilitating neurodegenerative disorder. [See blog post here] More collaborations are in the works and we’ll be talking about them as soon as we can.

We look forward to the results of these and other collaborations as leading institutions around the world make efforts to leverage the power of advanced sequencing technology to solve some of the greatest unanswered questions in medicine.

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A Standard Database Architecture Will Build a Stronger Foundation for Genome Discoveries

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big data genome sequencing hannes smarason

The general adoption of the Genomically-Ordered Relational database (GOR) as a data standard for storing genomic data may greatly accelerate the spread of sequencing and its effectiveness as a tool for advancing medicine.

It is widely accepted that the ability to share the analysis and insights from DNA sequencing will be a key driver of discovery and innovation. But one current limitation to extending this knowledge is that sequencing and analysis platforms, as well as samples, are often proprietary to and stored at different institutions. Perhaps more important, the structures and formats in which genomic data has customarily been stored—the relational databases developed by the likes of IBM and Oracle—make it unwieldy to analyze as the amount of data grows, and very difficult to share. The upshot is that institutions cannot easily share and consolidate information to generate more robust analyses and clinically relevant insights. This presents a serious hurdle to discovery both in rare disorders, where samples need to be gathered in order to generated adequate analytical power, and in complex ones, where truly massive studies can tease apart different facets of disease and reveal their causes.

Over the past decade, a novel and comprehensive database model has been developed to solve this bottleneck, offering a flexible and fast means to overcome these problems. It is called the Genomically-Ordered Relational database, or GOR, and was designed to manage and query the detailed genomic data amassed by deCODE genetics in Iceland – the world’s first and still by far largest and most comprehensive population-based genomic database.

The thinking behind the GOR is as simple as it is revolutionary. Genomic data is a sort of big data but one with an important difference: It is divided up in distinct packets—the chromosomes—and then arranged within each chromosome in linear fashion. The GOR makes use of this by storing and querying sequence data according to its unique position in the genome, rather than as huge files as long as the sequence. This radically reduces the data burden of querying even large numbers of whole genomes, at the same time making it possible to store and visualize instantly the raw sequence underlying an analysis.

In practice, the GOR thereby enables researchers to home in on specific variants without having first to call up entire patient genomes, and separates raw data from annotations to focus in on only the most relevant search components. It’s these types of functions and features that can be consistently applied across data storing systems to allow for more multi-institutional, collaborative research and consistency in outcomes worldwide.

Leaders in the genomic research community are now beginning to create coalitions and working groups to underpin and coordinate the adoption of standards for sharing genomic data. As these groups create flexible and efficient policy frameworks, the GOR is tested and ready to support the fundamental data requirements of global data sharing and the acceleration of discoveries in genome-based medicine. The general adoption of the GOR as a data standard for storing genomic data may greatly accelerate the spread of sequencing and its effectiveness as a tool for advancing medicine around the world.

Genomics-Based Medicine Coming Into View

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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

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£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.