Gene expression profiling of biphenotypic acute leukemia
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Aniko Szabo
PROVIDER: E-MTAB-5014 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Acute lymphoblastic leukemia (ALL) is characterized by the accumulation of somatic genetic alterations in B- or T-lymphoid precursor cells eventually resulting in overt leukemia. Contrary to paediatric ALL, its adult counterpart is rather scarcely researched. Early studies demonstrated that gene expression profiling (GEP) is a valuable tool for subgroup identification and risk stratification. This submission of 192 ALL (137 B-cell ALL [B-ALL] and 55 T-cell ALL [T-ALL]) cases characterized on gene expression microarrays serves as a repository for multiple studies examining the leukemogenic mechanisms underlying overt ALL establishment. After informed consent, bone marrow aspirates or peripheral blood samples of a representative cohort of 192 adult ALL patients were collected. Eligible patients had a diagnosis of primary ALL confirmed by cytological examination and immunophenotyping of blood and bone marrow. The majority of these cases were treated following the HOVON (Dutch-Belgian Hematology-Oncology Co-operative group) protocols (http://www.hovon.nl). All studies were approved through the institutional ethics review board and all patients provided written informed consent in accordance to the declaration of Helsinki. Survival data for these patients are captured but not shared publicly for data protection purposes, and will only be available on a case-by-case basis upon specific request, which are likely to be made in a collaborative structure. Blasts and mononuclear cells were purified by Ficoll-Hypaque (Nygaard, Oslo, Norway) centrifugation and cryopreserved. All samples contained 80-to-100 percent blast cells after thawing, regardless of the blast count at diagnosis. RNA isolation was performed as previously described (Valk et al., Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia, New England Journal of Medicine, 2004). <br>Complementary genotyping data from the same study have also been deposited at ArrayExpress, under accession number E-MTAB-5036 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5036/ ). A supplementary file 'DNA_RNA_link_numbers.xlsx' is also provided allowing RNA samples in this submission to be mapped against equivalent DNA sample in E-MTAB-5036.</br>
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Project description:The pretreatment karyotype of leukemic blasts is currently the key determinant in therapy decision-making in acute myeloid leukemia (AML). However, approximately fifty percent of AML patients, often carrying a normal karyotype, are currently unclassifiable based these established methods. Gene expression profiling has proven to be valuable for risk stratification of AML. This is a repository of 662 adult AML cases characterized on gene expression microarrays and used for different studies investigating the mechanisms underlying leukemogenesis. Bone marrow aspirates or peripheral blood samples of three independent representative cohorts of de novo AML patients, comprising 277, 256 and 129 cases respectively, were collected at diagnosis. Gene expression profiling was performed on 662 adult AML patients who have been treated according to Dutch-Belgian Hemato-Oncology Cooperative Group and the Swiss Group for Clinical Cancer Research (HOVON/SAKK) AML-04, -04A, -29, -32, -42, -42A, -43 and -92 protocols (available at http://www.hovon.nl). All patients provided written informed consent in accordance with the Declaration of Helsinki, and the study was approved by all participating institutional review boards. Blast cell purification and RNA isolation were performed as previously described (Valk et al., Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia, New England Journal of Medicine, 2004).
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