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.
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.
AMD Training Opportunities
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.
If you are interested in obtaining a membership, apply today!
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.
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 (Archived Webinar)
The Long and Short of Long-Read Sequencing (Archived Webinar)
Bioinformatics Learning Modules (on APHL Learning Center)
- Introduction to Bioinformatics
- Introduction to Genome Assembly
- Introduction to Phylogenetics
Accessing the APHL Learning Centerfor the first time (You must have an APHL account, if you do not have an account, you will need to
create a free APHL account using your work email address. Contact firstname.lastname@example.org with any login or account questions.
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.