Precision Medicine from Birth

Tute 2How many lives could be saved or significantly improved if precision medicine began at birth? Tute Genomics is aspiring to answer this question. Yesterday, Tute announced that they are working with Newborn Screening Ontario (NSO), part of the Children’s Hospital of Eastern Ontario (CHEO), to establish new next-generation sequencing (NGS) testing capabilities in Ontario, Canada. Tute, a leading genome annotation and interpretation platform, provides clinical sequencing informatics and interpretation to deliver meaningful reports of a patient’s full genomic profile to researchers and clinicians. Tute is providing its clinical customers, like Newborn Screening Ontario, with an end-to-end solution – taking raw sequence data through genome interpretation in a single step – DNAnexus is proud to be a part of that solution.

NSO 2NSO operates one of the largest and most modern newborn screening programs in the world.  In the past decade, NSO has tested more than one million newborns for serious but treatable rare diseases, making it the highest volume molecular lab in Canada. Working in conjunction with Tute, organizations like NSO can easily perform best practice data analysis in a single environment, avoiding the hassle of transferring large datasets between analysis and interpretation platforms, or deploying costly local solutions.

Tute is passionate about making genomics more accessible to healthcare providers and scientific researchers in order to advance precision medicine. Through integration with the DNAnexus Platform, Tute offers its customers upstream primary and secondary analyses and downstream interpretations in a seamless fashion. The NSO’s new genetic testing project is a perfect end-to-end example, connecting sequencing instruments, LIMS (UNIConnect), downstream clinical reporting software and report delivery.   Ultimately, these Tute employed services will help make medical intervention and care decisions faster and more effective for newborns suffering from genetic illness.

Email us directly to learn how DNAnexus can help data interpretation tool providers operate in a secure, compliant, and scalable platform on which they can deploy and expand their product portfolios.

Cloud-based Genomics at the White House

The Launch of precisionFDA Consistency Challenge

Last week the White House held a Precision Medicine Initiative (PMI) Summit, where government agencies discussed their progress on genomics-based personalized care, real people shared their success stories with precision medicine, and President Obama himself reiterated his vision for precision medicine. It was thrilling for DNAnexus to hear precisionFDA, the “online, cloud-based portal” that DNAnexus built for the FDA, based upon FDA requirements, specifically acknowledged (29:45-30:33). You can watch full coverage of the PMI Summit here.

PMI_Obama

It is no surprise that we have finally reached the era where cloud-based genomics is making it into White House announcements. The announcement also included the launch of the first precisionFDA consistency challenge, calling on members of the genomics community to assess their bioinformatics software on supplied reference human datasets. Called the precisionFDA Consistency Challenge, the goal is to engage genomics innovators to improve reproducibility and accuracy of next-generation sequencing (NGS) pipelines in order to achieve more consistent results from genetic tests and advance precision medicine.

PURPOSE OF THE CHALLENGE
Currently a single NGS test can identify genetic variants ranging from thousands to in the millions. The results, in some instances, are already being used to diagnose and treat disease. While NGS tests are currently used in clinical applications in oncology, non-invasive prenatal testing (NIPT), and rare disease, there is still room to improve consistency as they become more broadly adopted in clinical practice. A better understanding of accuracy and reliability of the results for specific NGS tests will help us get closer to personalized treatments and improve patient care.

Multiple sequencing technologies (Illumina XTen, Illumina HiSeq, PacBio RSII) can be used for human whole genome sequencing, and each has their own accuracy or reproducibility error profiles for different parts of the genome. The means to establish methodologies to assess the accuracy of a technology for specific variant types or regions across the genome would help advance evaluation of novel NGS-based tests for clinical applications. Unfortunately, there are still inconsistencies where an NGS-based test can report differing results. However, by establishing appropriate standards, inter-test variation can be minimized, allowing patients and physicians to place greater confidence in test results and the resulting treatments.

The FDA has delivered a new approach, precisionFDA, to help establish standards around secondary analysis – the process of mapping, aligning, and calling the variants of DNA sequence data. To jumpstart the engagement and improve techniques on the precisionFDA platform, the FDA’s first challenge is focused on consistency.

CHALLENGE DETAILS
The process of human WGS pipeline development and validation typically relies on mapping the sequenced reads to a well-known reference genome, then identifying the differences between the results and the reference dataset. Participants who join the challenge are asked to download two FDA-provided datasets (one contributed by the Garvan Institute of Medicine, and one by Human Longevity Inc. — both corresponding to sequencing of the well-characterized NA12878 sample), process it through their pipelines, upload results back to precisionFDA, and compare them to other files. The challenge provides a common frame of reference for measuring some of the aspects of reproducibility and accuracy of the participant’s pipeline.

precisionFDA Challenge

WHO CAN PARTICIPATE?
The challenge is open to all innovators in the field of human genomics. If you’re not already a member of precisionFDA, you will need to request access to get started. You have until April 25th to submit your software assessments.

DETERMINING WINNERS*
Results will be ranked on the precisionFDA website for achievements in eight categories. See the Determining Winners section on the challenge webpage for full details. In addition to exclusive bragging rights, your results, comparisons, and methods will be featured on the precisionFDA platform highlighting your technical contributions.

DNAnexus is incredibly excited about this challenge – the idea of genomics innovators working together to advance quality standards is something that gets us fired up. As of this blog post, precisionFDA hosts more than 1000 community members on the platform representing nearly 500 organizations. We are proud to support this novel community-contribution model for evaluating bioinformatics pipelines to help address the challenges of precision medicine.

* Winning a precisionFDA category is an acknowledgement by the precisionFDA community and does not imply FDA endorsement of any organization, tool, software, etc.

The Future of Precision Medicine

Collaboration, Integration, Participationprecision medicine initiative

Today the White House hosted the Precision Medicine Initiative (PMI) Summit, celebrating the first year since the President’s announcement of the Precision Medicine Initiative. The entire team at DNAnexus shares President Obama’s sense of excitement as we reflect upon what’s been accomplished; even as we roll our up sleeves and get busy doing the hard work the lies ahead. John Holdren, Director of the White House Office of Science and Technology kicked off the event announcing the progress of a few remarkable initiatives 1) the NIH advancing cancer clinical trials through the development of large research cohorts, 2) the Million Veteran Program which has enrolled 150,000 vets to date and is now open to active duty women and men, and 3) the precisionFDA community platform for NGS assay evaluation and regulatory science, which just launched its first “Consistency Challenge”.

There were a number of inspirational stories from patients and families recalling their own struggle with disease and how precision medicine aided in diagnosis and treatment. It is so rewarding to see real-life examples of how genomic sequencing is being used to diagnose genetic disorders in the clinic and advance treatment and, ultimately, help patients lead healthy and happy lives.

What resonated most for us from the White House PMI panel was the President’s remarks on the healthcare system. Although it is a system labeled for “health care”, it is actually a “disease care” system. The U.S. healthcare system has been designed based on patient passivity; patients wait until they are sick and then it’s the doctor’s job to treat the disease/condition. Instead, we need to transform the healthcare industry to play a more active role in health and get health information into the hands of consumers. This will allow patients to remain healthy and keep disease from manifesting in the first place.

In order to make the President’s PMI a reality, we need to make anonymized patient data available to researchers and to merge information from different studies in order to advance medical research. We believe in a secure and unified platform; one that connects thousands of scientists around the world. True scientific breakthroughs are possible when researchers are able to collaborate openly, securely, and transparently around petabyte-sized datasets.

It’s been a remarkable twelve months for DNAnexus. , We’ve had the opportunity to contribute to a range of efforts expected to advance the science of precision medicine and accelerate its translation into tangible clinical benefits. Examples include:

Looking ahead, we believe that the realization of precision medicine’s promise requires the intelligent integration of genetic data with electronic health record data and a range of other data types. Successfully doing this requires the technology to effortlessly collaborate around large volumes of data in a secure and compliant fashion – which DNAnexus provides. But meaningful progress also requires the commitment to share relevant data, which we believe is developing, especially as (a) stakeholders increasingly recognize the scientific advantages of collaboration as opposed to a history of secrecy and data silos; (b) stakeholders begin to appreciate the ease and security of cloud computing in this process; (c) patients appropriately demand and belatedly receive more ownership of their own (damn!) data, and can easily elect to contribute that data to scientific research.

We’ve been privileged to be so deeply involved in the mission of precision medicine, and are excited by the opportunities to drive this work forward. As a business, and as a U.S. business, we are excited to see President Obama’s vision for precision medicine and improved health care align with our own.