Webinars in 2015

Informatics 101-06: Leveraging the Electronic Health Record to Implement Genomic Medicine

Thursday, October 22, 2015

Presenter: Marc S. Williams, MD
Genomic Medicine Institute
Geisinger Health System
Danville, PA

Host: Nilesh G. Dharajiya, MD
AMP T&E Committee Member
Sequenom Center for Molecular Medicine, LLC
San Diego, CA

Description:
This presentation will focus on the importance of the electronic health record as a tool to support the implementation of genomic medicine. In particular the importance of moving beyond passive representation of laboratory results to results tied to knowledge and action will be explored. Use of clinical decision support to promote evidence based best practices will be demonstrated using genomic medicine use cases. Opportunities and barriers to implementation will be covered. Future opportunities including direct engagement with patients and families will be also presented.

Learning Objectives:

• Define genomic, personalized and precision medicine
• Identify the differences between passive, asynchronous and active clinical decision support
• Discuss genomic medicine applications that utilize the functionality of electronic health records to impact patient care

Level of Instruction: Basic

Number of Contact Hours: 1.0

NGS 101: Validation and Implementation of Clinical Next Generation Sequencing Based Tests for Inherited Disorders

Thursday, September 10, 2015

Presenter: Avni B. Santani, PhD
The Children's Hospital of Philadelphia
Philadelphia, PA

Host: Matthew Hiemenz, MD, MS MAC liaison to the T&E Committee
BioReference Laboratories, Inc.
Elmwood Park, NJ

Description:
Next generation sequencing technologies are widely being adopted by laboratories for the diagnosis of inherited genetic disorders and in oncology. Although diagnostic laboratories are incorporating novel instruments and bioinformatics tools, laboratory directors are facing increasingly complex challenges in choosing appropriate approaches for assay selection and in developing comprehensive validation methods that examine the pre-analytical, analytical and post analytical phases of an assay. This webinar will present general considerations for approaches used for assay selection and validation of next-generation sequencing based tests for inherited genetic disorders.

Learning Objectives:

• Identify the key considerations used for assay selection and validation.
• Describe the current approaches for validation testing of next-generation sequencing based tests for inherited genetic disorders.
• Define the major performance metrics for validation testing and identify use of reference standards in defining performance metrics

Level of Instruction: Basic

Number of Contact Hours: 1.0

The Informatics of Whole Exome Sequencing for Individualized Medicine: Applications for Clinicians and Research Models

Wednesday, September 9, 2015

Presenter: Eric W. Klee, PhD
Mayo Clinic
Rochester, MN

Host: Christopher D. Watt, MD, PhD
AMP T&E Committee Member
Hospital of the University of Pennsylvania
Philadelphia, PA

Description:
Discover how clinicians can apply information gathered from molecular-level data to diagnose and treat individual medical conditions. In this webinar, hear how clinicians can use bioinformatics to support clinical test development, implementation, quality control and interpret results.

Learning Objectives:

• Discuss the availability and role of phenotype to gene association tools to support whole exome sequencing (WES) testing for undiagnosed disease
• Gain familiarity with the different types of analytics that are possible when using WES
• Describe the utility in using protein modeling to explore the impact of VUSs
• Gain awareness of the role of routine functional analysis to support VUS characterization from WES analysis

Level of Instruction: Basic

Number of Contact Hours: 1.0

Using Integrated Genome Viewer (IGV) to View Next Generation Sequencing Data

Wednesday, August 19, 2015

Presenter: Ahmet Zehir, PhD
Memorial Sloan Kettering Cancer Center
New York, NY

Host: Jill Hagenkord, MD
23andMe
Los Altos, CA

Description:
This webinar will demonstrate how to use Integrated Genome Viewer in viewing and interpreting NGS data. We will specifically talk about data from DNA sequencing experiments and how IGV can be used to identify potential sequencing artifacts.

Learning Objectives:

1. Navigate through the IGV user interface
2. Load sequencing files and view different types of variants
3. Identify sequencing artifacts

Level of Instruction: Basic

Number of Contact Hours: 1.0

Practical Applications of Next-Generation Sequencing in Clinical Microbiology

Tuesday, August 11, 2015

Presenter: Stephen J. Salipante, MD, PhD
University of Washington
Seattle, WA

Host: Benjamin Pinsky, MD
Stanford University School of Medicine
Stanford, CA

Description:
This webinar will be a discussion about current and future applications of next-generation sequencing technologies in clinical microbiology laboratories. A special focus will be placed on assays that are currently validated for clinical use.

Learning Objectives:

1. Recognize the major sequencing technologies currently used in clinical laboratories.
2. Describe the current applications of next-generation sequencing data in clinical laboratories.
3. Identify future opportunities for integration of next-generation sequencing technologies into clinical laboratories.

Level of Instruction: Intermediate

Number of Contact Hours: 1.0

Development and Optimization of Genomic Analysis Pipelines Using Next Generation Sequencing Technologies

Wednesday, July 1, 2015

Presenter: Raghu Metpally, PhD
Weis Center for Research, Geisinger Health System, Danville, PA

Host: N. Sertac Kip, MD, PhD
Geisinger Health System, Danville, PA

Description:
This webinar will introduce the basic steps of bioinformatics pipeline development process for the genomic analysis of Next Generation Sequencing data. The presentation will focus on how NGS based analysis pipelines are built, tool selection and parameter optimization, especially for variant calling approaches to generate results in clinical context.

Learning Objectives:

1. Identify bioinformatics analysis pipelines and hardware selections
2. Discuss the selection of aligners and variant callers
3. Discuss various approaches to variant calling and optimization
4. Describe the importance of variant filtering steps in clinical setup

Level of instruction: Basic

Contact Hours: 1.0

Next-Generation Sequencing (NGS) Technologies for HIV Drug Resistance Testing

Thursday, June 18, 2015

Presenter: Robert W. Shafer, MD
Stanford University School of Medicine, Stanford, CA

Host: Benjamin Pinsky, MD
Stanford University School of Medicine, Stanford, CA

Description:
HIV-1 exists within individuals as a complex mixture of variants often referred to as a quasispecies. During the past 10 years, there have been many studies of the distribution and clinical significance of "low-abundance" or "minority" drug-resistance variants present in plasma in proportions below 20% to 30% -- the limit of detection of standard genotypic resistance testing using dideoxy-terminator "Sanger" sequencing. HIV-1 "deep" sequencing using NGS technologies have been widely used in research settings to study the clinical significance of low-abundance drug resistance mutations. In addition, NGS is commercially available for several niche clinical applications such as determining HIV-1 tropism before using a CCR5 inhibitor.

In this webinar, Dr. Shafer will review the scenarios in which low-abundance HIV-1 drug-resistance mutations are most clinically relevant, the most influential studies of NGS for HIV-1 drug resistance testing, and the practical aspects of NGS that have so far slowed its widespread adoption for most routine HIV-1 genotypic resistance testing.

Learning Objectives:

1. Describe the prevalence and clinical significance of low-abundance HIV-1 drug resistance testing in newly infected antiretroviral naive patients and in patients with a history of antiretroviral treatment failure.
2. Explain the promises and limitations of NGS deep sequencing for HIV-1 drug resistance testing including the published experience with the 454, Ion Torrent, PacBio, and Illumina sequencing platforms.
3. Recognize the practical laboratory and bioinformatic considerations that must be understood before implementing NGS deep sequencing for research or clinical applications

Level of Instruction: Basic

Number of Contact Hours: 1.0

An Introduction to Bioinformatics Methodologies: How to Process NGS Data into Clinically Meaningful Results

Thursday, May 7, 2015

Presenter: Sharanya Raghunath, PhD
Intermountain Healthcare, St. George, UT

Host: N. Sertac Kip, MD, PhD
Geisinger Health System, Danville, PA

Description:
The purpose of this webinar is to introduce the application of bioinformatics to molecular data generated in clinical laboratories. The lecture will focus on how various approaches can help generate clinically relevant results.

Learning Objectives:

1. Compare the different types of NGS approaches in clinical care: whole exome sequencing, hotspot sequencing, and whole genome sequencing.
2. Describe the tools and process of the standard bioinformatics workflow.
3. Explain the methods and clinical lab standards for measuring quality reads in a sequencing run.
4. Identify variant calling methods and the significance of variant annotation and interpretation.

Level of Instruction: Basic

Contact Hours: 1.0

Introduction to Bioinformatics for NGS Analysis

Thursday, March 26, 2015

Presenter:: Donavan Cheng, PhD
Memorial Sloan Kettering Cancer Center, New York, NY

Host: Maria E. Arcila, MD
Memorial Sloan Kettering Cancer Center, New York, NY

Description:
Next-generation sequencing (NGS) technology enables the unbiased identification of mutations across the genome with high sensitivity and specificity. NGS platforms routinely produce high volumes of data, which are amenable to analysis using specialized bioinformatics algorithms and methods. The goal of this webinar is to introduce the steps in a typical DNASeq bioinformatics analysis workflow, to illustrate the progression from raw FASTQ files to annotated variant calls. Basics of sequence alignment will be introduced, and an overview of variant calling methods for single nucleotide variants (SNVs), short insertions and deletions (indels), copy number variants (CNVs) and structural variants will be presented.

Learning Objectives:

1. Describe various sequencing platforms (Illumina, Ion Torrent)
2. Discuss the various steps in a typical DNASeq bioinformatics analysis workflow
3. Demonstrate an understanding of basics of sequence alignment, an appreciation of the BLAST algorithm

Level of Instruction: Basic

Contact Hours: 1.0

AMP Genomic Sequencing Procedure Cost and Value Models Tutorial

Friday, February 13, 2015

Presenters:
Aaron D. Bossler, MD, PhD, University of Iowa
Chair, Economic Affairs Committee
Charles Matthews, Vice President, Boston Healthcare

Panelists:
Linda M. Sabatini, PhD, HCLD, Northshore University Health System
Katherine Tynan, PhD, Tynan Consulting

Description:
CMS announced late last year that it will gap-fill all of the new Genomic Sequencing Procedure (GSP) CPT codes. While the new codes were made available on January 1, 2015, Medicare payment rates for GSP codes will not be finalized until November 2015 and national payment rates will not go into effect until January 1, 2016.

This means that labs need to work with Medicare Administrative Contractors (MACs) and commercial payers to ensure adequate pricing/reimbursement for these codes.

MAC values for these codes need to be submitted to CMS on or about April 1, 2015. MACs around the country have started to request input from providers to help ensure appropriate allowances are established.

To help AMP members estimate the cost basis of their GSP services, AMP initiated a micro-costing and health economic evaluation of several of these CPT codes. The availability of these tools will help AMP members who want to participate in this growing field articulate the cost and value of these procedures.

Learning Objectives:

1. Learn the coding for new genomic sequencing procedures
2. Receive an overview of the cost and value project
3. Discover how to put the tools into practice

Level of Instruction: Basic