Category Archives: genomic medicine

Domain Expertise: Jumpstarting Artificial Intelligence in Biomedicine

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Is artificial intelligence the “single most transformative technology in modern history?” That’s the view of Tom Chittenden, who leads WuXiNextCODE’s AI program. And Tom is not alone in his enthusiasm, as numerous analysts are predicting this technology will be one of the fastest growing fields in the world.

In recent talks at Boston’s BioIT World and the EmTech conference in Hong Kong, Tom described some of the strides we’ve been making with our DeepCODE AI tools. Their power is in part thanks to a novel, causal statistical-learning method and deep-learning classification strategy. But another advantage is that they were built on—and are extending the reach of—our global platform for genomic data. That means that Tom’s team has that rare combination of both of the key ingredients to AI making an impact in biomedicine: cutting-edge algorithms AND deep domain expertise and access to the biggest datasets.

Tom—who also holds appointments at Harvard, MIT, and Boston Children’s Hospital—and his growing team have the former in spades; our platform and expertise in genomics provide a key edge in the latter. Our platform has been built over more than 20 years and today underpins the majority of the world’s largest genomics efforts and includes all major global reference databases. It stores, manages, and integrates any type of genomic data and correlates it with phenotype, ‘omics’, biology, outcome, and virtually any other type of data that may be relevant to a particular medical challenge.

That means that we can routinely train and test our AI tools on some of the most comprehensive data sets in the world, such as that in The Cancer Genome Atlas (TCGA). “Today we can take ‘omics data and clinical information and map those to curated resources such as SNOMED CT and biomedical ontologies, and then use AI to identify patterns that lead us to novel findings,” Tom says.

This is a powerful approach to tease out which of hundreds of genetic variants are really involved in a particular disease, based on which ones are actually associated with aberrant expression pathways. You may find hundreds of genetic mutations in a single type of breast cancer tumor, for example, but it is determining which ones are drivers of the disease that matters.

Put simply, AI can lead us to both better diagnoses and easier discovery of more and better drug targets, by taking a range of genomic data and marrying it to clinical information and scientific knowledge. AI is not just going to better match patients to the right drugs, it is going to help further our understanding of the relationships between genes and complex molecular signaling networks, one of the most challenging arenas in our field and the most sought-after starting point for discovering validated pathways and targets.

Valuable insights in real-world medical challenges are already emerging from this AI effort uniquely developed on and applied to the genomic and medical data that counts.

WuXi NextCODE  recently presented preliminary data from analyses using our novel AI technology to diagnose subtypes of tumors. Our DeepCODE tools were validated on six patient-derived tumor xenografts from mouse models, and then tested against approximately 8,200 human tumors from a collection of 22 cancer types in The National Cancer Institute’s TCGA collection. That study included five ‘omics data types. We achieved 98% accuracy overall, and our analyses of human breast and lung cancer subtypes were accurate in 96% and 99% of cases, respectively. This points to an improvement over current methods for matching patients to treatments for their particular cancer, and we have refined that accuracy further still. This capability is also going to be central to the development of liquid biopsies.

http://hannessmarason.com/blog/2017/04/04/a-perfect-pairing-ai-and-precision-medicine/

In another oncology study, using the same multi-omics data, DeepCODE identified a signal predictive of survival across 21 cancers, pointing to novel and holistic pathways for developing broad oncotherapies.

A recent study published in Nature, meanwhile, describes a potential new role for a well-known growth factor. That report, led by Yale University scientist Michael Simons, looked at blood vessel growth regulation—a crucial process in some very common conditions, including cardiovascular disease and cancer. Our Shanghai team provided RNA sequencing for this study. Our Cambridge AI team drove some of the key insights pointing to novel disease mechanisms.

Simons’ team studied knockout mice, whose fibroblast growth factor (FGF) receptor genes were turned off. They proved, for the first time, that FGFs have a key role in blood vessel growth, uncovering some metabolic processes that were “a complete surprise,” according to scientists on the team. Further, they mapped out pathways that could help provide new drug leads.

http://hannessmarason.com/blog/2017/05/15/bringing-artificial-intelligence-cardiovascular-medicine-cancer-genomics-action/

Our AI team is just getting started. We’re looking forward to many more intriguing findings from this group as they leverage their expertise and massive amounts of the relevant data to improve medicine and healthcare.

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As Cancer Databases Grow, A Global Platform Leaps the Big Data Hurdle

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As massive cancer databases like The Cancer Genome Atlas (TCGA) proliferate and expand worldwide, WuXi NextCODE expects to see—and to drive—a boom in discoveries of cancer biomarkers that will advance our ability to treat cancer and improve outcomes for patients.

One of the fastest-growing areas in medicine today is the creation of massive cancer databases. Their aim is to provide the scale of data required to unravel the complexity and heterogeneity of cancer—the key to getting patients more precise diagnoses faster, and to getting them the best treatments for their particular disease.

In short, this data has the potential to save lives.

Such databases are not new, but they are now proliferating and expanding at an unprecedented pace. Driven by governments, hospitals, and pharmaceutical companies, they catalogue a growing range of genetic data and biomarkers together with clinical information about their effects on disease, therapy, and outcomes.

Only with such data can we answer the key questions: Does a certain marker suggest that a cancer will be especially aggressive? Does it signal that the tumor responds best to particular treatments? Are there new pathways involved in particular cancers that we can target to develop new drugs?

It’s the cutting edge of oncology, but to be powered to answer these questions, these databases have to be very, very big. They have to bring together whole-genome sequence data on patients and their tumors as well as a host of other ‘omics and biological data. One of the biggest challenges to realizing this potential is to manage and analyze datasets of that scale around the world. It’s one we are addressing in a unique manner through our global platform.

One of the most renowned and widely used of these is The Cancer Genome Atlas, a collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI). TCGA data is freely available to those who qualify, and there is a lot of it. It already comprises 2.5 petabytes of data describing tumor tissue and matched normal tissues for 33 tumor types from more than 11,000 patients. Researchers all over the world can apply to use this data for their own studies, and many have.

Yet asking questions of TCGA alone can take months for most groups and requires sophisticated tools. At Boston’s recent Bio-IT World conference, WuXi NextCODE’s director of tumor product development, Jim Lund, explained how we have put TCGA on our global platform—providing a turnkey solution with integrated analytics to transform the data into valuable findings.

Jim and his team have imported into WuXi NextCODE’s cloud platform virtually all key TCGA data: raw whole exome sequence data from patients and tumors, as well as variant calls using MuTect2 and Varscan2; RNA and microRNA sequence and expression data; and data on copy number variation, methylation arrays, and some 150 different clinical attributes. But this data isn’t just hosted in the cloud: it can all now be queried directly and at high speed online, enabling researchers to quickly ask and answer highly complex questions without having to download any data or provide their own bioinformatics software.

To demonstrate the power of this approach, Jim’s team decided to run the same queries in a recent published study that looked at sequence data from the exons of 173 genes in 2,433 primary breast tumors (Pereira et al., Nature 2016). They were specifically looking for driver mutations of cancer’s spread and growth. In a matter of minutes, rather than months, they were able to replicate key mutations identified in the study. That analysis was then extended to all cancer genes, and additional driver genes were found. More important, because they were able to correlate these mutations with clinical outcomes data, they were also able to begin systematically matching specific mutation patterns to patient outcomes.

Next, Jim’s team looked at the genomics of lung adenocarcinoma, the leading cause of death from cancer worldwide. Following up on the findings in another published study (Collison et al., Nature 2014), they profiled the 230 samples examined in the paper and immediately made several observations. Eighteen genes were mutated in a significant number of samples; EGFR mutations (which are well known) were more common in samples from women; and RBM10 mutations were more common in samples from men. These results were extended to 613 samples and shown to be robust. But because they had a wide range of data including mRNA, microRNA, DNA sequencing, and methylation, Jim’s team was further able to suggest some actual biological processes that may be fueling the origin and growth of lung adenocarcinomas.

What’s making this type of research possible? It’s our global platform for genomic data. The platform spans everything required to make the genome useful for helping patients around the world, from CLIA/CAP sequencing to the world’s most widely used system for organizing, mining, and sharing large genomic datasets. At its heart is our database—the Genomically Ordered Relational database (GORdb). Because it references sequence data according to its position on the genome, it makes queries of tens of thousands of samples computationally efficient, enabling the fast, online mining of vast datasets stored in multiple locations.

That’s how we are making the TCGA—and every major reference dataset in the world—available and directly minable by any researcher using our platform. Those users can combine all that data with their own to conduct original research at massive scale.

These breast and lung cancer studies are just two of more than a thousand that have been carried out so far on TCGA data. As more such datasets become available, we expect to see—and to drive—a boom in discoveries of cancer markers that will advance our ability to treat cancer and improve outcomes for patients. For those who want to go further still, our proprietary DeepCODE AI tools offer a means of layering in even more datasets to drive insights even deeper into the biology of cancer and other diseases. And that’s a topic I’ll return to in the weeks ahead.

Genomics: Forging Patient-Centric Communities

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Genomics has become a foundation for virtual patient-centric communities involving patients, caregivers, clinicians, and researchers worldwide.

In recent years, genomics has become a foundation for virtual patient-centric communities – communities built on the Internet and through social media that:

  • Connect people touched by a disease or disorder; or
  • Reach out to broad populations affected by rare diseases, many of whom are undiagnosed.

These patient-centric communities are dedicated to sharing information and providing support in order to break down the barriers of isolation and uncertainty that can compromise care and adversely affect quality of life for patients and their families.  As we learn more about the genetic variations that contribute to diverse conditions, virtual communities that are fueled by genomics contribute an ever-expanding resource.

Virtual communities have greatly affected patients and caregivers worldwide, and the relationships forged through genomics are essential to clinicians and researchers as well.  Genomics not only serves to link patients to each other but also to connect those patients to research initiatives that use genetic sequencing to diagnose conditions and guide treatment, thus improving patient outcomes today while influencing research for better therapies tomorrow.

RareConnect, for example, is an online platform that connects patients, caregivers, clinicians, and researchers in more than eighty disease-specific communities.  Another leader in this arena is PatientsLikeMe, which has activities that encompass more than 400,000 members with over 2,500 conditions.  Many diseases and conditions are identified by genetic abnormalities or characteristics.  Participants in RareConnect, PatientsLikeMe, and similar sites are drawn in part to the ways in which genomics could contribute to an accurate diagnosis, a novel treatment, and ultimately a cure.

The use of genomics to build communities has been especially important for rare diseases.  For patients and caregivers affected by the rarest of rare diseases – the disorders so rare that only a handful of known cases exist worldwide – the transformative role of genomics is that much more powerful.

An excellent article in The Atlantic tells the story of one young woman whose experience illustrates this phenomenon.  A genomic study identified the genetic mutation that underlies Lilly Grossman’s movement disorder.  The information provided by genomics has enabled the formation of a virtual community.

Lilly’s case has acted as a magnet for others with the same mutation. Families with the same problem read about Lilly’s case and contacted the Grossmans. Doctors and geneticists looked at their own patients and saw a new explanation behind puzzling symptoms. Before, there were isolated pockets of people around the world, dealing with their own problems, alone for all they knew. Now, there’s a community.

The connections forged through genomics are essential to patients, often children, and their caregivers, often families.  Genomics can provide the vital link, the piece of information that identifies individuals with similar experiences – the community of people who understand.  Patient-centric communities are one way in which the increasing availability of cost-effective genetic sequencing is transforming patient experiences, shortening diagnostic odysseys, and improving clinical care.

Many such communities are also critical for advocacy and fundraising.  Parent Project Muscular Dystrophy (PPMD), for instance, has worked effectively to promote Duchenne muscular dystrophy research and speed the discovery of potential treatments. PPMD has demonstrated how parents and caregivers can effect meaningful change, raising both awareness and financial resources – and even being a leading voice in support of FDA approval of therapeutics.

The intersection of genomics and social media increasingly drives progress, too. The Charlotte & Gwyneth Gray Foundation, for example, has raised an estimated $3.5 million to support CLN6-Batten disease research – through a crowdfunding initiative launched less than a year ago.

And coalitions of patient-centric communities can achieve significant advances through the power of numbers. Thus Genetic Alliance, a network of more than 10,000 organizations, was a key player in passage of the Genetic Information Nondiscrimination Act and in development of the National Patient-Centered Clinical Research Network.

Initiatives run the gamut from efforts to identify a handful of individuals with rare diseases to projects that aim to enroll thousands of participants.  Earlier this month, the University of Washington launched MyGene2, a site where families with rare conditions can publicly post their stories, establishing connections not only with those who share similar stories but also with clinicians and researchers.  At the other end of the spectrum, 23andMe has partnered with a number of Parkinson’s community groups on a project to gather genetic data from more than 11,000 individuals.

And, in the last year, the Simons Foundation Autism Research Initiative (SFARI) launched SPARK, a project to collect genomic information from 50,000 people with autism and their families.  At WuXi NextCODE we are delighted to participate in this endeavor by providing direct online access to the data.

Genomics has played a critical role in the evolution of patient-centric communities.  Groups that have developed resources and advice for patients and families are increasingly collaborating with clinicians and researchers.  Through voluntary contributions of personal knowledge – and genomic data – participants in patient communities are expanding the impact of genomics on medicine.  The growing power of virtual communities has facilitated numerous initiatives to improve patient outcomes through improved diagnosis, optimized standards of care, and new directions for promising research.

From rare diseases to disorders that affect millions, all stakeholders increasingly use genomics to translate individual experiences and expertise into meaningful improvements in the lives of patients and their caregivers.  Genomics sits at the powerful nexus between evidenced-based medicine and the empowered patient.  At WuXi NextCODE we are proud to advance the role of genomics not only in patient care but also in the evolution of strong, effective patient-centric communities.

Marking Progress in Genomics: Reflections and Prospects

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Progress in Genomics WuXi NextCODEAs leaders of our field gather in Vancouver for the annual American Society of Human Genetics Meeting (ASHG 2016), it is an excellent time to take stock of the past and clarify our perspectives for the future. For the field of genomics, this is an opportunity both to reflect on our accomplishments over the last few years and to consider what we can achieve in the years ahead.

Indeed, our accomplishments have been numerous and our goals are ambitious, yet achievable. Here, I would like to summarize five significant ways in which our work in genomics has been revolutionizing medicine and improving patient outcomes.  In addition, I would like to share my thoughts about five areas in which I believe our field can drive meaningful change over the next few years.

What We Have Achieved
1. Improvements in Sequencing Technology and Analytical Tools
The ever-increasing volume of genomic data is testimony to the dramatic increases in sequencing speed and efficiency over recent years.  At the same time, novel methods of analysis, like the powerful genomics platform employed here at WuXi NextCODE, have considerably advanced our understanding of genetic variations and their clinical significance.

2. Transformations in Cancer Treatment
As I have discussed here, the expanding use of genomic data to guide treatment decisions in oncology is transforming the way clinicians approach cancer treatment.  In addition, our growing understanding of genetic predispositions for certain cancers is helping high-risk individuals make informed choices about preventive care.

3. Progress in Rare Diseases
Genomic data has brought new hope to families struggling with rare diseases by shortening diagnostic odysseys, guiding treatment, and building communities.  I provide examples of the game-changing power of genomics in the diagnosis of rare diseases here.

4. Empowerment of Patients and Consumers
Patients and consumers are increasingly informed about the innovative and meaningful ways in which genomic data can guide healthcare decisions.  The successes in our field are empowering individuals to pursue personalized medicine and generating interest in direct-to-consumer testing.  I offer my thoughts about DTC genetic testing here.

5. Innovations in Cloud-Based Analysis
The vast and ever-growing quantity of genomic data and related information necessitates new approaches to storage and analysis.  As I have previously discussed, cloud-based computing is essential to continued success in genomics.  WuXi NextCODE’s Exchange is at the forefront of the accelerated research made possible by real-time collaboration and analysis in the cloud.

What We Can Achieve in the Years Ahead

1. Effective Communication and Collaboration
Realizing the full potential of big data and cloud-based computing will require new efforts to dismantle “data silos.”  I am encouraged by recent initiatives to facilitate collaboration in cancer research, and – as I have recently discussed – call upon researchers and clinicians throughout the field of genomics to improve communication among all stakeholders.

2. Policies for Research with Patient Data
Our field derives its greatest power from careful analysis of genomic data, and access to data is critical to effecting meaningful change in healthcare.  In order to gather this game-changing data – from patients, from consumers, and from population-wide studies – we need to develop and embrace policies that lead to consider the ‘biorights’ of patients.  Individuals who wish to contribute information for research should have the opportunity to do so, and all parties should clearly communicate the purposes and extent of data-sharing.

3. Integration for Clinical Trials
I perceive significant movement toward the development of clinical trials that test the efficacy of treatments tailored to specific genetic anomalies – and use genetic information to screen participants.  This is an area in which genomics will dramatically accelerate the development of personalized therapies that will surely improve patient outcomes.

4. Actionable Information from Population-Wide Genomic Studies
I believe that in the near future we will reap significant rewards from projects that gather population-wide genomic information.  Analysis of the data we are collecting around the world, which I describe here, is an essential step to reshaping healthcare practices worldwide.

5. Globalization of Genomic Products: ‘Think Globally, Act Locally’
The power of genomic information is now known throughout the globe, and can be applied in a multitude of positive ways.  With such widespread potential, individual countries and cultures will choose to advance and roll-out genomics in their own distinct ways for the benefit of their citizens.  Companies that develop genomic products will need to adapt and design their products for use in specific markets.  At WuXi NextCODE, the first focus of our product portfolio for individual patients and families is in China, where we are delivering three offerings: population-optimized diagnostics, carrier screening, and whole-genomic wellness scans.

Together these initiatives build upon our recent accomplishments and further the creation of data and analysis necessary for meaningful change in healthcare.

The genomic revolution in medicine that we envisage will be achieved through applied use of research and development that is:

  • Fueled by big data, including data provided by informed consumers and patients and data derived from population-wide studies;
  • Supported by clinical trials crafted to assess the safety and efficacy of treatments tailored to individual characteristics; and
  • Enabled by collaborative work and effective communication.

At WuXi NextCODE, we are energized by the prospects for genomics in the years to come. We are proud to be at the cutting edge, providing the tools and resources that researchers and clinicians need to harness the transformative power of genomic data. And—importantly—we are confident that our field will continue to drive meaningful changes in healthcare that improve patient outcomes.

Genomic Information and the Importance of Communication

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Communicating clinically useful results both to doctors and patients will drive success

genomics-communications-hannes-smarasonAround the world, researchers and clinicians are taking on the challenge of integrating genomic analysis into medical practice. Physicians and patients are increasingly aware of the potential utility of genomic data. As genomics continues to become a more powerful tool in healthcare, there is a clear and compelling need for a commitment to excellence in communication.

At WuXi NextCODE, we are proud to provide sequencing and analysis resources that help doctors:

  • Shorten diagnostic odysseys, as I have discussed here; and
  • Improve treatment choices, as I have discussed here.

Maximizing the opportunities afforded by the ‘big data’ of genomics necessitates collaboration and communication, which I discuss in more detail here. As part of our genomics business, we are dedicated to the highest standards of communication – indeed, we view effective communication as central to how our technologies will improve health in both the near and the long term.

The task of harnessing the vast and expanding quantity of genomic data to improve clinical care requires interpretation and discovery powered to translate the data into clinically useful information. Leveraging that information to improve patient outcomes also requires clear and accurate communication:

  • Between researchers and clinicians;
  • Between specialists in different medical fields;

And, increasingly,

  • Between doctors and patients.

As the recent CLARITY Undiagnosed competition highlighted, applying genomic data to medical practice involves interpreting the sequenced genomes and identifying molecular diagnoses – and a third step: communicating clinically useful results both to doctors and to patients.

The CLARITY challenge winners, including WuXi NextCODE, were explicitly recognized for the quality and clinical utility of their reports.

Studies and surveys have shown that many people favor greater access to genetic information. Individuals want analysis of their genomes in order to:

  • Reveal their unique risk factors for inherited diseases;
  • Pinpoint a diagnosis if they are ill; and
  • Guide their decisions if they are seeking treatment.

Genomics is helping to inform patients in all these ways.

In addition, genomics demonstrates enormous potential to empower individuals.

The hundreds of thousands of people who purchase genomic testing through direct-to-consumer businesses like 23andMe are demonstrating a robust enthusiasm for gathering genomic information. And patients enrolled in clinical trials and donors participating in population-wide genomic studies express a desire to be more informed. Patients and consumers consistently seek resources that transform their personal genomic signatures into information they can use to make better healthcare and lifestyle decisions.

And most patients and consumers are willing – often eager – to share their genomic information to aid medical research and discovery. 23andMe reports, for example, that 80% of its customers consent to share their genomes for research.

It is unmistakably clear that, in the not-too-distant future, every individual in many countries around the world will have their genome sequenced. Throughout a person’s life, medical professionals will be able to access genomic information to guide health decisions – from identifying inherited conditions to assessing risk for complex diseases to calculating appropriate treatments, drugs, and even dosages for truly personalized healthcare.

The more effectively we communicate – the more we share information within the research community and parlay that into clinically useful information for patients – the greater the benefit to all.

As much as people understandably prefer simple, definitive answers to questions about their personal health, the information that genomics provides can be complex and even ambiguous. A genetic variant might be identified, for example, that can be tied to family medical history and translated into a probability or likelihood. This was the case for Angelina Jolie Pitt, who noted in her New York Times piece that her genomic analyses “gave [her] an estimated 87 percent risk of breast cancer and a 50 percent risk of ovarian cancer.” Percentage risks are nuanced, and individual perceptions of acceptable risk vary considerably. It is therefore difficult to define precisely the circumstances under which a genetic variant becomes clinically actionable.

Or a genetic variant might be identified which gives physicians clues but does not explicitly identify a specific disease. For example, a patient seeking a diagnosis may have a genetic variant that correlates to a number of diseases involving dysregulation of lipid metabolism. Identifying the variant provides physicians and caregivers with a clear direction for further analysis and treatment, but does not yield a conclusive diagnosis or prognosis.

Or a genetic variant might be identified which has yet to be understood as causing or playing a role in disease. Such a variant may occur by chance and have no medical relevance, or its meaning may be uncovered as science in the field advances. But for the person who is having the genomic information analyzed today, it offers no actionable information.

As all of these examples illustrate, effective communication about genomic information can be a significant challenge. There is a risk that poor communication will be a barrier to the adoption of genomic medicine, but if we strive to communicate clearly with patients and the public, our successes will likely accelerate more widespread use of genomics. The role of genomics in transforming health care will grow exponentially as we all endeavor to improve communication with patients, their families, and the public at large.

Our work at WuXi NextCODE is advancing the transformation of medical practice through genomics. As part of that vision, we recognize the critical importance of facilitating effective communication among all stakeholders. We provide the resources that enable researchers and clinicians to identify disease and inform treatment decisions. And we strive to add additional value by communicating about genomic information accurately and proactively, all with the ultimate goal of meaningfully improving patient outcomes.

Genomics: Big Data Leading to Big Opportunities

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The Big Data of Genomics

WuXi NextCODE Exchange

The big data of genomics will continue to expand, and our approaches to analyzing genomic data need to continue to evolve to meet the growing demands of clinicians and researchers. Cloud-based platforms such as WuXi NextCODE’s Exchange are essential to address the fundamental big data challenge of genomics.

Beyond question, we are in the midst of an explosion of “Big Data” in many facets of human endeavors. In fact, data-storage leader IBM asserts that roughly 2.5 quintillion bytes of data are generated every day and 90% of the world’s data was created in the last two years.

An outpouring of articles in scientific journals and major newspapers has highlighted the promising potential of big data in medicine, including a special section in the current issue of Nature.  Genomics has become a major source of the growth of such big data, particularly as the cost of sequencing genomes has plummeted. The raw sequence data for just one person’s whole genome use as much as 100GB—and already hundreds of thousands of individual genomes have been sequenced.  With more than 2,500 high-throughput sequencing instruments currently used in 55 countries across the globe, more genomes are added every day. The aggregate amount of genomic data is growing explosively, and next-generation sequencing (NGS) sequencing data are estimated to have doubled in volume annually since 2007.

The accumulation of genomic data is a worldwide phenomenon.  Impressive population-wide sequencing efforts are leading the way, from 100,000 genomes in England, Saudi Arabia, and Iceland to 350,000 in Qatar to a million in both China and the U.S.

And earlier this month, the CEO of the Cleveland Clinic predicted that soon children will routinely have their whole genomes sequenced at birth, implying a near-future in which 10s of millions of new genomes are sequenced annually.

Turning Data into Resources

But sequencing genomes is not enough, and the creation of genomic big data is just the beginning.

Thanks to the analysis of big data in genomics and associated informatics, we are seeing meaningful progress in cancer care and the diagnosis of rare diseases, as I have discussed here and here. We clearly have a tremendous opportunity to use the big data of genomics to continue to drive a revolution in healthcare.

Yet there is a broad consensus that a ‘data bottleneck’ is hampering collaboration and discovery. Not all researchers and physicians confronting the current onslaught of genomic big data can readily determine how to use genetic information to prevent or treat disease. To succeed, researchers and physicians clearly need resources that:

  • Draw together useful data from disparate sources;
  • Facilitate analysis and collaboration; and
  • Improve clinical practice.

The power of genomic analysis needs to expand outward from major research centers and hospitals to the myriad clinics and community hospitals where many patients receive care. To have the greatest impact on the broadest population, clinicians throughout the world’s health systems need access to the big data generated by DNA sequencing, even—or perhaps especially—if they are not affiliated with research institutions. They also need to be able to make sense of the data they have access to.

Answers in the Cloud

Sequencing provides the raw data to uncover the genetic variants that contribute to disease. But the datasets are too big to transfer repeatedly—and too big even for smaller hospitals, labs, or clinics to store onsite. Key medical advancements require not only big data, but also tools and resources to generate, interpret, and share analysis of millions of genomes.

Cloud-based platforms—such as WuXi NextCODE’s Exchange—are essential to address the fundamental big data challenge of genomics. Collaboration in the cloud works to dismantle existing “data silos”—genomic information hosted only on local servers and analyzed on idiosyncratic, closed platforms. The NextCODE Exchange, in contrast, is a browser-based hub that affords secure, seamless collaboration with colleagues around the world. Moreover, users get access to NextCODE’s tools for making the critical links between variation in the genome and disease and other phenotypes, backed by harmonized links to the the most important public reference data.

And cloud-based computing is inherently scalable: resources for data storage and analysis expand as needed, allowing researchers and physicians to leverage massive datasets to improve patient care in the clinic. The big data of genomics will continue to expand, and our approaches to analyzing genomic data need to continue to evolve to meet the growing demands of clinicians and researchers.

At WuXi NextCODE, we have built upon our heritage of conducting the largest analysis of genomic data (deCODE’s path-breaking Icelandic analysis) by assembling an ever-growing database of human genomes. We are committed to driving the movement of sequence data into patient diagnosis and care through user-friendly, leading-edge analysis and informatics. I am confident that data analysis and collaboration in the cloud will revolutionize healthcare, and exceptionally proud that WuXi NextCODE’s Exchange is at the forefront of this exciting advancement.

Genomics in Cancer: Continuing to Push the Leading Edge

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Genomics is helping to prevent and treat cancer at an accelerating rate, supporting the goal of oncologists to dramatically improve cancer patient outcomes.

The progress in the use of genomics to help prevent and treat cancer continues to grow at a pace that is impressive. Indeed, there is expanded use of genomics to drive patient care and improve outcomes across an ever-expanding number of cancers by a growing number of oncologists.

Genomic Knowledge Can Clearly Drive Better Care

Applying genomics to cancer treatment is a powerful clinical application, as genomics can provide a window into how to best treat a patient’s particular cancer as it:

  1. may help better understand the genetics of the tumor itself, and
  2. can provide insight into how cancerous tumors may grow and spread over time.

With a genomic-based approach to cancer care, oncologists can more personally tailor anti-cancer treatments to an individual tumor’s mutations, thus molecularly targeting the specific cancer’s Achilles heel. Already, there are well-documented successes of molecularly targeted anti-cancer agents, such as cancer drugs that target certain genes—HER2, EFGR, ALK, and others.

In 2015, the pace of adoption of genomics in clinical oncology has advanced significantly. Recent evidence of the accelerating use of genomics to help fight cancer includes:

  • Evolving from ‘why’ to ‘how’ to use genomics at leading cancer centers. At the top cancer care facilities, genomics has become part of the programmatic approach to provide certain cancer patients with optimal care—care that is fundamentally designed to lead to the best outcomes. The question for leading medical centers globally has evolved over the last few years from “do we need genomics?” to “for which cancer types and at what stages of cancer treatment and diagnosis can we best use genomic sequencing and analysis?”—an evolution from “why?” to “how?” at a very fundamental level. The accelerating use and deployment of genomics by leading medical facilities validates that they are deriving significant value from genomics, and that value is resulting ultimately in meaningfully advancing better care for cancer patients.
  • Expanding potential applications of genomics within different types of cancers, broadening the types of cancers and tumors that can potentially benefit from genomics. Researchers and clinicians continue to publish a wealth of information validating the potential of genomics to improve outcomes in certain types of cancer patients. In 2015 alone, highlights of these advancements include certain prostate cancers, brain cancers, rare types of pediatric kidney cancers, and even potential targets in certain non-small cell lung cancers.
  • Broadening acceptance in cancer prevention. Driven in part by the education of oncologists and physicians generally and in part by the empowerment of knowledgeable patients, people are seeking and benefiting from genetic tests that reveal their personal risk for certain tumors (such as BRCA for breast or ovarian cancers). 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 is—for certain individuals with specific family histories and genetics—driving appropriate medical decisions for patients who may be at high risk for certain cancers.
  • Powering clinical trials with genomics. The use of genomics in cancer clinical trials – whether for inclusion in data-gathering or even screening of patients—has gone from rare to commonplace over recent years, and is improving knowledge around the safety and efficacy of drugs in cancer and beyond. Two large-scale cancer trials have been initiated in 2015 with the bold goal of substantially advancing the understanding and use of genomics in cancer care. The anti-cancer treatments being tested in both trials were selected for their activity on a specific molecular target, independent of tumor location and histology. The two trials are actively enrolling and are (1) an American Society of Clinical Oncology (ASCO)-sponsored study, called TAPUR (Targeted Agent and Profiling Utilization Registry) and National Cancer Institute (NCI) and is called NCI-MATCH (Molecular Analysis for Therapy Choice). These trials and any subsequent follow-on trials will doubtless provide insightful information to drive the growing use of genomics in improving cancer care.

In summary, genomics is helping to prevent and treat cancer at an accelerating rate, supporting the goal of oncologists to dramatically improve cancer patient outcomes. There are at least four frontiers where we can see substantial progress in the use of genomics in cancer care, including expanded use in leading medical centers, increased potential applications within cancer, widespread acceptance in cancer prevention, and an increase in the use of genomics within clinical trials. I am personally committed to continue to drive and accelerate this genomic revolution to continue to bring true progress in improving cancer care to patients in need globally.

2015: An Inflection Point for Genomics Adoption Around the Globe

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2015 genomics hannes smarason

2015 is shaping up to be a significant year in the advancement and adoption of genome sequencing and personalized medicine around the globe.

The year 2015 is shaping up to be an inflection point in the advancement and adoption of genome sequencing and personalized medicine.  While private initiatives are often the centerpiece of media coverage, leading governments clearly have advanced a number of important initiatives this year.  Indeed, many governments around the globe are actively promoting widespread utilization of genomics, supporting academic research, establishing industry guidelines, and raising public awareness.

Governments Serving as Catalysts for Genomics Progress

The efforts of officials worldwide to engage with and support the private sector’s tremendous potential have helped to make 2015 a significant year for expanding the use of genomics in clinical care.  A few highlights of 2015 include:

— In the U.S., President Obama made precision health one of the centerpieces of his State of the Union address in January. Obama’s administration kicked this effort off by requesting a $215M investment in a Precision Medicine Initiative with the following key attributes:

  • The cornerstone of Obama’s proposal is the plan to collect and analyze genomic data from a million or more volunteers;
  • The initiative further supports genomics through expanded research into the genetic mutations that drive cancer;
  • Additional funding is earmarked to maintain databases and develop industry standards.

— Germany and the U.K. expanded eligibility for government-funded genetic testing for breast cancer patients.

— Israel announced its intent to establish a government-sponsored genetic database.

— Through the National Institutes of Health and the National Cancer Institute, the U.S. federal government proposed dozens of new funding opportunities to support research in genetic sequencing and analysis.

— Japan launched an Initiative on Rare and Undiagnosed Diseases to provide genomic analysis and expert consultation for up to 1,000 individuals with childhood onset of undiagnosed conditions.

— Through Genomics England (which I described in further detail here), the U.K. Department of Health tapped WuXi NextCODE and others to begin interpretation in its groundbreaking 100,000 Genomes Project.

In news today, the trend toward globalization of genomics continues, as private sector leaders aligned to meet the needs of the forward-looking government health initiatives of Qatar:

— WuXi NextCODE and the Sidra Medical and Research Center partner to power population genomics and precision medicine in Qatar. Our partnership will:

  • Facilitate clinical diagnostics;
  •  Accelerate research; and
  • Support the Qatar Genome Project.

As I have discussed in an earlier post, large-scale population studies are an essential step in harnessing the power of genomics to improve health worldwide.  Since WuXi NextCODE’s foundational heritage as part of deCODE Genetics’ landmark analysis of Icelanders, we have always developed the tools to help translate sequence data into precision medicine on a large scale.  In our work with Genomics England, our collaboration with Fudan Children’s Hospital to diagnose rare diseases in China, and now our partnership with Sidra, the team at WuXi NextCODE is leading the effort to realize the potential of genomics on a truly global scale. The increasing interest in supporting those efforts shown by leading governments across the globe is helping to drive the successful use and application of genomics worldwide.

Genomics for Rare Diseases: Going Global and Shifting the Care Paradigm

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The use of genomics in rare disease diagnosis and treatment is going global

The benefits of genomics in rare diseases are increasingly making a difference to patients, their families, and their physicians, and they are being scaled globally.

The trend of accelerating the use of genomics in rare disease diagnosis and treatment is going global, driven by the important goal of reaching all people around the world, no matter where they live.

Active programs have now been deployed and exist in many populous countries around the world.

For instance, WuXi NextCODE has established active collaborative efforts in three continents, most recently adding Fudan Children’s Hospital as a partner in its efforts to lead whole genome diagnostics for rare diseases in China.

Over the coming weeks, I expect WuXi NextCODE to continue have news of its dedicated efforts to spread the application of genomics for rare diseases to all geographies.

Diagnosing Rare Diseases: Genomics Shifts the Paradigm

Rare diseases are an area of significant advancement for genomics, as the opportunity for improved diagnosis and treatment through the use of genomics is truly remarkable.

According to the National Institutes of Health (NIH), there are over 7,000 rare diseases affecting between 25 and 30 million Americans, which is nearly 1 in 10 people, making the overall prevalence of rare diseases significant. Since NIH believes that approximately 80 percent of rare diseases have genetic origins, the potential for genomic sequencing, interpretation, and analysis to offer a solution here is truly game-changing.

Every day there are new cases of children with “unknown” diseases, many of which are likely related to a hereditary genetic disorder. Sadly, these children and their families often spend years undergoing testing and experimental treatments for a wide range of diseases in an attempt to properly diagnose and treat them; usually, this so-called “diagnostic odyssey” is accompanied by a very high financial and emotional burden.

Genomics offers the potential to deliver a correct and precise diagnosis for rare diseases that have identifiable genetic causes. Indeed, case studies are rapidly accumulating that show that, by offering genomic sequencing and analysis services 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.  A recent article in Bloomberg BusinessWeek highlighted medical histories of two patients who recently received a diagnosis informed by genomics. In both these representative examples, genomic analyses provided an end to the burden, cost, and stress of their multidecade-long diagnostic odyssey:

  • Jackie Smith, 35, spent the 32 years from age 3 unable to receive a correct diagnosis that could account for her weak limbs and turned-in ankles, despite seeing many doctors on numerous occasions. Indeed, Jackie’s parents were told to “take the 3-year-old girl home and enjoy her while they could” …”[her disease] would probably kill her before she was old enough to drive.”  This past February, using genomic interpretation and analyses from Wuxi NextCODE, Claritas Genomics definitively identified her condition as centronuclear myopathy in less than three weeks.
  • Dustin Bennett, 24, would tremble and violently jerk for hours or days at a time and had been developmentally delayed since childhood. After dozens of doctor visits and incorrect diagnoses—seizures, muscle disorders, mental health problems—a Mayo Clinic genomic-based analysis showed he has episodic ataxia type I, a neurological disease characterized by hours-long attacks with no clear trigger. Dustin, a 24-year-old who functions at a first-grade level, is now on the second round of a medication doctors say should help reduce the frequency and severity of his episodes.

The benefits of genomics in rare diseases – to individuals, their families, and their physicians – are increasingly making a difference to patients.  These benefits are being seen in case after case – and they are being scaled globally, as leading medical centers in many countries around the world are using genomics to support their efforts in diagnosing and treating rare diseases.  I believe passionately in the game-changing potential of genomics to help rare disease patients and I am dedicated to advancing world-leading genomics globally to uncover new solutions for patients.

Genomics Offers Game-Changing Solution to Rare Disease Diagnosis, Costs

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Hannes Smarason Wuxi NextCODE

As genomics is used more and supported by ever-more robust analysis and interpretation, its potential to offer a solution to diagnosing rare diseases is truly game-changing.

I believe strongly and have previously blogged on the potential for genomics to shift the care paradigm for rare diseases, and here I’d like to detail in particular the huge potential value genomics can add to rare disease diagnosis. According to the National Institutes of Health (NIH), there are over 7,000 rare diseases affecting between 25 and 30 million Americans, which is nearly 1 in 10 people, making the overall prevalence of rare diseases significant. Rare diseases can be chronic, progressive, debilitating, disabling, severe, and life-threatening.

When a patient presents with a spectrum of unusual symptoms, a costly scramble naturally begins to diagnose the patient’s disease. Some people refer to this diagnosis process for rare diseases as a “diagnostic odyssey,” as patients and their families are subjected to test after test while being handed from one doctor to another, oftentimes to medical centers far from their home. Too often, this odyssey yields no concrete diagnosis or—worse—misdiagnosis. The direct medical costs can be significant, and the indirect costs—the frustration and disillusion felt by the patients and the family—can be extraordinary.

Since NIH believes that approximately 80 percent of rare diseases have genetic origins, the potential for genomic sequencing, interpretation, and analysis to offer a solution here is truly game-changing. A recent article in Bloomberg BusinessWeek highlighted medical histories of two patients who recently received a diagnosis informed by genomics. In both these examples, genomic analyses provided an end to the burden, cost, and stress of their multidecade-long diagnostic odyssey:

  • Jackie Smith, 35, spent the 32 years from age 3 unable to receive a correct diagnosis that could account for her weak limbs and turned-in ankles, despite seeing many doctors on numerous occasions. Indeed, Jackie’s parents were told to “take the 3-year-old girl home and enjoy her while they could”…”[her disease] would probably kill her before she was old enough to drive.”  This past February, using genomic interpretation and analyses from Wuxi NextCODE, Claritas Genomics definitively identified her condition as centronuclear myopathy in less than three weeks.
  • Dustin Bennett, 24, would tremble and violently jerk for hours or days at a time and had been developmentally delayed since childhood. After dozens of doctor visits and incorrect diagnoses—seizures, muscle disorders, mental health problems—a Mayo Clinic genomic-based analysis showed he has episodic ataxia type I, a neurological disease characterized by hours-long attacks with no clear trigger. Dustin, a 24-year-old who functions at a first-grade level, is now on the second round of a medication doctors say should help reduce the frequency and severity of his episodes.

As genomics is used more and supported by ever-more robust analysis and interpretation, I expect these types of clear successes to become even more commonplace. And the value to the healthcare system and the patient is clear, expressed powerfully in the Bloomberg BusinessWeek piece:

While there isn’t yet a cure, Smith is participating in research that may one day lead to treatments or more supportive care. “Just being connected feels good. I felt alone for a long time,” she says. “And I want to do it for the bigger picture, too. Not just for myself, but so I can be counted.”