16758 results for "sec+and+unspecified+malignant+neoplasm"

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• 2015 AML-ETO WGS analysis result

  This data is belong to 2015 AML-ETO patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001004011

• 2015 AML-ETO WGS additional analysis result

  This data is belong to additional 2015 AML-ETO patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 2 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001004012

• 2014 sequenced Korean WES-Lung Cancer sample 36 pair

  This data is belong to WES-Lung Cancer patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 36 paired tumor/normal samples from Samsung Hospital. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001004027

• Total RNA sequencing of 32 chronic lymphocytic leukemia (CLL) patients

  Peripheral blood mononuclear cells (PBMC) of CLL patients were isolated by density-gradient centrifugation over Linfosep (Biomedics, Madrid, Spain). B cells were purified with a CD19+ magnetic-bead system (MidiMACS, Miltenyi Biotec, Bergish Gladbash, Germany) according to the manufacturers’ instructions. Mean B-cell purity was >99% and the mean percentage of CD5+/CD19+ cells after purification was >98%, as measured by flow cytometry. Total RNA was extracted from purified cells in a single step using TriPure Isolation Reagent (Roche Applied Science, Vilvoorde, Belgium).Whole transcriptome sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Libraries underwent 2 × 76 bp paired-end sequencing on a HiSeq 2500 instrument (Illumina). The median number of paired-end reads was 60.5 million (range, 49.7-79.7 million).

  Dataset EGAD00001004047

• Whole exome sequencing data of tumor/normal pairs for the study "TGF-β attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells"

  Tumor DNA was extracted from formalin-fixed and paraffin embedded tumors of a large cohort of bladder cancer patients before treatment with anti-PD-L1. Normal DNA was extracted from matched PBMCs. Whole exome sequencing was performed. This is a subset of patients for which RNA sequencing is also provided (with more detailed phenotypic information).

  Dataset EGAD00001004218

• Pharmacogenomics of HIV Therapy - Atazanavir Bilirubin-related Side Effects

  This is an evaluation of genetic associations with atazanavir (ATV) discontinuation for bilirubin-related causes within 12 months of treatment. Patients were treated at an HIV primary care clinic in Nashville TN from 1998 to 2012. A previously known SNP in UGT1A1 (rs887829) was used to define metabolizer genotypes (extensive, intermediate, slow metabolizer). Over 500,000 SNPs from genome-wide genotyping were used to define MDS (Multidimensional Scaling) coordinates to account for population stratification. Patients were defined as cases if they discontinued ATV for bilirubin-related causes within 12 months of treatment, otherwise they were defined as controls if they did not stop treatment. Among 321 evaluable patients, 15 (4.6%) had bilirubin-related atazanavir discontinuation within 12 months. Homozygosity for rs887829 T/T was present in 28.1% of black, 21.4% of Hispanic, and 8.6% of white patients. Among all patients the hazard ratio (HR) for bilirubin-related discontinuation with T/T versus C/C genotype was 7.3 (95% C.I.: 1.7 to 31.5; p = 0.007). Among 152 white patients the HR was 14.4 (95% CI: 2.6 to 78.7; p = 0.002), but among 153 black patients the HR was 0.8 (95% C.I. 0.05 to 12.7; p = 0.87).

  Study phs001484

• CIDR Whole Exome Sequencing in Joubert Syndrome

  The purpose of this study is to identify new genetic causes of neurodevelopmental diseases (NDDs) in the Joubert syndrome (JS) spectrum. Joubert syndrome is a recessive disease characterized by cerebellar vermis hypoplasia. Our currently funded NINDS award entitled "Molecular characterization of Joubert syndrome" seeks to identify new genetic causes through a variety of molecular strategies. Although our previous strategies involved whole genome SNP-scans, followed by candidate gene sequencing to arrive at identification of new JS causes, we have recently moved to Whole Exome Sequencing (WES) as a highly efficient methodology that is optimized for recessive disease. In this pilot project, CIDR has sequenced DNA on probands from 20 inbred families with JS spectrum disorders in which known causes have been excluded, that have not previously undergone genome-wide SNP scans. These paired end reads will be subject to our established bioinformatics pipeline including HOMOZGYOSITY, SNP and INDEL callers in our lab to identify potentially deleterious sequence changes (PDSC). This is followed by analysis to include testing each PDSC for segregation in the whole pedigree, for occurrence in a ethnically-matched cohort, as well as a defined patient cohort patients, in order to validate new NDD genes.

  Study phs000382

• Synovial Fibroblast Gene Expression in Response to Fibronectin Fragment

  Osteoarthritis (OA) is a prevalent joint disease characterized by the progressive degradation of articular cartilage, hypertrophy of neighboring bone, and varying degrees of synovial inflammation. Recent research has highlighted the potential role of synovial fibroblasts in the pathogenesis of OA, particularly their inflammatory properties that disrupt cartilage homeostasis. Notably, degraded cartilage matrix components, such as fibronectin fragments (FN-f), have been identified in the synovial fluid of OA patients, suggesting that FN-f signaling influences the synovium where synovial fibroblasts reside. Despite affecting over 500 million individuals globally, our limited understanding of the underlying mechanisms of OA has significantly impeded the development of effective treatment strategies. To investigate this, we obtained deidentified surgical waste material from individuals undergoing knee replacement for OA. Synovial tissue was used to isolate synovial fibroblasts for cell culture studies. We generated bulk RNA-seq data from primary synovial fibroblasts (N=5 individuals) treated at passage 3 with either Phosphate-Buffered Saline (PBS) as control or FN-f for 18h to model the OA synovial fibroblast phenotype. We identified differentially expressed genes at an adjusted p-value of

  Study phs003999

• Increased mutation accumulation during fetal development in Down syndrome

  Children with Down syndrome (DS) show a high incidence of leukemia, which is preceded by transient myeloproliferative disorder (TMD) in neonates. TMD is characterized by mutations in GATA1 that accumulate during fetal development, indicating that additional mutagenesis is required for leukemogenesis. Abnormalities in chromosome numbers can result in a mutator phenotype. However, it is unknown whether a trisomy of chromosome 21 (T21) results in enhanced mutation accumulation during human development. Here, we determined the mutational consequences of a constitutive T21 in DS fetuses compared to disomy 21 cells (D21) of D21 fetuses. We found that D21 fetal HPSCs had a higher somatic mutation rate compared to healthy adults HSPCs. Moreover, we observed an increase in somatic mutation load in T21 cells of DS fetuses, which was already apparent during the first cell divisions of embryogenesis. The mutation load could be explained by processes that are active during normal fetal development and were similar to those observed in TMD blast cells. Our study shows that T21 causes an increase in somatic load in fetal cells of DS fetuses, which may contribute to leukemia development early in life.

  Study EGAS00001003982

• Biased allelic expression in human primary fibroblast single cells.

  The study of gene expression in mammalian single cells using genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We have used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblast cells over 133,633 unique heterozygous single nucleotide variants (hetSNVs). We have observed that at the snapshot of analyses each cell contains mostly transcripts from one allele from the majority of genes; indeed 76.4% of the hetSNVs display stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibit haplotype consistent allelic ratio; in contrast distant sites located in two different genes are independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in majority of the single cells at a given time point are rare and enriched in highly expressed genes. The relative abundance of each allele in a cell is controlled by some regulatory mechanisms since we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability.

  Study EGAS00001001009

• Allele-specific expression of GATA2 due to epigenetic dysregulation in double mutated CEBPA AML

  Transcriptional deregulation is a central event in the development of acute myeloid leukemia (AML). To identify potential disturbances in gene regulation, we conducted an unbiased screen of allele-specific expression (ASE) in 209 AML cases. The gene encoding GATA binding protein 2 (GATA2) displayed ASE more often than any other myeloid or cancer-related gene. GATA2 ASE was strongly associated with CEBPA double mutations (CEBPA DM), with 95% of cases presenting GATA2 ASE. In CEBPA DM AML with GATA2 mutations, the mutated allele was preferentially expressed. We found that GATA2 ASE is a somatic event lost in complete remission, supporting the notion that it plays a role in CEBPA DM AML. Acquisition of GATA2 ASE involved silencing of one allele via promoter methylation, compensated by overactivation of the other allele, thereby preserving expression levels. Notably, promoter methylation was also lost in remission together with GATA2 ASE. In summary, we propose that GATA2 ASE is acquired by epigenetic mechanisms and is a prerequisite for the development of AML with CEBPA DM. This finding constitutes a novel example of an epigenetic hit cooperating with a genetic hit in the pathogenesis of AML.

  Study EGAS00001004684

• Germline variants in patients with rare cancers - control samples WGS and WES

  The control samples (mostly blood) of 351 samples (paired WGS and WES sequencing) are in this dataset. The WGS was in nearly all cases at an Illumina HighSeq X Ten with the Illumina TruSeq Nano DNA Kit. The WES mostly on Illumina HighSeq 4000 with the Agilent SureSelect V5 plus UTRs Kit.

  Dataset EGAD00001010047

• Blueprint Data Access Committee.

  Access to the sequence and alignment and genotype level data produced by the Blueprint Consortium is controlled by the Blueprint Data Access Committee (DAC). Access to data will be granted to qualified investigators for appropriate use. Please email blueprint-dac@ebi.ac.uk to request the Data Access Application and Data Access Agreement.

  Dac EGAC00001000135

• Variability in immune response genes and prediction of severe SARS-CoV-2 infection (INMUNGEN-Cov2 project)

  Genetic factors may contribute to explain the variable clinical response to SARS-CoV-2 infection. To this end we sequenced the DNA of 392 COVID-19 patients from Spain. Whole Exome Sequencing (WES) was performed at two different sequencing centers. Half of the samples were sequenced at a commercial service, NIMGenetics, whereas the other half were sequenced by the EASI-Genomics consortium. Finally, Variant Call Format (VCF) files for each sample was also obtained.

  Study EGAS50000000066

• Progressive supranuclear palsy - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=42 samples. Tissue samples correspond to donors with pathologically confirmed progressive supranuclear palsy. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002623

• Multiple system atrophy - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=35 samples. Tissue samples correspond to donors with pathologically confirmed multiple system atrophy. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13). N=6 samples are overlapping with EGAS50000000301.

  Dataset EGAD50000002624

• Alzheimer's disease - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=72 samples. Tissue samples correspond to donors with pathologically confirmed Alzheimer's disease. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002625

• Dementia with Lewy bodies - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=80 samples. Tissue samples correspond to donors with pathologically confirmed dementia with Lewy bodies. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002626

• Parkinson's disease - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=448 samples. Tissue samples correspond to donors with pathologically confirmed Parkinson's disease. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13). N=81 samples are overlapping with EGAS50000000301.

  Dataset EGAD50000002627

• Controls - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=283 samples. Tissue samples correspond to health control donors. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13). N=21 samples are overlapping with EGAS50000000301.

  Dataset EGAD50000002628

• Corticobasal degeneration - bulk RNA seq of prefrontal cortex

  Dataset corresponding to the bulk RNA-seq dataset from prefrontal cortex for a total of N=17 samples. Tissue samples correspond to donors with pathologically confirmed corticobasal degeneration. RNA-seq was carried out using ribosomal depletion. Dataset contains paired fastq files, sample metadata and downstream quantification files. Quantification was performed with salmon v1.3.0 with Gencode 35 (GRCh38.p13).

  Dataset EGAD50000002629

• Single nuclei ATAC-Seq data from the human ganglionic eminences

  Data generated through single nuclei ATAC sequencing on whole ganglionic eminences from 3 human fetuses (two of 16 and one of 17 gestational weeks). Tissue was acquired from the MRC-Wellcome Trust Human Developmental Biology Resource with ethical approval. snATAC-Seq libraries were prepared from ~8,000 nuclei per sample using Chromium Next GEM Single Cell ATAC (v1.1) reagents (10X Genomics). Quality control of libraries was performed using the Agilent 5200 Fragment Analyzer before sequencing on an Illumina NovaSeq 6000 to a depth of at least 617 million read pairs per library. Raw sequencing data were converted into FASTQ files. For a full description of data generation, please see Cameron et al, Schizophrenia Bulletin 2024, https://doi.org/10.1093/schbul/sbae083. Please note that 10X generated BAM files, rather than FASTQ files, have been uploded. FASTQ files can be regenerated using the 10X Genomics bamtofastq tool. https://support.10xgenomics.com/docs/bamtofastq

  Dataset EGAD50000000601

• EGAD00010000730

  WTCCC2 Psychosis Endophenotype samples from UK, Germany, Holland, Spain and Australia using the Affymetrix 6.0 array

  Dataset EGAD00010000730

• Chondrosarcoma Targeted Sequencing Study

  This Study uses a focused bespoke bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.

  Dataset EGAD00001000265

• Osteosarcoma Targeted Sequencing Study

  This Study uses a focused bespoke bait pull down library method to target findings of Osteosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these findings in a larger set of patient samples.

  Dataset EGAD00001000266