Genetics Microarray Comparative Genomic Hybridization To Detect Abnormalities In Children With Acute Lymphoblastic Leukemia

Childhood acute lymphoblastic leukemia is the most commonchildhood malignancy, accounting for30%of childhood cancer.Division of different risk groups depends on age of onset, whiteblood cell count at diagnosis, immunology, cytogenetics, andprednisone induced reaction. Chemotherapy based on differentrisk groups improved prognosis significantly, especially acutelymphoblastic leukemia (ALL),which clinical cure rateapproaching80%, but15-20%of ALL will relapse eventually andbecome the most common cause of cancer-related death，which5-year disease-free survival is only10-40%.Unfortunately,Small number of children with the low-risk or good cytogeneticmarkers would be faced with treatment failure or relapse,indicating that the leukemia concealed submicroscopicaberration of genetic material. The conventional cellular andmolecular genetic techniques have their own advantages in thedetection of chromosomal numeriacal or structuralabnormalities， but are restricted in the detection ofsubmicroscopic and cryptic genomic lesions. For example，theG-banding karyotype analysis technology may complete the macroanalysis of the full set of chromosomal number and structure,but the failure of the leukemia cell culture andovergrowth of the normal cell account for40%of cases,theresolution is less than5-10Mb， and the interpretations of thekaryotype between different laboratories are not entirelyconsistent. Fluorescence in situ hybridization (FISH) candetect submicroscopic chromosomal structural abnormalities(the resolution determined by the probe size is about100Kb),but can detect only established or suspected chromosomalabnormalities. Therefore, only a few targeted probes can usefor the detection of genomic variations in targeted regions,can not do the whole genome screening. Microarray comparativegenomic hybridization (array CGH) is a genome-wide screeningtechniques with high-resolution, high-throughput, highefficiency,which can detect submicroscopic chromosomalabnormalities (microduplications or microdeletions),candefine accurately the positioning of breaking point and improvethe resolution to100kb.Array CGH is a powerful tool todetecting unbalanced chromosomal aberrations and cancompensate for the limitations of the conventional approaches.In this study,this technology is used for detecting the geneticabnormalities in childhood acute lymphoblastic leukemia and weassess the value of genetic diagnosis using the technology in children with acute lymphoblastic leukemia.一、 Objection1Analysis the genetic abnormalities of children with acutelymphoblastic leukemia by array CGH,investigation of theapplication value of detecting for genetics abnormalities ofleukemia.2Screening the genome-wide DNA copy number aberrations in thechildren with acute lymphoblastic leukemia,finding the newrecurring chromosomal abnormalities.二、Method1All of19DNA samples were perfomed genome-wide hybridizationand scanning according to the standard operation procedure ofCytoScan HD Array(Affymetrix) and performed analysis of copynumber variants using Chromosome Analysis Suite software.2To query database and retrive literature(1) Querying database of genomic variants(http://projects.tcag.ca/variation; GRCh37, Feb2009),to exclude the copynumber polymorphism.(2) Querying OMIM、NCBI、Ensembl,to study whether the relatedgene or chromosomal segments associated with leukemia.(3) To retrive literatures using the search terms “leukemia”、“cancer”、“Acute lymphoblastic leukemia”、“childhood”、 “copy number aberration/variants”、“array Comparative GenomicHybridization”、“genetics”、and gene or chromosomal segmentsrelated copy number variants such as“1q44”、“IKZF1”in Pubmedand to compare to the results in this study.三、Results1、Copy number changes were detected in every children，whichinvoling chromosome numbers is from4to11, the most commonlyabnormalities involving the minimal common regions of copynumber changes (MCR) were1q44,8p11.22,9p21.3,12p13.31,12q21.3,14q32.33,22q11.22.2、Several leukemia-related genes and cancer candidate genes,including CDKN2A, CDKN2B, PAX5, BTG1, IKZF1, OR2C3, VPREB1weredetected in small samples，while ETV6(often involved in thetranslocation, lesser in the loss)、 JAK2(gene mutation),ARID5B could not be detected， might be related to the smallnumber of samples。3、Patient0819251was diagnosed with ALL-L2,Pro-B,HR andBCR-ABL1negative,the loss of CDKN2A/CDKN2B (9p21.3)、PAX5(9p) and IKZF1(7p12.2) were detected by array CGH and the sizesof the copy numbers were101Kb、118Kb、109Kb， respectively.Loss of copy numbers of these genes would resulted in theprogression or early recurrence of disease. Early recurrence and progress quickly were observed in the patient.The sizes ofcopy numbers were below200Kb, which confirming the highsensitivity and high resolution of the technology.四、Conclusion1、Olig-array CGH is a new technology with important value inthe genetic analysis of leukemia, it can easily detect <5Mbsubmicroscopic and cryptic chromosomal abnormalities thatinvolved candidate genes or related gene of disease,and candefine accurately the positioning of the breaking point.2、Olig-chip is restricted in genetic analysis of tumors, ifcopy number variation of the leukemia is research purpose，the calculation method of analysis software or the biologicalcomplexity of the sample should be improved.