AMP Certificate Program: Next Generation Bioinformatics: Beyond Simple Variant Calling

This content was created in 2020, but has been reviewed and approved by the Training & Education Committee as useful, accurate, and relevant. Please note that in the time since this material was posted, there may have been additional developments, advancements, and/or more current publications in this field.

AMP Education is constantly updating our educational offerings, and will remove or replace content that is no longer accurate. Please be sure to use the search function to find related or updated material available in our catalogue at The Training and Education Committee works with AMP Education Programs to bring you the most up-to-date and cutting-edge information on molecular pathology research, applications, and training.

This webinar does not contain continuing education credit (CME and CMLE)

This AMP certificate program contains ~6 hours of lecture content, the associated pdf slides of the lectures, a pre-course exam, a post-course exam, and an AMP Certificate of Completion.


This certificate program is designed to give participants a deep dive into the challenges and proposed solutions in bioinformatics for next generation sequencing (NGS) testing. The talks go beyond the typical basics in bioinformatics of detecting simple point mutations and small indels into harder-to-detect genomic anomalies.

The talks in this Certificate Program discuss common problems and challenges seen in NGS data. These include strand bias, false positives, homology to interpretation challenges with databases, and HGVS nomenclature and proposed solutions for each of these. Speakers present a closer look at complex bioinformatics pipelines from selected laboratories, as well as an overview of advanced methods and technologies to detect complicated genomic anomalies. These anomalies include structural variants, copy number calling and fusion detection using both short and long read sequencing, as well as DNA and RNA assays.

Learning Objectives:

  • Describe the principles of a bioinformatics pipeline, including its complexities and caveats with examples and case studies.
  • Explain some of the technical challenges in short NGS reads such as those due to homology, strand bias, false positive calls, pseudogenes, etc. 
  • Design integrative modules to detect complex genomic anomalies such as large insertion/deletion mutations, structural variants and gene fusions. 
  • Describe the strengths and shortcomings of using short and long read technologies and bioinformatics methods to detect structural variants.
  • Describe the advantages and challenges of using RNA sequencing in detection of gene fusions in cancer. 

Target Audience: Molecular pathologists, informatics professionals, lab directors, and trainees.

Duration: 6.25 hours
Level: Intermediate

AMP Certificate Program Launched: July 15, 2020

TOPICS COVERED: Click here for a detailed course outline of the certificate program.

The video below is an excerpt from the welcome message and discusses the topics that will be covered in the Certificate Program. 




Sabah Kadri, PhD
Content Director 
 Catherine E. Cottrell, PhD Birgit Funke, PhD, FACMG Kevin Halling, MD, PhD
Marcin Imielinski, MD  Vincent Magrini, PhD  Ryan Mills, PhD Mark Routbort, MD, PhD
 Avni B. Santani, PhD  Jeremy Segal, MD, PhD  Ahmet Zehir, PhD   Justin M. Zook, PhD

This certificate program was planned and coordinated by the Content Committee: 

Sabah Kadri, PhD 
Content Director
Ann & Robert H. Lurie Children’s Hospital of Chicago


Weiwei Zhang, PhD
University of Nebraska Medical Center

and supported by the Training and Education Committee

"[The course] is very comprehensive and informative in the most challenging aspects of sequence bioinformatics. Every talk in the course brings a unique perspective to the audience for understanding the "hard" parts of bioinformatics."
- Somak Roy, MD University of Pittsburgh Medical Center


CME/CMLE is not available for this course.




About AMP Certificate Programs: AMP Certificate Programs are thematically bundled packages containing some repurposed and some newly recorded content and does not necessarily build on previous recordings. It is designed to help you develop knowledge and skills needed for success in molecular pathology and diagnostics. Each program is reviewed, vetted, and curated by expert content directors. All certificate programs include a post-course final exam and an AMP Certificate of Completion. Some certificate programs are also available for CME or CMLE credit. 

Note: Members of AMP can access this webinar for a discount. Join the AMP Family!


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