Clinical Variant Analysis for Cancer

Applying AMP Guidelines to Analyze Somatic Variants

Clinical Variant Analysis for Cancer eBook

The clinical utilization of Next-Generation Sequencing data to diagnose cancer has taken off, resulting in the need to standardize the interpretation and reporting of observed genomic variations. This eBook explores the entire clinical diagnostic process. It demonstrates how Golden Helix software can support clinicians with their decisionmaking in concordance with the guidelines issued by the College of American Pathologists (AMP). In this revision, I have also included a few examples of our new Drugs & Trials functionality and some information about the new annotation sources we have been curating.

In this eBook, I have summarized the key concepts of these guidelines, including:

  • What defines a pathogenic and benign variant respectively, and everything in between
  • Scoring mechanisms that allow us to classify a variant clinically
  • A few interesting cases of variants and their classifications

I encourage you to read this eBook in the context of two others. The first is “Genetic Testing for Cancer”, describing the general background of NGS-based tests in this field. It outlines how we zero in on variants and Copy Number Variants (CNVs) of interest with the help of a state-of-the-art secondary and tertiary analytics pipeline.

The second eBook is called “Clinical Variant Interpretation – Applying ACMG guidelines to Analyze Germline Diseases”.  It is relevant for clinicians who need to report on hereditary cancer types such as BRCA1 and BRCA2. This topic is also covered briefly in this eBook.

About the Author

Dr. Andreas Scherer is CEO of Golden Helix. The company has been delivering industry-leading bioinformatics solutions for the advancement of life science research and translational medicine for over a decade. Its innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from next-generation sequencing. With its solutions, hundreds of the world’s hospitals and testing labs are able to harness the full potential of genomics to identify the cause of disease, develop genomic diagnostics, and advance the quest for personalized medicine. Golden Helix products and services have been cited in thousands of peer-reviewed publications. Golden Helix is also on the Inc 5000 list of the fastest-growing private companies in the US. 

He is also Managing Partner of Salto Partners, Inc., Inc., a management consulting firm headquartered in Nevada.  He has extensive experience successfully managing growth as well as orchestrating complex turnaround situations. His company, Salto Partners, advises on business strategy, financing, sales, and operations. Clients are operating in the high-tech and life sciences space. 

Dr. Scherer holds a Ph.D. in computer science from the University of Hagen, Germany, and a Master of Computer Science from the University of Dortmund, Germany. He is author and co-author of over 20 international publications and has written books on project management, the Internet, and artificial intelligence. His latest book, “Be Fast Or Be Gone”, is a prizewinner in the 2012 Eric Hoffer Book Awards competition, and has been named a finalist in the 2012 Next Generation Indie Book Awards!