How is genotype testing performed in the workup of cystic fibrosis (CF)?

Updated: Oct 30, 2018
  • Author: Girish D Sharma, MD, FCCP, FAAP; Chief Editor: Kenan Haver, MD  more...
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Answer

More than 1893 CF mutations have been identified. [12] In the commercially available CF gene sequencing method, the entire coding region, splice junction sites, and promoter region of the CFTR gene are amplified from genomic DNA by polymerase chain reaction (PCR) and then subjected to nucleotide sequence analysis on an automated capillary DNA sequencer.

A finding of 2 CFTR mutations in association with clinical symptoms is diagnostic. This test can detect more than 98% of disease-causing mutations in whites; the detection rate is lower in black, Hispanic, and Asian populations. Therefore, failure to find 2 abnormal genes does not exclude the disease.

In November 2013, the FDA approved 4 next-generation gene sequencing devices for clinical use in CF. Two of the devices are used to screen and diagnose CF by detecting DNA changes in the CF transmembrane conductance regulator (CFTR) gene [43, 44] : the Illumina MiSeqDx Cystic Fibrosis 139-Variant Assay, which checks specific points in the patient's CFTR gene sequence to detect known variants in the gene, and the Illumina MiSeqDx Cystic Fibrosis Clinical Sequencing Assay, which sequences a large portion of the CFTR gene to detect any difference in the CFTR gene compared with a reference CFTR gene.

The other 2 FDA-approved devices are the Illumina MiSeqDx instrument platform, which analyzes the genes, and the Illumina Universal Kit reagents, which isolate and create copies of the genes of interest from patient blood samples. [43, 44] These 2 devices comprise the first FDA-regulated test system that allows laboratories to develop and validate sequencing of any part of a patient’s genome. [43, 44]


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