Thalassaemia intermedia caused by coinheritance of a β‐thalassaemia mutation and a de novo duplication of α‐globin genes in the paternal allele

Heterozygous Beta Thalassemia with Segmental Duplication of chr16p13.3 Leading to Thalassemia Intermedia Phenotype: A Report of 2 Cases with Review of Literature

Heterozygous β-thalassemia is typically asymptomatic, but when accompanied by α-globin gene multiplication, patients may exhibit clinical symptoms. We present two rare cases of heterozygous β-thalassemia where segmental duplications on chr16p13.3 led to increased α-globin gene copies, resulting in a thalassemia intermedia phenotype. One patient exhibited a novel de-novo duplication spanning 2.57 MB, while the other had a 173.8 KB duplication at the chr16p13.3 locus. These two cases are presented to underscore the significance of thorough and systematic evaluation in diagnosing rare forms of thalassemia accurately. Our study also compiles all reported cases of heterozygous β-thalassemia with large segmental duplications on chr16p13.3, leading to an excess of α-globin genes. A total of ten studies have been published in the literature so far. Importantly, the 2.57 MB segmental duplication identified in our study is a novel variant not previously documented in the literature.

Application value of long-read sequencing in full characterization of thalassemia-associated structural variations: identifying a novel large segmental duplication and literature review

BACKGROUND

Thalassemia is one of the most prevalent monogenic disorders in tropical and subtropical regions, imposing significant familial and social burdens on local populations. It is caused by point mutations or structural variations (SVs) in the α- or β-globin gene clusters. Due to the complex structure, full characterization of SVs has always been the focus and difficulty of molecular diagnosis of thalassemia patients.

METHODS

Peripheral blood of a Chinese boy with β-thalassemia intermedia phenotype and his family members were collected. Multiplex ligation dependent probe amplification (MLPA), long-read sequencing (LRS) and Sanger sequencing were used to analyze the variant in this family.

RESULTS

A novel large duplication (αααα280) was identified using LRS technique and validated by Sanger sequencing. Additionally, we conducted a systematic review of known SVs and evaluated the advantages and disadvantages of various methods in analyzing complex SVs.

CONCLUSIONS

Our study identified a novel SV in the α-globin gene cluster and demonstrated that LRS was a superior approach for detecting novel rare SVs. The appropriate use of LRS significantly improves diagnostic accuracy when conventional methods are not capable of completely identifying complex SVs.

Identification of a β-Globin Gene Mutation with the Genotype β-28(A > G), IVS-I-5(G > A)/βCD 71/72(+A) Using Third-Generation Sequencing

This study presents the hematological and genetic analysis of a child with severe β-thalassemia harboring triple heterozygous mutations. The child, diagnosed with anemia at the age of 1 year, became transfusion-dependent and maintained a hemoglobin level of 72.00-84.00 g/L following regular blood transfusions. At the age of 9 years, genetic analysis was conducted using PCR-reverse dot blot (PCR-RDB), Sanger sequencing, and third-generation nanopore sequencing. Sanger sequencing identified a triple heterozygous mutation in the β-globin gene: -28(A > G) (HBB:c.-78A > G), IVS-I-5(G > A) (HBB:c0.92 + 5G > A), and CD 71/72(+A) (HBB:c.216_217insA). Nanopore sequencing further confirmed the genotype as β-28(A>G), IVS-I-5(G>A)/βCD 71/72(+A). The combination of these mutations represents a rare β-thalassemia genotype in China, contributing to the β-globin gene mutation database for the Chinese population. This study highlights the importance of employing family analysis or third-generation sequencing technologies to clarify complex mutation linkages when Sanger sequencing alone cannot determine the relationship between multiple mutations.

Beta-thalassaemia intermedia due to a complex alpha-globin rearrangement and a heterozygous beta thalassaemia mutation

The alpha-thalassaemia alleles are very frequent in the world's population. The main molecular mechanism is a large deletion with the loss of one or two alpha genes. Another type of rarer abnormality exists: the gain of alpha genes. The consequence of a gain is an overproduction of alpha-globin chains, which aggravates a beta-thalassaemia trait into an intermedia phenotype (non-transfusion-dependent thalassaemia, NTDT). Here, we report the case of a young girl referred for a beta-NTDT with a combination never described in the literature: a heterozygous beta-thalassaemia mutation associated with a copy number gain of the alpha-globin locus and -alpha 3.7 deletion on the same allele.

Comparison of Third-Generation Sequencing and Routine Polymerase Chain Reaction in Genetic Analysis of Thalassemia

CONTEXT.—

Thalassemia is the most widely distributed monogenic autosomal recessive disorder in the world. Accurate genetic analysis of thalassemia is crucial for thalassemia prevention.

OBJECTIVE.—

To compare the clinical utility of a third-generation sequencing-based approach termed comprehensive analysis of thalassemia alleles with routine polymerase chain reaction (PCR) in genetic analysis of thalassemia and explore the molecular spectrum of thalassemia in Hunan Province.

DESIGN.—

Subjects in Hunan Province were recruited, and hematologic testing was performed. Five hundred four subjects positive on hemoglobin testing were then used as the cohort, and third-generation sequencing and routine PCR were used for genetic analysis.

RESULTS.—

Of the 504 subjects, 462 (91.67%) had the same results, whereas 42 (8.33%) exhibited discordant results between the 2 methods. Sanger sequencing and PCR testing confirmed the results of third-generation sequencing. In total, third-generation sequencing correctly detected 247 subjects with variants, whereas PCR identified 205, which showed an increase in detection of 20.49%. Moreover, α triplications were identified in 1.98% (10 of 504) hemoglobin testing-positive subjects in Hunan Province. Seven hemoglobin variants with potential pathogenicity were detected in 9 hemoglobin testing-positive subjects.

CONCLUSIONS.—

Third-generation sequencing is a more comprehensive, reliable, and efficient approach for genetic analysis of thalassemia than PCR, and allowed for a characterization of the thalassemia spectrum in Hunan Province.

Investigation of the mechanism of copy number variations involving the α-globin gene cluster on chromosome 16: two case reports and literature review

Thalassemia is one of the most common single-gene disorder worldwide. An important genetic cause of thalassemia is copy number variations (CNVs) in the α-globin gene cluster. However, there is no unified summary and discussion on the detailed information and mechanisms of these CNVs. In this study, two novel CNVs, a tandem duplication (αααα¹⁵⁹) and deletion (--²⁵⁹), were identified in two Chinese families with thalassemia patients, according to the results of hematologic analysis, routine genetic testing for thalassemia, multiplex ligation-dependent probe amplification (MLPA), next-generation sequencing (NGS) and other molecular methods. Co-inherited with β^CD41-42 mutation and --^SEA deletion separately, αααα¹⁵⁹ and --²⁵⁹ resulted in a patient with β-thalassemia intermedia and a lethal fetus with Hb Bart's hydrops fetalis syndrome, respectively. Next, a literature review was performed to summarize all known CNVs involving the α-globin gene cluster. The molecular structure characteristics of these CNVs were analyzed and the possible mechanism was explored. It is the first time to analyze the generation mechanism of genome arrangements in the α-globin gene cluster systematically.

A novel rearrangement of the α-globin gene cluster containing both the -α3.7 and ααααanti4.2 crossover junctions in a Chinese family

BACKGROUND

Thalassemia is one of the most common hemoglobinopathies. Thalassemia is mainly caused by the loss and/or deficiency of one or more globin chains in hemoglobin. The copy number variant (CNV) of α-globin gene is one of the important factors affecting the clinical phenotype of β-thalassemia. The precise detection for this type of variation is needed.

METHODS

Peripheral blood of a 33-year-old man and his family members were collected. Complete blood counts and serum iron levels were measured for participants. Genomic DNA was extracted from all family members. Routine genetic analysis of thalassemia was performed to determine the genotype. Additional PCR-electrophoresis and Multiplex ligation dependent probe amplification (MLPA) were conducted. Single-molecule real-time technology(SMRT) was then performed as a validation assay and further characterization of the variant for family members.

RESULTS

PCR-electrophoresis and MLPA found a new variant, but the exact genotype could not be determined. At last, SMRT identified the new variant as a rearrangement of the α-globin gene cluster named αHKαα (NC_000016.9:g.169818_174075dup169818_174075dup173302_177105del), which contained both the -α3.7 and ααααanti4.2 crossover junctions. Carriers of the novel CNV show normal clinical phenotype according to the hematological results.

CONCLUSION

We have identified an unreported CNV (αHKαα) in α-globin gene cluster. The novel CNV not only demonstrates the accuracy and efficiency of our combining strategy in detecting unknown CNVs, but also enriched the variant spectrum of thalassemia.

The hemoglobinopathies, molecular disease mechanisms and diagnostics

Hemoglobinopathies are the most common monogenic disorders in the world with an ever increasing global disease burden each year. As most hemoglobinopathies show recessive inheritance carriers are usually clinically silent. Programmes for preconception and antenatal carrier screening, with the option of prenatal diagnosis are considered beneficial in many endemic countries. With the development of genetic tools such as Array analysis and Next Generation Sequencing in addition to state of the art screening at the hematologic, biochemic and genetic level, have contributed to the discovery of an increasing number of rare rearrangements and novel factors influencing the disease severity over the recent years. This review summarizes the basic requirements for adequate carrier screening analysis, the importance of genotype–phenotype correlation and how this may lead to the unrevealing exceptional interactions causing a clinically more severe phenotype in otherwise asymptomatic carriers. A special group of patients are β‐thalassemia carriers presenting with features of β‐thalassemia intermedia of various clinical severity. The disease mechanisms may involve duplicated α‐globin genes, mosaic partial Uniparental Isodisomy of chromosome 11p15.4 where the HBB gene is located or haplo‐insufficiency of a non‐linked gene SUPT5H on chromosome 19q, first described in two Dutch families with β‐thalassemia trait without variants in the HBB gene.

Characterization of a Novel 71.8 kb α0-Thalassemia Deletion and Subsequent Summary of a Practical Procedure for Thalassemia Molecular Diagnosis

Thalassemia is the most common monogenic disorder around the world. Based on the principle of genotype-phenotype correlation, identification of thalassemia mutations is the essential prerequisite for clinical diagnosis and management. Because only common mutations are routinely detected, the identification of rare or undetermined mutations is a challenge for clinical laboratories. Herein, a proband presenting with inconsistent phenotype-genotype correlation after routine molecular screening was investigated by multiplex ligation-dependent probe amplification (MLPA), targeted-next generation sequencing (targeted-NGS), gap-polymerase chain reaction (gap-PCR) and Sanger sequencing. Eventually, a novel 71.8 kb deletion (- -^71.8) was identified and characterized, which included HBZ (ζ), HBA2 (α2), and HBA1 (α1) genes and was causing α⁰-thalassemia (α⁰-thal). Furthermore, we summarized a practical procedure based on accumulated experience in studies and clinical practice, which can be a guide for molecular screening and clinical diagnosis of thalassemia, especially for identification of undetermined or novel mutations.