Invitae’s method of variant classification is a systematic process for assessing the evidence gathered during variant review and applying a formal variant classification based on this evidence.
Invitae’s team of scientists, physicians, and genetic counselors works together to provide high-quality and rigorous variant classifications. Our method (published in Genetics in Medicine) adheres closely to the recommendations from the American College of Medical Genetics (ACMG).1,2 Invitae communicates the evidence and logic behind the classification to the clinician through an interpretive report.
The first step of variant interpretation is to collect and research evidence related to each variant.
The following evidence types are included in this review:
After the relevant information has been gathered and the variant has been thoroughly researched, a formal variant classification is assigned.
A formal classification is meant to help answer two questions about the clinical significance of the variant.
The ACMG has recommended a five-tier classification system. According to this system, a variant can be classified as:
Three additional classifications are also periodically invoked to capture variable expressivity:
Increased risk allele: This variant is not expected to cause disease. However, substantial association data exists suggesting that the presence of this variant may be indicative of increased risk for either a related disease or a completely separate condition.
Pseudodeficiency allele: This variant can lead to false positive results on biochemical enzyme studies, but is not known to cause clinical symptoms or lead to disease. Enzyme studies cannot differentiate between true pathogenic variants and pseudodeficiency alleles, so these must be distinguished by molecular studies.
Variants are assigned a formal classification based on:
Our clinical report:
The report includes:
The field of genetics is constantly evolving, often revealing new evidence relevant to variant interpretation. When new evidence on a variant becomes available, we review our variant interpretation and, if indicated, we will reclassify the variant and issue an amended report to the ordering clinician. If a report is amended, the ordering clinician will receive a notification via phone or email.
Genetic testing can have health implications not only for an individual, but for an entire family. Invitae offers family variant testing at no additional charge for all first-degree relatives of patients who undergo gene or panel testing for a hereditary condition at Invitae and are found to have a pathogenic or likely pathogenic variant. To help resolve variants of uncertain significance (VUS) in our test results, Invitae also offers complimentary follow-up testing to select family members of patients tested at Invitae when informative data can be obtained.
*Benign variants and silent and intronic variants with no evidence towards pathogenicity are not included in the report but are available upon request.
While the ACMG-AMP guidelines were a major step toward establishing a common framework for variant classification, several aspects of the guidelines lack specificity or are subject to varied interpretations. Our clinical genomics group developed Sherloc: a set of semiquantitative, hierarchical evidence-based rules for locus interpretation.
Using the ACMG-AMP guidelines to classify more than 40,000 clinically observed variants, we refined the classification criteria to add greater clarity to subjective rules, and capture edge cases and exceptions.
|Certain ACMG-AMP rules conflate concepts that should be considered separately.||Expands overly encumbered criteria into a set of discrete but related rules that can be weighted separately. This reduces subjectivity and increases consistency in the variant classification.|
|Certain pairings of ACMG-AMP rules capture types of evidence that contribute to the same basic argument, which creates a “double counting” effect.||Groups evidence criteria into broader categories so that only the strongest piece of evidence from the category is counted. This prevents inflated classifications due to “double counting” weak pieces of evidence.|
|The “clinical criteria” style of the ACMG-AMP guidelines introduce difficulty in intuitively understanding the cumulative strength of the evidence. As a result, it is difficult to appreciate how much additional evidence is needed to move to a more definitive classification.||Substitutes the “clinical criteria” style with a categorical framework and numerically weighted evidence criteria. The sum of the weighted evidence represents the strength of the argument for pathogenicity, supporting a more intuitive understanding of the evidence required for a definitive variant classification.|
In the case of family segregation, Sherloc takes a vague notion of supporting evidence that "may be used as stronger evidence” in certain situations, and distills it down into quantifiable scores that can be combined with other pieces of evidence to arrive at a final variant classification.
Invitae’s state-of-the-art Functional Modeling Platform (FMP) provides clarity for patients with variants of uncertain significance (VUS). By pulling in many lines of evidence from both lab experiments and computational analyses, FMP can accurately predict how some VUS will affect gene function. For 1 in 40 (or 2.5%) of Invitae patients, that means we can provide a more definitive variant classification (benign, likely benign, likely pathogenic, or pathogenic), rather than a VUS.