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Chromosomal Aberrations in ETV6/RUNX1-positive Childhood Acute Lymphoblastic Leukemia using 244K Oligonucleotide Array Comparative Genomic Hybridization

Zubaidah Zakaria1*, Mohd Fadly Md Ahid1, Azli Ismail1, Ten Sew Keoh1, Nooraisyah Mohamad Nor1, Nor Rizan Kamaluddin1, Ezalia Esa1, Lam Kah Yuen1, Eni Juraida Abdul Rahman2 and Raudhawati Osman3

Author Affiliations

1 Hematology Unit, Cancer Research Center, Institute for Medical Research, Kuala Lumpur, 50588, Malaysia

2 Pediatrics Institute, Kuala Lumpur Hospital, Kuala Lumpur, 50588, Malaysia

3 Department of Pathology, Kuala Lumpur Hospital, Kuala Lumpur, 50588, Malaysia

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Molecular Cytogenetics 2012, 5:41  doi:10.1186/1755-8166-5-41

Published: 15 November 2012



Acute lymphoblastic leukemia (ALL) is a heterogeneous form of hematological cancer consisting of various subtypes. We are interested to study the genetic aberration in precursor B-cell ALL with specific t(12;21) translocation in childhood ALL patients. A high resolution 244K array-based Comparative Genomic Hybridization (array-CGH) was used to study eleven ETV6/RUNX1-positive childhood acute lymphoblastic leukemia (ALL) patients.


155 chromosomal aberrations (119 losses, 36 gains) were reported in the array findings, corresponding to 76.8% deletions and 23.2% amplifications. The ETV6 gene deletion occurred in 4 of the patients, corresponding to 45% of the sample. The most common alterations above 1 Mb were deletion 6q (13%), 12p (12%) and 9p (8%), and duplication 4q (6%) and Xq (4%). Other genes important in ALL were also identified in this study including RUNX1, CDKN2A, FHIT, and PAX5. The array-CGH technique was able to detect microdeletion as small as 400 bp.


The results demonstrate the usefulness of high resolution array-CGH as a complementary tool in the investigation of ALL.

Array-based Comparative Genomic Hybridization; Acute lymphoblastic leukemia; ETV6/RUNX1