Modelling the spread of cystic fibrosis in Brittany using genealogical data over five centuries.

BACKGROUND: The French region of Brittany presents one of the highest cystic fibrosis (CF)-causing allele frequency in Europe. Here, we tested two hypotheses: i) CF-causing allele carriers arrived by sea in the middle of the 1st millennium AD, and ii) a selective advantage for healthy carriers explains this high rate. METHODS: From the census of cystic fibrosis patients, frequency maps of the most widespread alleles were established. A mathematical model was developed, based on birth date and place of the ancestors of these patients over 5 centuries, to determine the distribution of local migrations and their parameters for inter-generational intervals of 32 years. This model was applied to simulate the spread of CF-causing variant carriers, according to different scenarios that corresponded to the immigration of a given number of variant carriers at different times (year) and places, and to compare their results to current frequency maps. RESULTS: Migrants carrying a CFTR variant settled in several locations, around which they spread, notably in Central Brittany (F508del variant), Léon (G551D variant) and Cornouaille (1078delT variant). Until the end of the 18th century, the spreading of disease-causing allele carriers was relatively slow, and allele frequencies progressively increased. Then, the mean migration distances increased rapidly, leading to a decline in local frequencies. CONCLUSIONS: The main CFTR variants could only have reached their current frequencies through a selective advantage for healthy carriers of the order of 4-6 % at each generation. For the most widespread variant (F508del), the model supports the hypothesis that it appeared around 190 generations ago.

Lessons from the on-site quality audit of data transmitted to the French cystic fibrosis registry.

BACKGROUND: The French Cystic Fibrosis Registry takes a census of the population of patients and records their annual data transmitted by Cystic Fibrosis Centers (CFCs). Quality of patient data has been a focus in the past years, with the implementation of automated controls before data integration. The objective was to assess, at the 14 CFCs trained in the quality improvement named Hospital Program to Improve Outcomes and Expertise in Cystic Fibrosis (PHARE-M), the quality of the 2012 and 2013 data transmitted to the French Registry with respect to the rules established to obtain forced expiratory volume in 1 second (FEV1%) and anthropometric data. METHODS: The clinical researcher selected 20 patients at each CFC from age ranges corresponding to different visit frequencies and measurement procedures in order to reach saturation of error causes. The control consisted in comparing source data, pulmonary function tests (PFTs), patient records, and data in the Registry. RESULTS: The audit focused on 242 patients, 2455 consultations and 1855 PFTs. Less than 5% of data concerning weight, height, or FEV1 (L) in the patient records files had discrepancies with source data. Discrepancies on patient height between patient records and PFT files were found in 11% of cases. For one hundred and ten patients (45%), anomalies were found between the patient record and the Registry for the FEV1% and the associated anthropometric measurements mainly related to the interpretation of the selection rule of the venue corresponding to the "best spirometry in the year" and the reference standard used (local standards versus Knudson reference equations). For the 33 children in the age range of 6-17 years old (27% out of 120 children records controlled), the FEV1% value in the Registry presented an average deviation of +4.25% (min. = -9.3%; max. = +16.9%; median = 4%) with the value from the Patient record. CONCLUSIONS: This first on-site quality audit of the data transmitted to the Registry pointed out variability in the measurement process at the CFCs. The rule for selecting the data for the Registry was applied differently at some CFCs, and various local References for the FEV1% calculation were used. Avenues for improvement have been identified.

Fine-scale human genetic structure in Western France.

The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendée Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses.