Tag Archives: DNA Sequencing

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.

Rare Disease Research Focuses Charcot-Marie-Tooth Syndrome, Guided by DNA Sequencing

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rare diseases nextCODE hannes smarasonGenome sequencing is a relatively young technology and has been in active use in the research space for just over a decade. Yet already it has found very meaningful applications in clinical care, supporting the world’s leading researchers in discovering answers to some of the most rare and confounding diseases. The interface between the research and clinical realms is seeing some of the most exciting and fruitful applications of the power of sequencing. The ANZAC Research Institute in Sydney, Australia sits right at this nexus and is using the latest DNA sequencing and interpretation technology from NextCODE to mine genomes in search of genetic mutations that are associated with X-linked Charcot-Marie-Tooth syndrome (CMTX). CMTX is a rare, progressively debilitating neurodegenerative disorder that can be caused by mutations in many different places in the genome, including the X chromosome. At present there is no cure or drug treatment available. The team at the ANZAC Research Institute, recognized for their expertise in familial genetics, sought out the unique capabilities of the NextCODE analysis platform to investigate spaces outside the normal coding areas of genes. The aim is as pioneering as the technology: to identify not just just single SNPs but also structural variants that conventional approaches have not been able to search for systematically and link to CMTX. With dedicated research minds and the latest technology, the program aims to better understand this disease and potentially find novel targets for the development of therapies. This is one great example of the many opportunities to improve lives that are being generated by insights gained through the rapidly evolving field of genome sequencing.