Clinical Variant Analysis for Cancer

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.