Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA167468 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated.
2013-01-16 | GSE38228 | GEO
Project description:The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated. The whole-gene expression profile of 14 SCC of the vulva was compared to 5 normal vulvar samples to identify genes that were deregulated in the tumors genome. Vulvar hyperplasia 03-48 not further analyzed and not included in the normalized data but included in the non-normalized data
2013-01-16 | E-GEOD-38228 | biostudies-arrayexpress
Project description:Primary tumor recurrence occurs commonly after surgical resection of lung squamous cell carcinoma (SCC). The aim of this study was to identify genes involved in recurrence in lung squamous cell carcinoma patients. Array comparative genomic hybridization (aCGH) was performed on DNA extracted from tumour tissue from 62 patients with primary lung squamous cell carcinomas. aCGH data was analysed to identify genes affected by copy number alterations that may be involved in SCC recurrence. Candidate genes were then selected for technical validation based on differential copy number between recurrence and non-recurrence SCC tumour samples. Genes technically validated advanced to tests of biological replication by qPCR using an independent test set of 72 primary lung SCC tumour samples. 18q22.3 loss was identified by aCGH as significantly associated with recurrence (p=0.038). Although aCGH copy number loss associated with recurrence was found for seven genes within 18q22.3, only SOCS6 copy number loss was both technically replicated by qPCR and biologically validated in the test set.
2011-12-25 | GSE32058 | GEO
Project description:Primary tumor recurrence occurs commonly after surgical resection of lung squamous cell carcinoma (SCC). The aim of this study was to identify genes involved in recurrence in lung squamous cell carcinoma patients. Array comparative genomic hybridization (aCGH) was performed on DNA extracted from tumour tissue from 62 patients with primary lung squamous cell carcinomas. aCGH data was analysed to identify genes affected by copy number alterations that may be involved in SCC recurrence. Candidate genes were then selected for technical validation based on differential copy number between recurrence and non-recurrence SCC tumour samples. Genes technically validated advanced to tests of biological replication by qPCR using an independent test set of 72 primary lung SCC tumour samples. 18q22.3 loss was identified by aCGH as significantly associated with recurrence (p=0.038). Although aCGH copy number loss associated with recurrence was found for seven genes within 18q22.3, only SOCS6 copy number loss was both technically replicated by qPCR and biologically validated in the test set. DNA copy number profiling using 44K element array comparative genomic hybridization microarrays of 62 primary lung squamous cell carcinomas.
2011-12-25 | E-GEOD-32058 | biostudies-arrayexpress
Project description:The array comparative genomic hybridization (aCGH) was perform to identify regions with genomic imbalance in lung cancer.The aCGH analysis detected a total of 325 regions with genomic imbalance in all 8 lung cancer samples, ranging from focal rearrangements (70 kb–5 Mb) to chromosome-arm alterations with chromosomal segments amplification or deletion. Among these mutations, a total of 115 genomic imbalances were discovered occurring at high frequency varying from 25% to 50%.
2016-11-17 | GSE89927 | GEO
Project description:High-resolution array-CGH was performed to identify differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC). On a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2-q29, 12p13.2-p13.33, and 19p13.3, as well as losses at 3p26.2-p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2-q25.2 occurred in AC (P < 0.05). The most striking difference between SCC and AC was gains at 3q26.2-q29, occurring in 86% (19/22) of SCCs, but in only 21% (3/14) of ACs.
2009-06-19 | GSE16597 | GEO
Project description:The majority of patients with squamous cell lung cancer (SCC) die because of metastatic disease. The genomic mechanisms underlying this metastatic behaviour are underexposed. We analyzed a cohort of patients with primary squamous cell carcinoma (SCC) using array-based comparative genomic hybridization (aCGH) to identify which genomic aberrations were related metastatic behaviour. The cohort consisted of 34 patients with a follow-up of at least 5 years, including 15 without any metastases, 8 with metastases in regional lymph nodes only, and 11 with metastases exclusively in distant organs within two years after surgery. Common alterations observed in at least 40% of all SCC were gains at 3q13-q29, 5p11-p15, 8q24, 19q13, 20p12-p13, 22q11-q13, and losses at 3p12-p14, 3p24, 4p15, 4q33-q35, 5q14-q23, 5q31-q35, 8p21-p22, 9p21-p24. Amplifications were observed at 2p15-p16, 3q24-q29, 8p11-p12, 8q23-q24, and 12p12, containing candidate oncogenes such as BCL11A, REL, ECT2, PIK3CA, ADAM9, MYC, and KRAS. Gains at 7q36, 8p12, 10q22, 12p12, loss at 4p14 and homozygous deletions at 4q33-q34.1 occurred significantly more frequent in SCC from patients with lymph node metastases. SCC from patients with distant metastases showed a significantly higher frequency of gain at 8q22-q24 and loss of 8p23 and 13q21, and a significantly lower frequency of gain at 2p12 and 2p16 and loss at 11q25 as compared to SCC from patients without metastases. In conclusion, we identified specific genomic aberrations in primary SCC that are related to lymph node or distant metastases. These loci can be further explored for their potential use as predictive or prognostic markers.
2008-10-01 | GSE12280 | GEO
Project description:Parallel aSNP and aCGH analyses were performed on 22 samples from MDS patients with a normal karyotype. 55 overlapping alterations, most of these corresponding to CNVs were identified with both methods. Putative tumour specific imbalances were found with both methods in three cases, a deletion of TET2, a larger deletion containing DNMT3A and one complex molecular karyotype. In two cases putative tumour specific imbalances were only seen with aCGH: a 16p deletion in a low number of cells and a small homozygous deletion in WWOX. Telomeric UPDs were only detected with aSNP in two cases: one affecting chromosome 3q and in the other, two UPD regions were present on 4q and 5p. In total, putative relevant tumour specific genomic alterations were found in seven cases (32%). Three small aberrations only detected by aCGH were present in T-cells, suggestive of germ line alterations which may confer a risk for MDS development. This part contains the aCGH analyses, for aSNP see GSE49004.
2017-01-01 | GSE50897 | GEO
Project description:Chromosomal instability is one of the hallmarks of tumors, which can result in the gain or loss of specific genomic regions or even entire chromosomes. These copy number aberrations (CNAs) play an important role in carcinogenesis and malignant progression through CNA-induced gene expression alterations and, subsequently, key cancer-specific processes. In the current study, we applied aCGH analysis to screen out CNAs with potential prognostic value in lung SCC patients. Depending on their survival time, 100 patients with primary SCC were separated into high- or low-risk groups of prognosis, and copy number aberration (CNA) were analyzed by array-comparative genomic hybridization (array-CGH).
2015-09-22 | E-GEOD-43131 | biostudies-arrayexpress
Project description:High-resolution array-CGH was performed to identify differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC). On a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2-q29, 12p13.2-p13.33, and 19p13.3, as well as losses at 3p26.2-p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2-q25.2 occurred in AC (P < 0.05). The most striking difference between SCC and AC was gains at 3q26.2-q29, occurring in 86% (19/22) of SCCs, but in only 21% (3/14) of ACs. Array-CGH was performed to compare the different patterns of genetic alterations. DNA from NSCLC patients (n=36) and human reference DNA (Promega) were differentially labeled and cohybridized on the array. The Fisher exact test utilized two categories, normal and abnormal (loss and gain), with the null hypothesis that the relative proportions of each of the two imbalance categories would be expected to be the same in the groups. The counts of abnormal versus normal were summarized by subtype of NSCLC for each BAC, providing 2x2 tables for analysis. A multiple testing correction (Benjamini-Hochberg false discovery rate (FDR)) was applied to correct for the high number of false positive calls.
2010-05-18 | E-GEOD-16597 | biostudies-arrayexpress