Girl With 3 Different Mutations Captures ‘Pitfalls’ in Diagnosing CF

Marisa Wexler, MS avatar

by Marisa Wexler, MS |

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The complex diagnostic journey of a girl with cystic fibrosis (CF) and three different disease-causing mutations was described in a report by scientists in Italy.

“This case well illustrates possible pitfalls in the clinical and molecular diagnosis of CF,” the researchers wrote.

Their report, “Things come in threes: A new complex allele and a novel deletion within the CFTR gene complicate an accurate diagnosis of cystic fibrosis,” was published in the journal Molecular Genetics & Genomic Medicine.

A 6-year-old girl of Albanian descent, with no remarkable family history but “affected by an undefined syndrome,” was referred to medical geneticists.

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As a newborn, the girl had experienced meconium ileus, a condition where a baby’s meconium, or first feces, are thick and block the intestines. Newborn screening for CF at the time of her birth had been negative, as it identified only one CF-causing mutation in one copy of the CFTR gene. CF does not develop unless disease-causing mutations are in both copies of this gene (one inherited from each biological parent).

As she grew, the girl had chronic constipation and cough. She also showed multifaceted signs of growth delay, such as unusually short limbs and bones that were less developed than would be typical for her age. Some unusual physical features, like mild frontal bossing (an unusually prominent forehead) and curves in the bones of the lower legs, were also present in the girl’s father and paternal grandfather.

This constellation of signs and symptoms “led us to hypothesize a dominantly inherited skeletal dysplasia (SD) and/or CF,” the researchers wrote. Skeletal dysplasia is a group of conditions that affect bone development, neurological function, and cartilage growth.

Further investigations failed to identify genetic changes known to give rise to skeletal dysplasia. However, a sweat test showed abnormally high chloride levels, which is indicative of CF.

“Our patient fell within the several cases of false-negative CF NBS [newborn screening] documented,” the researchers wrote. “In this situation, a SCT [sweat chloride test] could have been decisive to resolve the CF suspicion” due to meconium ileus and poor weight gain in early life, “but it was performed only at patient’s age of six, indeed providing a positive result.”

Genetic sequencing of the CFTR gene followed. The initial newborn screening had identified a F508del mutation, which is the most common CF-causing mutation. Further analysis confirmed the presence of this mutation, and also identified a second, rarer CF-causing mutation called c.1420G>A.

Theoretically, two disease-causing mutations might have been enough to confirm a CF diagnosis. However, an additional test called segregation analysis showed that both the F508del and the c.1420G>A mutation were actually present on the same copy of the CFTR gene — the one that the girl had inherited from her mother.

This means that these two mutations alone could not have caused CF in the girl — if she had CF, then there must have been at least one other mutation affecting the CFTR copy that she inherited from her father.

A battery of further studies were taken to look for such mutations. In particular, the scientists looked at copy number data, a type of analysis useful for detecting deletions and amplifications, where large chunks of DNA get erroneously removed or copied.

Results now revealed that the girl’s paternal copy of the CFTR gene had a deletion, dubbed c.3158_3468+3219del.

“Taken together, these results stress the importance to perform segregation analysis, and to consider CNVs [copy number variations] among the disease-causing mutations for accurate CFTR genotyping,” the researchers concluded.