Cystic fibrosis mutation frequencies in an Irish population

Cystic Fibrosis-Related Diabetes Mellitus and Pregnancy: A Retrospective Study

INTRODUCTION

Cystic fibrosis-related diabetes mellitus (CFRDM) is becoming a more common issue in pregnancy care as the life expectancy of females living with cystic fibrosis has improved, with an increasing number of pregnancies in this population. Despite the Republic of Ireland having the highest incidence of cystic fibrosis globally, there is limited Irish data on pregnancy outcomes for those with CFRDM. This study aimed to retrospectively review maternal and foetal outcomes of pregnancies affected by maternal CFRDM.

METHODS

The patient records of all women with CFRDM who attended the National Maternity Hospital Dublin for obstetric care between 2015 and 2019 were retrospectively reviewed.

RESULTS

A search of patient records identified 15 pregnancies in 12 women with CFRDM during the study period. CFRDM was diagnosed pre-conception in ten of the 15 pregnancies. Median neonatal weight at birth was lower in women with CFRDM diagnosed pre-conception compared to women diagnosed during pregnancy (2.8 vs. 3.02 kg). The median weight gain in women with CFRDM diagnosed pre-conception was 10.9 kg compared to 11.9 kg for those diagnosed during pregnancy. The majority of women (62.5%) with CFRDM diagnosed pre-conception delivered via caesarean section. Admission for CF exacerbations during pregnancy in women with CFRDM diagnosed pre-conception was very common (87.5%) compared with 75% of those diagnosed during their pregnancy.

CONCLUSION

Women diagnosed with CFRDM were likely to require caesarean section, to be treated with insulin, and to be frequently admitted to hospital for CF exacerbations. Our review highlights the importance of good glucose control, stable cystic fibrosis before pregnancy and a multidisciplinary team approach.

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343-3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter-gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026-1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

The prevalence of alpha-1 antitrypsin deficiency in Ireland

Background

Alpha-1 antitrypsin deficiency (AATD) results from mutations in the SERPINA1 gene and classically presents with early-onset emphysema and liver disease. The most common mutation presenting with clinical evidence is the Z mutation, while the S mutation is associated with a milder plasma deficiency. AATD is an under-diagnosed condition and the World Health Organisation recommends targeted detection programmes for AATD in patients with chronic obstructive pulmonary disease (COPD), non-responsive asthma, cryptogenic liver disease and first degree relatives of known AATD patients.

Methods

We present data from the first 3,000 individuals screened following ATS/ERS guidelines as part of the Irish National Targeted Detection Programme (INTDP). We also investigated a DNA collection of 1,100 individuals randomly sampled from the general population. Serum and DNA was collected from both groups and mutations in the SERPINA1 gene detected by phenotyping or genotyping.

Results

The Irish National Targeted Detection Programme identified 42 ZZ, 44 SZ, 14 SS, 430 MZ, 263 MS, 20 IX and 2 rare mutations. Analysis of 1,100 randomly selected individuals identified 113 MS, 46 MZ, 2 SS and 2 SZ genotypes.

Conclusion

Our findings demonstrate that AATD in Ireland is more prevalent than previously estimated with Z and S allele frequencies among the highest in the world. Furthermore, our targeted detection programme enriched the population of those carrying the Z but not the S allele, suggesting the Z allele is more important in the pathogenesis of those conditions targeted by the detection programme.

APCR, factor V gene known and novel SNPs and adverse pregnancy outcomes in an Irish cohort of pregnant women

Background

Activated Protein C Resistance (APCR), a poor anticoagulant response of APC in haemostasis, is the commonest heritable thrombophilia. Adverse outcomes during pregnancy have been linked to APCR. This study determined the frequency of APCR, factor V gene known and novel SNPs and adverse outcomes in a group of pregnant women.

Methods

Blood samples collected from 907 pregnant women were tested using the Coatest^® Classic and Modified functional haematological tests to establish the frequency of APCR. PCR-Restriction Enzyme Analysis (PCR-REA), PCR-DNA probe hybridisation analysis and DNA sequencing were used for molecular screening of known mutations in the factor V gene in subjects determined to have APCR based on the Coatest^® Classic and/or Modified functional haematological tests. Glycosylase Mediated Polymorphism Detection (GMPD), a SNP screening technique and DNA sequencing, were used to identify SNPs in the factor V gene of 5 APCR subjects.

Results

Sixteen percent of the study group had an APCR phenotype. Factor V Leiden (FVL), FV Cambridge, and haplotype (H) R2 alleles were identified in this group. Thirty-three SNPs; 9 silent SNPs and 24 missense SNPs, of which 20 SNPs were novel, were identified in the 5 APCR subjects. Adverse pregnancy outcomes were found at a frequency of 35% in the group with APCR based on Classic Coatest^® test only and at 45% in the group with APCR based on the Modified Coatest^® test. Forty-eight percent of subjects with FVL had adverse outcomes while in the group of subjects with no FVL, adverse outcomes occurred at a frequency of 37%.

Conclusions

Known mutations and novel SNPs in the factor V gene were identified in the study cohort determined to have APCR in pregnancy. Further studies are required to investigate the contribution of these novel SNPs to the APCR phenotype. Adverse outcomes including early pregnancy loss (EPL), preeclampsia (PET) and intrauterine growth restriction (IGUR) were not significantly more frequent in subjects with APCR compared to normal pregnant women however Pregnancy induced hypertension (PIH) was found to be associated with FVL in our study group.

Analysis of the CFTR gene in Iranian cystic fibrosis patients: identification of eight novel mutations

BACKGROUND

Cystic fibrosis (CF) is the most common inherited disorder in Caucasian populations, with over 1400 mutations identified in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. Mutations in the CFTR gene may be also causative for CBAVD (Congenital Bilateral Absence of the Vas Deferens). The type and distribution of mutations varies widely between different countries and/or ethnic groups, and is relatively unknown in Iran. We therefore performed a comprehensive analysis of the CFTR gene in Iranian CF patients.

METHODS

69 Iranian CF patients, and 1 CBAVD patient, were analysed for mutations in the complete coding region, and its exon/intron junctions, of their CFTR genes, using different methods, such as ARMS (amplification refractory mutation system)-PCR, SSCP (single stranded conformation polymorphism) analysis, restriction enzyme digestion analysis, direct sequencing, and MLPA (Multiplex Ligation-mediated Probe Amplification).

RESULTS

CFTR mutation analysis revealed the identification of 37 mutations in 69 Iranian CF patients. Overall, 81.9% (113/138) CFTR genes derived from Iranian CF patients could be characterized for a disease-causing mutation. The CBAVD patient was found to be homozygous for the p.W1145R mutation. The most common mutations were p.F508del (DeltaF508) (18.1%), c.2183_2184delAAinsG (2183AA>G) (6.5%), p.S466X (5.8%), p.N1303K (4.3%), c.2789+5G>A (4.3%), p.G542X (3.6%), c.3120+1G>A (3.6%), p.R334W (2.9%) and c.3130delA (2.9%). These 9 types of mutant CFTR genes totaled for 52% of all CFTR genes derived from the 69 Iranian CF patients. Eight mutations, c.406-8T>C, p.A566D, c.2576delA, c.2752-1_2756delGGTGGCinsTTG, p.T1036I, p.W1145R, c.3850-24G>A, c.1342-?_1524+?del, were found for the first time in this study.

CONCLUSIONS

We identified 37 CFTR mutations in 69 well characterized Iranian CF patients, obtaining a CFTR mutation detection rate of 81.9%, the highest detection rate obtained in the Iranian population so far. These findings will assist in genetic counseling, prenatal diagnosis and future screening of CF in Iran.

Pulmonary abnormalities on high-resolution CT demonstrate more rapid decline than FEV1 in adults with cystic fibrosis

BACKGROUND

FEV1 may remain stable while high-resolution CT (HRCT) appearances deteriorate in children with cystic fibrosis (CF). However, spirometry results commonly decline in older age groups.

OBJECTIVES

To compare the rate of decline in HRCT abnormalities and spirometry results over time in an adult cohort with CF.

METHODS

The HRCT scans of 39 consecutive patients (19 males and 20 females; mean age, 22 years; range, 16 to 48 years) with two HRCT scans > 18 months apart were randomly and blindly scored using a modified Bhalla scoring system by two independent chest radiologists. Age, body mass index, spirometry, and sputum cultures were recorded at the time of both HRCTs. Rates of change in clinical parameters and HRCT abnormalities were calculated and compared using repeated-measures analysis of variance.

RESULTS

Mean FEV1 declined at a rate of - 2.3% per year, while mean HRCT total score declined at a rate of -2.7% per year. Several individual HRCT abnormalities as well as HRCT total scores declined significantly faster than FEV1 (p < 0.001). Six patients showed stable spirometry results but worsening HRCT scores. Mucus plugging and extent of bronchiectasis deteriorated at a more rapid rate in the group with mildly impaired lung function. Air trapping, collapse/consolidation, peribronchial thickening, severity of bronchiectasis, and generations of bronchial divisions involved deteriorated at a more rapid rate in the group with moderate-to-severely impaired lung function.

CONCLUSIONS

Adult CF patients have more rapid rates of decline in HRCT abnormalities than in spirometry results. Individual HRCT abnormalities decline at different rates depending on the degree of lung function impairment.

A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population

A single population test applied in a genomic context reveals evidence of selection on three biologically interesting genes in the Irish population.

Background

In this study we present a single population test (Ewens-Waterson) applied in a genomic context to investigate the presence of recent positive selection in the Irish population. The Irish population is an interesting focus for the investigation of recent selection since several lines of evidence suggest that it may have a relatively undisturbed genetic heritage.

Results

We first identified outlier single nucleotide polymorphisms (SNPs), from previously published genome-wide data, with high F_ST branch specification in a European-American population. Eight of these were chosen for further analysis. Evidence for selective history was assessed using the Ewens-Watterson's statistic calculated using Irish genotypes of microsatellites flanking the eight outlier SNPs. Evidence suggestive of selection was detected in three of these by comparison with a population-specific genome-wide empirical distribution of the Ewens-Watterson's statistic.

Conclusion

The cystic fibrosis gene, a disease that has a world maximum frequency in Ireland, was among the genes showing evidence of selection. In addition to the demonstrated utility in detecting a signature of natural selection, this approach has the particular advantage of speed. It also illustrates concordance between results drawn from alternative methods implemented in different populations.

Hyperpolarized 3helium magnetic resonance ventilation imaging of the lung in cystic fibrosis: comparison with high resolution CT and spirometry

The purpose of this study was to compare hyperpolarized 3helium magnetic resonance imaging (3He MRI) of the lungs in adults with cystic fibrosis (CF) with high-resolution computed tomography (HRCT) and spirometry. Eight patients with stable CF prospectively underwent 3He MRI, HRCT, and spirometry within 1 week. Three-dimensional (3D) gradient-echo sequence was used during an 18-s breath-hold following inhalation of hyperpolarized 3He. Each lung was divided into six zones; 3He MRI was scored as percentage ventilation per lung zone. HRCT was scored using a modified Bhalla scoring system. Univariate (Spearman rank) and multivariate correlations were performed between 3He MRI, HRCT, and spirometry. Results are expressed as mean+/-SD (range). Spirometry is expressed as percent predicted. There were four men and four women, mean age = 31.9+/-9 (20-46). Mean forced expiratory volume in 1 s (FEV)1 = 52%+/-29 (27-93). Mean 3He MRI score = 74%+/-25 (55-100). Mean HRCT score = 48.8+/-24 (13.5-83). The correlation between 3He MRI and HRCT was strong (R = +/-0.89, p < 0.001). Bronchiectasis was the only independent predictor of 3He MRI; 3He MRI correlated better with FEV1 and forced vital capacity (FVC) (R = 0.86 and 0.93, p < 0.01, respectively) than HRCT (R = +/-0.72 and +/-0.81, p < 0.05, respectively). This study showed that 3He MRI correlates strongly with structural HRCT abnormalities and is a stronger correlate of spirometry than HRCT in CF.

Thin-Section CT in Patients with Cystic Fibrosis: Correlation with Peak Exercise Capacity and Body Mass Index

PURPOSE

To evaluate whether thin-section chest computed tomographic (CT) findings correlate with exercise capacity, body mass index (BMI), dyspnea, and leg discomfort in patients with cystic fibrosis (CF).

MATERIALS AND METHODS

Institutional ethics committee approval was obtained, and patients provided written informed consent. Twenty-two patients (13 male and nine female patients; mean age, 22 years +/- 5.9; age range, 17-41 years) with stable CF underwent thin-section CT and exercise testing on a cycle ergometer. Three radiologists blinded to the clinical severity of disease and the spirometric findings of all patients independently and randomly scored all scans with a modified Bhalla scoring system. The primary measurement of the outcome of exercise testing was percentage of predicted peak O2 uptake. Univariate (Spearman rank correlation) and multivariate analyses were used to compare thin-section CT, clinical (age, sex, spirometric data, and BMI), and exercise measurements.

RESULTS

The correlation between total thin-section CT score and percentage of predicted peak O2 uptake was stronger than the correlation between the percentage of predicted peak O2 uptake and any clinical measurement (R = -0.60, P < .01). The thin-section CT structural abnormalities that had the strongest correlation with percentage of predicted peak O2 uptake were severity of bronchiectasis and presence of sacculations or abscesses (R = -0.70 and -0.71, respectively; P < .01). Multivariate analysis showed total thin-section CT score to be the only significant predictor of exercise capacity, accounting for 42% of the variance in percentage of predicted peak O2 uptake.

CONCLUSION

In patients with CF, the correlation between thin-section CT score and exercise limitation is stronger than that between spirometry results or BMI and exercise limitation.

Giant inflammatory polyposis coli as a manifestation of Crohn's disease in patients with coexistent cystic fibrosis

Crohn's disease (CD) arising in children with cystic fibrosis (CF) is well recognized. Indeed, reports suggest that CD is significantly more common in patients with CF than in the general population. Giant inflammatory polyposis is a rare manifestation of idiopathic inflammatory bowel disease and may complicate both ulcerative colitis and CD. Giant inflammatory polyposis has not been specifically reported in patients with coexistent CF and CD. Herein, we report the occurrence of giant inflammatory polyposis in 2 boys attending a tertiary care hospital, with an established diagnosis of CF who subsequently developed CD. Both boys required surgical treatment for CD. In addition to classical features of CD, both colonic resection specimens showed giant inflammatory polyposis. The appearances were modified by the presence of a layer of thick mucus. It is suggested that the coexistence of CF in patients with CD may predispose to the development of giant inflammatory polyposis. In addition to contributing to their development, it also appears that there is a propensity for CF to alter the morphological appearance of giant inflammatory polyposis. This may lead to diagnostic confusion when examining endoscopic biopsies.