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Series GSE147381 Query DataSets for GSE147381
Status Public on Mar 24, 2020
Title Clinical significance of recurrent copy number abnormalities revealed by SNP array in childhood T-cell acute lymphoblastic leukemia
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary T-cell acute lymphoblastic leukemia (T-ALL) is a genetically highly heterogeneous disease, and numerous genetic aberrations in the leukemic genome are responsible for the biological and clinical differences among particular ALL subtypes. However, there is limited knowledge about the association of whole genome copy number abnormalities (CNAs) in childhood T-cell ALL with the course of leukemia and outcome. The aim of study was identification the pattern of whole genome CNAs in 86 newly diagnosed childhood T-ALL using a high-density single-nucleotide polymorphism (SNP) array.A series of bone marrow aspirates from 86 children with newly diagnosed T-ALL were analysed prior to any oncological treatment.
 
Overall design The researched material was the genomic DNA extracted from bone marrow samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany). The median leukemic cell count in collected bone marrow at diagnosis assessed by flow-cytometry was 82.43% (range 30–100). The concentration and quality of isolates were determined by spectrophotometry (NanoDrop 8000, Thermo Fisher Scientific, Waltham, United States). The microarray analyses were performed with the use of a CytoScan HD array (2 670 000 markers, including 750 000 single-nucleotide polymorphism (SNP) and 1 900 000 nonpolymorphic copy number variant (CNV) markers) (Applied Biosystems part of Thermo Fisher Scientific, Waltham, United States). All laboratory procedures were carried out according to the manufacturers' protocols.In total, 250 ng of the genomic DNA was analyzed in accordance with the manufacturers' protocols. The study was based on an analysis of scanned data files that was generated with the Chromosome Analysis Suite v 3.3 (ChAS, Thermo Fisher Scientific, Waltham, MA). Furthermore, the copy numbers of altered regions (CNAs) were calculated, and the data were normalized to a reference model (Thermo Fisher Scientific) of baseline reference intensities, NA 33 (hg19/CRCh37). The copy number states (CNS) and their breakpoints were determined with the use of the hidden Markov model (HMM) software package. The threshold levels of log2 ratio ≥0.5 and ≤0.5 were used for the categorization of the altered chromosomal regions as CNV gains and losses, respectively. The identification of normal diploid markers in the cancer samples constituted an essential part of the algorithm, which was particularly significant in highly sample-induced aberrations. Furthermore, unaltered diploid markers were used for the calibration of signals, resulting in a log2 ratio of 0 (e.g., copy number 2). The algorithm also indicated that the identified unaltered diploid markers could correspond with CN=4. In such a case, the log2 ratio was readjusted, and the chromosomal ploidy of 4 was reported. The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukemia-associated region/gene-specific CNAs (leukemia genes_all_20150505; Fullerton Overlap Map_hg19). The minimal number of probes was applied to determine the CNAs were 50 probes for duplication (gain) and 25 probes for deletion (loss). Copy number-neutral loss of heterozygosity is reported when greater than 3000 kbp in length. To further identify the genes involved in the CNVs, two databases were applied: the UCSC database (http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org). For microarray results copy number polymorphisms were excluded based on comparison with the Database of Genomic Variants (http://projects. tcag.ca/variation/)
 
Contributor(s) Lejman M, Włodarczyk M, Pastorczak A
Citation(s) 32766158
Submission date Mar 23, 2020
Last update date Aug 24, 2020
Contact name Monika Szelest
E-mail(s) m.wlodarczyk214@gmail.com
Phone +48515509301
Organization name Medical University of Lublin
Department Laboratory of Genetic Diagnostics
Street address ul. Antoniego Gębali 6
City Lublin
ZIP/Postal code 20-093
Country Poland
 
Platforms (1)
GPL16131 [CytoScanHD_Array] Affymetrix CytoScan HD Array
Samples (91)
GSM4427422 blast cells, bone marrow, 1478
GSM4427423 blast cells, bone marrow, Y02335
GSM4427424 blast cells, bone marrow, 907
Relations
BioProject PRJNA614469

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE147381_RAW.tar 10.9 Gb (http)(custom) TAR (of CEL, CYCHP)
Processed data included within Sample table
Processed data provided as supplementary file
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