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Affymetrix SNP array data for B-lineage acute lymphoblastic leukemia

ABSTRACT: To shed light on the molecular bases of B-lineage acute lymphoblastic leukemia lacking known rearrangements (B-NEG ALL) and the differences between children and adults, we analyzed 168 B-NEG ALLs - including children, adolescents/young adults (AYA) and adults by genome-wide technologies, namely Next-generation sequencing and copy number aberration (CNA). Affymetrix SNP array analysis was performed according to the manufacturer's directions on DNA extracted from bone marrow sampled at diagnosis and paired germline DNA extracted from peripheral blood/bone marrow at complete remission or saliva.

ORGANISM(S): Homo sapiens

PROVIDER: GSE67405 | GEO | 2016/03/01

SECONDARY ACCESSION(S): PRJNA279840

REPOSITORIES: GEO

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Affymetrix SNP array data for B-lineage acute lymphoblastic leukemia

Project description:To shed light on the molecular bases of B-lineage acute lymphoblastic leukemia lacking known rearrangements (B-NEG ALL) and the differences between children and adults, we analyzed 168 B-NEG ALLs - including children, adolescents/young adults (AYA) and adults by genome-wide technologies, namely Next-generation sequencing and copy number aberration (CNA). Affymetrix SNP array analysis was performed according to the manufacturer's directions on DNA extracted from bone marrow sampled at diagnosis and paired germline DNA extracted from peripheral blood/bone marrow at complete remission or saliva. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 13 B-NEG ALL samples and their paired normal (non-tumoral) DNA samples, included in the discovery panel, processed in the same experiment and deposited.

2016-03-01 | E-GEOD-67405 | biostudies-arrayexpress

miRNA expression profile in pediatric and adolescent and young adult rhabdomyosarcomas

Project description:Adolescents and young adults (AYA) with rhabdomyosarcoma (RMS) form a subgroup of patients whose optimal clinical management and best possible access to care remain a challenge and survival lacks behind that of children while diagnosed with histologically similar tumors. Understanding the tumor biology that differentiate children from AYA-RMS could provide critical information and drive new initiatives to improve their final outcome. MiRNA profile was evaluated in a RMS series of 49 tumor and 13 non-neoplastic tissues. MiRNAs analysis identified miR-223 over-expression and mir-431 down-regulation in AYA, validated by Real-Time PCR and miRNA ISH.

2019-11-05 | GSE135518 | GEO

Gene expression profiling in pediatric and adolescent and young adult rhabdomyosarcomas

Project description:Adolescents and young adults (AYA) with rhabdomyosarcoma (RMS) form a subgroup of patients whose optimal clinical management and best possible access to care remain a challenge and survival lacks behind that of children while diagnosed with histologically similar tumors. Understanding the tumor biology that differentiate children from AYA-RMS could provide critical information and drive new initiatives to improve their final outcome. Gene expression profiling was evaluated in a RMS series of 48 tumor and 13 non-neoplastic tissues. GEP analysis detected 793 age-correlated genes in tumors. NOTCH2, FGFR1 were significantly down-modulated in AYA-RMS. GEP showed an increase in CD4 memory resting cells and a decrease in γδ T-cells in AYA-RMS. IHC analysis demonstrated an increase of infiltrated CD4, CD8 and neutrophils in AYA-RMS tumors.

2019-11-05 | GSE135517 | GEO

Transcription profiling of composite bone marrow from healthy humans to investigate age related gene expression changes

Project description:Human bone marrow is a complex, diversified and well-organized hematopoietic network changing composition with age. The purpose of this study was to analyze variations in relative precursor B cell abundance in bone marrow with age by means of global gene expression profiling. RNA was isolated from composite bone marrow from 25 healthy children, adolescents and adults age 2 months to 28 years. As reference transcript for precursor B cells we used recombination activating gene RAG1 exploring the data for other transcripts showing the same profile as RAG1 with age. We identified 54 genes with correlated expression profiles to RAG1 (r ? 0.9, p = 0), characterized by high expression at 3 - 20 months followed by a fast decline to lower signal levels maintained until early adulthood. Immunophenotyping from a similar healthy age-matched cohort (n = 37) showed a comparable decrease of precursor B cells. Of the 54 genes 15 were characteristically B cell associated representing cell surface molecules (CD19, CD72, CD79A, CD79B, CD180, IGL@, IGLL1, VPREB1, VPREB3), a signal transduction molecule (BLNK) and transcription factors (DNTT, EBF1, PAX5, POU2AF1, RAG2). Of the remaining transcripts some may represent novel B cell transcripts or genes involved in control of B cells. Bone marrow was obtained from healthy children eligible for elective minor surgery and voluntary health care workers. The bone marrow samples (2.5ml) were immediately after aspiration transferred to PAXgene tubes for mRNA stabilization before RNA extraction and hybridization on Affymetrix microarrays. To that end, the study presents a picture of the total marrow activity with minimal manipulation that would otherwise influence gene expression results. We used microarrays to determine age-related changes in precursor B cell transcripts in bone marrow from 25 healthy children and adults and searched for other transcripts showing the same expression profile with age.

2009-12-30 | E-GEOD-11504 | biostudies-arrayexpress

Long-read transcriptome sequencing reveals expression characteristics of osteosarcoma

Project description:Osteosarcoma is the most common primary bone cancer in children, adolescents and young adults. It is a rare cancer type. To comprehensively reveal the transcriptomic characteristics of osteosarcoma, we performed Oxford Nanopore Technologies (ONT) long-read RNA-Seq of tumor and adjacent normal tissues from 23 patients with osteosarcoma.

2023-07-19 | GSE218035 | GEO

Full-length, single cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity

Project description:Here, we investigate the extent to which individual cells within the total bone marrow (tot-BM) and the lineage negative (Lin-neg) populations exhibit this isoform diversity and whether distinct subpopulations in tot-BM and Lin-neg cells intersect based on transcript isoform usage. We extracted healthy donor human bone marrow tissues from discarded harvesting filters. From this total bone marrow cell preparation (tot-BM) we enriched for lineage-negative progenitor cells (Lin-neg) by magnetic selection as described earlier (Deslattes Mays et al. 2019). We then analyzed total and Lin-neg cell populations by droplet-based single cell RNA sequencing (10xGenomics). In order to increase the number of mRNA molecules detectable per cell we reduced the cell input to approximately 500 cells for each experiment. After single-cell selection, the barcoded cDNA libraries were equally divided and each pool was analyzed in parallel by short-read sequencing (Illumina) and by single-molecule real-time (SMRT) full-length RNA sequencing (Pacific Biosciences).

2023-04-06 | GSE181160 | GEO

In silico analyses of survival-associated microRNA signatures in pediatric osteosarcoma

2016-03-22 | GSE79181 | GEO

In silico analyses of survival-associated microRNA signatures in pediatric osteosarcoma

Project description:Osteosarcoma is the most common bone tumor in children, adolescents, and young adults. In contrast to other childhood malignancies, no biomarkers have been consistently identified as predictors of outcome. This study was conducted to assess the microRNAs (miRs) expression signatures in pre-treatment osteosarcoma specimens and correlate with outcome to identify biomarkers for disease relapse The cohort consisted of 25 patients of 70% Mexican-American ethnicity. High-throughput RT-qPCR approach was used to generate quantitative expression of 754 miRs in the human genome.

2016-03-22 | E-GEOD-79181 | biostudies-arrayexpress

Project description:Children, Adolescents, and Young Adults with Solid Tumors

| PRJNA559601 | ENA

Project description:Human bone marrow is a complex, diversified and well-organized hematopoietic network changing composition with age. The purpose of this study was to analyze variations in relative precursor B cell abundance in bone marrow with age by means of global gene expression profiling. RNA was isolated from composite bone marrow from 25 healthy children, adolescents and adults age 2 months to 28 years. As reference transcript for precursor B cells we used recombination activating gene RAG1 exploring the data for other transcripts showing the same profile as RAG1 with age. We identified 54 genes with correlated expression profiles to RAG1 (r ≥ 0.9, p = 0), characterized by high expression at 3 - 20 months followed by a fast decline to lower signal levels maintained until early adulthood. Immunophenotyping from a similar healthy age-matched cohort (n = 37) showed a comparable decrease of precursor B cells. Of the 54 genes 15 were characteristically B cell associated representing cell surface molecules (CD19, CD72, CD79A, CD79B, CD180, IGL@, IGLL1, VPREB1, VPREB3), a signal transduction molecule (BLNK) and transcription factors (DNTT, EBF1, PAX5, POU2AF1, RAG2). Of the remaining transcripts some may represent novel B cell transcripts or genes involved in control of B cells. Bone marrow was obtained from healthy children eligible for elective minor surgery and voluntary health care workers. The bone marrow samples (2.5ml) were immediately after aspiration transferred to PAXgene tubes for mRNA stabilization before RNA extraction and hybridization on Affymetrix microarrays. To that end, the study presents a picture of the total marrow activity with minimal manipulation that would otherwise influence gene expression results.

2009-12-31 | GSE11504 | GEO

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