INFORMATICS
New Analysis Services for Public Health in Next Generation Sequencing
By Brian Garrett , product manager , Datapult ; Millie Malai , technical producted manager , Datapult ; and Patina Zarcone , director , Datapult
Next generation sequencing ( NGS ) is heralded as the frontier in public health surveillance . Today , new technologies capable of analyzing pathogen genomes are unlocking positive outcomes for public health . In 2020 , the
US Centers for Disease Control and Prevention ( CDC ) launched its
Data Modernization Initiative ( DMI ) positing five priorities ; among them is “ accelerating data into action .” Hundreds of millions of dollars have been allocated to support public health , data modernization and surveillance efforts . Meanwhile , NGS data analytics programs have been generally out of reach for public health , with software and pipeline support focusing on more lucrative markets .
Datapult , an APHL Company , recognized public health ’ s dire need for technological modernization upon its creation in 2020 . Utilizing APHL proficiency , and a group of public health bioinformaticians , Datapult got to work on its NGS suite of services .
A New Way Forward …
While evaluating existing solutions , it was discovered that no single , off-theshelf solution would meet public health ’ s requirements . What is needed is a secure , trusted , cloud-based NGS data pipeline management system that could allow organizational hierarchy as well as interorganizational collaboration ; a sandbox environment for innovation and a simple launchpad for daily analytics . The catch ? To operate within the functions of public health and utilize existing analytics programs , an individual requires an exceedingly rare combination of bioinformatics expertise and serious programming chops .
The solution is complex in its simplicity — break up the minimum requirements . For Datapult , that meant splitting the “ work ” and leaning on the expertise of
NGS InSight ’ s value is the ability to efficiently analyze pathogen genomes , enabling laboratories to recognize differences in a pathogen ’ s genotypes .
three parties . Datapult ’ s NGS InSight is the result of a collaboration with Seqera and Two Bulls , leveraging three expertly developed elements .
Seqera ’ s Nextflow Core and Tower addresses pipeline management and organizational needs by simplifying the writing and deployment of compute and data-intensive pipelines , is scalable and agnostic . State bioinformaticians can easily create , share and manage reliable and reproducible scientific workflows .
Easy Genomics , implemented by Two Bulls , is a graphic user interface that plugs into Tower and removes much of the technical complexity for easy system administration and automation . It further automates Tower , making a great NGS analysis tool even easier to utilize in daily capacities and amplifies InSight ’ s capabilities . Lastly , Datapult ’ s utilization of the APHL Informatics Messaging Services ( AIMS ) platform provides a cloud platform for housing a public health centric NGS analysis solution .
AIMS is a cloud platform strictly maintained to the security protocols governed by the National Institute of Standards and Technology ( NIST ); earning it FISMA Moderate compliance and inherited FedRAMP controls . Rigorous HIPAA compliance for other services on AIMS means that NGS InSight benefits from the scrutiny and protections necessary for guaranteeing the privacy of private health information .
… With Multiple Uses
As an extension of InSight , NGS TB Pipeline permits access to the
Mycobacterium tuberculosis analysis pipeline created by the
New York State Department of Health Wadsworth Center . This pathogen genome analysis pipeline predicts drug resistance for M . tuberculosis isolates for clinical reporting . The pipeline was originally deployed on APHL ’ s AIMS Platform in a proof-of-concept pilot project managed by the APHL Infectious Diseases Program .
NGS TB Pipeline has incorporated lessons learned from the pilot ’ s proof-of-concept to enhance its new configuration and onboarding process . The white-glove onboarding process ensures that there is the right technical support from kickoff to go-live . Access to this M . tuberculosis pipeline is available exclusively through Datapult .
Datapult ’ s NGS InSight & NGS TB Pipeline are easy , secure ways to access pre-packaged pipelines and workspaces tailored to public health sequencing needs . NGS InSight ’ s value is the ability to efficiently analyze pathogen genomes , enabling laboratories to recognize differences in a pathogen ’ s genotypes . That information is actionable in protecting public health . Datapult ’ s vision for the future of NGS InSight includes adding functionality for sharing data across states or with other partners . g
28 LAB MATTERS Spring 2023