CYSTIC FIBROSIS SEQUENCING AND VARIANT CLASSIFICATION

The Division of Consolidated Laboratory Services performs second tier screening for Cystic Fibrosis following an abnormal first tier screen for elevated immunoreactive trypsinogen (IRT). By sequencing the gene associated with Cystic Fibrosis (CFTR) and looking for the presence of known variants, often referred to as mutations, DCLS can identify babies with an increased risk of developing Cystic Fibrosis.

My baby was identified as a carrier of Cystic Fibrosis. What does this mean?

First, if your child has been identified as a possible carrier of Cystic Fibrosis, they should be evaluated by a specialist to officially confirm their carrier status and rule out disease.

Cystic Fibrosis is an autosomal recessive disorder, meaning that an affected baby must receive one copy of an affected Cystic Fibrosis gene from each of their parents. If a baby only receives a copy from one parent, they are considered a carrier. A carrier of Cystic Fibrosis has an increased risk of passing Cystic Fibrosis to their future children, so carriers should see a genetic counselor when they start thinking about having children of their own.

What Cystic Fibrosis variants are included in the screen?
The Division of Consolidated Laboratory Services (DCLS) screens for over 1000 variants in the CFTR2 database classified as either “CF-Causing” or “Varying Clinical Consequence”. Several large deletions and complex variants are not included in the DCLS screen due to limitations in the testing method. For a current list of variants included on the DCLS screening panel, see here.
What do the classifications on my baby’s Cystic Fibrosis results mean?

The Division of Consolidated Laboratory Services (DCLS) relies on the CFTR2 database to determine the classification of a variant. A variant refers to a change in the genetic code, but not all variants cause disease. The following characterizations and their definitions are assigned by the CFTR2 database unless otherwise specified. For more information on the CFTR2 database characterization process, see here.

  • CF-causing: A variant in one copy of the CFTR gene that always causes CF, as long as it is paired with another CF-causing variant in the other copy of the CFTR gene.
  • Varying clinical consequence: A CFTR2 variant that may cause CF, when paired with a CF-causing variant in the other copy of the CFTR gene.
  • Non CF-causing: A CFTR2 variant in one copy of the CFTR gene that does NOT cause CF, even when it is paired with a CF-causing variant in the other copy of the CFTR gene.
  • Not classified: A reportable variant identified by DCLS that is not classified in the CFTR2 database. This variant classification is provided as supplemental information and is intended for review by your medical care provider.
My baby received sequencing, but no variants were found. What does this mean?

The process of sequencing for Cystic Fibrosis allows for the identification of a predetermined number of known variants within the CFTR gene. When a result of "No Variants Found" is reported, this indicates that none of those predetermined variants were identified within the infant’s CFTR gene. Within the limits of the screen, this result means that no known indicators of Cystic Fibrosis were detected.

The aim of a newborn screening test is to identify infants that may be at 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 in order to filter out those with no known genetic characteristics of a disorder.

What are the limitations of second tier sequencing for Cystic Fibrosis?

The process of sequencing for Cystic Fibrosis identifies a predetermined number of known variants within the CFTR gene. While sequencing can detect an extensive list of variants, it cannot rule out the presence of all Cystic Fibrosis variants. Other known limitations of the Cystic Fibrosis newborn screening sequencing test include:

  • Genetic variants that interfere with the amplification of the test panel targets may result in false negative results.
  • Phasing of detected variants cannot be predicted without parental testing.
  • This test does not include complex or structural variants (like large deletions/duplications) larger than 50 bases.
  • Results are not confirmed using an alternative technology.

Due to these known limitations, regardless of the screening test results, a physician should immediately evaluate any infant or child who exhibits symptoms consistent with CF.