If you’re running NGS data analysis pipelines for diagnostic purposes, then you know how important it is to have up-to-date insights into both the wet lab and bioinformatics stages of your pipeline. These insights empower teams to identify pipeline bottlenecks and deliver accurate results in a more timely manner. However, this type of visibility into pipeline progress is often difficult to achieve across various stakeholders, including executives, lab bioinformaticians, and clinicians.
To solve these challenges, we’re excited to introduce the Case Management Portal – a powerful new solution built for sequencing service providers and diagnostic companies to monitor data analysis throughout the bioinformatics process, and automate critical workflow steps.
How Does it Work?
The Case Management Portal enables customizable monitoring throughout all steps in your bioinformatics pipeline.
DNAnexus can help customize the dashboard for executives and team leads to show key metrics to review, identify pipeline bottlenecks, and understand the overall efficiency of the production pipeline.
The dashboard also provides an overview of the diagnostics pipeline for bioinformaticians and lab technicians, broken down by each app or stage. It can show how many samples have completed analysis, and how many are being actively processed on DNAnexus. With additional configuration, the portal can connect to LIMS to pull in additional metadata from the wet lab stages to reveal how many samples are ready to be analyzed in DNAnexus. The dashboard also includes a search feature, so users can easily find a specific sample of interest.
When samples have completed the bioinformatics pipeline, clinical experts can use the dashboard to review results, make changes or comments if necessary, and approve or make adjustments before sending it out to a physician.
Get Started Using the Case Management Portal Start monitoring your pipelines today. If you are a DNAnexus customer, reach out to your Account Manager for additional details. If you are new to DNAnexus, please send us a note at firstname.lastname@example.org, and we’ll chat about your goals.
Outcomes for many with neuromuscular disease have improved dramatically in recent years, with the launch of Biogen’s Spinraza drug and Novartis’ gene therapy Zolgensma for spinal muscular atrophy treatments among those making recent headlines.
We are proud that our platforms can play an integral role in helping to fuel research and drug development in neuromuscular disease through a new partnership with the Muscular Dystrophy Association (MDA).
MDA has doubled down on efforts to ensure those able to directly impact the lives of people living with neuromuscular disease have state-of-the-art tools to share data, and at the core of that is a new visualization and analysis platform powered by DNAnexus.
The neuroMuscular ObserVational Research (MOVR) Visualization and Reporting Platform (VRP) will enable 37 MDA Care Centers to analyze data from the MOVR Data Hub – MDA’s HIPAA-compliant, CDISC-formatted registry that collects longitudinal data in seven disease indications: amyotrophic lateral sclerosis, spinal muscular atrophy, Duchenne muscular dystrophy, Becker muscular dystrophy, facioscapulohumeral muscular dystrophy, limb-girdle muscular dystrophy and Pompe disease.
In order to extract value from the MOVR Data Hub, a comprehensive data harmonization and ingestion strategy was required. DNAnexus has worked with other leading organizations like UK Biobank, City of Hope, and now MDA, working with a multitude of common data models such as OMOP, CDISC, and other data schemas to support each customer’s unique use case. Now that the MOVR data has been ingested researchers can now unleash the power of this tremendous dataset.
Created both with clinicians and researchers in mind, the MOVR VRP features an intuitive and customizable interface, allowing different levels of analysis, from overviews of disease progression and outcomes across sites, to in-depth dives into clinical parameters across large cohorts of neuromuscular patients.
This level of correlative analyses could ultimately stimulate new drug, biologics and gene therapy discoveries. Exploration of deeply curated neuromuscular disease cohorts in the MOVR VRP could also help in clinical trial design, by enabling clinical researchers to rapidly identify populations that meet specific clinical criteria.
DNAnexus’ hallmark security, compliance and collaboration components will also enable increased accessibility of MOVR data to the wider neuromuscular clinical and research communities. And the platform is expected to make it easier for MDA to carry out training, fulfill data requests, review publications, encourage peer-to-peer collaboration and publishing, and share learnings across multiple channels.
The MOVR VRP currently leverages phenotype data from the MOVR Data Hub, but it has been developed to handle a wide range of EHR and genetic data types, enabling the platform to scale up as needed.
“The MOVR database, combined with the visualization and analysis platform from DNAnexus, allows us to make the most of this data in a way that really brings it to life to aid in developing new therapeutics.”
MDA’s President & CEO, Lynn O’Connor Vos
We are proud to serve as the technology platform bringing together MDA researchers and their partners to advance cures for this collection of neuromuscular diseases.
Although we’ll miss the chance to spend some time in San Diego, we’re excited for the opportunity to expose our research to the wider world, as the popular annual meeting of the American Society of Human Genetics (ASHG) goes virtual this year.
From pharmacogenomics to frameworks for benchmarking, the DNAnexus research team will be presenting posters on a number of exciting topics. We’ve included them all below, for easy reference.
Are you susceptible to adverse drug reactions?
Pharmacogenomics (PGx) is an embodiment of precision medicine. Yet gene-drug specific dosing guidelines are still limited. Using LightGBM – a decision-tree based gradient boosting machine learning framework – and UK Biobank phenotypic and genomic data, Chiao-Feng Lin and colleagues from the xVantage and Apollo Data Science teams investigated whether it is possible to predict an individual’s risk to adverse drug reactions, irrespective of drugs. Check out her Reviewers Choice Award poster to learn what they found, and how the Apollo Cohort Browser can make sample selection simpler. Poster 3591
The Portable Workflow Environs: Cloud-scale workflows with nano-scale effort
As the field of bioinformatics is largely converging on open standards, such as Workflow Description Language (WDL), for the development of workflows, we have developed a suite of tools that can be leveraged for their efficient and scalable development and deployment. Join John Didion as he introduces PoWEr (The Portable Workflow Environs), an open-source ecosystem of tools to simplify and accelerate the full life-cycle of workflow development and deployment. Poster 2217
Direct-to-risk: A scalable framework for end-to-end GWAS, fine-mapping and risk prediction on UK Biobank
While polygenic risk score (PGS) analyses seem straightforward, they consist of a plethora of disparate steps, each with their own datasets, methods, and hidden assumptions. DNAnexus Apollo can be used to conduct end-to-end PGS analyses with semi-automation, scalability, traceability, interoperability, and iterability. Peter Nguyen will demonstrate how, using the framework to conduct PGS analyses for type 2 diabetes by processing phenotypic and genomic data across 500,000 thousand UK Biobank participants and 90 million variants. Poster 3802
A WDL-based framework for benchmarking germline variant calling pipelines for high-throughput sequencing data
Wondering which variant caller would work best for you? We developed a WDL-based framework and benchmarked six variant callers for their accuracy and runtime. Join Yih-Chii Hwang as she describes the flexible framework and how it can be further customized and applied to benchmark any bioinformatics pipelines of interest. Poster 2018
In addition to our own research, we were proud to contribute to the following work by our customers and partners:
A new Genome in a Bottle benchmark for hard to assess and medically important genes
We were proud to contribute to this project, whose goal was to create a high quality benchmark variant call set for medically relevant genes, to help researchers and clinical related applications with the next gene sequencing. Be sure to check out the Reviewers Choice Award poster by the multi-institutional Genome In a Bottle team. Poster 2009
Automated repeat characterization of filaggrin from PacBio Sequel HiFi long reads
Filaggrin (FLG) is a medically important protein coding gene, associated with dermatitis, atopic, ichthyosis vulgaris, and other conditions. This poster demonstrates how to do efficient variant calling for this repeat-rich gene using a new method based on PacBio SMRT Sequencing. A DNAnexus applet was also created to help our collaborators at the Regeneron Genetics Center process thousands of samples for their research work on the related diseases. Poster 2046
Doubly Confused: Evaluation of splicing variant impact assessment with computational prediction, and vice versa
Many variants affecting splicing remain of unknown significance in the absence of definitive molecular and/or clinical data. Using data from three carefully chosen genes — HPRT, BRCA1, and ABCA4 — we helped scientists at the University of Maryland assess the quality of splice variant impact assessment software. Check out the poster to see which software came ahead. Poster 2088
Sequencing Quality Control Phase II: Inter and intra variability of NGS and its implication on structural variation detection
Genomic structural variation (SV) includes several different classes of mutations, including deletions, insertions, translocations, duplications, inversions and complex rearrangements. The complexity of these different events continues to make the detection of SV challenging. This is amplified by the usage of different sequencing technologies, centers, or across replicates within and between cohort studies. To better understand the impact of variability due to preparation, sequencing and analysis, we helped Baylor scientists compare the sequence of DNA from a Chinese family consisting of two identical twins and their parents at three different sequencing centers with three replicates each as part of the Sequencing Quality control Phase II (SEQC2) study. We utilized multiple analytical pipelines and compared the resulting 288 data sets within and across the family members. Check out the poster to see what was found. Poster 2202