35549e9c-f1f9-4722-8181-ec8c3cd8fbbf - samples
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ABSTRACT:
PROVIDER: EGAD00001005120 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:MASQ targeted amplicon sequencing of AML blood or bone marrow at presentation, and relapse, when available, for 5 patients. Remission samples of both blood and bone marrow are included for 5 patients. Multiple batches (b1,b2) are used for 2 patients. There are 25 assays of AML data. MASQ data demonstrating sensitivity, input range, and batch size are also included, as 12 assays. All data is provided in paired FASTQ files.
| EGAD00001005121 | EGA
Project description:Mutations in the nucleophosmin 1 (NPM1) gene are considered as a founder event in the pathogenesis of acute myeloid leukemia (AML). To address the role of clonal evolution in relapsed NPM1 mutated (NPM1mut) AML, we applied high-resolution genome-wide single-nucleotide polymorphism (SNP) array profiling to detect copy number alterations (CNA) and uniparental disomies (UPD) and performed comprehensive gene mutation screening in 53 paired bone marrow/peripheral blood samples obtained at diagnosis and relapse. At diagnosis, 15 aberrations (CNAs, n=10; UPDs, n=5) were identified in 13 patients (25%), whereas at relapse 56 genomic alterations (CNAs, n=46; UPDs, n=10) were detected in 29 patients (55%) indicating an increase in genomic complexity. Recurrent aberrations acquired at relapse included deletions affecting tumor suppressor genes [ETV6 (n=3), TP53 (n=2), NF1 (n=2), WT1 (n=3), FHIT (n=2)] and homozygous FLT3 mutations acquired via UPD13q (n=7). DNMT3A mutations (DNMT3Amut) showed the highest stability (97%). Persistence of DNMT3Amut in 5 patients who lost NPM1mut at relapse suggests that DNMT3Amut may precede NPM1mut in AML pathogenesis. Of note, all relapse samples shared at least one genetic aberration with the matched primary AML sample implying common ancestral clones. In conclusion, our study reveals novel insights into clonal evolution in NPM1mut AML. Bone marrow or peripheral blood samples from diagnosis, remission and relapse of 53 NPM1 mutated AML patient were analyzed on the Affymetrix Genome-Wide Human SNP 6.0 Array. Raw data (CEL-Files) were transformed to genotyping files (CHP) with Genotyping Console Version 4.2 from Affymetrix. Bioinformatic evaluation of CNAs was performed using dChipSNP and circular binary segmentation .
2013-05-30 | E-GEOD-46951 | biostudies-arrayexpress
Project description:In high income countries 90% of the patients achieve complete remission after induction chemotherapy. However, 30-40% of these patients suffer from relapse. These patients face a dismal prognosis, as the majority (>60%) of relapsed patients die within 5 years. As a result, outcome for pediatric acute myeloid leukemia (AML) patients remains poor and has stabilized over the past 15 years. To prevent or better treat relapse of AML is the best option to improve outcome. Despite patient specific differences, most patients do respond to initial therapy. This suggests that at relapse, mechanisms are active that cause the altered response to chemotherapy. Detailed understanding of mechanisms that cause relapse remain largely elusive. To gain insight in the molecular pathways that characterize relapsed AML, we performed genome wide gene expression profiling on paired initial diagnosis and relapsed AML samples of 23 pediatric AML patients. We used pathway analysis to find which molecular pathways are involved in altered gene expression between diagnosis and relapse samples of individual AML patients. 23 paired diagnosis and relapse bone marrow or peripheral blood samples were collected and cryo-preserved. They were later thawed and processed for hybridization to Affymetrix U133 Plus 2.0 arrays.
2015-05-07 | E-GEOD-52891 | biostudies-arrayexpress
Project description:Genome-wide analysis of single nucleotide polymorphisms in 64 acute myeloid leukemias has revealed that 20% exhibited large regions of homozygosity that could not be accounted for by visible chromosomal abnormalities in the karyotype. Further analysis confirmed that these patterns were due to partial uniparental disomy (UPD). Remission bone marrow was available from five patients showing UPD in their leukemias, and in all cases the homozygosity was found to be restricted to the leukemic clone. Two examples of UPD11p were shown to be of different parental origin as indicated by the methylation pattern of the H19 gene. Furthermore, a previously identified homozygous mutation in the CEBPA gene coincided with a large-scale UPD on chromosome 19. These cryptic chromosomal abnormalities, which seem to be nonrandom, have the characteristics of somatic recombination events and may define an important new subclass of leukemia. Patient No. from Table 1 of Raghavan et al 2005 and Sample name; Patient No: 1 = Sample name: AML sample 35 diagnosis; Patient No: 1 = Sample name: AML sample 107 remission; Patient No: 2 = Sample name: AML sample 37 diagnosis; Patient No: 3 = Sample name: AML sample 10 diagnosis; Patient No: 3 = Sample name: AML sample 44 remission; Patient No: 4 = Sample name: AML sample 20 diagnosis; Patient No: 5 = Sample name: AML sample 65 diagnosis; Patient No: 6 = Sample name: AML sample 69 diagnosis; Patient No: 6 = Sample name: AML sample 94 remission; Patient No: 7 = Sample name: AML sample 40 diagnosis; Patient No: 7 = Sample name: AML sample 41 remission; Patient No: 8 = Sample name: AML sample 64 diagnosis; Patient No: 9 = Sample name: AML sample 7 diagnosis; Patient No: 10 = Sample name: AML sample 49 diagnosis; Patient No: 10 = Sample name: AML sample 106 remission; Patient No: 11 = Sample name: AML sample 76 diagnosis; Patient No: 12 = Sample name: AML sample 79 diagnosis Experiment Overall Design: DNA from 64 diagnostic AML samples were analysed using Affymetrix 10K SNP arrays. Large regions of homozygosity were identified and compared with remission bone marrow where available.
2008-06-15 | E-GEOD-7490 | biostudies-arrayexpress
Project description:Genome-wide DNA methylation profiling of diagnosis, complete remission and disease relapse samples of an AML case with complex and unusual DNMT3A mutational profile. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs from bone marrow samples at the three different conditions of disease.
2022-05-10 | GSE202488 | GEO
Project description:In this study, serum from bone marrow and peripheral blood was collected from patients with newly diagnosed MM (NDMM), RRMM, and MM in remission as well as healthy controls. Mass spectrometry-based tandem mass tag-labeled quantitative proteomics was applied to measure the levels of more than 1000 proteins in the serum. The results revealed the low expression of thrombospondin-1 (THBS1) and lactoferrin (LTF) in the bone marrow serum of patients with RRMM, indicating that these proteins are associated with MM relapse. The enzyme-linked immunosorbent assay (ELISA) results also revealed that THBS1 and LTF were downregulated in the bone marrow serum of patients with RRMM compared with the findings in patients with NDMM, and their levels in peripheral blood serum in the RRMM group were much lower than those in the NDMM, MM in remission, and healthy control groups. Based on the proteomics and ELISA data, the protein signature THBS1/LTF could contribute to the prediction of MM relapse.
2023-09-22 | PXD045583 |
Project description:Acute myeloid leukemia (AML) is an aggressive blood cancer with poor prognosis. We performed a comprehensive proteogenomic analysis of bone-marrow biopsies from 252 uniformly treated AML patients to elucidate the molecular pathophysiology of AML in order to inform future diagnostic and therapeutic approaches. In addition to in-depth quantitative proteomics, our analysis included cytogenetic and mutation profiling, and RNA sequencing. This identified five proteomic AML subtypes, each reflecting specific biological features spanning genomic boundaries. Two of these subtypes were correlated with patient outcome, but none exclusively associated with specific genomic aberrations. Remarkably, one subtype (Mito-AML), which was only captured in the proteome, was characterized by high expression of mitochondrial proteins and showed poor outcome, with reduced remission rate and shorter overall survival upon treatment with intensive induction chemotherapy. Functional analyses revealed that Mito-AML is metabolically wired towards stronger complex Idependent respiration and is more responsive to treatment with the BCL2-inhibitor venetoclax.
2022-03-08 | PXD028007 | Pride
Project description:Gene expression profile at single cell level of bone marrow (BM) T cells and hematopoietic stem and progenitor cells (HSPCs) of acute myeloid leukemia patients post allogeneic stem cell transplantation (alloSCT) of patients in complete remission (CR) and relapse (REL).
2024-01-11 | GSE216187 | GEO
Project description:We analyzed transcriptome data from above 50K single leukemia bone marrow cells across 3 patients during newly diagnosed, complete remission and relapse stages. These 3 patients belong to M4 or M5, according to French-American-British classification. We analyze heterogeneity of acute myeloid leukemia during progression and identify novel relapse subgroups in these heterogeneous populations.
2025-04-17 | GSE201966 | GEO
Project description:Identification of de novo copy number abnormalities arising in relapsed paediatric ALL in matched presentation and relapse samples. We identified deletions of BACH2, (BTB and CNC homology 1, basic leucine zipper transcription factor 2) at relapse. To study the role of Bach2 in pre-B ALL in a genetic experiment, we transformed pre-B cells from Bach2–/– mice with BCR-ABL1. Our findings identify Bach2 as a novel tumor suppressor upstream of p53 in pre-B ALL. 64 arrays (32 250K Nsp and 32 250K Sty) are included in this study. DNA was extracted from the presentation and relapse samples from 11 paediatric patients and DNA was extarcted from the remission samples from 10 patient and hybridised to the Affymetrix Human Mapping 500K Array Set.
2013-12-21 | E-GEOD-43060 | biostudies-arrayexpress