Affymetrix SNP array data for acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS)
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Ayana Kon
PROVIDER: E-GEOD-47682 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen tissues. To obtain a profile of copy number alterations in RMS, we studied 65 samples in 60 RMS cases. Other data of 38 samples are deposited in GSE41263: GSM1528059 GSM1528057 GSM1528061 GSM1528058 GSM1528054 GSM1528060 GSM1012723 GSM1012722 GSM1012746 GSM1528055 GSM1528056 GSM1530028 GSM1012751 GSM1012724 GSM1012726 GSM1012747 GSM1012725 GSM1012716 GSM1012735 GSM1012713 GSM1012736 GSM1012737 GSM1012738 GSM1012730 GSM1012739 GSM1012740 GSM1012750 GSM1012717 GSM1012718 GSM1012719 GSM1012741 GSM1012732 GSM1012715 GSM1012720 GSM1012742 GSM1012721 GSM1012743 GSM1012744 Copy number analysis of Affymetrix 250K or Cytoscan_HD SNP arrays was performed for 27 rhabdomyosarcoma samples.
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Project description:To elucidate the pathogenesis of rhabdomyosarcoma (RMS), particularly for different subgroups, we performed a SNP array-based copy number analysis of 46 RMS specimens from primary cases with ERMS (N = 21), ARMS (N = 14), unclassified RMS (N = 1), and RMS of unknown histology (N = 3) together with 7 RMS-derived cell lines. The ERMS subtype was characterized by hyperploidy and was significantly associated with gains of chromosomes 2, 8, and 12, whereas majority of ARMS cases exhibited near-diploid copy number profiles. Recurrent loss of heterozygosity (LOH) of chromosomes 3 (28.6%) and 15q (35.7%) was detected in ARMS. Uniparental disomy/polysomy of 11p was commonly found in both tumor types. Focal gains/amplifications were associated mostly with PAX3-FOXO1 (5/10) or PAX7-FOXO1 (6/6) fusions, but novel amplified regions were also found, including the IRS2 in 2 ARMS. Gain of 13q was significantly associated with good patient outcome in ERMS. These findings not only illustrate genetic differences between ARMS and ERMS but also provide novel insights into the pathogenesis of RMS. Copy number analysis of Affymetrix 50K/250K SNP arrays was performed for 46 RMS samples.
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Project description:ALK fusion positive tumor constitutes a unique entitiy in lung adenocarcionmas. We compared the allelokaryotypes of ALK fusion positive and negative tumors with SNP array to get insight into the difference of genomic background of them. Copy number analysis with Affymetrix 250K SNP arrays of 35 ALK fusion positive and 95 ALK fusion negative lung adenocarcinomas was performed with annonymous references.
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Project description:Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. We determined the genomic landscape of 52 NPC cases with SNP-array analysis. This approach identified multiple recurrent SCNVs, with the most frequent deletion peak spanning the CDKN2A gene on 9p21. Additional SCNVs involving established cancer genes including CCND1, AKT2, MYC and TP53 were observed. Notably, we identified that one component of the SWI/SNF complex, ARID1A, was frequently deleted in NPC. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen nasopharyngeal carcinoma biopsy tissues Copy number analysis of Affymetrix 250K SNP arrays was performed for 52 nasopharyngeal carcinoma samples. Please note that the sample characteristics 'primary tumor size, metastasis, and regional lymph node' represents T, M and N in WHO TNM staging of nasopharyngeal cancer (according to American Joint Committee on Cancer (AJCC)), respectively.
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Project description:Transient abnormal myelopoiesis (TAM) is a clonal pre-leukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, IL-2Rγnull mice. In serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from murine bone marrow (hCD45 sorted) or human peripheral blood samples. Copy number analysis of Affymetrix 500K SNP arrays was performed for xenografted TAM samples of 3 patients. There are also 3 samples from TAM patients in remission, which were used as references for copy number inference.
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