Miroslava Balascakova

Correlation between Genetic and Geographic Structure in Europe

Understanding the genetic structure of the European population is important, not only from a historical perspective, but also for the appropriate design and interpretation of genetic epidemiological studies. Previous population genetic analyses with autosomal markers in Europe either had a wide geographic but narrow genomic coverage [1, 2], or vice versa [3-6]. We therefore investigated Affymetrix GeneChip 500K genotype data from 2,514 individuals belonging to 23 different subpopulations, widely spread over Europe. Although we found only a low level of genetic differentiation between subpopulations, the existing differences were characterized by a strong continent-wide correlation between geographic and genetic distance. Furthermore, mean heterozygosity was larger, and mean linkage disequilibrium smaller, in southern as compared to northern Europe. Both parameters clearly showed a clinal distribution that provided evidence for a spatial continuity of genetic diversity in Europe. Our comprehensive genetic data are thus compatible with expectations based upon European population history, including the hypotheses of a south-north expansion and/or a larger effective population size in southern than in northern Europe. By including the widely used CEPH from Utah (CEU) samples into our analysis, we could show that these individuals represent northern and western Europeans reasonably well, thereby confirming their assumed regional ancestry.

Mutations in the Amiloride-Sensitive Epithelial Sodium Channel in Patients With Cystic Fibrosis-Like Disease

We investigated whether mutations in the genes that code for the different subunits of the amiloride‐sensitive epithelial sodium channel (ENaC) might result in cystic fibrosis (CF)‐like disease. In a small fraction of the patients, the disease could be potentially explained by an ENaC mutation by a Mendelian mechanism, such as p.V114I and p.F61L in SCNN1A. More importantly, a more than three‐fold significant increase in incidence of several rare ENaC polymorphisms was found in the patient group (30% vs. 9% in controls), indicating an involvement of ENaC in some patients by a polygenetic mechanism. Specifically, a significantly higher number of patients carried c.–55+5G>C or p.W493R in SCNN1A in the heterozygous state, with odds ratios (ORs) of 13.5 and 2.7, respectively.The p.W493R‐SCNN1A polymorphism was even found to result in a four‐fold more active ENaC channel when heterologously expressed in Xenopus laevis oocytes. About 1 in 975 individuals in the general population will be heterozygous for the hyperactive p.W493R‐SCNN1A mutation and a cystic fibrosis transmembrane conductance regulator (CFTR) gene that results in very low amounts (0–10%) functional CFTR. These ENaC/CFTR genotypes may play a hitherto unrecognized role in lung diseases. Hum Mutat 30:1–11, 2009.

Comparison of different IRT-PAP protocols to screen newborns for cystic fibrosis in three central European populations

BACKGROUND In recent years different IRT/PAP protocols have been evaluated, but the individual performance remains unclear. To optimize the IRT/PAP strategy we compared protocols from three regional CF newborn screening centers (Heidelberg, Dresden, and Prague). METHODS We evaluated the effect of elevating the IRT-cut-off from 50 to 65 μg/l (~97.5th to ~99.0th percentile), the need of a failsafe protocol (FS, IRT ≥ 99.9th percentile) and the relative performance using either two IRT-dependent PAP-cut-offs or one PAP-cut-off. FINDINGS Elevation of the IRT cut-off to 65 μg/l (~99.0th percentile) increased the PPV significantly (Dresden: 0.065 vs. 0.080, p < 0.0001, Prague: 0.052 vs. 0.074, p < 0.0001) without reducing sensitivity. All three IRT/PAP protocols showed a trend towards a higher sensitivity with FS than without and when using one PAP-cut-off instead of two IRT-dependent PAP-cut-offs. CONCLUSIONS For best performance we suggest an IRT/PAP protocol with an IRT-cut-off close to the 99.0th percentile, FS, and a single PAP-cut-off.

An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population

Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene–disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309 790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.

Rituximab resistant evans syndrome and autoimmunity in Schimke immuno-osseous dysplasia

Autoimmunity is often observed among individuals with primary immune deficiencies; however, the frequency and role of autoimmunity in Schimke immuno-osseous dysplasia (SIOD) has not been fully assessed. SIOD, which is caused by mutations of SMARCAL1, is a rare autosomal recessive disease with its prominent features being skeletal dysplasia, T cell deficiency, and renal failure. We present a child with severe SIOD who developed rituximab resistant Evans syndrome (ES). Consistent with observations in several other immunodeficiency disorders, a review of SIOD patients showed that approximately a fifth of SIOD patients have some features of autoimmune disease. To our best knowledge this case represents the first patient with SIOD and rituximab resistant ES and the first study of autoimmune disease in SIOD.

Pilot newborn screening project for cystic fibrosis in the Czech Republic: defining role of the delay in its symptomatic diagnosis and influence of ultrasound-based prenatal diagnosis on the incidence of the disease.

The objective need for cystic fibrosis (CF) newborn screening (NBS) in the Czech Republic has recently been substantiated by a significant delay of its symptomatic diagnosis. This trend most likely resulted from the process of decentralisation of health care which led to the deterioration of care for patients who need specialised approaches. Applied newborn screening model (IRT/DNA/IRT) was efficacious enough to detect CF cases with median age at diagnosis of 37 days. The incidence of CF (1 in 6946 live births) ascertained in this project was lower than that established previously by epidemiological studies (1 in 2700-1 in 3300). However, adjustment for broadly applied ultrasound-based prenatal diagnosis (PND) in the 2nd trimester of pregnancy, that was performed within the period of the project (1/2/2005-2/11/2006), rendered an incidence estimate of 1 in 4023. This value is closer to that observed in other CF NBS programmes and reflects influence of PND on the incidence of CF.

A product of immunoreactive trypsinogen and pancreatitis-associated protein as second-tier strategy in cystic fibrosis newborn screening.

BACKGROUND In cystic fibrosis newborn screening (CFNBS), immunoreactive trypsinogen (IRT) and pancreatitis-associated protein (PAP) can be used as screening parameters. We evaluated the IRT×PAP product as second-tier parameter in CFNBS in newborns with elevated IRT. METHODS Data on 410,111 screened newborns including 78 patients with classical cystic fibrosis (CF) from two European centers were retrospectively analyzed by discrimination analysis to identify a screening protocol with optimal cutoffs. We also studied differences in PAP measurement methods and the association of IRT and PAP with age. RESULTS PAP values differed systematically between fluorometric and photometric assays. The IRT×PAP product showed better discrimination for classical CF than PAP only as second-tier screening parameter (p<0.001). In CF patients, IRT decreased while PAP values remained high over years. In newborns without CF, IRT decreased after birth over weeks while PAP increased within days. CONCLUSIONS The IRT×PAP product performs well as second-tier cutoff parameter for CFNBS. Screening quality parameters depend on the analytic method and on age at blood collection.

25 Cystic fibrosis (CF) prevalence derived from CF newborn screening (CFNBS) in the Czech Republic: comparison of previous epidemiological and current CFNBS-based disease prevalence data

Objectives: This study reviews parental views on how they were informed of the probable CF diagnosis, following neonatal screening, and explores which method parent’s found most acceptable. Methods: Retrospective questionnaires were used to find parents’ views on how they were told that their child had a probable diagnosis of CF, who told them initially, were they told at home or by the GP followed by hospital, how acceptable was the mode of information sharing? Results: 40 parents of children with CF were studied. Most parents (9 out of 12) who had been informed by their GP recall receiving inaccurate information about the condition. All parents (28 out of 28) who had received a home visit to be told about the CF diagnosis felt that the information received had been accurate and found it easier to accept. Conclusion: Our qualitative study confirms that parents who were given accurate information by CF professionals during a home visit found this an acceptable means of being informed of the probable diagnosis of CF. Parents reported less negative recollections of that time than parents who were informed by their GP and met CF professionals in hospital. We consider that this is a superior method of sharing the information about the diagnosis of CF.

17 Cystic fibrosis newborn screening (CF NBS): 4 year experience of the Prague Centre with the IRT/DNA/IRT protocol

Background: Cystic Fibrosis Newborn screening (CFNBS) as a pilot study started at the Institute of Mother and Child (IMC) Centre in 1999 and 444 063 newborns were examined until 2003. Current CFNBS has started gradually in Poland in 2006, covering the whole country in 2009 and is ongoing. 582 693 children were screened until the end of 2011. During CFNBS different protocol’s strategies were used. Aim: Impact of the implementation of NBS on the age of CF diagnosis. Methods: The study involved children diagnosed and treated only in IMC CF Centre (from 1999 until the end of 2011). Three groups were formed: 1. Pilot group (p-NBS) − 56 children, according to protocol strategy IRT/IRT and IRT/IRT/DNA, only F508del mutation was assessed; 2. Current group (c-NBS) − 92 children, IRT/IRT/DNA and IRT/DNA protocol, with expanded DNA analysis panel; 3. Patient diagnosed clinically (non-NBS) − 56 children. Moreover, DNA analysis in c-NBS group contains also frequent mutation in Polish population: 3849+10kbC>T, which is combined with low sweat test values. All patients underwent sweat tests. Results: The age of diagnosis was significantly lower (both p T than p-NBS and non-NBS group (both 0.9%). Conclusion: IRT/DNA strategy with extended DNA analysis provides an opportunity of earlier CF diagnosis even in children with normal sweat test values.