Fast and Accurate Cystic Fibrosis Test Developed for Newborns

The new method detects virtually all mutations in the cystic fibrosis gene, preventing missed diagnoses that delay babies’ ability to begin receiving essential treatment.

Cystic fibrosis (CF), which causes mucus to build up in the lungs, pancreas and other organs, is the most common fatal genetic disease in the USA, affecting 30,000 people. To develop the disease, a child must inherit two mutated copies of the CF gene, one from each parent. Newborns in every state of the USA have been screened for CF since 2010, but the current tests have limitations.

Scientists at the Stanford University Medical Center (CA, USA) and their colleagues have developed a highly sensitive, specific, rapid and cost-effective assay for comprehensive cystic fibrosis transmembrane conductance regulator gene (CFTR) analysis from dried blood spots, the common newborn screening specimen. The unique design of CFseq, as the assay is called, integrates optimized dried blood spot sample processing, a novel multiplex amplification method from as little as one nanogram of genomic DNA, and multiplex next-generation sequencing of 96 samples in a single run to detect all relevant CFTR mutation types.

Sequence data analysis utilizes publicly available software supplemented by an expert-curated compendium of more than 2000 CFTR variants. Validation studies across 190 dried blood spots demonstrated 100% sensitivity and a positive predictive value of 100% for single-nucleotide variants and insertions and deletions and complete concordance across the polymorphic poly-TG and consecutive poly-T tracts. Additionally, they accurately detected both a known exon 2,3 deletion and a previously undetected exon 22,23 deletion. CFseq is thus able to replace all existing CFTR molecular assays with a single robust, definitive assay at significant cost and time savings and could be adapted to high-throughput screening of other inherited conditions.

Curt Scharfe, MD, PhD, a professor and senior author of the study, said, “The assays in use are time-consuming and don't test the entire cystic fibrosis gene. They don't tell the whole story. Ultimately, we would like to develop a broader assay to include the most common and most troublesome newborn conditions, and be able to do the screening much faster, more comprehensively and much more cheaply.” The study was published on January 28, 2016, in the Journal of Molecular Diagnostics.

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