Invitae Cystic Fibrosis Newborn Screening Confirmation Test


Test description

The Invitae Cystic Fibrosis Newborn Screening Confirmation test analyzes the CFTR gene; which is associated with cystic fibrosis (CF). This test is intended for any individual with an elevated immunoreactive trypsinogen (IRT) on newborn screening (NBS), a positive sweat chloride test (sweat test), or a suspected diagnosis of a cystic fibrosis based on clinical presentation. Cystic fibrosis has strong genotype/phenotype correlations and the combination of specific variants may provide guidance as to expected outcomes.

Pathogenic variants in the CFTR gene inhibit the function of chloride channels across cell membranes. This disrupts the ability of the cells to regulate the flow of water and chloride ions and results in the buildup of a thick sticky mucus that can clog airways and organs such as the pancreas and intestine.

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Primary panel (1 gene)


CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C>T (also known as 3849+10kbC>T), c.1210-34TG[12]T[5] (also known as T5TG12), c.1210-34TG[11]T[5] (also known as T5TG11), and c.1679+1634A>G.

Cystic fibrosis (CF)
CFTR-related disorders

Cystic fibrosis (CF) is a complex multisystemic disorder caused by the buildup of thick, viscous secretions on the lining (epithelia) of many different organ systems. This buildup damages organ function over time. Classically affected individuals often present with pulmonary symptoms, including lower airway inflammation, recurrent pulmonary infections, airway damage, and the buildup of scar tissue in the lungs (lung fibrosis). Historically, pulmonary failure was a common cause of childhood morbidity, but with improved preventive treatment, individuals with CF now frequently live into adulthood.

Individuals with CF may also present with digestive problems associated with the pancreas and the intestine. The reduced production of insulin and digestive enzymes by the pancreas (pancreatic insufficiency) can lead to nutritional deficiencies. In infants with CF, excess mucus production in the intestine can cause a blockage called meconium ileus.

CFTR-related disorders encompasses a broad clinical spectrum from single organ manifestations to individuals with abnormal IRT and/or sweat test results, but mild or absent clinical symptoms.

CFTR is the only gene known to be associated with cystic fibrosis and the CFTR-related disorders. Sequencing identifies more than 98% of CFTR pathogenic variants.

All CFTR-related conditions are inherited in an autosomal recessive pattern.

CF is considered to have incomplete penetrance and variable expression. Genotype/phenotype correlations have been well studied and account for much of this variability.

In the United States, cystic fibrosis occurs most frequently in the Caucasian population, with an incidence of 1 in 2,500 to 1 in 3,500 newborns. CF is less common in other ethnic groups, occurring in approximately 1 in 15,000 to 1 in 17,000 African Americans and 1 in 31,000 Asian Americans.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
CFTR* NM_000492.3

CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C>T (also known as 3849+10kbC>T), c.1210-34TG[12]T[5] (also known as T5TG12), c.1210-34TG[11]T[5] (also known as T5TG11), and c.1679+1634A>G.