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Cytogenomic landscape of adult Philadelphia chromosome-positive acute lymphoblastic leukemia in Malaysia.

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Τίτλος: Cytogenomic landscape of adult Philadelphia chromosome-positive acute lymphoblastic leukemia in Malaysia.
Συγγραφείς: Phan CL; Department of Haematology, Hospital Ampang, Jalan Mewah Utara, Pandan Mewah, 68000 Ampang, Selangor, Malaysia; Ministry of Health Malaysia; Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: chinleephan@gmail.com., Zakaria Z; Ministry of Health Malaysia; Haematology Unit, Cancer Research Centre (CaRC), Institute for Medical Research, National Institute of Health, Block C, No.1, Jalan Setia Murni U13/52, Seksyen U13 Setia Alam, 40170 Shah Alam, Selangor, Malaysia. Electronic address: drzubai@gmail.com., Yegappan S; Department of Haematology, Hospital Ampang, Jalan Mewah Utara, Pandan Mewah, 68000 Ampang, Selangor, Malaysia; Ministry of Health Malaysia. Electronic address: mani14141@gmail.com., Khang TF; Institute of Mathematical Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: tfkhang@um.edu.my., Ng CC; Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: ccng@um.edu.my.
Πηγή: Cancer genetics [Cancer Genet] 2026 Sep; Vol. 306-307, pp. 54-62. Date of Electronic Publication: 2026 May 20.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Elsevier Country of Publication: United States NLM ID: 101539150 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2210-7762 (Print) NLM ISO Abbreviation: Cancer Genet Subsets: MEDLINE
Imprint Name(s): Original Publication: New York, NY : Elsevier
Ιατρικοί όροι (MeSH): Precursor Cell Lymphoblastic Leukemia-Lymphoma*/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma*/pathology , Philadelphia Chromosome*, Humans ; Malaysia ; Female ; Comparative Genomic Hybridization ; Adult ; Male ; Middle Aged ; DNA Copy Number Variations ; Polymorphism, Single Nucleotide ; Chromosome Aberrations ; Young Adult ; Aged ; Adolescent
Περίληψη: Background: Philadelphia chromosome-positive acute lymphoblastic leukemia (-Ph+ ALL) is a high-risk leukemia often accompanied by additional genomic abnormalities beyond BCR::ABL1.
Methods: We analyzed 74 newly diagnosed adult -Ph+ ALL patients. Additional chromosomal abnormalities (ACAs) were assessed by conventional cytogenetics in 51 patients and copy number variations (CNVs) by combined array comparative genomic hybridization plus single nucleotide polymorphism (array-CGH+SNP) in 43 patients.
Results: ACAs were detected in 31 cases (60.8%), including complex karyotypes in 11 (35.5%). CNVs were identified in 38 cases (88.4%) and were predominantly deletions (69.2%). Recurrent abnormalities included double Ph chromosome, monosomy 7, chromosomal gains at 8q, 9q34, 22q11, and losses at 7p, 9p, and 20q. The t(3;9;22) was the most frequent t(9;22) variant (12.9%), despite being rare in previous studies of adult Ph+ ALL. IKZF1 deletions were most frequent (91.7%), followed by CDKN2A/B (44.4%), PAX5 (38.9%) and RB1 (30.6%). IKZF1 co-deletions with CDKN2A/B and/or PAX5 occurred in 66.7%. IKZF1 and 22q11.22 co-deletions occurred in 34.2%, and VPREB1 deletions in 15.8%; both have been associated with adverse outcomes in ALL. Copy-neutral loss of heterozygosity >5 Mb was detected in 16.3%, frequently involving chromosome 9p and encompassing the CDKN2A/B loci.
Discussions: Adult Ph+ ALL in this multi-ethnic cohort exhibited marked genomic heterogeneity, with frequent submicroscopic alterations detectable only through integrated genomic profiling. Comprehensive genomic characterization is needed to better understand leukemogenesis and refine risk stratification.
(Copyright © 2026 Elsevier Inc. All rights reserved.)
Competing Interests: Declaration of competing interest The authors have no competing interest.
Contributed Indexing: Keywords: Acute lymphoblastic leukemia; Additional chromosomal aberrations; Array-CGH+SNP; Cytogenomic; Philadelphia chromosome-positive
Entry Date(s): Date Created: 20260605 Date Completed: 20260824 Latest Revision: 20260824
Update Code: 20260825
DOI: 10.1016/j.cancergen.2026.05.006
PMID: 42247916
Βάση Δεδομένων: MEDLINE
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  Data: Cytogenomic landscape of adult Philadelphia chromosome-positive acute lymphoblastic leukemia in Malaysia.
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  Data: <searchLink fieldCode="AU" term="%22Phan+CL%22">Phan CL</searchLink>; Department of Haematology, Hospital Ampang, Jalan Mewah Utara, Pandan Mewah, 68000 Ampang, Selangor, Malaysia; Ministry of Health Malaysia; Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: chinleephan@gmail.com.<br /><searchLink fieldCode="AU" term="%22Zakaria+Z%22">Zakaria Z</searchLink>; Ministry of Health Malaysia; Haematology Unit, Cancer Research Centre (CaRC), Institute for Medical Research, National Institute of Health, Block C, No.1, Jalan Setia Murni U13/52, Seksyen U13 Setia Alam, 40170 Shah Alam, Selangor, Malaysia. Electronic address: drzubai@gmail.com.<br /><searchLink fieldCode="AU" term="%22Yegappan+S%22">Yegappan S</searchLink>; Department of Haematology, Hospital Ampang, Jalan Mewah Utara, Pandan Mewah, 68000 Ampang, Selangor, Malaysia; Ministry of Health Malaysia. Electronic address: mani14141@gmail.com.<br /><searchLink fieldCode="AU" term="%22Khang+TF%22">Khang TF</searchLink>; Institute of Mathematical Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: tfkhang@um.edu.my.<br /><searchLink fieldCode="AU" term="%22Ng+CC%22">Ng CC</searchLink>; Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address: ccng@um.edu.my.
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  Data: <searchLink fieldCode="JN" term="%22101539150%22">Cancer genetics</searchLink> [Cancer Genet] 2026 Sep; Vol. 306-307, pp. 54-62. <i>Date of Electronic Publication: </i>2026 May 20.
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Elsevier%22">Elsevier </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>101539150 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>2210-7762 (Print) <i>NLM ISO Abbreviation: </i>Cancer Genet <i>Subsets: </i>MEDLINE
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  Data: <searchLink fieldCode="MM" term="%22Precursor+Cell+Lymphoblastic+Leukemia-Lymphoma%22">Precursor Cell Lymphoblastic Leukemia-Lymphoma*</searchLink>/<searchLink fieldCode="MM" term="%22Precursor+Cell+Lymphoblastic+Leukemia-Lymphoma+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Precursor+Cell+Lymphoblastic+Leukemia-Lymphoma%22">Precursor Cell Lymphoblastic Leukemia-Lymphoma*</searchLink>/<searchLink fieldCode="MM" term="%22Precursor+Cell+Lymphoblastic+Leukemia-Lymphoma+pathology%22">pathology</searchLink> <br /><searchLink fieldCode="MM" term="%22Philadelphia+Chromosome%22">Philadelphia Chromosome*</searchLink><br /><searchLink fieldCode="MH" term="%22Humans%22">Humans</searchLink> ; <searchLink fieldCode="MH" term="%22Malaysia%22">Malaysia</searchLink> ; <searchLink fieldCode="MH" term="%22Female%22">Female</searchLink> ; <searchLink fieldCode="MH" term="%22Comparative+Genomic+Hybridization%22">Comparative Genomic Hybridization</searchLink> ; <searchLink fieldCode="MH" term="%22Adult%22">Adult</searchLink> ; <searchLink fieldCode="MH" term="%22Male%22">Male</searchLink> ; <searchLink fieldCode="MH" term="%22Middle+Aged%22">Middle Aged</searchLink> ; <searchLink fieldCode="MH" term="%22DNA+Copy+Number+Variations%22">DNA Copy Number Variations</searchLink> ; <searchLink fieldCode="MH" term="%22Polymorphism%2C+Single+Nucleotide%22">Polymorphism, Single Nucleotide</searchLink> ; <searchLink fieldCode="MH" term="%22Chromosome+Aberrations%22">Chromosome Aberrations</searchLink> ; <searchLink fieldCode="MH" term="%22Young+Adult%22">Young Adult</searchLink> ; <searchLink fieldCode="MH" term="%22Aged%22">Aged</searchLink> ; <searchLink fieldCode="MH" term="%22Adolescent%22">Adolescent</searchLink>
– Name: Abstract
  Label: Abstract
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  Data: Background: Philadelphia chromosome-positive acute lymphoblastic leukemia (-Ph+ ALL) is a high-risk leukemia often accompanied by additional genomic abnormalities beyond BCR::ABL1.<br />Methods: We analyzed 74 newly diagnosed adult -Ph+ ALL patients. Additional chromosomal abnormalities (ACAs) were assessed by conventional cytogenetics in 51 patients and copy number variations (CNVs) by combined array comparative genomic hybridization plus single nucleotide polymorphism (array-CGH+SNP) in 43 patients.<br />Results: ACAs were detected in 31 cases (60.8%), including complex karyotypes in 11 (35.5%). CNVs were identified in 38 cases (88.4%) and were predominantly deletions (69.2%). Recurrent abnormalities included double Ph chromosome, monosomy 7, chromosomal gains at 8q, 9q34, 22q11, and losses at 7p, 9p, and 20q. The t(3;9;22) was the most frequent t(9;22) variant (12.9%), despite being rare in previous studies of adult Ph+ ALL. IKZF1 deletions were most frequent (91.7%), followed by CDKN2A/B (44.4%), PAX5 (38.9%) and RB1 (30.6%). IKZF1 co-deletions with CDKN2A/B and/or PAX5 occurred in 66.7%. IKZF1 and 22q11.22 co-deletions occurred in 34.2%, and VPREB1 deletions in 15.8%; both have been associated with adverse outcomes in ALL. Copy-neutral loss of heterozygosity >5 Mb was detected in 16.3%, frequently involving chromosome 9p and encompassing the CDKN2A/B loci.<br />Discussions: Adult Ph+ ALL in this multi-ethnic cohort exhibited marked genomic heterogeneity, with frequent submicroscopic alterations detectable only through integrated genomic profiling. Comprehensive genomic characterization is needed to better understand leukemogenesis and refine risk stratification.<br /> (Copyright © 2026 Elsevier Inc. All rights reserved.)
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  Data: Declaration of competing interest The authors have no competing interest.
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  Data: <i>Keywords: </i>Acute lymphoblastic leukemia; Additional chromosomal aberrations; Array-CGH+SNP; Cytogenomic; Philadelphia chromosome-positive
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        Text: English
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        Type: general
      – SubjectFull: Malaysia
        Type: general
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      – SubjectFull: Philadelphia Chromosome
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