Colorectal tumor DNA vs. normal control DNA
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Ian Brock
PROVIDER: E-GEOD-41813 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on Array Comparative Genomic Hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal (GI) carcinoids. In contrast to the relatively stable karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in SCLC tumors and cell lines in cytogenetic bands encoding JAK2, FGFR1, and MYC family members. In some of those samples, the CN of these genes exceeded 100, suggesting that they could represent driver alterations and potential drug targets in subgroups of SCLC patients. Recurrent CN alterations of a total of 203 genes, including the RB1 gene, and 59 microRNAs, most of which locate in the DLK1-DIO3 domain, were observed in SCLC tumors, bronchial carcinoids and carcinoids of GI origin; in contrast, CN alterations of the TP53 gene and the MYC family members were observed more frequently in SCLC. These findings suggest the existence of partially shared tumor-specific CN alterations in these tumors. Furthermore, we demonstrated that the aCGH profile of SCLC cell lines highly resemble that of clinical SCLC specimens. Finally, by analyzing potential drug targets, we provide a genomics based rationale for targeting the AKT-mTOR and apoptosis pathways in SCLC. Carcinoids, including 19 bronchial carcinoids and 9 carcinoid of gastrointestinal origin, and small cell lung cancer, including 33 patients' tumor samples and 13 cell line samples, were compared.
2010-04-22 | E-GEOD-21468 | biostudies-arrayexpress
Project description:To assess the performance of our custom-designed pan-genome microarray and characterize the differences in gene content between JP2 and non-JP2 genotypes of A. actinomycetemcomitans. Comparative genomic hybridization reactions were carried out to assess the performance of our pan-genome microarray by using genomic DNA of 11 previously sequenced Aggregatibacter actinomycetemcomitans strains (I23C, SCC1398, ANH9381, HK1651, D7S-1, D11S-1, I63B, SCC393, D18P-1, SCC2302, and D17P-2). The microarray was subsequently used for comparative genomic hybridization of 6 strains of JP2 (S067, A26, G111-1, G121-2, D41S-1, and HK1651) and 6 strains non-JP2 (I23C, SCC1398, ANH9381, ATCC29524, 194, and G104-2) genotypes of Aggregatibacter actinomycetemcomitans. Two biological duplicates were carried out for each strain.
2012-09-28 | E-GEOD-39143 | biostudies-arrayexpress
Project description:To analyze the gain and lost of genes in Aggregatibacter actinomycetemcomitans during short-term persistent infection in the same host The microarray was used to compare gene contents of 4 different pairs of Aggregatibacter actinomycetemcomitans strains (SCC393 vs A160, SCC1398 vs SCC4092, SCC2302 vs AAS4a, and S23A vs I23C), where each pair was isolated from an individual over time. Two biological duplicates were carried out for each strain.
2013-12-31 | E-GEOD-42953 | biostudies-arrayexpress
Project description:MicroRNAs are a wide class of ~22 nt non-coding RNAs of metazoans capable of inhibiting target mRNAs translation by binding to partially complementary sites in their 3âUTRs. Due to their regulatory potential, miRNAs are implicated in functioning of a broad range of biological pathways and processes. Here we investigate the functions of the miR-959-964 cluster expressed predominantly in testes of Drosophila melanogaster. The deletion of miR-959-964 resulted in male sterility due to the disturbance of the spermatid individualization process. Analysis of the transcriptome by microarray followed by luciferase reporter assay revealed didum, for, fdl and CG10512 as the targets of miR-959-964. Moreover, the deletion of miR-959-964 is accompanied by a decreased the expression of genes responsible for microtubule-based movement and spermatid differentiation. Thus, we suggest that miR-959-964 can control the process of spermatid individualization by direct and indirect modulating the expression of different components of the individualization process. In addition, we have shown that in comparison to other miRNAs, the rate of evolution of the testis-specific miR-959-964 cluster is unusually high, indicating its possible involvement in speciation via reproductive isolation.
2015-10-29 | E-MTAB-3214 | biostudies-arrayexpress
Project description:The genomic DNA sample of monkey PG-haESCs were compared to the female adipose cells by comparative genomic hybridization. The data confirmed that these haploid cells sustained genome integrity. The analysis was performed on a Agilent aCGH G3 Rhesus Macaque 4x180K array to analyse the copy number variations in monkey PG-haESCs, and the genomic DNA of femal monkey adipose was used as control, which had the same background with haploid ESCs.
2013-06-26 | E-GEOD-43979 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-06-26 | E-GEOD-43980 | biostudies-arrayexpress
Project description:Objective: To evaluate the clinical impact of chromosomal microarray (CMA) on the management of paediatric patients in Hong Kong Methods: We performed NimbleGen 135k oligonucleotide array on 327 children with intellectual disability (ID)/ developmental delay (DD), autism spectrum disorders (ASD), and/or multiple congenital anomalies (MCAs) in a university-affiliated paediatric unit from January 2011 to May 2013. The medical records of patients were reviewed in September 2013, focusing on the pathogenic/likely pathogenic CMA findings and their “clinical actionability” based on established criteria. Results: Thirty-seven patients were reported to have pathogenic/likely pathogenic results, while 40 had findings of unknown significance. This gives a detection rate of 11% for clinically significant (pathogenic/likely pathogenic) findings. The significant findings have prompted clinical actions in 28 out of 37 patients (75.7%), while the findings with unknown significance have led to further management recommendation in only 1 patient (p<0.001). Nineteen out of the 28 management recommendations are “evidence-based” on either practice guidelines endorsed by a professional society (n=9, Level 1) or peer-reviewed publications making medical management recommendation (n=10, Level 2). CMA results impact medical management by precipitating referral to a specialist (n=24); diagnostic testing (n=24), surveillance of complications (n=19), interventional procedure (n=7), medication (n=15) or lifestyle modification (n=12).
2014-08-31 | E-MTAB-2883 | biostudies-arrayexpress
Project description:Objective: To evaluate the clinical impact of chromosomal microarray (CMA) on the management of paediatric patients in Hong Kong Methods: We performed NimbleGen 135k oligonucleotide array on 327 children with intellectual disability (ID)/ developmental delay (DD), autism spectrum disorders (ASD), and/or multiple congenital anomalies (MCAs) in a university-affiliated paediatric unit from January 2011 to May 2013. The medical records of patients were reviewed in September 2013, focusing on the pathogenic/likely pathogenic CMA findings and their “clinical actionability” based on established criteria. Results: Thirty-seven patients were reported to have pathogenic/likely pathogenic results, while 40 had findings of unknown significance. This gives a detection rate of 11% for clinically significant (pathogenic/likely pathogenic) findings. The significant findings have prompted clinical actions in 28 out of 37 patients (75.7%), while the findings with unknown significance have led to further management recommendation in only 1 patient (p<0.001). Nineteen out of the 28 management recommendations are “evidence-based” on either practice guidelines endorsed by a professional society (n=9, Level 1) or peer-reviewed publications making medical management recommendation (n=10, Level 2). CMA results impact medical management by precipitating referral to a specialist (n=24); diagnostic testing (n=24), surveillance of complications (n=19), interventional procedure (n=7), medication (n=15) or lifestyle modification (n=12).
2014-09-04 | E-MTAB-2884 | biostudies-arrayexpress
Project description:Background: Array-Comparative-Genomic-Hybridization (aCGH) is recommended as first-tier genetic test for children with autism spectrum disorder (ASD). However, result interpretation can be challenging as copy number variants (CNVs) in non-European ASD patients is not well studied. To address this literature gap, we report the CNV findings in a cohort of Chinese children with ASD. Methods DNA samples were obtained from 258 Chinese ASD patients recruited from a child assessment center between January 2011 and August 2014. aCGH was performed using NimbleGen-CGX-135k or Agilent-CGX 60k oligonucleotide array. Results were classified based on existing guidelines and literature. Results: Ten pathogenic and one likely-pathogenic CNVs were found in nine patients, with an overall diagnostic yield of 3.5%. A 138kb duplication involving 3â exons of DPP10 (hg[19]chr2:116534689-116672358), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of unknown significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified amongst our ancestry-matched control with frequency of 6/653 (0.92%) as well as from literature and genomic databases. Conclusions: DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings.
2017-04-07 | E-MTAB-5665 | biostudies-arrayexpress
Project description:Current therapy has turned HIV infection into a chronic condition. Clinically, some patients suffer prematurely from ailments associated with advanced age; however, the relationship between HIV and aging is unclear. Here we have collected a large cohort of HAART treated HIV+ subjects with both recent and chronic infection and recapitulated the shared phenotype of HIV and age. To further understand this signal, we applied validated models of DNA methylation-based biological age to establish a clear link between HIV infection and molecular age advancement. We then show this result to be robust to HIV duration, cellular composition, and general methylome disorder. Finally we show a pattern of hypomethylation in HIV+ individuals at the HLA locus. Together these results lead to a much-needed better understanding of the epigenetic consequences and gerontological aspects of chronic HIV infection. To determine whether HIV is associated with signs of aberrant biological aging, samples of whole blood were collected from HIV-infected, HAART-treated but otherwise healthy non-Hispanic white males (no hepatitis C co-infection, no diabetes, and strict adherence to therapy) and healthy non-Hispanic white male controls. DNA was extracted from whole blood and genome-wide methylation profiles of each sample were determined using the Illumina Infinium HumanMethylation450 BeadChip array. As a validation, a second cohort of subjects was profiled by flow-sorting cells and measuring methylation in pure-cell populations. Data were normalized and controlled for quality using standard techniques. Please note that the following samples were excluded from the data processing by quality control steps; METI-6 METI-7 352_CD4 381_CD4 however, their raw data was provided so that the full pipeline could be reproduced.
2016-04-03 | E-GEOD-67705 | biostudies-arrayexpress