22 PDX of triple-negative breast cancer genotyped with Affymetrix Cytoscan HD
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Elisabetta Marangoni
PROVIDER: E-MTAB-8653 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To characterize Homologous recombination deficiency (BRCAness) in triple-negative breast cancer PDX models genomic signature was utilized. After normalization using Genotyping Console we obtained absolute copy number profiles using the GAP software (Popova et al, Genome Biol, 2009). The number of Large-scale State Transitions (LSTs) was used to annotate PDX as BRCAness or not (Popova et al, Cancer Res 2012).
2020-01-01 | E-MTAB-8654 | biostudies-arrayexpress
Project description:The uploaded results of two samples were SNParray results in our research of which fetal CNVs were detected by noninvasive prenatal test (NIPT) and confirmed by microarray results. Sample ZNY162 received prenatal diagnosis because at 17 gestational week the pregnant woman received NIPT showing 23Mb microdeletion in Chr18. Later ultrasound examination showed developmental anomalies of feet and the 13th ribs. The pregnant woman received amniocentesis and SNParray at the 21st gestational week, which confirmed the existence of the microdeletion in Chr18. DNA was extracted from 10ml amniotic fluid and tested by Affymetrix CytoScan HD array to detect CNVs in whole genome, showing arr 18q22.3q23(69,461,933-78,014,123) Ã1. Sample LMQ155 received prenatal diagnosis because of advanced maternal age and NIPT result of a 2.29Mb microduplication in Chr13 at 15 gestational week. Amniocentesis was performed at the 17th gestational week. Affymetrix CytoScan HD array were used to detect fetal CNVs in whole genome, which showed arr 13q21.2(60,399,612-61,730,194) Ã3 that was consistent with NIPT result.
2016-11-16 | E-MTAB-4738 | biostudies-arrayexpress
Project description:Autosomal dominant polycystic liver disease (ADPLD) is caused by mutations in PRKCSH, SEC63, and LRP5, while autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1, and PKD2. Liver cyst development in these disorders is explained by somatic loss-of-heterozygosity (LOH) of the wild type allele in the developing cyst. We hypothesize that we can use this mechanism to identify novel disease genes that reside in LOH regions. In this study, we aim to map abnormal genomic regions using high-density SNP microarrays to find novel polycystic liver disease genes. We collected 46 cysts from 23 patients with polycystic or sporadic hepatic cysts, and analyzed DNA from those cysts using high-resolution microarray (n=24) or Sanger sequencing (n=22). We here focused on regions of homozygosity on the autosomes (>3.0Mb), and large CNVs (>1.0Mb). We found frequent LOH in PRKCSH (22/29), and PKD1/PKD2 (2/3) cysts of patients with known heterozygous germline variants in the respective genes. In the total cohort, 12/23 patients harbored abnormalities outside of familiar areas. In individual ADPLD cases, we identified germline events: a 2q13 complex rearrangement resulting in BUB1 haploinsufficiency, a 47XXX karyotype, chromosome 9q copy number loss, and LOH on chromosome 3p. The latter region was overlapping with an LOH region identified in two other cysts. Unique germline and somatic abnormalities occur frequently in and outside of known genes underlying cysts. Each liver cyst has a unique genetic makeup. LOH driver gene BUB1 may imply germline causes of genetic instability in PLD. 24 liver cysts from 23 patients
2016-06-30 | E-GEOD-78808 | biostudies-arrayexpress
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Project description:The contribution of copy number (CN)-altered genes in cervical carcinogenesis is unknown owing to a lack of correlation with gene expression. We mapped CN-altered genes in 31 cervical cancers (CCs), and investigated the expression of 21,000 genes in 55 CCs using microarrays. Biological processes associated with genes deregulated by gene dosage and the relationship between gene dosage and patient survival were investigated. CN-altered genome (CN-AG) percentages varied widely among tumors from 0% to 32.2% (mean = 8.1 ± 8.9). Tumors were classified as low (mean = 0.5 ± 0.6, n = 11), medium (mean = 5.4 ± 2.4, n = 10), or high (mean = 19.2 ± 6.6, n = 10) CN. The highest %CN-AG was found in 3q, which contributed an average of 55% of all CN alterations. Genome-wide, only 5.3% of CN-altered genes were deregulated by gene dosage; by contrast, the rate in fully duplicated 3q was twice as high. Amplification of 3q explained 23.6% of deregulated genes in whole tumors (r2 = 0.236, p = 0.006; analysis of variance), including those in 3q and other chromosomes. A total of 862 genes were deregulated exclusively in high-CN tumors, but only 22.9% were CN altered. This result suggests that the remaining genes are not deregulated directly by gene dosage but by mechanisms induced in trans by CN-altered genes. Anaphase-promoting complex/cyclosome (APC/C)-dependent proteasome proteolysis, glycolysis, and apoptosis were upregulated, whereas cell adhesion and angiogenesis were downregulated exclusively in high-CN tumors. The high %CN-AG and upregulated gene expression profiles of APC/C-proteasome-dependent proteolysis and glycolysis were associated with poor patient survival, although only the first 2 correlations were statistically significant (p < 0.05, log-rank test). The data suggest that inhibitors of APC/C-dependent proteasome proteolysis and glycolysis may be useful treatments in these patients. In this study 31 tumors and 25 reference controls were used for analysis of copy number alterations using the 500K microarray. The results obtained from 500K array analysis were validated in 15 of the 31 tumors with a higher density microarray (Cytoscan HD). For the analysis of gene expression 55 cervical tumors (27 of them belong to the group of 31 tumors analyzed for copy number) and 17 exocervical controls were used. Please note that the sample R397 in the CytoScanHD_Array set corresponds to the R392 sample in the other data sets (due to an error in file name).
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2015-06-04 | E-GEOD-52904 | biostudies-arrayexpress
Project description:To identify the molecular causes of heterotaxy syndrome patients with congenital heart defects, an Affymetrix CytoScan HD array was used to identify possible pathogenic CNVs in 63 patients. A total of 59 samples passed initial quality control.
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Project description:In T-cell acute lymphoid leukemia (T-ALL) several oncogenes and tumour suppressor (TS) genes have been described. Deregulation of these genes mostly results from genomic aberrations, including translocations, amplifications and deletions. To identify novel cancer-related genes targeted by copy number alterations we performed genomic profiling of eight T-ALL cell lines. In three of these (HPB-ALL, JURKAT, MOLT-14) we identified a shared deletion at chromosomal position 2p16.3-p21. Within the minimally deleted region we recognized several candidate TS genes, including FBXO11 (component of the ubiquitin-pathway) and FOXN2 (developmental transcription factor). Furthermore, an additional deletion at 14q23.2-q32.11 (in cell line RPMI-8402) included FOXN3, highlighting this class of FOX genes as potential TS. Accordingly, quantitative expression analyses of FBXO11, FOXN2 and FOXN3 confirmed reduced transcript levels in the indicated cell lines. Moreover, reduced expression of these genes was also observed in about 7 % of T-ALL patients from a public dataset (GSE26713), showing their clinical relevance in this malignancy. Bioinformatic analyses of these patient data revealed concurrent reduction of FOXN2 and/or FOXN3 together with homeobox gene ZHX1. Consistently, knockdown experiments and reporter gene assays demonstrated that both FOXN2 and FOXN3 directly activated transcription of ZHX1 in T-ALL. ZHX1 target gene analysis via expression profiling after siRNA-mediated knockdown indicated regulation of several genes involved in the ubiquitin-pathway including CUL4A. Taken together, we identified novel TS genes which form a regulatory network improving our understanding of T-cell development and leukemogenesis.
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