Efficient detection of Mediterranean β-thalassemia mutations by multiplex single-nucleotide primer extension

ANXA5 and VEGFA Gene Variants in Women with Early Pregnancy Losses from North Macedonia

Early pregnancy loss (EPL) is the most common pregnancy complication, found in approximately 15% of all clinically recognized pregnancy complications. Up to date, various maternal as well as fetal factors are reported as a cause of EPLs. However, in approximately 50% of EPL cases, the exact cause is not clearly identified and these cases are referred as idiopathic. The aim of our study was to examine the association of four distinct variants in the ANXA5 gene and two variants within the VEGFA gene in a cohort of women with EPLs from North Macedonia. This group was compared to a control group of women matched by ethnic background without pregnancy loss and at least one live birth. We also aimed to establish an effective and cost-efficient method for their detection based on multiplex single-base extension. Among 190 women experiencing EPLs, and 190 samples from women without a history of pregnancy loss (control group), our results demonstrated a statistically significant prevalence of heterozygotes for the M2/ANXA5 haplotype in women with EPLs, compared to the control group (p=0.0006). In the analyses comparing genotypic frequencies for the variants in the VEGFA gene, higher frequencies were generally observed among women experiencing EPLs, however without statistical significance. Our study aligns with multiple studies showing that M2 and M1 ANXA5 haplotypes are more prevalent in patients with pregnancy loss and presents an affordable genotyping technique for the specific ANXA5 and VEGFA variants.

Global distribution of β-thalassemia mutations: An update

One excellent illustration of how a single gene abnormality may result in a spectrum of disease incidence is the incredible phenotypic variety of β-thalassemia, which spans from severe anemia and transfusion needs to an utterly asymptomatic sickness. However, genetic causes of β-thalassemia and how the anemia's severity might be altered at various stages in its pathophysiology have been well investigated. There are currently known to be more than 350 mutations that cause genetic disease. However only 20 β thalassemia mutations account for more than 80% of the β thalassemia mutation across the globe due to phenomenon of geographical clustering where each population has a few common mutations together with a varying number of rare ones. Due to migration of the population, the spectrum of thalassemia mutation in changing from time to time. In this review, efforts are made to collate β globin gene mutations in different countries and populations.

Identification of thalassemia gene cluster deletion by long-read whole-genome sequencing (LR-WGS)

INTRODUCTION

At present, a variety of molecular detection methods are obtained to diagnose thalassemia accurately. Although exome sequencing or specific panels have been widely used in clinical diagnosis of genetic diseases, the positive rate is about 25%-30%. Because the detection range is limited to exons and splice sites, and the read length is usually 100-150 bp, there are limitations in the detection of globin gene clusters with pseudogenes.

METHODS

In this study, seven thalassemia patients were selected to perform whole-genome sequencing (WGS) with long read at 400 bp to make accurate detection for thalassemia deletions. And we used PCR and Sanger sequencing to confirm the gene deletions in the patients.

RESULTS

WGS analysis detected a rare 172 kb deletion on the α-globin gene cluster at chr16: 57 009-330 001, 19 kb deletion at chr16: 215 396-234 699, 11 kb deletion at chr16:220 861-231 981; and 27 kb deletion on the β-globin gene deletion at chr11: 5 222 878-5 250 288, 21.4 kb deletion at chr11: 5 236 361-5 257 771, 78.9 kb deletion at chr11: 5 191 121-5 270 050. All the seven patients carried heterozygous deletions, including three in α-gene cluster, three in β-gene cluster, and one in both globin clusters.

CONCLUSION

Our results indicate that long-read WGS will be beneficial to the diagnosis of genetic diseases with pseudogenes or highly duplicated sequences and will enable clinical geneticists to inform high-risk couples and provide prenatal diagnosis.

First Cases of Hb Agrinio Described in Patients from the Republic of Macedonia

Previous molecular analyses of α-thalassemia (α-thal) in the Republic of Macedonia have identified the following genetic defects: -α^3.7 (rightward), -(α)^20.5 and - -^MED I deletions and Hb Icaria [α142, Term→Lys (α2), HBA2: c.427T>A] and polyadenylation signal (polyA) [AATAAA>AATGAA (α2), HBA2: c.*92A>G] point mutations. Here, we report two unrelated patients from the Romani population in the Republic of Macedonia, homozygotes for the α2-globin gene variant Hb Agrinio [α29(B10)Leu→Pro; HBA2: c.89T>C]. To date, Hb Agrinio has been described only in individuals of Greek, Cypriot and Spanish origin. Both of our patients had early presentation of the disease (3.5 years and 2 months, respectively) with frequent blood transfusions from early infancy. They have a severe intermediate phenotype of thalassemia (Hb H disease) with hemoglobin (Hb) levels of 7.8 and 7.7 g/dL, respectively. Although the HBA2: c.89T>C mutation results in an α⁺ allele, the severe phenotype of the homozygotes is due to the production of hyperunstable α chains that undergo post translational precipitation. This leads to a greater degree of red cell damage and hemolytic anemia. The detection of Hb Agrinio in two unrelated families of Romani ethnic origin, may suggest it is a founder mutation in this population living in the Republic of Macedonia. Considering the severity of the clinical presentation of the homozygotes or compound heterozygotes for this rare Hb variant, a targeted molecular screening for Hb Agrinio mutation carriers should be considered in all patients of Romani ethnic origin with manifested microcytosis.

Presence of the IVS-I-6-Mutated Allele in Beta-Thalassemia Major Patients Correlates with Extramedullary Hematopoiesis Incidence

Extramedullary hematopoiesis (EMH) results from the extension of hematopoietic tissue beyond the confines of the bones. Since the initiation of regular transfusion programs from an early age for all thalassemia major (ΤΜ) patients, EMH has not been considered a clinical issue anymore. The present study aims to record the prevalence of EMH in chronically transfused ΤΜ patients followed at our institution and to investigate possible risk factors associated with its occurrence. The project was designed as a retrospective, nonexperimental, descriptive, exploratory study. In total, the study enrolled 104 patients. EMH was revealed in 15/104 (14%) patients. The presence of intravening sequence (IVS)-I-6 was significantly related with the development of EMH (p < 0.05). No other demographic or biological factor studied was found to be related with the presence of EMH. The study stresses a profound incidence of asymptomatic EMH in a solid group of well-transfused ΤΜ patients. Given the high incidence of the IVS-I-6 allele in the Mediterranean and Middle Eastern region, high-quality, prospective, multicenter studies could confirm the association of EMH occurrence with the presence of the IVS-I-6 mutation and further evaluate the exact role of this mutation in the EMH process.

SNaPshot assay for the detection of the most common CFTR mutations in infertile men

Congenital bilateral absence of vas deferens (CBAVD) is the most common CFTR-related disorder (CFTR-RD) that explains about 1-2% of the male infertility cases. Controversial data have been published regarding the involvement of CFTR mutations in infertile men with non-obstructive azoospermia and oligozoospermia. Here, we describe single base extension (SNaPshot) assay for detection of 11 common CFTR mutations: F508del, G542X, N1303K, 621+1G->T, G551D, R553X, R1162X, W1282X, R117H, 2184insA and 1717-1G->A and IVS8polyT variants. The assay was validated on 50 previously genotyped samples and was used to screen a total of 369 infertile men with different impairment of spermatogenesis and 136 fertile controls. Our results show that double heterozygosity of cystic fibrosis (CF) and CFTR-related disorder (CFTR-RD) mutations are found in a high percentage (22.7%) of infertile men with obstructive azoospermia, but not in other studied groups of infertile men. The SNaPshot assay described here is an inexpensive, fast and robust method for primary screening of the most common CFTR mutations both in patients with classical CF and CFTR-RD. It can contribute to better understanding of the role of CFTR mutations in impaired spermatogenesis, ultimately leading to improved management of infertile men.

Novel Βeta (β)-Thalassemia Mutation in Turkish Children

Beta (β)-thalassemia is the most frequently observed hereditary blood disorder in the world. It is characterized by deficiency of hemoglobin β-globin gene and is also a profoundly heterogeneous both at the molecular and clinical level. In the case of β-thalassemia, there is reduced (β(+) type) or absent (β(o) type) synthesis of the beta chains of hemoglobin. β-Thalassemia clinically occurs in three main forms: major, intermedia and minor according to requirement of transfusion. The objective of this study was to evaluate β-thalassemia mutations in 89 patients ranging from 2 months to 16 years of age, who enrolled to Medical School Research and Training Hospital, Gaziantep University. The direct DNA sequence analysis was performed for mutation scanning of β-globin gene. 89 children with β-Thalassemia including all types were analyzed, 16 different β-thalassemia mutations were detected. We have also identified a novel mutation (HBB.c.-80delT, rs397509430) in the promoter region (-30 TATA box) of β-globin gene, and clinical data of patient having novel mutation was given. The β-Thalassemia mutations were determined as β-Thalassemia major type in 42 patients (47.19 %), β-Thalassemia intermedia in 4 (4.49 %), β-Thalassemia minor in 43, (48.31 %) patients. The most frequent mutation was IVS I-110 G>A, followed by IVS I-1 G>A, IVS I-6 T>C, IVS II-1 G>A, respectively.