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Impaired B-lymphocyte immunity in acute myeloid leukemia patients after chemotherapy

ABSTRACT: We analyzed via microarray gene expression profiles in de-identified, clinically annotated samples from Ficoll-purified peripheral blood samples from 10 acute myeloid leukemia (AML) patients in remission and 10 healthy donors collected under IRB-approved protocols.

ORGANISM(S): Homo sapiens

PROVIDER: GSE97485 | GEO | 2017/08/11

SECONDARY ACCESSION(S): PRJNA381960

REPOSITORIES: GEO

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Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues.

Project description:We analyzed using quantitative real-time PCR (qRT-PCR), gene expression of 65 potential leukemia associated antigens in de-identified, clinically annotated samples from ficoll purified peripheral blood samples from 30 newly diagnosed untreated AML patients collected under IRB-approved protocols from three NCCN cancer centers.

2016-11-24 | GSE52756 | GEO

Expression of putative targets of immunotherapy in acute myeloid leukemia and healthy tissues.

Project description:We analyzed using quantitative real-time PCR (qRT-PCR), gene expression of 65 potential leukemia associated antigens in de-identified, clinically annotated samples from ficoll purified peripheral blood samples from 22 newly diagnosed untreated AML patients collected under IRB-approved protocols from three NCCN cancer centers.

2017-01-21 | GSE53948 | GEO

The Immunome in Two Inherited Forms of Pulmonary Fibrosis

Project description:We analyzed via microarray gene expression profiles from patients with familial pulmonary fibrosis and HPS-1 pulmonary fibrosis collected under IRB-approved protocols.

2018-01-10 | GSE107797 | GEO

Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Affymetrix SNP array data]

Project description:Background: Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries. Methods: Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays and Illumina mRNA expression arrays as well as Illumina sequencing of the coding regions of 384 genes belonging to various pathways known to be altered in other cancers. Results: Genetic alterations were observed in the WNT, Hedgehog, cell cycle, DNA damage and epithelial-to-mesenchymal-transition pathways. Conclusions: The data suggests targeted therapies approved or in clinical development for gastric carcinoma would be of benefit to ~22% of the patients studied. In addition, the novel mutations detected here, are likely to influence clinical response and suggest new targets for drug discovery. DNA and RNA samples were obtained from hospitals in Russia and Vietnam according to IRB approved Protocols and with IRB approved consent forms from which informed consents were given for molecular and genetic analysis. The medical centres themselves also have internal ethical committees with reviewed the protocol and ICFs. The samples were sourced through Tissue Solutions Ltd (http://www.tissue-solutions.com/). Genotypes and copy number profiles were generated for each samples using 1 ug of DNA run on Affymetrix SNP V6 arrays using Affymetrix protocols.

2012-10-25 | E-GEOD-29996 | biostudies-arrayexpress

Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Illumina mRNA expression array data]

Project description:Background: Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries. Methods: Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays and Illumina mRNA expression arrays as well as Illumina sequencing of the coding regions of 384 genes belonging to various pathways known to be altered in other cancers. Results: Genetic alterations were observed in the WNT, Hedgehog, cell cycle, DNA damage and epithelial-to-mesenchymal-transition pathways. Conclusions: The data suggests targeted therapies approved or in clinical development for gastric carcinoma would be of benefit to ~22% of the patients studied. In addition, the novel mutations detected here, are likely to influence clinical response and suggest new targets for drug discovery. DNA and RNA samples were obtained from hospitals in Russia and Vietnam according to IRB approved Protocols and with IRB approved consent forms from which informed consents were given for molecular and genetic analysis. The medical centres themselves also have internal ethical committees with reviewed the protocol and ICFs. The samples were sourced through Tissue Solutions Ltd (http://www.tissue-solutions.com/). Gene expression profiles were generated using Illumina mRNA expression arrays.

2012-10-25 | E-GEOD-29998 | biostudies-arrayexpress

Transcription profiling of human cisplatin based chemotherarpy adult male germ cell tumor patients - validation set for prediction of outcome

Project description:This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 2003. The tumor samples consist of 34 NSGCT specimens. RNA was isolated, labeled, and hybridized to Affymetrix U133A and U133B microarrays using standard protocols. Data were processed by the RMA method.

2008-10-26 | E-GEOD-10783 | biostudies-arrayexpress

Expression data from human PBMCs from breast cancer patients and controls

Project description:We analyzed gene expression in human peripheral blood mononuclear cells (PBMCs) from breast cancer patients, patients with benign breast abnormalities, healthy cancer-free individuals as well as patients with other types of cancer (gastrointestinal and brain cancers). Peripheral blood mononuclear cell (PBMC) samples were collected from women with a suspect initial mammogram prior to undergoing a diagnostic biopsy procedure to determine whether the detected abnormality was benign or malignant. In total, we collected blood from 57 women with a diagnosis of breast cancer and 37 with a benign diagnosis. We also collected blood from 31 women with normal initial mammograms as negative controls and 15 breast cancer patients following surgery. All breast cancer patient samples were collected at the Duke University Medical Center (DUMC) under an institutional review board (IRB)-approved protocol (Duke eIRB#12025) after obtaining informed consent and were provided by Dr. Jeffrey Marks. PBMC samples from patients with various gastrointestinal cancers (n=15) were colelcted and stored at DUMC under IRB-approved protocols (Duke eIRB#12010 and 12025) and were provided by Dr. Jeffrey Marks. Peripheral blood leukocyte samples from patients with brain tumors (n=7) were provided by Dr. John Sampson and were collected by leukapheresis under Duke eIRB#00003877 and #00009403.

2011-03-01 | E-GEOD-27562 | biostudies-arrayexpress

head and neck squamous cell carcinoma samples

Project description:Patient selection and specimen collection. Thirty-six freshly frozen tumor samples were prospectively collected from patients undergoing surgery or biopsy for HNSCC at the University of North Carolina (UNC) at Chapel Hill (21 patients) and Vanderbilt University (15 patients). All tissues were snap-frozen in liquid nitrogen within 30 minutes of surgical resection or biopsy, and kept at -80oC until further processing. All patients consented to participation in this study under protocols approved by IRB at the two institutions. This set includes the samples previously deposited into GEO including 8 additional samples and adjustment for protocol changes. The original 36 before protocol changes (and thus unadjusted) are here: Slebos RJ, Yi Y, Ely K, et al. Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma. Clin Cancer Res 2006;12(3 Pt 1):701-9. Keywords: disease state analysis

2009-03-22 | GSE10300 | GEO

Immunohistochemical and Clinical Characterization of the Basal-like Subtype

Project description:3 fresh frozen Breast tumor from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. Each experimental sample was ssayed versus a common reference sample that was a modified version of the Stratagene Human Universal Reference (which was further augmented with a 1/10 amount of MCF7 mRNA and 1/10 amount of ME16C mRNA) Keywords = Agilent microarray Keywords = EGFR Keywords = keratin Keywords: parallel sample

2004-10-15 | GSE1319 | GEO

Expression data from skin biopsy samples from patients with moderate-to-severe psoriasis

Project description:A gene expression profiling sub-study was conducted in which skin biopsy samples were collected from 85 patients with moderate-to-severe psoriasis who were participating in ACCEPT, an IRB-approved Phase 3, multicenter, randomized trial. This analysis identified 4,175 probe-sets as being significantly modulated in psoriasis lesions (LS) compared with matched biopsies of non-lesional (NL) skin.

2012-07-26 | GSE30999 | GEO

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