POMPE AND MPSI SEQUENCING AND VARIANT CLASSIFICATION

The Division of Consolidated Laboratory Services (DCLS) has developed an extensive review process for assessing the clinical significance of a variant. This process begins with the collection of all available information on a variant. The information is reviewed and interpreted by a variant interpretation team at DCLS using criteria and rules derived from recommendations published by the American College of Medical Genetics and Genomics (ACMG) [1].

The ACMG guidelines define 28 criteria, and rules for combining those criteria to meet one of these five clinical significance classifications:

- Pathogenic - directly contributes to the development of disease
- Likely Pathogenic - very likely to contribute to the development of disease
- Uncertain Significance (VOUS) - insufficient or conflicting evidence
- Likely Benign - not expected to contribute to the development of disease
- Benign - does not contribute to the development of disease

These criteria take into account certain characteristics of a variant that suggest its effect within the human body and its role in disease, as well as, the general consensus of the scientific community. DCLS uses the most definitive criteria applicable to the disorder of interest.

Can a variant’s classification change?

New information on disease causing variants is discovered every day and, as a result, the process of variant interpretation and classification is an ongoing task. DCLS utilizes methods that perform searches for this new information on a weekly basis and, once identified, determines its clinical significance. DCLS will monitor and report any clinically significant classification changes by issuing an amended report. When there is new clinically significant information available, there are three types of variant classification amendments that can occur:

A benign amendment is any change to a variant's classification that maintains or strengthens an interpretation towards benign significance. These are the most common types of changes resulting from long term monitoring of variant classification.
A pathogenic amendment is any change to a variant's classification that maintains or strengthens an interpretation towards pathogenic significance.
A reversal of classification is any change to a variant's classification that opposes the previously reported classification. Reversals of classifications are rare due to the level and quality of evidence required to meet more certain classifications.

How accurate is a variant’s classification?

A variant's reported classification reflects the consensus of all the information currently available to the Newborn Screening Program at the time of the variant's detection. The process of determining a classification through the evaluation of that information requires that there are multiple lines of evidence in agreement. As the lines of evidence increase, so does our confidence in a variant's clinical significance, shifting the classification from unknown to likely until scientists can reach a definitive classification of either benign or pathogenic. When followed correctly, professional guidelines report a 90% likelihood associated with "likely" classifications [1,2].

References:

Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405‐424. doi:10.1038/gim.2015.30
Harrison, S. M., & Rehm, H. L. (2019). Is 'likely pathogenic' really 90% likely? Reclassification data in ClinVar. Genome medicine, 11(1), 72. doi:10.1186/s13073-019-0688-9

My baby received sequencing but no variants/mutations were found. What does this mean?

The process of sequencing for Lysosomal Storage Disorders identifies rare variants within the causative gene of interest for a screened disorder. DCLS defines a rare variant as those which are present in less than 5% of the population. When a result of "No Variants Found" is reported, this means that no rare variants, either pathogenic or benign, were identified within the associated causative gene. Within the limits of the screen, we can say that no known indicators of the screened disorder were found.

The aim of a newborn screen is to identify infants with results that suggest an increased risk for disease. The addition of second tier sequencing increases the specificity of the screen by taking a closer look at a subset of higher risk infants to filter out those with no known genetic characteristics of a disorder.

What does a classification of Uncertain Significance mean?

A classification of uncertain significance is applied to a variant in which there is currently insufficient, or conflicting information on the variant's role in disease. As more information is discovered about that variant, typically as a result of research and patient outcomes, laboratories are able to provide a more informative classification. This variant may, or may not be determined to be of clinical significance at a later date, so all babies detected by the Newborn Screening Program with a variant of Uncertain Significance are referred to genetic specialists for evaluation.

What is an amended report?

An Amended Report is issued by the screening laboratory when a change has occurred to laboratory testing results. For variant analysis results specifically, amended reports inform you of a change to a variant's classification due to updated scientific data.
The inheritable disease community is continuously discovering new information on disease-causing variants. As a result, variant interpretation and classification is an evolving process. When DCLS classifies a variant, it is classified based on the consensus of all scientific and medical information currently available to DCLS at that time. As new information is discovered and evaluated, it can result in classification changes that may have clinical significance. The following table highlights the three types of Amendments and the possible classification changes:

Virginia's Newborn Screening Program is committed to ensuring the most accurate variant classifications for newborn disorders screened for by DCLS. As such, we will issue amended reports to both the original submitter and care provider on record for any change to a variant's classification.

An amendment may change the overall interpretation of the previous results. It should be evaluated by the care provider cumulatively with all variant data reported for the patient.