Genomic landscape of childhood acute lymphoblastic leukemia in Malaysia: insights from array-CGH

Ismail A 1 , Ahid F 2 , Moi WN 3 , Kamaluddin NR 1 , Esa E 1 , Yusoff YM 1 Show all authors , Seman ZA 1 , Mohammed MA 1 , George E 4 , Isa A 5 , Zakaria Z 6

Affiliations 

  • 1 Hematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, 40170, Malaysia
  • 2 Centre for Medical Laboratory Technology Studies, Faculty of Health Sciences, Universiti Teknologi MARA, Puncak Alam, Selangor, 42300, Malaysia. fadlyahid@uitm.edu.my
  • 3 Medical Laboratory Technology College, Ministry of Health Malaysia, Kuala Lumpur, 50588, Malaysia
  • 4 Faculty of Medical and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400, Malaysia
  • 5 Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Pulau Pinang, 13200, Malaysia
  • 6 Premier Integrated Labs, Pantai Hospital Ampang, Kuala Lumpur, 55100, Malaysia
Mol Cytogenet, 2025 Mar 28;18(1):7.
PMID: 40155977 DOI: 10.1186/s13039-025-00709-4

Abstract

BACKGROUND: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, comprising approximately 25% of pediatric malignancies. Notably, chromosomal aberrations and genetic alterations play a central role in the pathogenesis of ALL, serving as critical diagnostic and prognostic markers. In this study, we use array-based comparative genomic hybridization (array-CGH) to explore the landscape of copy number variations (CNVs) and variants of uncertain significance (VUS) in 67 Malaysian childhood ALL patients with normal karyotype.

RESULTS: A total of 36 pathogenic CNVs (26 gains, 10 losses) were identified in 19 (28.4%) patients which harbor genes related to the development of ALL. The genes include the MLLT3 (9p21.3), ETV6 (12p13.2), RUNX1 (21q22.12), ERG (21q22.2) and DMD (Xp21.1). On the other hand, a total of 46 variants of uncertain significance (VUS) was observed in 34 (50.7%) patients.

CONCLUSIONS: Our study indicates that array-CGH is able to identify and characterize the CNVs responsible for the pathogenesis of childhood ALL. However, further studies are required to determine the pathogenic implications of VUS in the development of childhood ALL.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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