Cystic Fibrosis (CFTR) Sequencing and Deletion/Duplication

  • Use for individuals with symptoms of CF or a CFTR-related disorder
  • Not intended for routine obstetric carrier screening

For information on the screening tests for CF, see the Cystic Fibrosis (CFTR) 165 Pathogenic Variants Test Fact Sheet.

Cystic fibrosis (CF) is an autosomal recessive disorder caused by pathogenic variants in the CFTR gene. Age of onset, manifestations, and symptom severity vary greatly. Symptoms of classic CF include chronic sinopulmonary disease, pancreatic insufficiency, hepatic disease, prolapsed rectum, meconium ileus, obstructive azoospermia, and salt loss syndromes. Classic CF results in reduced life expectancy. CFTR-related disorders are less severe and may be characterized by isolated pancreatitis, bilateral absence of the vas deferens, chronic bronchiectasis, and/or nasal polyposis. These disorders typically present in adulthood and often do not decrease life expectancy.

Disease Overview

Incidence

  • Classic CF 
    • Ashkenazi Jewish: 1/2,300
    • Caucasian/White: 1/2,500
    • Hispanic American: 1/13,500
    • African American/Black: 1/15,100
    • Asian American: 1/35,100
  • Other CFTR-related disorders: unknown

Genetics

Gene

CFTR (NM_000492)

Inheritance

Autosomal recessive

Penetrance

  • Two severe variants on opposite chromosomes
    • Penetrance is complete
    • Causative for classic CF
  • Combinations of severe and mild, varying clinical consequences (VCC) and mild, or two mild variants on opposite chromosomes
    • Penetrance is incomplete
    • May or may not cause symptoms of a CFTR-related disorder

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as NGS) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage or known low quality, and in certain situations, to confirm variant calls.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Sensitivity/Specificity

Clinical Sensitivity

CFTR sequencing and deletion/duplication: 99%   

Analytical Sensitivity

Variant Class Analytical Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)
Analytical Specificity (NPA) (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc Deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [single exon]

>99.9

Exon-levelc Duplications

83.3 (56.4-96.4) [3 exons or larger]

>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA).

bVariants greater than 10 bp may be detected, but the analytical sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

Results

Result Variant(s) Detected Clinical Interpretation

Positive

Two severe pathogenic variants identified

Predicted to be affected with classic CF disease

Refer patient to a CF clinic and offer carrier screening to reproductive partner and family members

One mild pathogenic variant and another (mild, VCC, or severe) pathogenic variant on the opposite chromosome

Increased risk for a CFTR-related disorder; if a severe variant is present, offer carrier screening to family members and reproductive partner

One severe pathogenic variant identified

At least a CF carrier

Offer carrier screening to family members and reproductive partner

One mild pathogenic variant identified

At least a carrier of a CFTR-related disorder

Negative

No pathogenic variants identified

Risk for being affected with, or a carrier of, CF or a CFTR-related disorder is reduced

Uncertain

Variant(s) of uncertain identified

Unknown if variant(s) are disease causing or benign

Limitations

  • A negative result does not exclude a diagnosis of cystic fibrosis.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if this patient has had an allogeneic stem cell transplantation.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of the CFTR gene
    • Regulatory region and deep intronic variants other than 5T (IVS8), c.1680-886A>G (c.1679+1.6kbA>G), and c.3718-2477C>T
    • Breakpoints of large deletions/duplications
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by massively parallel sequencing
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Low-level somatic variants
    • Certain other variants due to technical limitations in the presence of pseudogenes and/or repetitive/homologous regions

References