Objective: Mutational analysis of BCR::ABL1 kinase domain (KD) is a crucial component of clinical decision algorithms for chronic myeloid leukemia (CML) patients with failure or warning responses to tyrosine kinase inhibitor (TKI) therapy. This study aimed to detect BCR::ABL1 KD mutations in CML patients with treatment resistance and assess the concordance between NGS (next generation sequencing) and Sanger sequencing (SS) in detecting these mutations. Results: In total, 12 different BCR::ABL1 KD mutations were identified by SS in 22.6% (19/84) of patients who were resistant to TKI treatment. Interestingly, NGS analysis of the same patient group revealed an additional four different BCR::ABL1 KD mutations in 27.4% (23/84) of patients. These mutations are M244V, A344V, E355A, and E459K with variant read frequency below 15%. No mutation was detected in 18 patients with optimal response to TKI therapy. Resistance to TKIs is associated with the acquisition of additional mutations in BCR::ABL1 KD after treatment with TKIs. Additionally, the use of NGS is advised for accurately determining the mutation status of BCR::ABL1 KD, particularly in cases where the allele frequency is low, and for identifying mutations across multiple exons simultaneously. Therefore, the utilization of NGS as a diagnostic platform for this test is very promising to guide therapeutic decision-making.

Malaysia is a multicultural and multiethnic country comprising numerous ethnic groups. From the total population of 32.7 million, Malays form the bulk of the Bumiputera in Malaysia comprise about 69.9%, followed by Chinese 22.8%, Indian 6.6%, and others 0.7%. The heterogeneous population and increasing numbers of non-citizens in this country affects the heterogeneity of genetic diseases, diversity, and heterogeneity of thalassaemia mutations. Alpha (α)-thalassaemia is an inherited haemoglobin disorder characterized by hypochromic microcytic anaemia caused by a quantitative reduction in the α-globin chain. A majority of the α-thalassaemia are caused by deletions in the α-globin gene cluster. Among Malays, the most common deletional alpha thalassaemia is −α^3.7 deletion followed by −−^SEA deletion. We described the molecular characterization of a new −−^GB deletion in our population, involving both alpha genes in cis. Interestingly, we found that this mutation is unique among Malay ethnicities. It is important to diagnose this deletion because of the 25% risk of Hb Bart’s with hydrops fetalis in the offspring when in combination with another α⁰- thalassaemia allele. MLPA is a suitable method to detect unknown and uncommon deletions and to characterize those cases which remain unresolved after a standard diagnostic approach.

Purpose Thalassemia is a major public health concern in Southeast Asia, particularly in Malaysia, where a high carrier rate places significant pressure on healthcare systems. Hereditary Persistence of Fetal Hemoglobin (HPFH) and delta-beta (δβ) thalassemia are genetic conditions associated with elevated levels of fetal hemoglobin (Hb F). This study aimed to determine the frequency of common beta (β)-globin gene cluster deletions among Malaysian carriers of HPFH or δβ thalassemia, while also providing an overview of the thalassemia burden in the region. Methods A retrospective study was conducted on 534 blood samples submitted to the Institute for Medical Research (IMR), Malaysia, for β-thalassemia genotyping between January 2017 and December 2019. Demographic data, including full blood count parameters and hemoglobin (Hb) analysis, were retrieved. Deoxyribonucleic acid (DNA) was extracted and analyzed using Multiplex Gap-Polymerase Chain Reaction (PCR) to detect large deletions in the β-globin gene cluster. Results Seven distinct deletions were identified among the 534 heterozygous carriers. The two most common deletions were ^Gγ(^Aγδβ)°-thalassemia Siriraj I (~ 118 kilobase pairs [kb]) and δβ°-thalassemia Thai (~ 12.5 kb), accounting for 30.0% and 29.8% of cases, respectively. The HPFH-6 deletion was observed in 20.0% of cases, followed by ^Gγ(^Aγδβ)°-thalassemia Asian-Indian Inversion-Deletion (Inv/Del) (14.2%), ^Gγ(^Aγδβ)°-thalassemia Chinese (~ 100 kb) (4.3%), HPFH-3 (0.9%), and ^Gγ(^Aγδβ)°-thalassemia Asian (~ 49.3 kb) (0.7%). The ethnic distribution showed a predominance among Malay patients (93.4%), with specific deletions suggesting ethnic clustering. Genotype–phenotype analysis revealed notable variations in hematological parameters: carriers of HPFH-3 had the highest Hb F levels (25.3 ± 3.1%) as measured by high-performance liquid chromatography (HPLC) and showed the least severe microcytosis, while carriers of δβ°-thalassemia Thai (~ 12.5 kb) demonstrated more pronounced hematological abnormalities. Findings were consistent with previous reports from Southeast Asia, underscoring the importance of incorporating molecular diagnostics into national screening programs. Although Multiplex Gap-PCR is robust, further studies using Next-Generation Sequencing (NGS) and Multiplex Ligation-dependent Probe Amplification (MLPA) are recommended to detect rare or undetected mutations. Conclusions This study provides crucial data on the molecular spectrum of HPFH and δβ thalassemia in Malaysia, contributing to improved diagnostic strategies and genetic counselling. Future research should explore additional genetic variants to enhance national thalassemia prevention programs.

Thalassemia is a significant health burden in Malaysia. This report presents a retrospective analysis of nationwide diagnostic data compiled over seven years, investigating β-thalassemia spectrum in 731 referred family trios. Genomic analysis used gap-PCR, ARMS-PCR, MLPA, Sanger sequencing, and exome sequencing to validate rare CNVs. We identified 468 at-risk couples, with 440 children inherited biallelic mutations. Heterogeneous mutations were recorded among Peninsular Malaysian children with 43 β-, four δ-, 11 α-thalassemia and variant types, and five α-globin duplications. Among children in Sabah, 15 β-, one δ-, and two α-thalassemia and variants, and one α-globin duplications were recorded. Sarawak exhibited lowest heterogeneity. In Peninsular Malaysia, β ^E was most prevalent among Malays, followed by IVS 1–5 (G > C), β ^Malay , and IVS 1–1 (G > T). IVS 2–654 (C > T) and − 28 (A > G) were observed only among Chinese individuals in this referred cohort, while Cd 41/42 -TTCT was common to both ethnicities. β ^E /β-thalassemia was the most frequent disease with 188 cases. In Sabah, homozygous β ^Filipino was the most frequent genotype across multiple ethnicities, with 35.2% (31/88) of these cases exhibiting concomitant -α ^3.7 . Overall, 15.2% (111/731) of children with HBB mutations had concomitant α-thalassemia, and 10 had α-triplications. These findings highlight the necessity of HBA genotyping for accurate genetic counseling. We present two novel mutation, codon 122 (TTC > TGC) mutation (HBB:c.368 T > G; p.Phe123Cys) named β ^{Tanah Merah} , and α-globin cluster duplication, ααα ⁹¹ (NC_000016.10:g.87820_179080dup). This comprehensive dataset is essential for improving molecular diagnostics and optimizing DNA analysis workflows in highly heterogeneous populations.

Poly A (AATAAA > AATA--) [HBA2:c.*93_*94delAA] is a rare α-variant reported in our population. It is caused by 2 bp deletion (--AA) in the α2 poly A sequence, leading to a significant α–thalassaemia phenotype. Background/Objectives: This study describes the haematological parameters, phenotype, and genotype characteristics of AATA(--AA) in the Malaysian population. Methods: The study was carried out on 17 177 cases referred to the Institute for Medical Research, Malaysia, for further diagnosis of α-thalassaemia in a five-year period. Alpha-Gap and ARMS-PCR were performed to detect common α-thalassaemia, followed by HBA1 and HBA2 genes sequencing and multiplex ligation-dependent probe amplification (MLPA). Haematological parameters among various groups with the AATA(--AA) allele were presented in this study. Results: Thirty-two patients with AATA(--AA) displaying an α–thalassaemia-like phenotype were analysed. They comprised 22 (68.75%) AATA(--AA) carriers, 2 (6.25%) compounds with 3.7 deletion, 2 (6.25%) compounds with --SEA deletion, 1 (3.12%) AATA(--AA) homozygote, and 3 (9.37%) compounds of Hb Adana, Hb CS, and Hb Pakse with co-inheritance Hb E, respectively. Most of the patients with AATA(--AA) compounds with the α-variant exhibited a significant phenotype between moderate to severe thalassaemia, especially cases with compound α^−AAα/α^Adanaα. Conclusions: AATA(--AA) is a significant pathogenic variant that should be diagnosed to prevent significant thalassaemia phenotype or transfusion-dependent thalassaemia.