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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
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)
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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