CGC 2020 Webinar Series


In an effort to provide high-quality online educational opportunities to our members and colleagues, we are excited to announce a new webinar series sponsored by the Cancer Genomics Consortium and the University of Wisconsin Collaborative Genomics Conference.

This three-lecture series will focus on new methods for detection of structural variants (copy number abnormalities and balanced rearrangements) in constitutional and cancer testing, and on interpretation of copy number abnormalities (CNAs) and copy-neutral loss of heterozygosity (CN-LOH) in cancer using the ACMG/CGC standards.


Recordings Available from Recent Webinars



Copy Number Abnormality Detection from Whole Genome Sequencing Data
Alka Chaubey, PhD, FACMG
Head of Cytogenomics, Perkin Elmer Genomics




Dr. Alka Chaubey will discuss the utilization of low pass genome sequencing as a new diagnostic approach for CNV detection across the entire genome. Dr. Chaubey will provide evidence from internal validation studies for CNGnome® test, which by utilizing 5x genome sequencing delivers an increased level of CNV detection when compared to traditional methods. Multiple case examples will be discussed in the webinar to demonstrate the clinical capabilities of CNGnome®. Several examples of whole genome sequencing (>30X depth) with pathogenic sequencing and copy number variants will also be discussed.

Interpretation of Copy Number Abnormalities (CNAs) and CN-LOH in Cancer using the ACMG / CGC Standards: Working through Complex Cases


This webinar provides practical guidance how to streamline interpretation of CNAs and CN-LOH in neoplasia using the current ACMG/CGC standards. Easy steps to generate clear, accurate and well organized reports will be illustrated. Using case examples, the speakers will explain challenging concepts including interpretation of genomic complexity, adjustment of ploidy, estimation of the percentage of involved cells and reporting of abnormalities suspected to be germline. 


Vanessa Horner, PhD, FACMG

Director, UW Cytogenetics and Molecular Genetics Services WSLH
Assistant Professor, Department of Pathology and Laboratory Medicine
University of Wisconsin-Madison

Fady M. Mikhail, MD, PhD, FACMG

Co-Director, Cytogenetics Laboratory
Professor, Department of Genetics
University of Alabama at Birmingham

Gordana Raca, MD, PhD, FACMG

Director of Clinical Cytogenomics, Center for Personalized Medicine,
Department of Pathology
Children's Hospital Los Angeles
Associate Professor, Clinical Pathology, Keck School of Medicine of USC



Optical Mapping and its Role as a Cytogenomics Tool in Cancer

Dr. Brynn Levy, MSc (Med), PhD, FACMG

Columbia University Medical Center, 
New York Presbyterian Hospital

Dr. Levy will describe the principles of optical mapping, illustrate the capacity of this technology to detect balanced structural rearrangements in different sample types, and compare its performance with classic cytogenetic approaches including karyotype analysis and fluorescence in situ hybridization testing.

Application of Optical Mapping for Comprehensive Assessment of Structural Rearrangements in Hematological Malignancies

Dr. Rashmi Kanagal-Shamanna, MD

The University of Texas MD Anderson Cancer Center

Dr. Kanagal-Shamanna will discuss the application of optical mapping in comprehensive genomic characterization of hematological malignancies and highlight the clinical utility of this technique in management of including myelodysplastic syndromes.

Registration Instructions

1. Create an account at ICEP (see pdf for detailed instructions):
2. Register for the GoToWebinar at

3. Once you have registered with GoToWebinar you will receive an e-mail with the link for the day of the conference.


Continuing Medical Education


Intended Audience

PhD, MD, RN, Genetic Counselors, and healthcare professionals who generate or use genomic/genetic data in their practice (laboratory directors, ABMGG Fellows, laboratory staff, etc.).

Global Objectives

As a result of this educational regularly scheduled series, learners will be able to:

1. Recognize both common and rare genetic abnormalities associated with developmental delay, infertility, prenatal ultrasound findings, and oncology specimens.
2. Demonstrate an improved ability to effectively communicate genetic information across healthcare team members from different professions and disciplines.
Examine performance and utility of novel testing approaches and standardized classification recommendations. 


Policy on Disclosure

It is the policy of the University of Wisconsin-Madison ICEP that the faculty, authors, planners, and other persons who may influence content of this CE activity disclose all relevant financial relationships with commercial interests* in order to allow CE staff to identify and resolve any potential conflicts of interest.  Faculty must also disclose any planned discussions of unlabeled/unapproved uses of drugs or devices during their presentation(s). For this educational activity, all conflicts of interest have been resolved and detailed disclosures are listed below.

* The University of Wisconsin-Madison ICEP defines a commercial interest as any entity producing, marketing, re-selling, or distributing health care goods or services consumed by, or used on, patients The University of Wisconsin-Madison ICEP does not consider providers of clinical service directly to patients to be commercial interests.

  Financial Relationship Disclosures


Discussion of Unlabeled/Unapproved
uses of drugs/devices in presentation?

COI completion date
Kaitlin Lenhart, PhD, CGC RSS Chair
No relevant financial
relationships to disclose
March 30, 2020
Lori Halverson, RSS Planner
No relevant financial
relationships to disclose
March 27, 2020
Xiangqiang Shao, PhD
No relevant financial
relationships to disclose
May 6, 2020
Daniel Kurtcyz, MD
No relevant financial
relationships to disclose
March 28, 2020
Vanessa Horner, PhD, FACMG
Wisconsin State Laboratory
of Hygiene (Employment),
School of Medicine and
Public Health,
University of Wisconsin-
Madison, (Employment)
March 31, 2020
Kimberly Anderson, MS, CGC
No relevant financial
relationships to disclose
March 31, 2020
Alka Chaubey, PhD, FACMG

Perkin Elmer, Inc (Stock option)
Bionano Genomics (Contractor)
Perkin Elmer, Inc (Employment

YesMay 15, 2020