Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters.

We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.

Reconstructing an African haploid genome from the 18th century.

A genome is a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Here, we reconstruct the genome of Hans Jonatan (HJ), born in the Caribbean in 1784 to an enslaved African mother and European father. HJ migrated to Iceland in 1802, married and had two children. We genotyped 182 of his 788 descendants using single-nucleotide polymorphism (SNP) chips and whole-genome sequenced (WGS) 20 of them. Using these data, we reconstructed 38% of HJ's maternal genome and inferred that his mother was from the region spanned by Benin, Nigeria and Cameroon.

Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname.

The transatlantic slave trade was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations. Throughout the Americas, thousands of enslaved Africans managed to escape captivity and establish lasting communities, such as the Noir Marron. We find that this population has the highest proportion of African ancestry (∼98%) of any African-descendant population analyzed to date, presumably because of centuries of genetic isolation. By contrast, African-descendant populations in Brazil and Colombia harbor substantially more European and Native American ancestry as a result of their complex admixture histories. Using ancestry tract-length analysis, we detect different dates for the European admixture events in the African-Colombian (1749 CE; confidence interval [CI]: 1737-1764) and African-Brazilian (1796 CE; CI: 1789-1804) populations in our dataset, consistent with the historically attested earlier influx of Africans into Colombia. Furthermore, we find evidence for sex-specific admixture patterns, resulting from predominantly European paternal gene flow. Finally, we detect strong genetic links between the African-descendant populations and specific source populations in Africa on the basis of haplotype sharing patterns. Although the Noir Marron and African-Colombians show stronger affinities with African populations from the Bight of Benin and the Gold Coast, the African-Brazilian population from Rio de Janeiro has greater genetic affinity with Bantu-speaking populations from the Bight of Biafra and west central Africa.

Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America.

Bantu languages are spoken by about 310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with local populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans.

Disease impact on general well-being and therapeutic expectations of European Type II and Type III spinal muscular atrophy patients.

Spinal muscular atrophy (SMA) is a neurodegenerative disorder showing a broad clinical spectrum and no cure to date. To design and select evaluation criteria for the potential assessment of drugs currently being developed, the patient's perspective is critical. A survey, aiming to obtain a view on the current clinical state of European Type II and Type III SMA patients, the impact of this situation on their quality of life and their expectations regarding clinical development, was carried out by SMA-Europe member organizations in July 2015. A questionnaire was set up, translated into 8 European languages and sent out directly via electronic mailing to the targeted SMA patient population by the respective European patient organizations. We were able to collect 822 valid replies in less than two weeks. The questionnaire captured the current abilities of the respondents, their perception of the disease burden which appeared very similar across Europe despite some regional variations in care. According to the great majority of the respondents, stabilization of their current clinical state would represent a therapeutic progress for a compelling majority of the respondents to the questionnaire.

Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups.

Ninety-six single nucleotide polymorphisms (SNPs) and seventeen short tandem repeat (STRs) were investigated on the Y-chromosome of 288 unrelated healthy individuals from populations in Benin (Bariba, Yoruba, and Fon) and the Ivory Coast (Ahizi and Yacouba). We performed a multidimensional scaling analysis based on FST and RST genetic distances using a large extensive database of sub-Saharan African populations. There is more genetic homogeneity in Ivory Coast populations compared with populations from Benin. Notably, the Beninese Yoruba are significantly differentiated from neighbouring groups, but also from the Yoruba from Nigeria (FST>0.05; P<0.01). The Y-chromosome dataset presented here provides new valuable data to understand the complex genetic diversity and human male demographic events in West Africa.

Future trends in cystic fibrosis demography in 34 European countries.

Median survival has increased in people with cystic fibrosis (CF) during the past six decades, which has led to an increased number of adults with CF. The future impact of changes in CF demographics has not been evaluated. The aim of this study was to estimate the number of children and adults with CF in 34 European countries by 2025. Data were obtained from the European Cystic Fibrosis Society Patient Registry. Population forecasts were performed for countries that have extensive CF population coverage and at least 4 years of longitudinal data by modelling future entering and exiting flows in registry cohorts. For the other countries, population projections were performed based on assumptions from knowledge of current CF epidemiology. Western European countries' forecasts indicate that an increase in the overall number of CF patients by 2025, by approximately 50%, corresponds to an increase by 20% and by 75% in children and adults, respectively. In Eastern European countries the projections suggest a predominant increase in the CF child population, although the CF adult population would also increase.It was concluded that a large increase in the adult CF population is expected in the next decade. A significant increase in adult CF services throughout Europe is urgently required.

Comparing Mycobacterium massiliense and Mycobacterium abscessus lung infections in cystic fibrosis patients.

BACKGROUND: Mycobacterium massiliense is closely related to Mycobacterium abscessus and is also a frequent cause of mycobacterial lung disease in patients with cystic fibrosis (CF). There has been no previous investigation of possible differences between M. massiliense and M. abscessus infections in the setting of CF. METHODS: We studied a prospective cohort of 16 M. massiliense and 27 M. abscessus lung infection cases with CF, with a mean follow-up of 6 years. RESULTS: M. massiliense cases were younger than M. abscessus cases (mean age: 12.8 vs 17.1 years; p=0.02) at the time of the first mycobacterial isolation and also had lower body mass index values (mean: 16.4 vs 19.3 kg/m(2), p=0.002). All M. massiliense cases, except one, had negative BMI Z-score values at the time of the first mycobacterial isolation (11/12 vs 16/23 M. abscessus cases, p=0.04). Clarithromycin-based combination therapies led to mycobacterial eradication in 100% of M. massiliense cases but only in 27% of M. abscessus cases (p=0.009). CONCLUSION: Our data show a particular link between M. massiliense and malnutrition specifically in CF patients. Unlike M. abscessus, the bacteriological response of M. massiliense to combination antibiotic therapies containing clarithromycin was excellent. Distinguishing between M. massiliense and M. abscessus has major clinical implications for CF patients.

CFTR p.Arg117His associated with CBAVD and other CFTR-related disorders.

BACKGROUND: The high frequency of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene mutation p.Arg117His in patients with congenital bilateral absence of the vas deferens (CBAVD) and in newborns screened for CF has created a dilemma. METHODS: Phenotypic and genotypic data were retrospectively collected in 179 non-newborn French individuals carrying p.Arg117His and a second CFTR mutation referred for symptoms or family history, by all French molecular genetics laboratories, referring physicians, CF care centres and infertility clinics. RESULTS: 97% of the patients had the intronic T7 normal variant in cis with p.Arg117His. 89% patients were male, with CBAVD being the reason for referral in 76%. In 166/179 patients with available detailed clinical features, final diagnoses were: four late-onset marked pulmonary disease, 83 isolated CBAVD, 67 other CFTR-related phenotypes, including 44 CBAVD with pulmonary and/or pancreatic symptoms and 12 asymptomatic cases. Respiratory symptoms were observed in 30% of the patients, but the overall phenotype was mild. No correlation was observed between sweat chloride concentrations and disease severity. Five couples at risk of CF offspring were identified and four benefited from prenatal or preimplantation genetic diagnoses (PND or PGD). Eight children were born, including four who were compound heterozygous for p.Arg117His and one with a severe CF mutation. CONCLUSIONS: Patients with CBAVD carrying p.Arg117His and a severe CF mutation should benefit from a clinical evaluation and follow-up. Depending on the CBAVD patients' genotype, a CFTR analysis should be considered in their partners in order to identify CF carrier couples and offer PND or PGD.

Mycobacterium avium and Mycobacterium abscessus complex target distinct cystic fibrosis patient subpopulations.

BACKGROUND: Clinical observations suggest that Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABSC) may affect cystic fibrosis (CF) patients with different characteristics and risk factors, but this has never been demonstrated within a single prospective cohort. METHODS: We studied 50 MABSC-positive and 23 MAC-positive patients from a French prevalence study of non-tuberculous mycobacteria (NTM) in CF. Risk factors specifically associated with MABSC and MAC were analyzed by nested case-control studies, with two NTM-negative controls matched by age, sex and center for each case. RESULTS: MAC-positive patients were significantly older than MABSC-positive patients (mean [SD] age, 23.1 [10.2] vs 17.4 [8.3] years, p=0.013), and were also older at CF diagnosis (mean [SD] age, 12.9 [16.1] vs 3.1 [7.7] years, p=0.015); they tended to be less frequent of the ΔF508/ΔF508 genotype (33.3 vs 61.1%, p=0.17) and to use pancreatic extracts less frequently (82.4 vs 97.6%, p=0.07). Risk factors identified by multivariate analysis were: i) in the MAC case-control study, an older age at CF diagnosis (p=0.004); ii) in the MABSC case-control study, at least one course of intravenous antibiotics (p=0.01) and more frequent isolation of Aspergillus (p=0.03). CONCLUSIONS: MAC affects adult patients with a mild form of CF, whereas MABSC affects younger patients with more severe CF and more frequent intravenous antimicrobial treatment.

Inhaled therapies, azithromycin and Mycobacterium abscessus in cystic fibrosis patients.

Cystic fibrosis (CF) patients are at particularly high risk of developing lung disease caused by Mycobacterium abscessus complex (MABSC). Over the last 10 years, changes in CF treatment, with increasing use of inhaled therapies and low-dose azithromycin, have been accompanied by an increase in the prevalence of MABSC infections in CF patients. There is therefore some concern about the role of new CF treatments in the emergence of MABSC infections. We addressed this issue by means of a case-control study including 30 MABSC-positive cases and 60 nontuberculous mycobacteria-negative CF controls matched for age, sex and centre. We also compared practices at the CF centres with the highest prevalence of MABSC with those at the other centres. No positive association was found between MABSC lung disease and the use of inhaled therapies or low-dose azithromycin in the 4 years preceding MABSC isolation. These treatments were not significantly more frequently used at the CF centres with the highest MABSC prevalence rates. In conclusion, there is no evidence for a link between M. abscessus complex lung disease and inhaled therapies or low-dose azithromycin in patients with CF.

Growth during puberty in cystic fibrosis: a retrospective evaluation of a French cohort.

OBJECTIVES: To assess the longitudinal growth pattern in a large French cohort of patients with cystic fibrosis (CF), to determine to what extent puberty contributed to final height and to explore a potential relationship between growth, nutritional status and respiratory function. METHODS: Retrospective data were drawn from the French CF registry from 1999 to 2004. Height, weight and forced expiratory volume in 1 s (FEV(1)) were recorded annually. Growth and velocity curves were compared with reference curves. RESULTS: 729 children with CF were included. In girls, height was similar to the reference population until age 11. Age at onset of puberty was the same as in reference girls. The pubertal spurt was lower than reference values and contributed less to the final adult height. In boys, the mean height was close to the reference mean until age 14 and was thereafter lower. Age at growth acceleration was similar to that in reference boys, but with an impaired peak height velocity (PHV). The final height was lower than in the general population (z score -0.73). No correlations were found between body mass index (BMI) and PHV. In girls, there was a weak but significant positive relationship between PHV and FEV(1) (r=0.17, p=0.02) CONCLUSIONS: In this cohort, children with CF had a normal age of onset of puberty and pubertal spurt, with a low PHV. Puberty contributed less to final adult height, and neither BMI nor FEV(1) had a significant effect on pubertal height gain.

Multicenter study of prevalence of nontuberculous mycobacteria in patients with cystic fibrosis in france.

We performed a multicenter prevalence study of nontuberculous mycobacteria (NTM) involving 1,582 patients (mean age, 18.9 years; male/female ratio, 1.06) with cystic fibrosis in France. The overall NTM prevalence (percentage of patients with at least one positive culture) was 6.6% (104/1,582 patients), with prevalences ranging from 3.7% (in the east of France) to 9.6% (in the greater Paris area). Mycobacterium abscessus complex (MABSC; 50 patients) and Mycobacterium avium complex (MAC; 23 patients) species were the most common NTM, and the only ones associated with fulfillment of the American Thoracic Society bacteriological criteria for NTM lung disease. The "new" species, Mycobacterium bolletii and Mycobacterium massiliense, accounted for 40% of MABSC isolates. MABSC species were isolated at all ages, with a prevalence peak between 11 and 15 years of age (5.8%), while MAC species reached their highest prevalence value among patients over 25 years of age (2.2%).

Long-term noninvasive ventilation in patients with cystic fibrosis.

BACKGROUND: The benefits of long-termnoninvasive positive pressure ventilation (NPPV) have not yet been evaluated in patients with cystic fibrosis (CF). OBJECTIVES: To evaluate the effect of 1 year of NPPV on lung function in patients with advanced CF. METHODS: Data were obtained from the French CF Registry. Patients who started NPPV (ventilated group, n = 41) were compared to matched controls (control group, n = 41). Each ventilated patient was matched to a control 1 year before the start of NPPV (year -1) for gender, CFTR genotype, age +/- 5 years and forced expiratory volume in 1 s (FEV(1)) +/- 10%. The ventilated group was compared to the control group at year -1, during the year of NPPV initiation (year 0) and 1 year after NPPV (year +1). RESULTS: At year -1, the two groups were comparable with regard to forced vital capacity (FVC; 43.7 vs. 49.1% in the ventilated group and the control group, respectively) and FEV(1) (28.2 vs. 28.5%). At year 0, the ventilated group had significantly greater declines in FVC (-3.6 +/- 9.2 vs. +0.8 +/- 8.9%, p = 0.03) and in FEV(1) (-3.0 +/- 6.7 vs. +2.6 +/- 4.4, p < 0.0001). At year +1, the decreases in FVC (-2.1 +/- 10.0 vs. -2.2 +/- 9.9%) and in FEV(1) (-2.2 +/- 6.7 vs. -2.3 +/- 6.2%) were similar in both groups. CONCLUSIONS: These data show that NPPV is associated with stabilization of the decrease in lung function in patients with advanced CF.

Cystic fibrosis mortality trends in France.

BACKGROUND: In 1992 France set up a national cystic fibrosis observatory (Observatoire national de la mucoviscidose, ONM) to monitor the state of health of patients on an annual basis. Using the ONM data, this study estimates the main indicators for life expectancy and assesses the total number of cystic fibrosis patients. METHODS: The data for the years 1994 to 2003 are divided into 3-year periods. Life tables are drawn up for these periods, from which mean and median lengths of life are determined. Using the most recent life table, the number of births in 2003 and the incidence of the disease, the total population of patients can be estimated, assuming a stationary population. RESULTS: In 2001-2003, life expectancy at birth of patients registered with the ONM was 39.1 years and median length of life was 36.4 years. These results, substantially better than those of 1994-1996, are linked to improved conditions of patient inclusion in the ONM database, to improvements in their healthcare, but also to the limitations of the life tables. Based on the 2003 data, the total theoretical number of patients is 6490, and coverage by the ONM database is thus 63.2%. CONCLUSIONS: These provisional results demonstrate the need to convert the ONM observatory into a registry providing exhaustive coverage of all patients.

Paternity in men with cystic fibrosis: a retrospective survey in France.

BACKGROUND: Because more patients reach adulthood, new questions as "what about having a child and/or paternity responsibility?" arose. METHOD: We performed a retrospective investigation based on the French CF registry. The context of the paternity and the health status of fathers were recorded. A comparison with clinical status of non-father patients and a compilation of follow-up data to evaluate its impact were done. RESULTS: Forty-eight men had 69 children. One fourth was said to be natural conceptions, 69% needed assisted reproduction techniques. No child had CF. Clinical status of men was satisfactory: mean BMI was 20.9 kg/m(2) and mean FEV(1) and FVC were 50.5% and 69.2% of predicted, respectively. When matched to CF non-fathers, few significant differences appeared. More non-fathers were F508del/F508del (p=0.03). Fathers' sputum cultures were positive for non-Pseudomonas aeruginosa strain (p=0.05), including Staphylococcus aureus (p=0.01). Mean age at diagnosis was higher, and based on minor evidence of sterility as first symptom leading to the diagnosis of CF (p=0.01) or aspergillosis (p=0.03). The 3-year follow-up showed no degradation of the clinical status. CONCLUSION: Men having paternity responsibility over children did not differ from the CF male population and neither did it seem to have an impact on the disease course.

Cystic fibrosis at the Reunion Island (France): spectrum of mutations and genotype-phenotype for the Y122X mutation.

BACKGROUND: The Reunion Island is a French administrative department located in the Indian Ocean between the islands of Madagascar and Mauritius. Its population is known to be at a high risk of cystic fibrosis (CF). METHODS: Data concerning all CF patients born at the Reunion Island was extracted from the French CF Registry. Twenty-eight DeltaF508/DeltaF508, 17 Y122X/DeltaF508, and 11 Y122X/Y122X were included in a genotype-phenotype study. RESULTS: The detection rate of the CFTR mutations was 83% among the CF patients born at the Reunion Island. Three CFTR mutations accounted for 75% of the detected CF alleles at the Reunion Island (DeltaF508, Y122X, and 3120 + 1G-->A.). The DeltaF508/DeltaF508, DeltaF508/Y122X, and Y122X/Y122X genotypes accounted for 60.2% of the CF patients. Patients carrying at least one Y122X mutation were pancreatic insufficient, had high sweat chloride values and significantly lower anthropometric measures. The mean anthropometric values in all three groups were lower that in the whole CF population followed in "continental" France. This may reflect the poor compliance and even the refusal of treatment noted by the clinicians. CONCLUSIONS: The distribution of CFTR mutations could be explained by the history of the Reunion Island: admixture of French settlers, African and Asian populations, founder effect and isolation followed by genetic drift. The Y122X allele appears to be associated with a severe phenotype.

Reproductive attitudes of couples having a child with cystic fibrosis in Brittany (France).

Cystic fibrosis (CF) has an incidence of one in 2,636 livebirths and a carrier rate of one in 26 inhabitants in Brittany. One objective of a major enquiry among parents having a CF child as well as CF adolescents and adults was to evaluate the reproductive behavior of 124 couples attending a CF care center. Knowledge of recurrence risk resulted in deciding against further progeny or in reducing the number of children (average number of children: 1.96; ideal mean number of children: 3.7). Thirty-five percent adopted or changed their method of contraception after the birth of their affected child, but the change was due to the birth of the CF child in only 14.3% of the couples. Prenatal diagnosis (PD) was favored by 95.1%, and 41.2% had used it; 68.6% were in favor of pregnancy interruption for CF and 76.2% would interrupt the pregnancy should PD reveal that their fetus had CF. All 123 respondents thought that genetic counseling was useful, but only 87.1% knew of its availability. Our results are quite different from those previously published. Although results could be population-specific, one cannot exclude the fact that they reflect a change of attitudes among parents, the other studies being much older.