Scaling to Meet the Demands of Rare Disease Genetics

rare disease clinical diagnostics

Approximately 350 million people worldwide face the life-changing impacts of a rare disease. The sheer number of people affected begs the question: are rare diseases really that rare?  According to Jussi Paananen, Chief Technology Officer at Blueprint Genetics, perhaps the only thing rare about them is how difficult they are to diagnose: “it’s like finding a needle in a haystack.”

It’s like finding a needle in a haystack.

Jussi Paananen, CTO Blueprint Genetics

Blueprint Genetics wants the process of diagnosing and understanding rare diseases to be more efficient and less challenging for patients. The global clinical diagnostics company focuses on rare disease genetics and offers single gene tests, panels, and whole exome sequencing in 14 medical specialties, including cardiology, ophthalmology, immunology, hereditary cancer, and malformations, to name a few. The result of Blueprint’s end-to-end testing operation is an easy-to-understand clinical report that physicians can share with their patients.

There’s been a notable surge in rare disease activity over the last few years, driven by reduced sequencing costs and several public sector initiatives that have increased our understanding. Blueprint experienced firsthand this surge and had to scale its operations rapidly to meet demand. When Paananen’s team added an Illumina NovaSeq™ 6000 system to its operations, the volume of samples increased, and so did the amount of data for each sample. By partnering with DNAnexus, Blueprint Genetics was able to scale in velocity and volume by moving its bioinformatics pipelines to the cloud. 

After samples are sequenced on the NovaSeq system, the raw data now runs through Blueprint’s proprietary bioinformatics pipelines on DNAnexus, which produces pre-processed variants that the in-house geneticists interpret and use as the basis for final clinical reports.

Blueprint Genetics: Scaling & Increasing Demand with DNAnexus

According to Paananen, they’ve been able to scale to the increased demand so that it’s no longer the sequencing and bioinformatics that are a bottleneck — it’s the interpretation. But Blueprint has a solution for this challenge as well: augmented intelligence.  Augmented intelligence, in which human expertise remains at the center of decision making with help from computer counterparts, will enable geneticists at Blueprint to automate as much as possible to increase interpretation speed and quality.

The bottle-neck in scaling clinical genetics is no longer in sequencing or bioinformatics, but on clinical interpretation of the data.

To learn more about how Blueprint Genetics has scaled its high-volume clinical diagnostics business, watch the video below:

Works Cited

1.Austin CP, Cutillo CM, Lau LPL, et al. Future of Rare Diseases Research 2017-2027: An IRDiRC Perspective. Clinical and translational science. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5759721/. Published January 2018. Accessed October 1, 2019.


DNAnexus Scoops European Innovations Award at SCOPE

We’ve always been proud of our innovative technology solutions, and recently we had the opportunity to celebrate our success with our European partners at the Summit for Clinical Ops Executives (SCOPE)-Europe in Barcelona, Spain. 

Preeti McGill, EMEA Account Director, was on hand to accept DNAnexus’ European Innovations Award, sponsored by Clinical Research News. Fellow awardees included the UK’s Guys and St. Thomas’ NHS trust and Tata Consultancy Services. 

The European Innovations Awards  program seeks to recognize outstanding examples of applied strategic innovation—partnerships, deployments, and collaborations that manifestly improve the clinical trial process. 

“These awards celebrate dedication and innovation in clinical research, and the winners chosen highlight the inspiring work being done in the industry,” said Allison Proffitt, Editorial Director of Clinical Research News. “The research community in Europe is increasingly open, and the projects showcased in this year’s award program prove their dedication to excellence.” 

One project in particular, the UK Biobank Consortium Data Delivery and Cohort Browser, was noted for its contribution to the scientific community. Part of the DNAnexus Apollo Platform, the cohort browser was designed to democratize data access to the UK Biobank, which has collected and developed a biospecimen and data resource on over 500,000 individuals. 

In collaboration with a consortium of pharma companies, the Regeneron Genetics Center has undertaken the exome sequencing and analysis of all 500,000 samples, using Apollo to host the dataset and run Regeneron’s software pipeline. We partnered with Regeneron to construct a combined database of the biobank genomic and phenotypic data to explore, with an innovative “geno/pheno cohort browser” user interface that gives diverse teams the ability to browse and build cohorts among 3,000 phenotypic fields and 15,000,000 genomic variants across 100,000 samples. 

“This resource has proven valuable to pharmaceutical companies, healthcare organizations and the scientific community, and has already led to more than 170 publications revealing novel associations with important epidemiological markers,” Clinical Research News noted.  

Data leads to new discoveries

The Sept. 18 award presentation came on the heels of another announcement: a £200 million expansion of the original £34 million pilot programme. The funding — half from government sources and half from biopharmaceutical and healthcare companies (Amgen, AstraZeneca, GlaxoSmithKline and Johnson & Johnson) — will enable each of the biobank’s 500,000 samples to undergo whole genome sequencing at the Wellcome Sanger Institute in Cambridge, UK, and the deCOde site in Iceland. 

“Today’s funding will support one of the world’s most ambitious gene sequencing programmes ever undertaken,” said UK Business Secretary Andrea Leadsom. “Its results could transform the field of genetic repeated research – unlocking the causes of some of the most terrible diseases and how we can best tackle them. It will be a major step forward for individually tailored treatment plans, and will help us better understand why some people get certain diseases while others don’t.”

Data from Regeneron’s exome sequencing efforts have already led to several scientific discoveries. One of the discoveries has been a better understanding of Type 1 diabetes. This is the most common form of diabetes in children, which has led to it being called ‘juvenile diabetes’. However, a study using information from UK Biobank revealed that type 1 diabetes is almost as common in adults as it is in children. This hasn’t been recognized previously because so many adults have a different kind of diabetes. Another study also shed light on the effect of diabetes on the heart. 

Scientists in Australia used the data to examine the prevalence of inbreeding in the UK (~13,200 people born to extreme inbreeding), and scientists at the Broad Institute used it to explore whether there are any genetic links involved in same-sex partnerships. Another team of researchers used both sequencing and imaging data from the UK Biobank to characterize the brain signature and genetic basis of left-handedness. 

“I am incredibly excited by the potential of genomics to change the way we think about disease and healthcare,” said UK Health and Social Care Secretary Matt Hancock. “In an ageing society with an increasing burden of chronic diseases, it is vital that we diagnose earlier, personalise treatment and where possible prevent diseases from occurring altogether. This project will help unlock new treatments and grow our understanding of how genetics affects our risk of disease.”

Researchers interested in applying for access to UK Biobank data should visit http://www.ukbiobank.ac.uk/register-apply/.

For more information about the UK Biobank Cohort Browser, visit https://www.dnanexus.com/product-overview/apollo/apollo-for-ukb

DNAnexus Navigation and UI Changes

To keep the DNAnexus platform easy enough for anyone to use and powerful enough for expert users, our team has made some layout and user interface (UI) changes. While these updates are relatively minor, they make the platform look different than you might be used to, so we’ve outlined them below to help you find your way around and see what’s new.

New Look

The first thing you’ll probably notice is that the user interface looks cleaner, flatter, and more modern. The visual updates to the interface make it easier to look at and faster to find what you’re looking for. Primary actions will be on the right of the screen and be immediately noticeable. Certain areas of the site won’t have this updated look yet, but every part of the site is getting revamped in the next few months, so if it hasn’t changed yet, it will soon.

Projects

Projects UI

We have redesigned the Project list page with an easily filterable list of all your projects. A new “pin” feature allows you to mark your favorite projects and they will remain on top of the list! 

Project List

Projects now display a line of summary text in the main list. You can add even longer text in the Descriptions section of the Info panel.

Reference Data List

Info Panel

We have added a new “info” panel which allows you to quickly inspect any project when you select its row. The info panel can be opened by clicking the “i” icon in the upper right. This shows information (metadata, project settings, project size, etc.) which is also available in the Project Settings. Now you can access this information directly from the Project list page. The info panel also lets you easily copy the project ID.

Pin Project


The context (three-dots) menu in each row gives you a shortcut to Leave or Delete a project (depending on your access level), share, pin and view project settings.

To view the contents of a project, click the project name and you will enter the Data Manager section.

Data Manager: Manage Tab 

The Manage section has many enhancements. Next to the Project name there is now a menu for quick access to common tasks such as Sharing projects. Also task such as Leaving or Deleting a project (tasks formerly found in Settings) are in the menu.

Data Manager

Project navigation has been enhanced with a collapsible tree as well as fully functional breadcrumbs.

Project Folder Tree

All action buttons have been consolidated to the right side of the screen (New Folder, New Workflow, Upload Data, Add Data, Copy data from project, Start Analysis)

Start Analysis Add Button

The filter bar has been redesigned and now defaults to searching within a project. 

Project Folders

Data Manager: Manage Tab: New “info” panel

We have added a new “info” panel which allows you to quickly inspect any file. The info panel can be opened by clicking the “i” icon in the upper right. You can then select any item, or multiple items, to display their properties. This shows information previously found in the info pop up window.

You can easily copy a file or path ID from this side panel by clicking the copy icon. 

Project Info Panel

Tables are now paginated.

New folders will now be created and show at the top of the list. After you enter a name, it will move to the appropriate place in the sort order.

Project Folder Rename

Projects can be renamed in the Settings tab or in the Info panel on the main project list page.

Data Uploading

The data uploading dialog has been split into three discrete functions.

Data Uploader

The ability to apply tags and properties in the dialog has been removed. Tags and properties can easily be added in the new Info panel. Select multiple items to apply the same tag or property to multiple objects at once.

Note: Settings & Visualize tabs are the same with minor visual updates.

Featured Projects

The Featured projects section has been removed and the projects in Resources have been updated to have useful reference files and demo data.

Featured Projects Section

Data Selection Dialog

The Data Selection dialog appears when you copy data, select projects or paths during app runs, and select inputs for workflows. It now allows you to filter, add/remove columns, and view pinned items.

Platform Data Selection

Within a project, filters allow for easier filtering to find files.

Platform Folder Selection

Start Analysis 

The start analysis dialog has enhanced to improve usability. It has the familiar filtering mechanism to easily locate an app, applet workflow or global workflow. You can now see the category and the author of the analysis tool. By selecting a row and opening the “i” Info panel, you can still view the inputs and outputs. 

Starting Analysis

Version can be toggled in the dropdown:

Allele Frequency Calculator

Open the tools details to see full information provided by the tool developer.

Tool Details Button

Tool Runner

The Tool Runner has been enhanced with a graphical representation of the analysis process. Each app or workflow has three areas that a you can configure: Settings, Analysis Inputs, Stage Settings.

Settings includes execution name, project location, output folder and optional advanced features.

Analysis inputs is where you can select appropriate inputs and can toggle to batch mode. Also, you can now view all inputs in one location.

Stage Settings contains information about each stage of a workflow, including app version, instance type and output folder. You can change these as desired.

Tool Runner

Data Manager: Monitor Tab

The Monitor Tab also has a fresh look with updated filter bar UI and action buttons consolidated to the right side. 

Monitor Tab

On the monitor details page, several actions have been moved or temporarily removed.

  • View info in not currently visibility (coming in our next release)
  • View input is removed as the inputs and outputs all shown on the page details.
  • Save as New Workflow has been removed.
  • Monitor tab is not indicating that a job is running (coming in next release)
  • Tags not showing on the Monitor table (coming in next release as its own column)

You can copy an execution ID to the clipboard by clicking the icon next to the ID.

Logs have a new Download button feature: 

Logs Download Feature