Evaluating the Clinical Utility of a Long-Read Sequencing-Based Approach in Prenatal Diagnosis of Thalassemia

Thalassemia genetic screening of pregnant women with anemia in Northern China through comprehensive analysis of thalassemia alleles (CATSA)

Thalassemia is an inherited blood disorder and traditionally considered more prevalent in Southern China. However, with increased migration and intermarriage, more and more thalassemia carriers had been reported in Northern China. The lack of screening for thalassemia carriers may also result in missed diagnosis in Northern China. Additionally, thalassemia carriers are usually asymptomatic or mild anemia, but their anemia can get worse during pregnancy. Iron deficiency anemia (IDA) is also one of the causes of anemia during pregnancy. In particular, both IDA and thalassemia are characterized by microcytic hypochromic anemia. The overlap of symptoms and the presence of thalassemia carriers with IDA may lead to misdiagnosis. In this study, long-read sequencing based approach termed comprehensive analysis of thalassemia alleles (CATSA) had been performed for 244 pregnant women in Northern China whose results of routine blood examinations were abnormal. As a result, 16.39 % (40/244) of the anemic pregnant women carried at least one mutation of thalassemia. One Hb H patient and a rare α-globin gene triplication combined with β-thalassemia were also identified. Of the 44 thalassemia variants detected, the -α3.7, -SEA and HBB:c.316-197C > T were the most common variants. CATSA is of great significance for determining exact genotype of 22.50 % (9/40) thalassemia carriers because 8 variants they carried were outside the detection range of routine genetic tests. It is noted that 2 novel deletions of HBA gene were identified, expanding the genotype spectrum of α-thalassemia. Our findings demonstrate the importance of thalassemia screening in Northern China. Future research should focus on expanding screening to include more diverse populations.

Long-Read Sequencing Solves Complex Structure of CYP21A2 in a Large 21-Hydroxylase Deficiency Cohort

CONTEXT

Genetic testing for 21-hydroxylase deficiency (21-OHD) is always challenging. The current approaches of short-read sequencing and multiplex ligation-dependent probe amplification (MLPA) are insufficient for the detection of chimeric genes or complicated variants from multiple copies. Recently developed long-read sequencing (LRS) can solve this problem.

OBJECTIVE

To investigate the clinical utility of LRS in precision diagnosis of 21-OHD.

METHODS

In the cohort of 832 patients with 21-OHD, the current approaches provided the precise molecular diagnosis for 81.7% (680/832) of cases. LRS was performed to solve the remaining 144 cases with complex chimeric variants and 8 cases with variants from multiple copies. Clinical manifestations in patients with continuous deletions of CYP21A2 extending to TNXB (namely CAH-X) were further evaluated.

RESULTS

Using LRS in combination with previous genetic test results, a total of 16.9% (281/1664) CYP21A1P/CYP21A2 or TNXA/TNXB chimeric alleles were identified in 832 patients, with CYP21A1P/CYP21A2 accounting for 10.4% and TNXA/TNXB for 6.5%. The top 3 common chimeras were CYP21 CH-1, TNX CH-1, and TNX CH-2, accounting for 77.2% (217/281) of all chimeric alleles. The 8 patients with variants on multiple copies of CYP21A2 were accurately identified with LRS. The prevalence of CAH-X in our cohort was 12.1%, and a high frequency of connective tissue-related symptoms was observed in CAH-X patients.

CONCLUSION

LRS can detect all types of CYP21A2 variants, including complex chimeras and pathogenic variants on multiple copies in patients with 21-OHD, which could be utilized as a first-tier routine test for the precision diagnosis and categorization of congenital adrenal hyperplasia.

Hotspots and status of Fetal Alpha-Thalassemia from 2009 to 2023: a bibliometric analysis

Objective

to evaluate the research status and development hotspots of fetal α-thalassemia by quantitatively analyzing the diagnostic status, key areas, related management measures and prospects of the disease by bibliometrics.

Methods

The global literature on fetal α-thalassemia and severe α-thalassemia from 2009-2023 in the Web of Science Core Collection (WOSCC) was visually analyzed by VOSviewer and CiteSpace.

Results

(1) The examination of the quantity of publications concerning fetal α-thalassemia indicates a rising tendency prior to 2018, followed by a decrease after 2018. (2)The United States, China, Italy, Thailand have published more papers, and the United States has more collaborating countries such as Italy and China. (3) Chiang Mai University and Harvard University are the top two institutions with the highest contribution. However, Chiang Mai University's H index (12) and citation frequency per article (8.05) are relatively low and the NC (6,342), H index (33) and citations per article (75.42) of Harvard University are higher than those of the other institutions. (4) Tongsong T, Gambari R and Fucharoen S are the top three prolific authors. Fucharoen S emerges as the most frequently cited author with 738 citations, excluding self-citations. (5) HEMOGLOBIN leading with 87 published papers (NC:601,IF: 0.82, H-index: 13), followed by BLOOD(58 papers, Nc: 3755, IF: 25.48, H-index: 40) and BLOOD CELLS MOLECULES AND DISEASES(39 papers, Nc: 729, IF: 2.37, H-index: 16). (6) The most cited article was published in science and the second and third cited articles were featured in the Proceedings of the National Academy of Sciences; the top 3 clusters of co-cited literature are "gene editing", "polymorphisms", "hydroxyurea". (7) Keywords analysis showe that the top two categories of keyword cluster focus on the prenatal diagnosis and the current treatment strategy of the disease, which remain the research hotspots.

Conclusions

Recent research on this topic has primarily focused on prenatal diagnosis and treatment strategies. A particular area of interest is the ongoing research on gene therapy.The advances in non-invasive diagnosis and therapeutic methods will change the current management approaches for fetal severe α-thalassemia in the future.

SNPscan Combined With CNVplex as a High-Performance Diagnostic Method for Thalassemia

OBJECTIVE

Thalassemia is a Mendelian-inherited blood disorder with severe consequences, including disability and mortality, making it a significant public health concern. Therefore, there is an urgent need for precise diagnostic technologies. We introduce two innovative diagnostic techniques for thalassemia, SNPscan and CNVplex, designed to enhance molecular diagnostics of thalassemia.

METHODS

The SNPscan and CNVplex assays utilize variations in PCR product length and fluorescence to identify multiple mutations. In the SNPscan method, we designed three probes per locus: two 5' and one 3', and incorporated allele identification link sequences into one of the 5' probes to distinguish the alleles. The detection system was designed for 67 previously reported loci in the Chinese population for a specific genetic condition. CNVplex identifies deletion types by analyzing the specific positions of probes within the globin gene. This innovative approach enables the detection of six distinct deletional mutations, enhancing the precision of thalassemia diagnostics. We evaluated and refined the methodologies in a training cohort of 100 individuals with confirmed HBA and HBB genotypes. The validation cohort, consisting of 1647 thalassemia patients and 100 healthy controls, underwent a double-blind study. Traditional diagnostic techniques served as the control methods.

RESULTS

In the training set of 100 samples, 10 mutations (Hb QS, Hb CS, Hb Westmead, CD17, CD26, CD41-42, IVS-II-654, --SEA, -α3.7 and -α4.2) were identified, consistent with those identified by traditional methods. The validation study showed that SNPscan/CNVplex offered superior molecular diagnostic capabilities for thalassemia, with 100% accuracy compared to 99.43% for traditional methods. Notably, the assay identified three previously undetected mutations in 10 cases, including two deletion mutations (Chinese Gγ(Aγδβ)0 del and SEA-HPFH), and one non-deletion mutation (Hb Q-Thailand).

CONCLUSIONS

The SNPscan/CNVplex assay is a cost-effective and user-friendly tool for diagnosing thalassemia, demonstrating high accuracy and reliability, and showing great potential as a primary diagnostic method in clinical practice.

Application of whole exome sequencing in carrier screening for high-risk families without probands

Purpose

This study aimed to screen the genetic etiology for the high-risk families including those with an adverse pregnancy history, a history of consanguineous marriages, or a history of genetic diseases, but lack of proband via whole exome sequencing (WES).

Methods

128 individuals from high-risk family were tested by WES. The candidate variants were analyzed according to the ACMG criteria to screen the potential carriers. At-risk couples (ARCs) who harbored the same causative gene were provided with precise fertility guidance to avoid the birth of children with birth defects.

Results

The total detection rate was 36.72%, with pathogenic/likely pathogenic (P/LP) variants found in 47 individuals, and variants of uncertain significance (VUS) were found in 34. Among couples with adverse pregnancy history: P/LP variants were found in 38 individuals, and VUS were found in 26, for a detection rate of 34.55%; among members of family history of genetic disease or consanguineous marriages: P/LP variants were found in nine individuals, and VUS were found in 8, for a detection rate of 50.00%. Otherwise, we detected 19 ARCs who both carried P/LP variants in the same gene, with a theoretical offspring prevalence of up to 7.42%.

Conclusion

In the absence of probands, carrier screening using WES can provide an efficient tool for screening the molecular etiology of high-risk families.

Case report: Identification of a novel triplication of alpha-globin gene by the third-generation sequencing: pedigree analysis and genetic diagnosis

BACKGROUND

Thalassemia, a common autosomal hereditary blood disorder worldwide, mainly contains α- and β-thalassemia. The α-globin gene triplicates allele is harmless for carriers, but aggravates the phenotype of β-thalassemia. Therefore, it is particularly crucial to accurately detect the structural variants of α-globin gene clusters.

CASE REPORT

We reported a 28-year-old man, the proband, with microcytic hypochromic anemia. From pedigree analysis, his mother and sister had hypochromic microcytosis, and his father was normal. Genetic testing of thalassemia identified a novel α-globin gene triplicate named αααanti4.2del726bp (NC_000016.10:g.170769_174300dupinsAAAAAA) by third-generation sequencing (TGS) in the proband and his father, which was further validated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. The genotypes of the proband's mother and sister were both -α3.7/αα compounded with heterozygous HBB:c.126_129delCTTT. They were categorized as silent α-thalassemia with co-inheritance of β-thalassemia trait. The proband's genotype additionally had the α-globin gene triplicates compared with his mother and sister, which increased the imbalance between α/β-globin, so the proband had more severe hematological parameters. The proband's wife was diagnosed as HBA2:c.427T > C heterozygosis, and his daughter had the novel α-globin gene triplicates compounded with HBA2:c.427T > C, therefore the girl might be asymptomatic.

CONCLUSION

The identification of the novel α-globin gene triplicates provides more insight for the research of thalassemia variants and indicates that TGS has significant advantages on genetic testing of thalassemia for the reliability, accuracy and comprehensiveness.

The comprehensive analysis of thalassemia alleles (CATSA) based on single-molecule real-time technology (SMRT) is a more powerful strategy in the diagnosis of thalassemia caused by rare variants

Thalassemia is one of the most widely distributed monogenic disorders in the world and affects the largest number of people. It can manifest a wide spectrum of phenotypes from asymptomatic to fatal, which is associated with the degree of imbalance between α- and β-globin chains. Therefore, individuals with different genotypes could present with a similar phenotype. Genetic analysis is always needed to make a correct diagnosis. However, routine genetic analysis of thalassemia used in the Chinese population identifies only 23 common variants, resulting in many cases undiagnosed or being misdiagnosed. In this study, we applied a long-read sequencing-based approach termed comprehensive analysis of thalassemia alleles (CATSA) to 30 subjects whose hematologic screening results could not be explained by the routine genetic test results. The identification of additional variants and the correction of genotypes allowed the interpretation of the clinical phenotype in 24 subjects, which have been confirmed to be correct by independent experiments. Moreover, we identified a novel 8.4-kb deletion containing the entire HBB and HBD genes as well as part of the HBBP1 gene, expanding the genotype spectrum of β-thalassemia. CATSA showed a great advantage over other genetic tests in the diagnosis of thalassemia caused by rare variants.

Molecular characterization of a novel 83.9-kb deletion of the α-globin upstream regulatory elements by long-read sequencing

Inherited deletions of upstream regulatory elements of α-globin genes give rise to α-thalassemia, which is an autosomal recessive monogenic disease. However, conventional thalassemia target diagnosis often fails to identify these rare deletions. Here we reported a family with two previous pregnancies of Hb Bart's hydrops fetalis and was seeking for prenatal diagnosis during the third pregnancy. Both parents had low level of Hemoglobin A2 indicating α-thalassemia. Conventional Gap-PCR and PCR-reverse dot blot showed the father carried -SEA deletion but did not identify any variants in the mother. Multiplex ligation-dependent probe amplification identified a deletion containing two HS-40 probes but could not determine the exact region. Finally, a long-read sequencing (LRS)-based approach directly identified that the exact deletion region was chr16: 48,642-132,584, which was located in the α-globin upstream regulatory elements and named (αα)JM after the Jiangmen city. Gap-PCR and Sanger sequencing confirmed the breakpoint. Both the mother and fetus from the third pregnancy carried heterozygous (αα)JM, and the fetus was normally delivered at gestational age of 39 weeks. This study demonstrated that LRS technology had great advantages over conventional target diagnosis methods for identifying rare thalassemia variants and assisted better carrier screening and prenatal diagnosis of thalassemia.

Third-generation sequencing for genetic disease

Third-generation sequencing (TGS) has led to a brave new revolution in detecting genetic diseases over the last few years. TGS has been rapidly developed for genetic disease applications owing to its significant advantages such as long read length, rapid detection, and precise detection of complex and rare structural variants. This approach greatly improves the efficiency of disease diagnosis and complements the shortcomings of short-read sequencing. In this paper, we first briefly introduce the working mechanism of one of the most important representatives of TGS, single-molecule real-time (SMRT) sequencing by Pacific Bioscience (PacBio), followed by a review and comparison of the advantages and disadvantages of different sequencing technologies. Finally, we focused on the progress of SMRT sequencing applications in genetic disease detection. Future perspectives on the applications of TGS in other fields were also presented. With the continuous innovation of the SMRT technologies and the expansion of their fields of application, SMRT sequencing has broad clinical application prospects in genetic diseases detection, and is expected to become an important tool for the molecular diagnosis of other diseases.

Case report: A novel 10.8-kb deletion identified in the β-globin gene through the long-read sequencing technology in a Chinese family with abnormal hemoglobin testing results

Background

Thalassemia is a common inherited hemoglobin disorder caused by a deficiency of one or more globin subunits. Substitution variants and deletions in the HBB gene are the major causes of β-thalassemia, of which large fragment deletions are rare and difficult to be detected by conventional polymerase chain reaction (PCR)-based methods.

Case report

In this study, we reported a 26-year-old Han Chinese man, whose routine blood parameters were found to be abnormal. Hemoglobin testing was performed on the proband and his family members, of whom only the proband's mother had normal parameters. The comprehensive analysis of thalassemia alleles (CATSA, a long-read sequencing-based approach) was performed to identify the causative variants. We finally found a novel 10.8-kb deletion including the β-globin (HBB) gene (Chr11:5216601-5227407, GRch38/hg38) of the proband and his father and brother, which were consistent with their hemoglobin testing results. The copy number and exact breakpoints of the deletion were confirmed by multiplex ligation-dependent probe amplification (MLPA) and gap-polymerase chain reaction (Gap-PCR) as well as Sanger sequencing, respectively.

Conclusion

With this novel large deletion found in the HBB gene in China, we expand the genotype spectrum of β-thalassemia and show the advantages of long-read sequencing (LRS) for comprehensive and precise detection of thalassemia variants.

Third generation sequencing transforms the way of the screening and diagnosis of thalassemia: a mini-review

Thalassemia is an inherited blood disorder imposing a significant social and economic burden. Comprehensive screening strategies are essential for the prevention and management of this disease. Third-generation sequencing (TGS), a breakthrough technology, has shown great potential for screening and diagnostic applications in various diseases, while its application in thalassemia detection is still in its infancy. This review aims to understand the latest and most widespread uses, advantages of TGS technologies, as well as the challenges and solutions associated with their incorporation into routine screening and diagnosis of thalassemia. Overall, TGS has exhibited higher rates of positive detection and diagnostic accuracy compared to conventional methods and next-generation sequencing technologies, indicating that TGS will be a feasible option for clinical laboratories conducting in-house thalassemia testing. The implementation of TGS technology in thalassemia diagnosis will facilitate the development of effective prevention and management strategies, thereby reducing the burden of this disease on individuals and society.

Applications of advanced technologies for detecting genomic structural variation

Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.