Next Generation Dx Summit

Short Course 3
NGS Data Analysis – Determining Clinical Utility of Genome Variants
Monday, August 18 | 9:00am - 12:00pm

 

Advances in NGS have provided unprecedented opportunities to mine genetic data from individuals to populations. The subsequent identification of genetic variants which may be implicated in disease is an important step in linking sequence data with disease and provides new approaches to improve human health. This course will explore the strategies of genomic data analysis and interpretation, an emergent discipline that seeks to deliver better answers from NGS data so that patients and their physicians can determine informed healthcare decisions.

Detailed Agenda: 

9:00 am Welcome

9:15 Clinical Grade Annotations: Public Data Resources for Interpreting Genomic Variants

Gabe Rudy, Vice President, Product Development, Golden Helix

NGS is providing affordable and data-rich assays for rare disease diagnosis, carrier screening, risk prediction, pharmacogenomics and oncology care. But the public sharing of clinically relevant annotations is not even across these applications. In this short course, I review the fundamental mechanics and challenges of annotating NGS data for clinical grade reporting and interpretations. We will cover resources such as OMIM, ClinVar, HDMD and COSMIC and how they curate and update their databases. Finally, we will go over hands-on examples of common mistakes in the variant interpretation process: false-positive variant calls, complex variant representations, genomic reference mapping errors and public data limitations.

10:30 Coffee Break

10:50 From Interpretation to Diagnosis: Working with the NGS Lab Report

Erica Ramos, MS, CGC, Clinical Genomics Specialist, Certified Genetic Counselor, New and Emerging Opportunities, Illumina, Inc.

In the world of whole-exome and whole-genome sequencing, clinical laboratories are compiling and interpreting incredible amounts of data related to sequence variation. The lab then faces the challenge of synthesizing that data into a concise, informative report for the clinician. As our knowledge about the impact of variation on human disease is incomplete, these reports will often contain uncertainty that clinicians and their patients then must address. This presentation focuses on the delivery of variant information back to the clinician, considerations for clinical decision making and the changing relationship between the clinician and the clinical lab.

11:25 Practical Considerations for the Clinical Interpretation of Germline Sequence Variants in the Era of NGS

Heather McLaughlin, Ph.D., MB(ASCP)CM, Instructor of Pathology, Massachusetts General Hospital and Harvard Medical School and Assistant Laboratory Director, Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine

The advent of NGS technologies has revolutionized the clinical genetics laboratory. Labs offering NGS technologies are faced with an onslaught of sequence variants which must be interpreted with respect to the patient’s indication for testing. In this presentation we will review the cornerstones of variant interpretation, discuss important considerations and common pitfalls, learn how to construct variant interpretations for clinical reports and review real case examples.

12:00 pm Close of Short Course


Speaker Biographies:

 

Heather McLaughlinHeather McLaughlin, Ph.D., MB(ASCP)CM, Instructor of Pathology, Massachusetts General Hospital and Harvard Medical School and Assistant Laboratory Director, Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine  

Dr. McLaughlin received a B.S. in Diagnostic Molecular Science from Michigan State University, a Ph.D. in Human Genetics from the University of Michigan and has just completed a Clinical Molecular Genetics Fellowship at the Harvard Medical School Genetics Training Program. She has recently accepted a position at Partners HealthCare Personalized Medicine’s Laboratory for Molecular Medicine, where she will serve as an Assistant Laboratory Director. Dr. McLaughlin’s clinical interests focus on molecular diagnostic testing for inherited cardiomyopathies and pulmonary disorders and the implementation of exome and genome sequencing into the clinical laboratory. She is also interested in exploring incidental findings in individuals undergoing genomic sequencing and developing reporting formats that will aid in the integration of genomic sequencing into clinical medicine.

Erica RamosErica Ramos, MS, CGC, Clinical Genomics Specialist, Certified Genetic Counselor, New and Emerging Opportunities, Illumina, Inc.
Erica Ramos received her Master’s degree in genetic counseling from the University of California, Irvine in 2001. After graduation, she worked as a prenatal and preconceptional genetic counselor for Genzyme Genetics in multiple Southern California clinics. In 2005, she moved to Las Vegas to help start Amigenics, a unique adult genetics specialty clinic. While at Amigenics, she helped to create an innovative breast cancer risk assessment program and was the first genetic counselor to focus on adult and cancer genetics in Las Vegas. In July 2012, Ms. Ramos joined Illumina as a Clinical Genomics Specialist, where she provides support and guidance to the Illumina Clinical Services Laboratory and its clients to advance the use of whole-genome sequencing in clinical care. Ms. Ramos is also active in the National Society of Genetic Counselors and was recently elected to the 2014 NSGC Board of Directors as a Director at Large. Additionally, she has served on the Education Committee, Cancer SIG Quality Initiative Task Force and Genetic Counseling Advanced Degree Task Force (GCADTF).

GabeRudyGabe Rudy, Vice President, Product Development, Golden Helix

Gabe is a 10-year veteran at Golden Helix and spends his days collaborating with a diverse set of scientists and building solutions to enable their research. An alumnus of Montana State, he earned his Master’s in Computer Science from the University of Utah before setting his sights on the fast-changing field of genomics and bioinformatics. Gabe has been involved in developing various algorithms from copy number segmentation to runs of homozygosity and rare variant association testing. Gabe blogs about the genomics field from the perspective of someone building solutions and curating genomic annotations and public databases. His series "A Hitchhiker’s Guide to Next Generation Sequencing" has become quite popular as a starter guide for those entering the field.



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