Alpha1-antitrypsin deficiency: epidemiology and prevalence

Computational Tools to Assist in Analyzing Effects of the SERPINA1 Gene Variation on Alpha-1 Antitrypsin (AAT)

In the rapidly advancing field of bioinformatics, the development and application of computational tools to predict the effects of single nucleotide variants (SNVs) are shedding light on the molecular mechanisms underlying disorders. Also, they hold promise for guiding therapeutic interventions and personalized medicine strategies in the future. A comprehensive understanding of the impact of SNVs in the SERPINA1 gene on alpha-1 antitrypsin (AAT) protein structure and function requires integrating bioinformatic approaches. Here, we provide a guide for clinicians to navigate through the field of computational analyses which can be applied to describe a novel genetic variant. Predicting the clinical significance of SERPINA1 variation allows clinicians to tailor treatment options for individuals with alpha-1 antitrypsin deficiency (AATD) and related conditions, ultimately improving the patient's outcome and quality of life. This paper explores the various bioinformatic methodologies and cutting-edge approaches dedicated to the assessment of molecular variants of genes and their product proteins using SERPINA1 and AAT as an example.

Population genetic testing and SERPINA1 sequencing identifies unidentified alpha-1 antitrypsin deficiency alleles and gene-environment interaction with hepatitis C infection

Alpha-1 antitrypsin deficiency (AATD), a relatively common autosomal recessive genetic disorder, is underdiagnosed in symptomatic individuals. We sought to compare the risk of liver transplantation associated with hepatitis C infection with AATD heterozygotes and homozygotes and determine if SERPINA1 sequencing would identify undiagnosed AATD. We performed a retrospective cohort study in a deidentified Electronic Health Record (EHR)-linked DNA biobank with 72,027 individuals genotyped for the M, Z, and S alleles in SERPINA1. We investigated liver transplantation frequency by genotype group and compared with hepatitis C infection. We performed SERPINA1 sequencing in carriers of pathogenic AATD alleles who underwent liver transplantation. Liver transplantation was associated with the Z allele (ZZ: odds ratio [OR] = 1.31, p<2e-16; MZ: OR = 1.02, p = 1.2e-13) and with hepatitis C (OR = 1.20, p<2e-16). For liver transplantation, there was a significant interaction between genotype and hepatitis C (ZZ: interaction OR = 1.23, p = 4.7e-4; MZ: interaction OR = 1.11, p = 6.9e-13). Sequencing uncovered a second, rare, pathogenic SERPINA1 variant in six of 133 individuals with liver transplants and without hepatitis C. Liver transplantation was more common in individuals with AATD risk alleles (including heterozygotes), and AATD and hepatitis C demonstrated evidence of a gene-environment interaction in relation to liver transplantation. The current AATD screening strategy may miss diagnoses whereas SERPINA1 sequencing may increase diagnostic yield for AATD, stratify risk for liver disease, and inform clinical management for individuals with AATD risk alleles and liver disease risk factors.

Development of genomic DNA reference materials for genetic testing of disorders common in people of ashkenazi jewish descent

Many recessive genetic disorders are found at a higher incidence in people of Ashkenazi Jewish (AJ) descent than in the general population. The American College of Medical Genetics and the American College of Obstetricians and Gynecologists have recommended that individuals of AJ descent undergo carrier screening for Tay Sachs disease, Canavan disease, familial dysautonomia, mucolipidosis IV, Niemann-Pick disease type A, Fanconi anemia type C, Bloom syndrome, and Gaucher disease. Although these recommendations have led to increased test volumes and number of laboratories offering AJ screening, well-characterized genomic reference materials are not publicly available. The Centers for Disease Control and Prevention-based Genetic Testing Reference Materials Coordination Program, in collaboration with members of the genetic testing community and Coriell Cell Repositories, have developed a panel of characterized genomic reference materials for AJ genetic testing. DNA from 31 cell lines, representing many of the common alleles for Tay Sachs disease, Canavan disease, familial dysautonomia, mucolipidosis IV, Niemann-Pick disease type A, Fanconi anemia type C, Bloom syndrome, Gaucher disease, and glycogen storage disease, was prepared by the Repository and tested in six clinical laboratories using three different PCR-based assay platforms. A total of 33 disease alleles was assayed and 25 different alleles were identified. These characterized materials are publicly available from Coriell and may be used for quality control, proficiency testing, test development, and research.

Prevalence of common HFE and SERPINA1 mutations in patients with hepatocellular carcinoma in a Moroccan population

BACKGROUND

Hereditary hemochromatosis and SERPINA1 mutation were reported to affect liver functions. Our objective was to estimate the prevalence of HFE and SERPINA1 (formerly known as alpha1-antitrypsin, AAT) mutations and assess their influence on hepatocellular carcinoma development.

METHODS

This study included 222 controls and 96 cases with hepatocellular carcinoma. PCR-RFLP was used to characterize S and Z alleles in SERPINA1, as well as C282Y/H63D alleles of HFE.

RESULTS

In healthy subjects and hepatocellular carcinoma patients as well, no homozygotes for the C282Y mutation were found. In controls, heterozygosity and homozygosity for the H63D mutation were 27 and 0.9%, respectively. Among patients, homozygosity for the H63D mutation was 3.1%, whereas heterozygosity for C282Y and H63D was 2.1 and 35.4%, respectively. Interestingly, albeit it does not reach significance (p=0.062), H63D was more prevalent in hepatocellular carcinoma patients than in controls (38.5 vs. 27.9%, respectively). The association was stronger when considering only male patients with hepatocellular carcinoma (47.1 vs. 23.6, p=0.001). Allele frequencies of S and Z in controls were 0.45% (95% CI=0.2-1.07) and 0.22% (95% CI=0.2-0.6), respectively, and 1 for S and 0% for Z in HCC. No significant difference was found between cases and controls.

CONCLUSIONS

We provide a novel appraisal of HFE and SERPINA1 mutations prevalence in the Moroccan population. Results are consistent with the worldwide spread of the H63D and S mutation and the north European restriction of the C282Y and Z. Our results show that H63D carriage is increased among hepatocellular carcinoma patients, suggesting that it may confer an increased susceptibility to hepatocellular carcinoma even in a heterozygous state. On the contrary, HFE C282Y and SERPINA1 mutations do not contribute to hepatocellular carcinoma development.

Alpha-antitrypsin genotypes in Korean patients with chronic obstructive pulmonary disease

OBJECTIVE

Alpha1-antitrypsin (AAT) deficiency is a recognized susceptible factor for chronic obstructive pulmonary disease (COPD) in Western countries, but its importance in Korea is unclear. To date, no definitive case of alpha1-antitrypsin deficiency has been reported in Korea. This study aimed to clarify whether alpha1-antitrypsin deficiency exists and to determine the distribution of alpha1-antitrypsin alleles in the Korean population.

METHODOLOGY

The serum concentrations of alpha1-antitrypsin were determined and polymorphisms of the alpha1-antitrypsin gene in 114 COPD patients and in 196 healthy controls were examined. Phenotyping by isoelectric focusing and the genotyping of alpha1-antitrypsin gene by polymerase chain reaction and restriction fragment length polymorphism were performed.

RESULTS

No alpha1-antitrypsin level abnormality was found in the patients. M1(Val)/M1(Val) was found to be the most frequent genotype in both groups (69.2% and 66.8%, respectively), and M1(Val) the most frequent allele. The distributions of alpha1-antitrypsin alleles were similar in the patient and control groups, and no S or Z allele was found.

CONCLUSION

Alpha1-antitrypsin deficiency is unlikely to be an important cause of chronic obstructive pulmonary disease in the Korean population.

[PI*S and PI*Z alpha 1-antitrypsin deficiency: estimated prevalence and number of deficient subjects in Spain]

BACKGROUND AND OBJECTIVE

Alpha-1-antitrypsin deficiency (AATD) is an hereditary disorder with increased risk of pulmonary emphysema and chronic liver diseases in children and adults. Since it is possible currently in Spain to apply alpha-1-antitrypsin replacement therapy to AATD patients, the objective of this study was to calculate the total number of subjects affected by PIS and PIZ AATD, and its phenotypic distribution. SUBJECTS, MATERIAL AND METHOD: Selection of published studies on allelic frequencies PIS and PIZ according to the following criteria: a) alpha-1-antitrypsin phenotyping performed by isoelectrofocusing; b) rejection of "screening studies"; c) statistic precision factor score of 5, and d) samples representative of the Spanish general population.

RESULTS

Four out 34 cohorts were selected. Mean gene frequencies (per 1,000) were: 104 (95% confidence interval [CI], 96-113) for PI*S and 17 (95% CI, 14-21) for PI*Z. These data indicated that it would exist in Spain 9,173,181 AATD subjects (95% CI, 9,167,966-9,178,398), with the following phenotypic distribution: 7,358,263 (95% CI, 6,696,222-8, 072,328) for PIMS; 1,222,041 (95% CI, 972,767-1,539,805) for PIMZ; 436,023 (95% CI, 369,057-514,244) for PISS; 144,827 (95% CI, 107,227-195,038) for PISZ; and 12,026 (95% CI, 7,788-18,493) for PIZZ. The global prevalence was 1 out of 4.4 individuals, with the following distribution: PIMS 1/5; PIMZ 1/33; PISS 1/92; PISZ 1/278; and PIZZ 1/3,344.

CONCLUSIONS

AATD is a frequent but underdiagnosed disease in Spain.

AAT as a diagnostic tool

Serum alpha-1-antitrypsin (AAT) concentration can be affected by both inflammatory and non-inflammatory conditions. This paper characterizes the nature of AAT in physiology and pathologic deficiency and increasing states. The relationships between the AAT concentration in different clinical materials (serum, urine, faeces) and various diseases connected with different organs were analyzed.

Genetic epidemiology of alpha-1 antitrypsin deficiency in North America and Australia/New Zealand: Australia, Canada, New Zealand and the United States of America

Alpha-1-antitrypsin deficiency (AAT deficiency) is one of the most common serious hereditary disorders in the world, as its affects all major racial subgroups worldwide, and there are an estimated 120.5 million carriers and deficient subjects worldwide. This genetic disease is related to susceptibility for development of jaundice in infants, liver disease in children and adults and pulmonary emphysema in adults. Moreover, AAT deficiency carrier phenotypes (PiMS and PiMZ) and deficiency allele phenotypes (PiSS, PiSZ and PiZZ) are suspected to predispose subjects to a variety of other adverse health effects. Because there is a limited database on the number of individuals affected by this disease worldwide, we have collected data on control cohorts in genetic epidemiological studies published on case-control studies in the peer-reviewed literature worldwide. Based on these data, we estimated the numbers of carriers and deficiency allele combinations for the two most common defective alleles, namely PiS and PiZ in 58 countries worldwide. The present paper focuses on the distribution of the PiS and PiZ deficiency alleles in Australia, Canada, New Zealand and the United States of America. A total of 31,042,232 individuals at risk for adverse health effects have been calculated in these four countries: 2,144,158 in Australia, 3,258,564 in Canada, 430,922 in New Zealand and 24,909,548 in the United States of America. The prevalences for all five phenotypic classes of AAT deficiency in each of these countries is as follows: Australia 1 out of 8.9, Canada 1 out of 9.8, New Zealand 1 out of 8.5 and the United States of America 1 out of 11.3. The geographical distribution of individual control cohorts and estimates of the numbers of carriers and deficiency allele phenotypes in each of these four countries are given in individual tables.

Influence of deficient alpha1-anti-trypsin phenotypes on clinical characteristics and severity of asthma in adults

Severe alpha1-anti-trypsin (AAT) deficiency implies a high risk of pulmonary emphysema development. The possible relationship between partial deficiencies of this enzyme and bronchial asthma remains controversial. The objective of this study was to ascertain the distribution of AAT phenotypes in a non-selected asthmatic patient population. Across-sectional study on a sample of 111 patients with asthma was carried out. Demographic and clinical variables were collected with serum IgE concentrations, plasma eosinophil number and serum AAT concentrations determined, together with the Pi phenotype. Asthma was mild in 36 (32.4%) patients, moderate in 45 (40.5%) and severe in 30 (27%). No differences were observed in eosinophil count or serum IgE or AAT concentrations among patients with different degrees of severity. Twenty-two (19.8%) asthmatics with deficient phenotypes for AAT were identified, distributed equally in all severity stages of the disease. No significant differences were found in clinical and functional characteristics, or in asthma morbidity between PiMM and PiMS patients or the heterozygote group (PiMS and PiMZ). Eosinophil count and IgE concentrations did not differ significantly between asthmatics with normal phenotype and heterozygotes. In conclusion, the distribution of AAT phenotypes in asthmatic patients did not differ from that found in the general population. Heterozygote phenotypes for the deficiency do not appear to confer greater severity or different clinical expression of asthma in adults.

Distribution of alpha1-antitrypsin PI S and PI Z frequencies in countries outside Europe: a meta-analysis

The objective of the present study was to review published surveys on allelic frequencies S and Z in countries outside Europe to evaluate the validity of the reported data. Studies on the topic, published from 1965 to May 2001, were retrieved using MEDLINE and bibliographic reference consultations. The criteria for the selection of the studies were the following: 1) sample size >or=250 individuals; 2) alpha1-antitrypsin phenotype determination performed by means of crossed antigen-antibody, isoelectric focusing in polyacrylamide gels, or polymerase chain reaction (PCR); 3) PI type determination performed without any previous screening procedure; 4) S and Z 95% CI of the reported outcomes within the limits of a calculated coefficient of variation. Forty-three out of 85 studies comply with the established criteria for being analysed. Worldwide maps of geographical distributions of PI S and PI Z frequencies have been designed by the authors by adding the data provided by these 43 selected studies to the 70 reported in a recent European meta-analysis.