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

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. It also includes CME and CMLE credits.

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
AMP Certificate of Completion Credit available: 6.25 hrs
Hours of CME or CMLE available: 6.25 hrs 
Last day to claim CME or CMLE Credit: March 20, 2022
Last day to complete the course: December 31, 2023

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, PhDBirgit 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 credit available: 6.25
CMLE credit available: 6.25
**Continuing Education Credit must be claimed by March 20, 2022. No partial credits will be awarded**


AMA PRA Category 1 Credit(s)™

This activity has been planned and implemented in accordance with the Essential Areas and policies of the Accreditation Council for Continuing Medical Education through the joint providership of American Society for Clinical Pathology (ASCP) and Association for Molecular Pathology (AMP). The American Society for Clinical Pathology (ASCP) is accredited by the ACCME to provide continuing medical education for physicians.

The ASCP designates this enduring material for a maximum of 6.25 AMA PRA Category 1 Credit(s)™. Physicians should claim only credit commensurate with the extent of their participation in the activity.


This continuing medical laboratory education activity is recognized by the American Society for Clinical Pathology for 6.25 hours of CMLE credit. ASCP CMLE credit hours are acceptable for the ASCP Board of Certification (BOC) Certification Maintenance Program (CMP). CMLE credit hours meet the continuing education requirements for the ASCP Board of Certification Credential Maintenance Program (CMP) and state relicensure requirements for laboratory personnel. Participants should claim only the credit commensurate with the extent of their participation in the activity. 

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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