Researchers have developed a more cost-effective supporting diagnostic test for hereditary angioedema (HAE) to detect genetic changes that are otherwise missed by current standard methods.
The study, “Gene mapping strategy for Alu elements rearrangements: Detection of new large deletions in the SERPING1 gene causing hereditary angioedema in Brazilian families,” was published in the journal Gene.
HAE is a rare genetic disease characterized by recurrent episodes of severe swelling — angioedema — and pain. The most commonly affected areas are the face, limbs, intestinal tract, and airways. HAE is mainly caused by mutations in the SERPING1 gene, which lead to low levels of C1 inhibitor protein (HAE type 1) or an abnormal defect in the protein (HAE type 2).
C1 inhibitor (C1-INH) prevents the activity of molecules of the complement system — part of the immune system with a crucial role in inflammation — and other enzymes involved in clotting. A deficiency in the protein leads to excessive inflammation and blood flow, which causes swelling.
More than 500 mutations in the SERPING1 gene have been associated with HAE. Most of the cases (65%) are caused by missense mutations — in which a change in a single nucleotide, the basic unit of DNA, leads to an alteration of the protein’s composition — and small deletions or insertions of nucleotides, while large gene rearrangements are responsible for 10% to 20% of cases.
While the standard genetic test (Sanger sequencing) is highly effective in detecting small changes — including substitutions, deletions, and insertions of nucleotides — it cannot detect large rearrangements, such as deletions or insertions of large sections of DNA.
Multiplex ligation dependent probe amplification (MLPA) is the standard technique for detecting these large rearrangements, but its use in many countries, including Brazil, is limited because it is time-consuming and expensive.
Researchers in Brazil have now developed a simple, rapid, and less expensive molecular diagnostic test — called exon quantification technique (EQT) — to detect large genetic rearrangements in the SERPING1 gene.
They performed EQT on blood samples of two women belonging to different families there with a medical history of HAE with C1-INH deficiency, but with no disease-causative mutations in the SERPING1 gene detected through standard genetic testing.
The new technique rapidly detected two distinct large DNA deletions in the SERPING1 gene of the two women (one deletion in each patient), and identified the exact length and position of the deletions within the gene. These alterations were likely to induce the production of C1-NHI protein with an abnormal structure, preventing it from being secreted.
The two deletions were also detected by the MLPA technique, thus validating the results of EQT and highlighting it as “a cheaper, faster and more direct technique, requiring no extensive computational resources and presenting a sensitive and precise result,” the researchers wrote.
Analysis revealed that both deletions were caused by a genetic event associated with Alu elements in the SERPING1 gene. Alu elements, the most abundant class of mobile repetitive sequences in the human genome, are frequently involved in DNA rearrangements and have been associated with approximately 0.1% of human genetic diseases.
The researchers noted that since the SERPING1 gene has a substantial number of Alu elements — making it prone to alterations — their results support the value of EQT in detecting rearrangements caused by these elements.
“Considering that Sanger sequencing does not detect these types of mutations, this mapping method is essential for identifying and diagnosing symptomatic patients and conducting family investigations of asymptomatic C1-INH-HAE carriers,” the researchers said.
They suggest that EQT could be implemented as a support test for the molecular diagnosis of HAE, and be used for the diagnosis of other genetic diseases involving large rearrangements.