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Series GSE190392 Query DataSets for GSE190392
Status Public on Dec 10, 2021
Title Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios [Omni2.5]
Organism Homo sapiens
Experiment type Genome variation profiling by array
SNP genotyping by SNP array
Summary Recurring genetic abnormalities have been identified in Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL). Among them, IKZF1 deletion was associated with poor prognosis in patients treated with imatinib-based or dasatinib-based regimens. However, the molecular determinants for clinical outcomes in ponatinib-treated patients remain unknown. We systematically analyzed genetic alterations in adults with Ph-positive ALL uniformly treated in clinical trials with dasatinib-based regimens or a ponatinib-based regimen and investigated the molecular determinants for treatment outcomes using pretreatment specimens collected from adults with Ph-positive ALL treated with Hyper-CVAD plus dasatinib or ponatinib. DNA sequencing and SNP microarray were performed and recurrent genetic abnormalities were found in 84% of the patients, among whom IKZF1 deletion was most frequently detected (60%). IKZF1 deletion frequently co-occurred with other copy-number abnormalities (IKZF1plus, 46%) and was significantly associated with unfavorable overall survival (OS) (false discovery rate < 0.1) and increased cumulative incidence of relapse (p = 0.01). In a multivariate analysis, dasatinib therapy, lack of achievement of 3-month complete molecular response, and the presence of IKZF1plus status were significantly associated with poor OS. The differential impact of IKZF1plus was largely restricted to patients given Hyper-CVAD plus ponatinib; dasatinib-based regimens had unfavorable outcomes regardless of the molecular abnormalities.
 
Overall design We report the results of SNP arrays using either IIllumina Infinium Omni-2.5 or Illumina Infinium CytoSNP-850K v1.2 BeadChip (Agilent Technologies, Santa Clara, CA, USA) for 99 samples obtained from patients with Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL).
We re-analyzed 99 individual hybridizations conducted on IIllumina Infinium Omni-2.5 and Illumina Infinium CytoSNP-850K v1.2 BeadChip.This series includes the 80 samples obtained from patients with Ph-positive ALL on Illumina Infinium Omni-2.5 Exome-8 Kit and 19 samples obtained from patients with Ph-positive ALL on Illumina Infinium CytoSNP-850K v1.2 BeadChip. Samples were either bone marrow aspirate or peripheral blood obtained from previously untreated patients.
Genomic DNA extracted from leukemic cell was genotyped using IIllumina Infinium Omni-2.5 Kit.
 
Contributor(s) Sasaki Y, Takahashi K, Uryu H
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Submission date Dec 07, 2021
Last update date Dec 11, 2021
Contact name Yuya Sasaki
E-mail(s) imagingbio0311@gmail.com
Organization name M.D. Anderson Cancer Center
Street address 1515 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77054
Country USA
 
Platforms (1)
GPL18952 Illumina HumanOmni2.5-8v1.1 beadchip
Samples (80)
GSM5722884 Bone marrow cells - SNP array (1003312-3)
GSM5722885 Bone marrow cells - SNP array (1009724-4)
GSM5722886 Bone marrow cells - SNP array (1012121-11)
This SubSeries is part of SuperSeries:
GSE190397 Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL)
Relations
BioProject PRJNA786931

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
GSE190392_Omni2.5_matrix.Processed.GEO.ID.txt.gz 1.7 Gb (ftp)(http) TXT
GSE190392_Omni2.5_matrix.Signal.GEO.ID.txt.gz 1.6 Gb (ftp)(http) TXT
GSE190392_RAW.tar 292.6 Mb (http)(custom) TAR
Processed data are available on Series record
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