Project description:Except for the well-known association with Down syndrome, there is little information on the genetic factors predisposing to acute myeloid leukemia. Germinal gene copy-number variations may represent risk factors for the disease. To identify copy number variants present in both normal and leukemic cells, we compared the Comparative Genomic Hybridization profiles of the blasts and healthy cells (CD3+ cells or peripheral lymphocytes during remission) of 13 patients (SET-A) and the blasts of a further 12 normal-karyotype acute myeloid leukemia patients (SET-B) for which only blasts DNA were available.
Project description:Pediatric patients with de novo acute myeloid leukemia. To define genomic architecture, we performed genome-wide copy number abberation analysis in 460 paired diagnostic-remission bone marrow aspirates. Illumina SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic and remission bone marrow samples.
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.
Project description:aCGH was performed on acute myeloid leukemia samples (vs constitutive Normal matched tissue) derived from a mouse model of mutant NPM1, NRAS and FLIT3 normal karyotype leukemia. The purpose of these assays was to identify common and potentially co-operative genetic phenomena in NPM1c positive mouse leukemias.
Project description:250k Sty, 250k Nsp, 250k Hind and 250k Xba Affymetrix SNP arrays for 50 leukemia remission samples used as controls for copy number analysis for GSE9109 and GSE9112. Keywords: Acute leukemia, BCR-ABL1, chronic myeloid leukemia, copy number analysis, loss-of-heterozygosity, genomics *** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***
Project description:Copy number and LOH analysis was performed for 56 chronic myeloid leukemia cases obtained from 23 CML cases obtained atchronic phase, accelerated phase, blast crisis, or remission. All caseswere genotyped with Affymetrix 250k Sty and Nsp arrays. Keywords: Acute leukemia, BCR-ABL1, chronic myeloid leukemia, copy number analysis, loss-of-heterozygosity, genomics *** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***
Project description:SNP profiling can reveal copy number abnormalities and loss of heterozygosity associated with distinct biologic subtypes of acute lymphoblastic leukemia (ALL). We performed SNP profiling of Down syndrome ALL cases and controls to identify unique biologic features of this ALL subgroup. Ficoll-enriched, cryopreserved bone marrow aspirate samples were obtained from patients with B-precursor ALL at diagnosis and in remission; and from control patients without 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.
Project description:Comparison of copy number variations of acute myeloid leukemia mononuclear cells and the given cell types collected during complete remission of the acute myeloid leukemia
Project description:We applied a novel approach of parallel transcriptional analysis of multiple, highly fractionated stem and progenitor populations from patients with acute myeloid leukemia (AML) and a normal karyotype. We isolated phenotypic long-term HSC (LT-HSC), short-term HSC (ST-HSC), and committed granulocyte-monocyte progenitors (GMP) from individual patients, and measured gene expression profiles of each population, and in comparison to their phenotypic counterparts from age-matched healthy controls.
