About Hannes Smarason

Hannes Smarason is CEO of NextCODE Health, a genomics leader. He is the former CEO of the FL Group (formerly Icelandair) and Chief Business Officer of deCODE Genetics, an Iceland-based genomics company.

WuXi NextCODE Partners with Google Cloud

We’re delighted to announce an alliance between WuXi NextCODE and Google Cloud. This partnership will provide our customers and partners yet another world-class option for accessing a growing genomic data analysis toolset capable of fueling real breakthroughs in research and clinical care.

WuXi NextCODE is building the global standard platform for using genomic data at scale and over the internet. Our offerings already include our pioneering GOR database management system; our own secondary analysis pipeline; the Sequence Miner case-control research application; and the Clinical Sequence Analyzer interpretation system.  Google, meanwhile, has one of the world’s leading cloud platforms as well as its own outstanding genomics tools, such as BigQuery the DeepVariant secondary analysis pipeline, as well as full integration with other open-source tools that many are eager to leverage in tandem with ours.

As pioneers of using the genome online, working with Google in genomics is clearly exciting. Through this partnership, Google Cloud will host the entire suite of WuXi NextCODE’s core offerings and make these available on the Google Cloud Launcher Marketplace. This will provide users our combined IT horsepower and a full range of tools to perform at the leading edge of genomic research and clinical interpretation.  We expect to launch our tools on Google Cloud in May, at the BioIT World Conference & Expo in Boston.

As we build the global standard platform for genomic data, WuXi NextCODE has been making crucial partnerships to ensure our clients have the most options for accessing the full range of tools they need, however they prefer to do so.

Read more about this remarkable partnership at the WuXi NextCODE Genomics Insights blog or in our press release.  It is an important step towards realizing our vision to provide people and organizations with the best tools for using genomic data – wherever they are and at internet speed.

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Rare Disease Day Spotlight: Dr. Christina Waters on how WuXi NextCODE is Using Global Genomics to Advance Diagnosis and Treatment

As we continue to build and expand the leading global platform for storing, sharing, and interpreting massive sets of genomic data, rare diseases are becoming an increasing focus for us.

So, today, on Rare Disease Day, we want to spotlight the role of Dr. Christina Waters, our new Senior Vice President for Rare Disease.

Christina founded the non-profit RARE Science in 2013.  With RARE Science she has succeeded in creating a framework to power rare disease research and bring together families across 38 countries who share one of the almost 400 conditions the organization is working on. Joining WuXi NextCODE has allowed Waters to help us increase our focus on rare diseases and take her non-profit’s goals to scale and help more patients with rare diseases receive definitive diagnoses and more effective treatments.

“The reality of rare disease means we must work globally if we are going to have enough patients in any of our studies to have an impact,” she explains.

Rare conditions are, after all, much harder to study because in any given place fewer people have them.  For some conditions, the number of known patients is fewer than 100 worldwide.

Still, overall, there are many rare conditions – about 7,000 and affecting hundreds of millions of people worldwide. Over half of rare disease patients are children, 30% of which will die before their fifth birthday.

Learn more about Christina and her aims for rare disease patients.

WuXi NextCODE Named one of the “Top 10 Most Innovative Companies in Biotech” by Fast Company for Creating the World’s Leading Platform for Genomic Data

One of fast company's most innovative companies 2018

Wuxi NextCODE has been named one of Fast Company’s “Top 10 Most Innovative Companies in Biotech” for being the world’s leading platform for storing, sharing, and interpreting massive sets of genomic data. With offices in Shanghai, Cambridge and Reykjavik, we provide the infrastructure underpinning many of the largest national genome projects and rare disease efforts underway worldwide.

One notable example of our capabilities cited by the editors of Fast Company is the RareCODE rare disease diagnostics platform we launched approximately one year ago in collaboration with Fudan Children’s Hospital in Shanghai. It’s hard to think of work that better taps, according to the magazine’s criteria, “both heartstrings and purse strings and uses the engine of commerce to make a difference in the world.”

RareCODE is the first platform that applies global gold standard genomics to the diagnosis of rare disease, at scale, in China. As a result of this program, Fudan Children’s has been able to quickly and accurately diagnose thousands of rare disease patients, allowing clinicians to optimize their treatment and care.

In just the first calendar year since its launch, RareCODE generated more than 12,000 clinical reports. We and our partners at Fudan also used it for some 2500 cases in their neonatal intensive care unit (NICU). We are now generating more than 1,000 new reports each month.  Thanks to this program, Fudan clinicians have been able to provide diagnoses to nearly 40% of patients tested and recommend treatment for nearly two-thirds of them. In short, this partnership is now carrying out sequencing and delivering diagnoses at a rate that is equivalent to that of the world’s leading laboratories.

We are delighted to join outstanding partners and colleagues on Fast Company’s Top Biotechs list, including Novartis, Biogen, GE Healthcare, Spark Therapeutics, and Sophia Genetics. The winners are selected by the magazine’s reporting team from thousands of enterprises reviewed each year.

Learn more about this award, and the breakthrough genomic platform that helped us earn it.

Genomic Power Tools: WuXi NextCODE Partners with 10x Genomics to Offer Advanced NGS Technologies

Genomics is advancing rapidly, and as the world’s only contract genomics organization, we make it our business to work closely with world-leading technology partners to make sure our customers can access all the best tools available for using the genome to derive the insights they need – from generating sequence data to storing it, querying it and sharing it, all in one place.

This week, 10x Genomics, Inc. announced new programs to deploy its innovative sequence data solutions to create a “global ecosystem of sequencing technologies and service providers who together span all aspects of the next-generation sequencing (NGS) workflow, from wet-lab to informatics,” said Edwin Hauw, senior director of strategic marketing at 10x Genomics, in their recent press release.  WuXi NextCODE is proud to be among the first partners in this strategy.

10x Genomics’ Certified Service Provider program will connect customers to a reliable network for outsourcing genomic and single cell analysis through global providers, leading off with WuXi NextCODE. The applications include 10x Genomics’ Chromium Single Cell Gene Expression, Immune Profiling Genome or Exome Solutions.

Their second initiative, Compatible Partnership Programs, will designate 10x compatible products, thereby helping customers identify ancillary NGS technologies that have been verified and validated as compatible with the company’s products. More details about the two new programs will be shared at this years’ Advances in Genome Biology and Technology Meeting (AGBT) held February 12 to 16 in Orlando, FL.

We at WuXi NextCODE already have considerable experience working with 10x Genomics. “We are proud to be among the first certified 10x service providers,” says Dr. Hongye Sun, WuXi NextCODE’s CTO and founder of our sequencing laboratory. “Our philosophy is to provide our customers with end-to-end solutions for using genomic data to improve health and medicine.

10x shares that vision, and their technology enables our customers to derive even more information and value from their sequencing data and to use other best-in-class laboratory tools and our informatics to generate novel insights. That’s the kind of innovation and collaboration that drives the field forward.”

It’s a strong partnership with a compelling rationale.  We at WuXi NextCODE are building the global standard platform for genomic data.  Our own capabilities include study design, sequencing, secondary analysis, storage, interpretation, scalable analytics, artificial intelligence and deep learning.

Meanwhile, as Sun says, “10x Genomics offers, among other tools, unique library methods in combination with short-read sequencing technologies that are very powerful for DNA/RNA sequencing from single cells to population scale. That means users can derive a range of key additional information, including on phasing, structural variation and gene expression. That will not be obtained with traditional short-read sequencing technologies alone.”

Once our partners have used 10x to generate the data they need, we are very pleased to be able to help them take it downstream according to their needs, to improve medicine and health around the world.

 

Another sequencing milestone for WuXi NextCODE partner Oxford Nanopore

Oxford Nanopore MinION

Over the last few months, Oxford Nanopore (ON) instruments have been used to achieve two major sequencing milestones.

First, in December, a group in Australia announced they had become the first to generate a DNA read longer than 1 Mb when they produced a 1.105 Mb read from Chromosome 19.

Then, just last week, a paper was published in Nature Biotechnology describing how scientists used a handheld ON sequencer – the MinION – to assemble an entire human genome by direct long reads. That accomplishment is another important first that demonstrates how this technology can power breakthroughs.

To learn more about this remarkable study and the Nanopore technology, see this post on the WuXi NextCODE Genomic Insights blog. It features comments and insights from our esteemed colleague Dr. Hongye Sun, our Chief Technology Officer and head of our sequencing lab in Shanghai.

WuXi NextCODE has a lot of experience working with Nanopore instruments.  In October of last year, we announced that our Shanghai sequencing laboratory would feature the first open-access installation of ON instruments in a laboratory in China.

2018 Kicks Off with a Bang: The Sequencing Boom Continues and the Dawn of China’s “Healthcare Moment”

The sequencing boom and the China’s burgeoning healthcare market were major topics of interest at the annual JP Morgan Healthcare Conference earlier this month. WuXi NextCODE looks forward to addressing these evolving topics further in the upcoming BIO CEO and Investor Conference in New York in February, BioCentury “Future Leaders” conference in New York in March, and Cowen & Co. Healthcare Conference in Boston in March.

Like thousands of people across the biotech, pharma, and healthcare industries, we started the year with an intense and very productive week at the annual JP Morgan Healthcare Conference. As ever, we were very pleased to meet with so many colleagues and partners—old, new, and future—and to speak to a truly packed audience during our presentation at the conference. We have returned to work excited for some of the trends in genomics that are clearly in the air.

It was no surprise to us that the sequencing boom was again one of the hot topics for 2018. The bigger question among healthcare experts was, “What companies will be riding this wave, and how will they harness the data to move the needle across healthcare?” Another interesting trend was growing recognition of how large, fast-growing, and innovative China’s healthcare market has become. That’s no surprise either, as China is actively working to become a leader in this field, and its healthcare market is now expected to grow to around $1 trillion by 2020.

WuXi NextCODE is playing a significant role in the evolution of both these fields. One of our main focuses is building our partnerships to ensure that our database management system continues to develop as the global standard. That, and our portfolio of products in China, are poised to play a key role in helping China vault to the fore of genomic medicine.

Regarding sequencing, a lot of the buzz at JP Morgan was around sales figures for instruments. Analysts have estimated that the world market for next-generation sequencing could reach more than $21 billion by 2025. But the challenges in sequencing have moved far beyond the original issues of speed and cost. Now, those at the forefront of the field are focusing on improving accuracy, integrating multi-omic and clinical data, and using advanced analytics to apply that data to healthcare challenges. High-throughput sequencing is flourishing in industry, academia, non-profits, and medical practice. The goals are to improve current treatment outcomes and to find new drugs and diagnostics.

Prominent sequencing instrument providers, such as Illumina, are bellwethers of this market. Analysts attributed that company’s current healthy sales to factors that include: the growth of the consumer genetics market, the continued rise of targeted cancer therapies, increasing numbers of countries pursuing large-scale genomic studies, advances in sequencing to diagnose rare diseases, uptake of non-invasive prenatal testing, and the dawn of liquid biopsies. We have leading and innovative offerings in all of these areas.

The recognition of China’s emergence as a major healthcare market also resonated with the Wuxi NextCODE team. In another recent report, Cannaccord analyst Mark Massaro pointed specifically to increased sales in China of Illumina’s sequencers as one of the factors influencing that company’s currently rosy outlook. He also highlighted our positioning to drive genomics forward there.

Many life sciences companies are starting to see the potential of China’s healthcare market, and Chinese healthcare providers are eager to provide the highest level of care possible. We at WuXi NextCODE have been privileged to be at the frontier of genomic medicine globally, but particularly in China, where we have multiple partnerships with leading hospitals and are quickly expanding our laboratory and sales presence. The breadth and promise of our work in China was recently highlighted in a roundup coming out of JP Morgan.

I’m sure that both sequencing and China’s healthcare marketplace will evolve further over this year and will be major stories again in the weeks and months ahead. And we’ll be telling our part of the story soon at the BIO CEO and Investor conference, BioCentury’s Future Leaders conference, and the Cowen & Co. Healthcare conference.

We look forward to seeing many of you there!

 

Louis Yuan Joins WuXi NextCODE to Lead Growth of China Businesses

Louis Yuan will lead the growth of WuXi NextCODE’s China businesses, sales, and other operations based out of the company’s Shanghai site.

I’m pleased to announce that Louis Yuan has joined WuXi NextCODE‘s team as senior vice president and China General Manager based in Shanghai. This is a major milestone for us, since further expansion and commercialization of our genomics platform in China is one of our strategic priorities, and Louis is the ideal person to lead that charge.

He has a stellar record of commercial success, scaling businesses, and managing sales teams more than 300 strong. He has also achieved multiple triple-digit revenue ramps in the past. Further, his experience supports our broader mandate as a fully integrated contract genomics organization (CGO) building the global standard platform for genomic data.

Among Louis’ outstanding accomplishments: He has held senior sales and marketing positions at such renowned businesses as Becton Dickinson, Sanofi Pasteur, and Pfizer, where he led the company’s launch of the blockbuster vaccine, Prevenar, in China.

For the complete announcement about his appointment and its significance, read more in our press release.

Using AI to Understand and Make Use of the Genetic Roots of Obesity

This week, we announced a breakthrough partnership applying artificial intelligence to the study of genetic variants associated with obesity. Rare metabolic syndromes cause excessive weight gain in some patients. These conditions are very difficult to treat and lead to related health risks. Now, WuXi NextCODE is working with Rhythm Pharmaceuticals to use AI to help advance the development of drugs to treat such patients.

We’re excited to be doing this work because several key genes are known in the MC4R pathway, which helps regulate weight by increasing energy expenditure and reducing appetite. We’re now working with Rhythm to determine which of these variants correlate with the greatest impact on risk of developing obesity through this pathway.

This is one of the frontiers of rare disease research, and we hope to make rapid progress with our novel AI tools, including our proprietary DeepCODESM algorithm for variant scoring. Learn more about this intriguing research here.

WuXi NextCODE Appoints Christina Waters to Expand Reach and Impact of the Global Platform for Rare Disease

Dr. Christina Waters’ expertise in translational medicine and building global networks and cohorts will extend the reach and benefits directly to patients, families, and disease organizations.

Connecting patients, advocacy organizations, researchers, and healthcare systems through world-leading genomics and massive data – to advance diagnosis, research and new therapies

  • WuXi NextCODE’s platform is the engine of choice for large-scale sequence-based rare disease diagnostics and research efforts on three continents
  • Dr Waters’ expertise in translational medicine and building global networks and cohorts will extend the reach and benefits directly to patients, families, and disease organizations

14 December 2017 – WuXi NextCODE today announced the appointment of Dr Christina Waters as senior vice president, focusing on our rare disease programs. Dr Waters will apply her two decades of experience to grow the company’s rare disease platform by reaching out to and integrating patients and patient communities, leveraging our capabilities and those of our partners to benefit even more people around the world.

WuXi NextCODE presently serves as the diagnostics engine for major research hospitals and national health systems and genome projects in the US, China, UK, Ireland, Singapore and Qatar, and has assembled the world’s leading knowledgebase of genome variation for diagnosing rare disease. Under Dr Waters’ leadership the company aims to extend the breadth and impact of its platform by using existing networks and global social media to identify and connect rare disease patients wherever they are. WuXi NextCODE plans to employ the full range of its capabilities – from sequencing through interpretation, AI and large-scale discovery – to generate new datasets, communities and cohorts that will make it possible to diagnose more cases, understand the biology of rare disorders, and drive therapeutic development.

“A central part of our mission as a company is to apply genomics to solve rare disease and we are thrilled that Christina Waters is joining us to realize this vision,” said Hannes Smarason, CEO. “Building on our large-scale work, she is going take our platform to the next level: putting it directly at the service of patients and families in urgent need. Connected with each other and armed with sequence and medical data, we and patients, partnering with research institutions, healthcare systems and pharmaceutical companies, are going to be able to solve and eventually treat more rare disease cases.”

“I am excited to be joining WuXi NextCODE at this promising moment in the genomics revolution,” said Dr Waters. “Pharmaceutical companies have very clear criteria for the data they need to begin working on developing new drugs but many families are on their own, scattered all over the world. WuXi NextCODE has the platform that can connect patients’ and families’ data globally to create a critical mass of knowledge for diagnosing more diseases and the cohorts for uncovering the biology and undertaking therapeutic development. We are uniquely placed to be the trusted partner for generating and assembling the data required. This is going to help countless families and I feel privileged to have the chance to help drive this effort.”

Dr Waters is founder and CEO of Rare Science, a non-profit staffed entirely by volunteers that serves as a resource and research hub working to find diagnoses and treatments for some 3000 children and their families with more than 350 rare disorders in 38 countries. She has been responsible for leading medical research in a broad range of organizations ranging from academia and disease – from non-profits to biotech and large pharmaceutical companies, including Novartis, aTyr Pharma, Cell Therapeutics and the Multiple Myeloma Research Foundation.
She holds a BS in molecular biology from San Diego State University, a PhD in genetics from UC Davis, an MBA from the Anderson School of Management at UCLA, and was awarded postdoctoral fellowships at UC Berkeley and CalTech.

WuXi NextCODE Takes on Cancer: Breakthroughs and Innovation in Sequencing using TCGA and AI

Hannes Smarason NextCODE TCGA cancer

Sequencing reads of a sample prepared by the traditional whole-genome sequencing workflow for fresh-frozen samples and data generated using the SeqPlus whole-genome FFPE method. The green and purple indicate reads sequenced in the forward and reverse directions, respectively, and yellow represents bases with non-reference sequence. The center of the image shows a C to A mutation in each of the tumor samples.

Cancer is one of the most active fields in genomics, spurring mountains of research papers and scores of clinical trials. WuXi NextCODE (WXNC) is committed to pushing this field forward and so we had a special “Genomes for Breakfast” session devoted to this topic at the recent ASHG17 event. Featured talks addressed our pathbreaking work in how to extract impactful findings from the renowned TCGA dataset; get better sequencing results from FFPE samples; and apply deep learning to drug discovery, drug repurposing, and identifying subtypes for diagnostics and clinical trials.

The Cancer Genome Atlas (TCGA) is one of the most useful public genomic cancer databases available and has already led to numerous critical discoveries, including entirely new drug targets as well as better insights into tumor origination, development, and spread. It includes data from approximately 11,000 patients and covers 33 cancer types. Data types include WES, RNA-Seq, mi RNA, CNV, Methylation array, and clinical sample data. The data is big and complex, and can include multiple samples from one patient, which is crucial to know when doing analyses.

During his ASHG talk, Jim Lund, WXNC’s Director of Tumor Product Development, shared some insights into how we put this rich data source to work in concert with our own unique data and analytical tools, in a process he dubs “multiomics analysis.” He described how we specially process the data and use our unique analytical platform to help scientists find just what they are looking for. Researchers can search the data by cancer type, age of diagnosis, sex, ethnicity, year of diagnosis, sample type (e.g. metastatic, new primary), and more.

Multiple pivotal studies using this dataset have already been published, including some examining the prevalence of specific mutations across human cancer types as well as in-depth profiling of specific tumors, such as breast cancer and lung adenocarcinoma. Layering different types of data, such as reads from DNA and RNA, allows much more accurate detection of features such as variants with allele-specific effects on gene expression. The user-friendly but sophisticated data interface makes it easier to see such findings. Over the years, our own database and our capabilities have both grown exponentially, creating a powerful tool for multiomics cancer research. You can see Jim putting the portal through its paces in a recent webinar.

In his talk, Shannon Bailey described how Whole Genome Sequencing (WGS) can be applied to formalin-fixed paraffin-embedded (FFPE) tumor samples, which are stored by the hundreds of thousands in repositories around the world. Shannon is the Associate Director of our Cancer Genetics division. He pointed out that while these samples are abundant and often paired with extensive clinical and outcome data, there are specific hurdles to using these for the type of large-scale retrospective studies many groups are eager to carry out.

For one thing the genetic material in such samples can be degraded, crosslinked, or in low quantities. Of all these problems, the biggest issue is getting sufficient quantity of quality DNA for sequencing. Numerous studies have found that these types of samples are difficult to work with and often provide very low success rates for gene sequencing studies. Clearly, fresh frozen samples provide much better results, but they are also much harder to obtain.

In response, our team has developed the WXNC SeqPlus FFPE extraction method, which provides substantially improved coverage compared to traditional methods and even approximates the results obtained with fresh frozen samples at 10X depth, with similar numbers of heterozygous and homozygous calls.

We tested SeqPlus in a study that comprised 516 tumor-normal pairs (i.e., 1,032 samples) that had been stored for 3 to 6 years. The targeted sequencing depth was 30X for the normal tissue and 70X for tumor tissue. The starting amount of DNA was 400 ng. The results were excellent, with SeqPlus delivering a coverage analysis just about 1% below what the fresh frozen control samples achieved. Further, a comparison of our analyses to results from the TCGA, using fresh frozen samples, showed striking similarity. These study results give us confidence that SeqPlus is a new “power tool” for FFPE sequencing studies. This webinar describes the process.

Sequencing reads of a sample prepared by the traditional whole-genome sequencing workflow for fresh-frozen samples and data generated using the SeqPlus whole-genome FFPE method. The green and purple indicate reads sequenced in the forward and reverse directions, respectively, and yellow represents bases with non-reference sequence. The center of the image shows a C to A mutation in each of the tumor samples.

Another area of great interest at WXNC is artificial intelligence (AI). We have been pioneers in AI for pulling novel insights out of massive multiple datasets. Leading this effort is Tom Chittenden, our Vice President of Statistical Sciences, Founding Director of the Advanced AI Research Labs, and a Lecturer on Pediatrics and Biological Engineering at Harvard Medical School and MIT. He also spoke at the breakfast series.

Our AI capabilities improve the tools we have and expand their capabilities. For example, using our AI tools, we can improve functional annotation of missense variants to an accuracy of >99%, integrate multiple types of data to discover new genes and elaborate pathways, and improve tumor subtype and drug-response classification accuracy by combining DNA- and RNA-seq, among other data types. These tools can be used for such varied purposes as target discovery, drug repurposing, and defining responders and non-responders in clinical trials.

We’ve already helped to develop breakthrough results, such as identifying an intriguing new target for both cardiovascular and cancer drug discovery. We’ve also classified breast and lung cancer subtypes with 97% to 100% accuracy, classified 8,200 tumors of 22 TCGA cancer types with >99% accuracy, and discovered a completely novel pan-cancer molecular survival signature.

The power of our deepCODE AI tools 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 our global platform for genomic data, which underpins the majority of the world’s largest genomics efforts and includes all major global reference databases. Our database 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.

If you want to know more, I recently gave an interview to WXpress outlining WXNC’s AI strategy. As we continue to deepen our commitment to this field, I’m sure we’ll have more exciting results to share.