Cystic fibrosis: Identification and frequency of mutations in a mixed population from a low‐income region in Northeastern Brazil

Current evidence points to the importance of a more personalized approach that takes into account the ethnicity of a population in the diagnosis of Cystic Fibrosis (CF). Recent studies have indicated that use of gene sequencing is a reliable approach to diagnose CF. Although this approach is extremely relevant, it is costly. The rational use of health resources is highly recommended, especially in low-incomeareas.Brazil is a country of continental dimensions and with great ethnic-racial heterogeneity. The state of Bahia, located in the Northeast of Brazil, presents a population with a high degree of miscegenation due to the characteristics of its ancestry: African (47.3%), European (36.4%), and Amerindian (16.3%). The population of this state is approximately 15.2 million, most of it with low income, and only two medical centers provide clinical care for CF patients; these centers are part of the public health system, which has universal coverage in this country. Our center is a multidisciplinary clinic, located at the teaching Hospital of the Federal University of Bahia. Since January 2008, we have enrolled and prospectively followed patients with CF from 0 to 20 years of age. Between 2012 and 2017, 50 patients with confirmed CF diagnosis by two positive sweat tests were submitted to molecular analysis for screening of seven mutations by conventional methods using peripheral blood samples (polymerase chain reaction and enzymatic digestion), or by next-generation sequencing of oral mucosa samples using Illumina HiSeq platform whenever it was not possible to determine the patients’ genotype through conventional analysis. Of the patients studied, 26 (52%) were male, 48 (96%) were nonwhite, median age of 6 years. Through conventional molecular techniques, five mutations were identified, allowing us to ascertain the genotype of 25 patients. The sequencing study identified 14 new mutations (including a new variant, not yet described in the literature), expanding to 43 (86%) the number of patients with known genotype. These findings allowed us to predict that by using a 20 mutation panel, we would be able to complete diagnostic genotyping from approximately 90% of our patients. Three patients had no mutant allele identified and whereas additional four patients presented with only one mutation. Genotypes and mutation frequencies are described in Table 1. Advances in precision medicine require knowledge of the genotypic profiles of CF patients. However, the routine performance of genetic testing is not a reality for the vastmajority of CF care centers in Brazil. Data from the Brazilian Registry of Cystic Fibrosis (REBRAFC) from 2015 indicated that only 46.2% from 3857 patients were submitted to any genetic study. Thus, it expansion in use of genetic testing is warranted to better diagnose CF. To optimize diagnosis without significantly increasing cost, we predict that development of a panel of mutations more specific to each region is highly recommended, since the use of a single panel may not be equally sensitive, particularly in regions with major heterogeneity in ethnicity such as Brazil. The results of our study revealed that despite the high degree of miscegenation of the study population, with 96% non-white patients, the initial investigation of only F508del mutation determined the genotype of approximately 30% of patients. This finding corroborates with the proposal of an initial investigation searching only for F508del mutation, as suggested for patients from the Brazilian southeast. In our population, subsequent investigation for G542X and 3120 + 1G>A mutations expanded the genotype knowledge to 50% of patients. Thus, the establishment of a step wise protocol, with the research of only three mutations, can optimize the use of public health resources and increase the access to molecular diagnosis techniques. The other mutations, found only through sequencing, can be incorporated into a specific panel for this region of Brazil, reserved only for patients whose genotype could not be determined by the initial investigation. Identifying the genotypes of our patients allowed us to discover that 42% of these were eligible for precision medicine treatment: 14 (28%) patients F508del/F508del—Lumacaftor/Ivacaftor or Tezacaftor/Ivacaftor combination; 3 (6%) patients were suitable to use Ivacaftor and 3 (6%) patients for the use of the association Tezacaftor/ Ivacaftor or Ivacaftor. Furthermore, due to low availability of other diagnostic resources such as CFTR function evaluation or periodic dosing of fecal elastase to investigate pancreatic insufficiency, genotype determination has firmly contributed to improve treatment strategies for our patients.