CDC’s Advanced Molecular Detection (AMD) initiative aims to improve the identification and characterization of infectious diseases by increasing critical next generation sequencing (NGS) and bioinformatics capacities at CDC and at state and local health departments.
APHL
works with CDC and other partners on both the implementation and use of NGS in
public health laboratories. APHL works
to address challenges laboratories may face including a changing landscape of workforce
and laboratory needs as they expand their use of NGS for disease detection and
surveillance. To this end, APHL continues
to develop tools, resources, and training, along with convening meetings and facilitating
constant dialogue with leaders in the public health laboratory arena.
AMD days
APHL is excited to be partnering with CDC OAMD again to co-host AMD days on September 12-14, 2023 on the CDC Roybal Campus in Atlanta, GA. For more information, please check out our AMD days website.
Upcoming AMD Training Opportunities
Easy Genomics + Nextflow Tower Training
Amazon Web Services (AWS) and Two Bulls, in collaboration with Wisconsin State Laboratory of Hygiene (WSLH), have developed a no-code, user-friendly tool called Easy Genomics that enables organizations to scale their bioinformatics capacity with limited technical expertise. The solution leverages Nextflow Tower APIs for an automated system that uses AWS serverless services, including AWS Lambda, Amazon API Gateway, and Amazon DynamoDB, to provide automatic scaling and built-in high availability. Users can securely login, upload single or multiple samples, select the appropriate analytic workflows, monitor sample progress, and receive the results directly via a browser or email.
The in-person training, scheduled for August 14-16, 2023 in Arlington, VA, will provide participants with a valuable opportunity to gain hands-on experience using both Easy Genomics and Nextflow processes. The training aims to help get a grasp of a fast and efficient solution for genomic sequencing analysis.
Applications are due on June 15, 2023. Apply now.
DataCamp Memberships
The Association of Public Health Laboratories (APHL) has DataCamp subscriptions available for state or local public health laboratorians. DataCamp is an online platform to take over 340 data science courses on a range of topics including Python, R, SQL, and more. DataCamp's modules cover a range of topics that can be customized to fit the computing infrastructure of each laboratory and provide assessments to gauge learning progress and proficiency. These trainings can assist public health laboratorians grow in their proficiency in a variety of coding skills that can be used for bioinformatics analysis, data visualization, and statistics.
Applications are due on June 20, 2023. Apply now.
NGS Quality Initiative
APHL and CDC's OAMD established the NGS Quality Initiative to develop a quality management system addressing many of the NGS challenges experienced by public health and clinical laboratories. APHL and CDC, together with state and local public health laboratories, are working to develop standard operating procedures and other NGS-based quality management tools that can be implemented within laboratories.
Building the AMD Workforce
Fellowships and Internships
APHL administers a number of fellowships including fellowships focused on training graduates with bioinformatics skills. The fellowship aims to train and prepare bioinformaticians to apply their expertise within public health and to design tools that will aid existing public health personnel in the use of bioinformatics. Applications are accepted on a rolling basis. Check out information on all of the APHL fellowships.
In addition, APHL sponsors a number of internship opportunities as well. The genomic data internship program will be launching summer 2023 and accepting applications for interns and host labs. This program would provide in-person or remote bioinformatics support to laboratories.
Building Bioinformatics Capacity
Building Bioinformatics Capacity Through Academic Partnerships
The increase in public health applications of NGS has created new challenges, including additional demands for bioinformatics computing power. One potential solution is to build bioinformatics capabilities in a public health laboratory through partnerships with academic institutions. There are several success stories for sharing sequencing resources and specimen collections can improve both the capacity and efficiency of public health laboratories.
Hiring a Bioinformatician
In addition to partnerships, many laboratories are also hiring bioinformaticians. For many laboratories, this may be the first time a position like this has been created. The bioinformatician recruitment guide can be a useful resource for creating a position description and identifying the skills required for a person in this role.
Training
APHL has created a webinar series that is available for free to state and local health department staff. Continuing education credits are available.
- Advanced Molecular Detection: Automation options for Next Generation Sequencing workflows
- Communication Strategies for Laboratorians and Epidemiologists on NGS Data
- The Long and Short of Long-Read Sequencing
- Bioinformatics Learning Modules available on the APHL Training Portal: Introduction to Bioinformatics, Introduction to Genome Assembly, and Introduction to Phylogenetics
Accessing the APHL Training Portal for the first time:
- Navigate to the APHL Training Portal.
- Select Login, then Create an Account.
Once you have a Training Portal Account:
- Navigate to the Catalog to view all available courses.
- Enroll in the Bioinformatics Series.
AMD Bioinformatics Training Leads and Regional Resources
Through the Epidemiology Laboratory Capacity (ELC) grant, using the PulseNet and ARLN regions, CDC OAMD has established regional bioinformatics resources and training leads. Each region has designated bioinformatics regional resource and training leads. In some cases, the same laboratory may serve as the bioinformatics regional resource and training lead. Training leads provide support and training for laboratories across the region on building their sequencing capacity.