2022 Forecast: Responding to the Rising Tide of Diagnostic Tests

Next-generation sequencing (NGS) has reached a turning point in diagnosing and treating rare and inherited diseases, and is overtaking traditional approaches in a wide variety of other indications as well, from cancer to rheumatology, transplants to non-invasive prenatal testing.  Lower sequencing costs improved reimbursement, and consumer demand is likely to drive the market even further. 

Businesses in this rapidly growing market sector have a lot to consider when it comes to technology. In a recent article in The Pathologist, David Fenstermacher, Vice President of Precision Medicine and Data Science, shares some tips to help laboratories leverage cloud-based informatics solutions. 

As he points out, cloud-based systems enable you to optimize analysis pipelines for quality, speed, runtime, and cost. They provide an environment that can flexibly scale to meet the demand for increased test volume, and are great for those looking to expand their footprint, either locally or globally.When it comes to security, compliance, and intellectual property (IP) protection, going with a purpose-built NGS informatics platform provided by a well-established, customer-focused, company can be invaluable. 

Ultimately, Clinical Diagnostics companies need to stay ahead of innovation. With a purpose-built NGS genomics platform, the latest technological advancements in cloud computing, analytics, knowledge or rich visualizations are already incorporated. Diagnostics teams can focus on what they do best, test development and delivery of results. 

Fenstermacher advises that labs ask themselves the following: 

  • How will the changing genetic testing landscape impact my operations and support needs?
  • Is my informatics system sufficient?
  • Is it scalable?
  • Does it give me the flexibility I need?
  • How does it handle quality, security, and compliance?
  • Can it help me improve my sample turnaround time or pipeline development?

“By keeping pace with technology and industry innovations in the NGS and genomics field, you can ensure that you are not only ahead of the tide, but making your own waves,” Fenstermacher said.

Read the full article here. 
Learn more about how DNANexus can help grow your diagnostic business.

Partnering with NVIDIA Clara Parabricks to Accelerate NGS Data Processing

Looking for ways to accelerate data processing and genomic analysis? By using graphics processing units (GPUs), it’s possible to achieve throughput comparable to nearly 40-50 CPU servers with just one GPU server reducing overall operating costs.

We’re excited to be working with NVIDIA Clara Parabricks to make the DNA and RNA pipelines available on our DNAnexus Titan or Apollo Platforms. For a limited time, we are offering license-free access to test, validate, and use the following Clara Parabricks pipelines (more on the way):

GATK4 and DeepVariant users will appreciate NVIDIA Clara Parabricks Pipelines. They provide equivalent results, but at much greater throughput and speed — 50-90 times faster. In fact, Parabricks Pipelines v3.0 achieved a record for the germline analysis of a whole human genome in under 20 minutes when running on the just-announced NVIDIA A100 GPUs. On DNAnexus today, GATK analyses which take nearly 30 hours of computation on a 32-vCPU machine complete, will complete in 30 minutes with identical results on an eight v100 GPU instance using Parabricks.  The Parabricks Pipelines are compatible with GATK4.1 and DeepVariant 0.10.0, the latest major releases for both analysis packages.

The tools are also fully configurable, so users can choose to run the full GATK4 best practices, for instance, or specific steps from the pipeline.

DNAnexus makes it easy to run NVIDIA Parabricks pipelines by providing an out-of-the-box solution. Users simply supply input files and receive results delivered in their DNAnexus project. Launching NVIDIA Parabricks apps is a seamless process, removing the hassle of provisioning GPU instances in the cloud manually or installing CUDA or NVIDIA Parabricks apps themselves.

For secondary analyses of sequencer-generated FASTQ files to variant call files (VCFs), we recommend you register today to take advantage of this limited-time, license-free opportunity to try out Parabricks available through June 30th

Being Productive during COVID-19 Quarantine

A new Linus Group study finds that many life science practitioners have had their work disrupted, with their labs and offices largely shut down due to COVID-19. However, many are taking advantage of working from home, to dive into writing, data analysis, planning for future work, even launching “in silico” studies.“1 

One of the biggest challenges people face while working from home is accessing the data, applications, and compute resources they need. For organizations where remote work is the exception rather than the rule, network bottlenecks and slow download times can quickly become a chronic problem, when the majority of employees are all using the  VPN every day. Moreover, not all applications may work properly and some data and resources may simply not be accessible to users who aren’t on-premise.

We’ve heard from many of our customers that they’re grateful that access to the DNAnexus Platform is efficient and straightforward. They’ve been able to shift to working from home without hiccups. Unlike most on-prem analytics setups, the DNAnexus Platform allows them to leverage any of a wide range of compute resources, provides cost-effective storage options, and enables secure, fluid collaboration and sharing with partners and peers around the globe. 

And thanks to the DNAnexus Cloud Workstation App, those working from home are able to keep working at speed. Accessible via SSH, it gives you the ability to explore and analyze your data, directly on the DNAnexus cloud platform, just as you would in a local Linux environment. There’s nothing to download, so your work won’t be slowed by network bandwidth constraints. Note as well that when accessing the app, your connection is secure, and encrypted end-to-end, and the DNAnexus environment ensures the right access controls and permissions, along with the strong compliance.  So you can work safely and efficiently at home, like you do in the office.

Everyone hopes that life – and work – will return soon, to something akin to normal. That will bring life science practitioners back to their labs and office.

1 – “How Scientific Research Progresses Amidst a Global Pandemic,” Linus Group, https://www.thelinusgroup.com/coronavirus-report-summary