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2020 Short Course - Essential Fundamentals - Next Generation Sequencing From The Beginning
About this course


Essential Fundamentals - Next Generation Sequencing from the Beginning – Short Course

Date of Release: May 1, 2020

Credits offered: CME, P.A.C.E.®
Expiration Date: May 1, 2023
Revised Expiration Date: August 31, 2025

A survey conducted by Hutton Kearney on the Cytogenetics listserv identified a significant educational need among laboratorians who are expected to understand, validate and review complex molecular technology-based assays for clinical patient care. Many currently practicing laboratorians completed their formal education before the advent of SNP chromosomal microarrays and next generation sequencing (NGS). The survey revealed that approximately half of responders feel they have some understanding or less of critical interpretative aspects related to molecular-based technologies; the largest need was indicated to be in NGS. This proposal is meant to begin addressing this educational gap in NGS by presenting the technology and its applications at the most fundamental level. This information is targeted for both beginners to NGS and for those who have some exposure but would benefit from filling in basic knowledge gaps.  Some of the concepts which will be highlighted include panel-based testing, exome and whole genome sequencing, secondary findings, and genome-wide copy number assessment.

The short course will be opened by Dr. Jennelle Hodge who will give an introduction and share the survey information that prompted development of this education initiative. Dr. Elaine Mardis will then provide a detailed overview of NGS technology, including explaining the fundamental principles, methods, as well as which features are common and differ between platforms. Dr. Susan Hsiao will expand on basic bioinformatics principles and terminology in NGS . Following a break, Dr. Mark Ewalt will describe approaches to NGS assay design, validation and technical artifact identification to deliver high quality results. Dr. Mardis will then conclude the didactic portion by describing what’s currently new in the NGS field including immunogenomics (estimating tumor burden using NGS to predict checkpoint blockade immunotherapy response) as well as single cell sequencing and long read sequencing technologies and applications.  Finally, the knowledge gained will be applied during a case-based audience-interaction to conclude the short course.

Target Audience

All healthcare professionals interested in the diagnosis, management, treatment and prevention of genetic conditions and increasing their understanding of the genetic basis of common, chronic health problems affecting both children and adults will find the programming applicable to their practice.



  • The Next Generation Sequencing Education Gap - Jennelle C. Hodge, PhD
  • Next Generation Sequencing Technologies - Elaine Mardis, PhD
  • Basic Principles in Bioinformatics for Identification and Interpretation of Genomic Alterations - Susan J. Hsiao, MD, PhD
  • Approaches to NGS Assay Design and Validation - Mark D. Ewalt, MD
  • What’s New in NGS- Elaine Mardis, PhD               
  • Case-Based Application


Learning Objectives

At the conclusion of this session, participants should be able to:

  1. Recognize the education gap within the genetics community related to NGS testing
  2. Describe the basic principles of NGS technology
  3. Contrast features of different NGS platforms
  4. Identify the strengths and limitations of different NGS platforms
  5. Explain the difference between whole genome sequencing, whole exome sequencing and targeted panels and identify the best option for clinical application
  6. Describe the basic principles of bioinformatics analysis of NGS data
  7. Explain the steps involved in a general NGS data analysis
  8. Recognize the difference between real variants and technical artifacts
  9. Explain the fundamentals of clinical validation for NGS assays
  10. Identify the relationship between sequencing coverage and depth
  11. Describe at least two key factors in delivering high quality NGS results
  12. Discuss publicly available resources for use in NGS data analysis
  13. Identify the role of NGS in immunogenomics
  14. Summarize the current state of single cell sequencing and long read sequencing technologies
  15. Recognize newly acquired knowledge during application to cases



Jennelle C. Hodge, PhD

Associate Professor of Clinical Medical & Molecular Genetics

Indiana University School of Medicine

ACMG 2020 Program Committee Chair

Elaine Mardis, PhD

Co-Executive Director of the Institute for Genomic Medicine at Nationwide Children’s Hospital and the Nationwide Foundation Endowed Chair of Genomic Medicine.

Susan J. Hsiao, MD, PhD

Assistant Professor in the Department of Pathology and Cell Biology at Columbia University Medical Center

Mark D. Ewalt, MD

Program Director for the University of Colorado Molecular Genetic Pathology Fellowship



Financial Disclosures

Disclosure Statement

It is the policy of the American College of Medical Genetics and Genomics to plan and implement all of its educational activities in accordance with the ACCME Essentials and Areas and ACCME® Policies to ensure balance, independence, objectivity and scientific rigor. In accordance with the ACCME® Standards for Commercial Support, everyone (speakers, moderators, committee members and staff) who is in a position to control the content of an educational activity certified for AMA PRA Category 1 Credit™ is required to disclose all financial relationships with any commercial interests (see definition below) within the past 12 months that creates a real or apparent conflict of interest. Disclosure must include financial relationships of the individual and those of their spouse/partner. Individuals who do not disclose will be disqualified from participating in a CME activity.

This disclosure pertains to relationships with ACCME-defined commercial interests whose products or services may be related to the subject matter of the presentation topic. Any real or apparent conflicts of interest related to the content of the presentations must be managed prior to the educational activity. ACMG will identify, review and resolve all conflicts of interests prior to an educational activity being delivered to learners.


  • ACMG will follow the ACCME’s expectation that no employees or owners of commercial interests will be involved as planners/faculty/presenters of a CME accredited activity.
  • The ACCME definition of a commercial interest is any entity producing, marketing, re-selling, or distributing health care goods or services consumed by, or used on, patients.
  • The ACCME does not consider providers of clinical service directly to patients to be commercial interests – unless the provider of clinical service is owned, or controlled by, an ACCME-defined commercial interest.
  • Diagnostic laboratories are not considered commercial interests unless they are owned by or have a sister organization which is a commercial interest.


Jennelle C. Hodge, PhD


Has no relevant financial relationships to disclose.


Elaine Mardis, PhD

Dr. Mardis has disclosed that she is a consult for Kiadis Pharmaceuticals NV, PACT Pharma LLC, Interpreta LLC; has major stockholder/ownership interest in Qiagen NV; and is part of the board of directors/supervisory board of Qiagen NV.


Susan J. Hsiao, MD, PhD

Dr. Hsiao has disclosed that she is a consult for Bristol Myers Squibb, and Loxo Oncology; she has external grant/research support from Bristol Myers Squibb.


Mark D. Ewalt, MD

Has no relevant financial relationships to disclose.


Educational Credit


Accreditation Statement

The American College of Medical Genetics and Genomics is accredited by the Accreditation Council for Continuing Medical Education (ACCME) to provide continuing medical education for physicians.


Designation Statement

The American College of Medical Genetics and Genomics designates this enduring activity for a maximum of 4.5 AMA PRA Category 1 Credits™. Physicians should claim only the credit commensurate with the extent of their participation in the activity.


P.A.C.E.® CEUs- Laboratory Directors and Laboratory Personnel

ACMG is approved as a provider of continuing education programs in the clinical laboratory sciences by the American Society for Clinical Laboratory Science (ASCLS) Professional Acknowledgment for Continuing Education (P.A.C.E.®) Program. The American College of Medical Genetics and Genomics designates this OnDemand course for a maximum of 4.5 contact hours. ACMG is approved by the Florida Board of Clinical Laboratory Personnel as CE Provider #50-11878. This course is registered # 20-775394 with CEBroker.  ACMG is approved by the California Department of Health Services through the ASCLS P.A.C.E.®


Claiming your Educational Credits

Complete the activity, score 80% or better on the post-test, and carefully complete the evaluation form.


HIPAA Compliance

The ACMG supports medical information privacy.  While the ACMG is not a “covered entity” under HIPAA 1996 and therefore is not required to meet these standards, ACMG wishes to take reasonable steps to ensure that the presentation of individually identifiable health information at ACMG-sponsored events has been properly authorized.  All presenters have completed a form indicating whether they intend to present any form of individually identifiable healthcare information.  If so, they were asked either to attest that a HIPAA-compliant consent form is on file at their institution, or to send ACMG a copy of the ACMG HIPAA compliance form. This information is on record at the ACMG Administrative Office and will be made available on request.


Content Validation

ACMG follows the ACCME policy on Content Validation for CME activities, which requires:


Content Validation and Fair Balance

  1. ACMG follows the ACCME policy on Content Validation for CME activities, which requires:
  1. All recommendations involving clinical medicine must be based on evidence that is accepted within the profession of medicine as adequate justification for their indications and contraindications in the care of patients.
  2. All scientific research referred to, reported or used in CME in support or justification of patient care recommendations must conform to the generally accepted standards of experimental design, data collection and analysis.


  1. Activities that fall outside the definition of CME/CE; “Educational activities that serve to maintain, develop, or increase the knowledge, skills, and professional performance and relationships that a physician uses to provide services for patients, the public, or the profession” (source: ACCME and AMA) will not be certified for credit. CME activities that promote recommendations, treatment, or manners of practicing medicine or pharmacy that are not within the definition of CME/CE or, are known to have risks or dangers that outweigh the benefits or, are known to be ineffective in the treatment of patients.
  2. Presentations and CME/CE activity materials must give a balanced view of therapeutic options; use of generic names will contribute to this impartiality.  If the CME/CE educational materials or content includes trade names, where available, trade names from several companies must be used.


Off-label Uses of Products

When an off-label use of a product, or an investigational use not yet approved for any purpose, is discussed during an educational activity, the accredited sponsor shall require the speaker to disclose that the product is not labeled for the use under discussion, or that the product is still investigational. Discussions of such uses shall focus on those uses that have been subject of objective investigation.



The ACMG does not endorse, or recommend the use of this educational program to make patient diagnoses, particular by individuals not trained in medical genetics. Adherence to the information provided in these programs does not necessarily ensure a successful diagnostic outcome. The program should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed at obtaining the same results. In determining the propriety of any specific procedure or test, a healthcare provider should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen.




Availability: On-Demand
Expires on Aug 31, 2025
Cost: ACMG Member: $100.00
Non-Member: $120.00
Postdoc/Trainee (M): $100.00
Postdoc/Trainee (NM): $120.00
Student (M): $100.00
Student (NM): $120.00
Credit Offered:
4.5 CME (AMA) Credits
4.5 CME (Other) Credits
4.5 Certificate of Participation Credits
4.5 P.A.C.E. Credits

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