Blog 5 min

Less Variation, More Standardization in Somatic Variant Interpretation and Reporting

Lisa Owen
July 13th, 2018

Preparing for our upcoming webinar -- A Practice-based Guide for Interpretation and Reporting of Sequence Variants in Cancer--caused us to think about the evolution of next generation sequencing (NGS) into the clinic and how there’s hasn't been a dull moment since this technology was first introduced.

Case in point: at 7:00 AM on a Saturday morning following a night of conference social events and cocktail parties, you might not expect a large group of people to assemble to talk about their work. But this is precisely what happened at the Association for Molecular Pathology (AMP) conference in November of 2016.1 Over 600 molecular pathologists, clinical oncologists, and other scientists and clinicians provided a standing-room only audience for a multidisciplinary group to announce newly recommended guidelines for the interpretation and reporting of sequencing variants in cancer. The joint consensus guidelines, created and published by AMP, along with key representation from the American Society of Clinical Oncology (ASCO), the American College of Medical Genetics and Genomics (ACMG), and College of American Pathologists (CAP), were previewed to AMP attendees before being published the following January.

NGS testing has become a powerful resource for this crowd. It’s given them the ability to individualize prevention, diagnosis, and treatment of diseases, including cancer. And this crowd is only going to get bigger. Based on 2017 figures, there are approximately 300 laboratories performing clinical NGS and this number is growing steadily.2

But the growth of clinical NGS testing has revealed just how challenging the act of identifying, classifying, and reporting variants can be, especially when it comes to cancer. To start, the sheer volume of what current NGS panels interrogate is daunting. They look at multiple genes and multiple mutations. When you add in different levels--including copy number variations, insertions and deletions, and point mutations, etc.--things get out of hand very quickly.

In a survey conducted by AMP and the working group, it became clear just how differently labs  interpret and create final variant reports. For example, some labs use a one percent cutoff for population databases, while others use higher or lower. The resulting set of variants can be different based on the thresholds used. The reporting tiers used at labs also seem to differ considerably. Some labs opt to use a simple, two-tiered approach, indicating whether a variant is a mutation or benign, while some labs use a 3-, 4-, or 5-tiered approach.

The working group also concluded that many labs seem to use their own nomenclature for variants in different contexts. When you consider the doctors who order the tests -- highly skilled individuals who have years of experience in oncology, surgery, or some other specialty, but who aren’t molecular pathologists--it becomes important to not only standardize the language but make it as free from ambiguity as possible. Wouldn’t the process of ordering these tests and applying their results in a clinical setting be more efficient if all reports were written similarly, with agreed upon conventions for language and classification?

As with the introduction of any new technology, there comes a time when more focus needs to be placed on developing standards so that the technology can be implemented more efficiently and adopted more broadly. This is the tipping point for NGS testing in cancer. We have the technology, but now we must collectively put the guidelines into practice so that we can all move forward in the same direction, ultimately providing better outcomes for patients.  

What’s in the Guidelines?

Armed with collective experience and survey results from clinical NGS testing labs about how they classify variants and prepare final reports, the working group led by AMP set out to develop the joint consensus guidelines. The result is a set of recommendations, published in the Journal of Molecular Diagnostics, that provide context on the necessity of the guidelines but then quickly delve into the specifics. How should the available databases be used? How should variants be annotated? How do in silico algorithms figure into the process? And what should the final report include and how should it be written?

Their recommendations are based on one fundamental principle: that interpretation of somatic variants should be focused on their impact on clinical care. According to the recommendations, pathologists must determine the clinical impact of the variant and whether it is diagnostic, prognostic, therapeutic, or preventive; collect evidence for the variant’s clinical significance; and evaluate the strength of the evidence for clinical impact, to ultimately classify the variant in one of the four tiers:

  • Tier 1: Variants with strong clinical significance
  • Tier 2: Variants with potential clinical significance
  • Tier 3: Variants of unknown clinical significance
  • Tier 4: Variants deemed benign, or likely benign3

Toward Standardization

Although the guidelines will go a long way toward creating standardization and a common language for labs, variant interpretation is somewhat of an art as well as a science. Laboratory directors still have the room to use their own discretion and judgement. Variant allele frequency is a perfect example -- somewhat standard is to have a cutoff of five percent, but some labs will lower this if they are doing testing to surveil for residual disease.

The guidelines also recommend that labs find a way to keep pace with the notoriously speedy clip of NGS testing developments and find ways to continually evaluate variants, acknowledging that this is a tall order.1,3  Indeed, properly applying the guidelines and keeping pace with the dynamism of NGS testing is a tall order and that’s when it helps to have expertise or partners you can call on for help.

Join us on Thursday, July 19th as Medical Director, Shalini Verma, and VP of Product, Andy Bredemeyer, break down the guidelines and put them into practice using real clinical examples.



  1. CAP TODAY. (2018). In cancer sequencing, a new lingua franca - CAP TODAY. [online] Available at: [Accessed 12 Jul. 2018].

  2. (2018). Bringing NGS Testing In-House. [online] Available at: [Accessed 12 Jul. 2018].

  3. Li, M. (2017). Clinical Implementation of the Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of AMP, ASO and CAP. Cancer Genetics, 214-215, p.36.

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