EGAS00001000743-sc-20140903 - samples
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ABSTRACT:
PROVIDER: EGAD00001000998 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Targeted capture of exonic and intronic regions of interest for the study of genomic alterations in multiple myeloma.
| EGAS00001000743 | EGA
Project description:High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecological malignancies in the world, has not significantly benefited from recent progress in cancer immunotherapy. While HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. The goal of this study was to establish the global landscape of HGSC tumor-specific antigens (TSAs) using a mass spectrometry pipeline that interrogates all reading frames of all genomic regions. In 23 HGSC tumors, we identified 113 TSAs. Classic TSA discovery approaches focusing only on mutated exonic sequences would have uncovered only seven of these TSAs. Other mutated TSAs resulted from out-of-frame exonic translation or from non-exonic sequences. The most interesting group of TSAs (n = 94) derived from aberrantly expressed unmutated genomic sequences which are not expressed in normal tissues. These aberrantly expressed TSAs (aeTSAs) derived primarily from non-exonic sequences, in particular intronic (31%) and intergenic (22%). Their expression was regulated at the transcriptional level by variations in gene copy number and DNA methylation. While mutated TSAs were unique to individual tumors, aeTSAs were shared by a large proportion of HGSCs. We conclude that, in view of their number and the fact that they are shared by many tumors, aeTSAs may be the most attractive targets for HGSC immunotherapy.
2020-02-18 | PXD014062 | Pride
Project description:Differential marking of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, histone density and H3K36me3 patterns in fission yeast
2011-03-16 | E-TABM-946 | biostudies-arrayexpress
Project description:To obtain a comprehensive genomic profile of presenting multiple myeloma cases we performed high resolution single nucleotide polymorphism (SNP) mapping array analysis in 114 samples alongside 258 samples analysed by U133 Plus 2.0 expression array (Affymetrix). We examined DNA copy number alterations and loss of heterozygosity (LOH) in order to define the spectrum of minimally deleted regions in which relevant genes of interest can be found. The most frequent deletions are located at 1p (30%), 6q (33%), 8q (25%), 12 (22%), 13q (59%), 14q (39%), 16q (35%), 17p (7%), 20 (12%) and 22 (18%). In addition, copy number-neutral LOH, or uniparental disomy, was also prevalent on 1q (8%), 16q (9%), and X (20%), and was associated with regions of gain and loss. Based on fluorescent in situ hybridisation (FISH) and expression quartile analysis, genes of prognostic importance were found to be located at 1p (FAF1, CDKN2C), 1q (ANP32E), and 17p (TP53). In addition, we identified common homozygously deleted genes which have functions relevant to myeloma biology. Taken together, the dysregulated genes from the myeloma genome indicate that the crucial pathways in myeloma pathogenesis include the NF-?B pathway, apoptosis, cell-cycle regulation and Wnt signalling.
2010-10-18 | GSE21349 | GEO
Project description:Small noncoding RNAs (sncRNA) are becoming recognized for their participation in a diverse range of cellular functions. In this study, their global characterization in human spermatozoa from donors with proven fertility was undertaken. Reads were analyzed in two classes, those mapping to unique locations and those that could be aligned to up to 10 genomic locations. All libraries showed comparable distribution of reads between intergenic, intronic and exonic genomic regions. Analysis of the sequences revealed the presence of multiple small RNA classes. The miRNAs retained in spermatozoa were found to be associated with promoter regions, suggestive of a role at the transcriptional level. Piwi-interacting sncRNAs as well as repeat-associated small RNAs were identified for the first time in mature spermatozoa from a mammalian species. Human spermatozoa retain a multifaceted population of small non-coding RNAs. Their presence is consistent with the view that they may function to stabilize the genome as part of the confrontation and consolidation of the genomes at fertilization. Examination of sperm samples from 3 individuals, sequenced individually
2011-10-15 | E-GEOD-21191 | biostudies-arrayexpress
Project description:To obtain a comprehensive genomic profile of presenting multiple myeloma cases we performed high resolution single nucleotide polymorphism (SNP) mapping array analysis in 114 samples alongside 258 samples analysed by U133 Plus 2.0 expression array (Affymetrix). We examined DNA copy number alterations and loss of heterozygosity (LOH) in order to define the spectrum of minimally deleted regions in which relevant genes of interest can be found. The most frequent deletions are located at 1p (30%), 6q (33%), 8q (25%), 12 (22%), 13q (59%), 14q (39%), 16q (35%), 17p (7%), 20 (12%) and 22 (18%). In addition, copy number-neutral LOH, or uniparental disomy, was also prevalent on 1q (8%), 16q (9%), and X (20%), and was associated with regions of gain and loss. Based on fluorescent in situ hybridisation (FISH) and expression quartile analysis, genes of prognostic importance were found to be located at 1p (FAF1, CDKN2C), 1q (ANP32E), and 17p (TP53). In addition, we identified common homozygously deleted genes which have functions relevant to myeloma biology. Taken together, the dysregulated genes from the myeloma genome indicate that the crucial pathways in myeloma pathogenesis include the NF-?B pathway, apoptosis, cell-cycle regulation and Wnt signalling. SNP data: 114 tumour samples (MM) analyzed by Affymetrix 500K array set (Nsp+Sty), of which 80 samples have matched peripheral blood (PB) (non-tumour) DNA performed on the same array types. Matched tumour and non-tumour samples have the same ID number, e.g. MM400 and PB400 Expression data: 258 expression samples from CD138+ cell selection
2010-11-02 | E-GEOD-21349 | biostudies-arrayexpress
Project description:Microarray-based enrichment of selected genomic loci is a powerful method for genome complexity reduction. Since the vast majority of exons in vertebrate genomes are smaller than 150 nt, we have explored the use of short fragment libraries (85-110bp) to achieve higher enrichment specificity by reducing carryover and adverse effects of flanking intronic sequences. These short fragment libraries were enriched for 1.69 Mb of exonic sequences, using custom 244K microarrays, and sequenced using AB/SOLiD. High enrichment specificity (60 M-bM-^@M-^S 75%) was obtained at 67-213x average coverage, with 77-92% and 90-98% of targeted regions covered with more than 25% and 10% of the average coverage, respectively. As a more appropriate measure of the evenness of coverage, which is relatively independent of sequencing depth, we introduce the evenness of coverage parameter E. E values up to 75% were achieved. To verify the accuracy of SNP/mutation detection we evaluated 384 known non-reference SNPs in the targeted regions. At ~ 200x average sequence coverage, we were able to survey 96.4% of 1.69 Mb of genomic sequence with only 4.2% false negative calls while 3.6% of targeted regions were marked as unsurveyed. A total of 1197 new variants were detected. Verification revealed only 8 false positive calls, resulting in an overall false positive rate of less than 1 per ~200,000 bp (0.0005%, equivalent to an overall phred score of 55). 4 samples + capture design file
2010-02-01 | E-GEOD-18542 | biostudies-arrayexpress
Project description:Small noncoding RNAs (sncRNA) are becoming recognized for their participation in a diverse range of cellular functions. In this study, their global characterization in human spermatozoa from donors with proven fertility was undertaken. Reads were analyzed in two classes, those mapping to unique locations and those that could be aligned to up to 10 genomic locations. All libraries showed comparable distribution of reads between intergenic, intronic and exonic genomic regions. Analysis of the sequences revealed the presence of multiple small RNA classes. The miRNAs retained in spermatozoa were found to be associated with promoter regions, suggestive of a role at the transcriptional level. Piwi-interacting sncRNAs as well as repeat-associated small RNAs were identified for the first time in mature spermatozoa from a mammalian species. Human spermatozoa retain a multifaceted population of small non-coding RNAs. Their presence is consistent with the view that they may function to stabilize the genome as part of the confrontation and consolidation of the genomes at fertilization.
2011-10-16 | GSE21191 | GEO
Project description:Multiple Myeloma Genomic Study (MMGS)
| PRJNA377962 | ENA