22974 results for "ega"

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• Genomic characterization of hepatocellular carcinoma in Hispanic patients

  The genomic DNA was extracted from paired tumor and adjacent non-tumor samples of 27 Hispanic HCC patients. The TruSeq Rapid Exome Library Prep kit (Illumina, CA) was used to capture the coding regions of the human genome. The 100 bp paired-end sequencing of every 6-plex whole exome library pool was performed on an Illumina HiSeq 3000 system according to the manufacturer’s recommended protocol to achieve an average coverage of ~100X. The paired-end reads were aligned to the human reference genome (hg19) with decoy sequences (as used in the 1000 Genomes Project) using BWA software. The duplicate reads were marked and removed using Picard and SAMtools, respectively. Local realignment around insertions/deletions (indels) and base quality recalibration were performed using GATK.

  Study EGAS00001007431

• RNA sequencing on intestinal biopsies from inflammatory bowel disease patients treated with vehicle control, MEK inhibitor, or infliximab

  By investigating an intergenic haplotype on chr21q22, independently linked to inflammatory bowel disease (IBD), ankylosing spondylitis, primary sclerosing cholangitis and Takayasu’s arteritis, we discover that the causal gene, ETS2, is a master regulator of inflammatory responses in human macrophages and delineate how the risk haplotype increases ETS2 expression. Using a database of cellular signatures, we identified drugs that could modulate this pathway. To validate the anti-inflammatory activity of one class of small molecules ex vivo, we obtained biopsies from patients with active IBD and cultured these biopsies with a selective, non-ATP competitive MEK inhibitor (PD-0325901), infliximab (positive control), or DMSO (vehicle control) for 18 hours, then performed RNA sequencing.

  Study EGAS00001007534

• Exploring the cell-free total RNA transcriptome in diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma patients as biomarker source in blood plasma liquid biopsies

  The goal of this study was to investigate cell-free RNA (cfRNA) biomarkers in DLBCL and PMBCL patients. Blood plasma samples (n=168) and matched diagnostic formalin-fixed paraffin-embedded (FFPE) tissue samples (n=69) of DLBCL patients, PMBCL patients and healthy controls were collected between 2016-2021. Plasma samples were collected at diagnosis, at interim evaluation, after treatment, and in case of refractory or relapsed disease. RNA was extracted from 200 µl plasma using the miRNeasy serum/plasma kit and from FFPE tissue using the miRNeasy FFPE kit. RNA was subsequently sequenced on a NovaSeq 6000 instrument using the SMARTer Stranded Total RNA-seq pico v3 library preparation kit.

  Study EGAS00001007585

• NOTCH1 fusion genes in pediatric T-cell lymphoblastic lymphoma hallmark a common high-risk subgroup with blood TARC levels as possible biomarker

  T-cell lymphoblastic lymphoma (T-LBL) is a common pediatric malignancy accounting for approximately 20% of the non-Hodgkin lymphomas during childhood. Survival rates of T-LBL are ~80%, but outcome after relapse is dismal, with salvage rates reaching only ~15. Considering the extremely poor prognosis after relapse and absence of clinically relevant high-risk genetics, there is an urgent need for the identification of molecular risk factors and new prognostic biomarkers in T-LBL, as well as identification of new therapeutic strategies. In this study we present a novel entity of high-risk pediatric T-LBL patients characterized by previously unknown NOTCH1 gene fusions and highly elevated blood TARC levels

  Study EGAS00001007703

• Clonal tracing with somatic epimutations reveals dynamics of blood aging

  In this study, we generated comprehensive single-cell multi-omic datasets from bone marrow samples collected from 13 donors spanning a wide age range. We applied the scTAMseq protocol to profile DNA methylation and nuclear mutations obtained from 7 total bone marrow aspirates (donors A.1-A.7) and 6 CD34+-enriched bone marrow samples ((donors B.1-B.5 & X.1). Complementary surface marker expression data were acquired by integrating CITE-seq into the scTAMseq workflow (scTAMseq_prot). Targeted RNA sequencing (scTAMARA_rna) was performed alongside scTAMARA_DNA on one CD34+-enriched sample (X.1). Additionally, a dedicated mitochondrial panel (TAMITO_seq) was employed on a peripheral blood sample from a healthy donor (X.2) to assess mitochondrial heterogeneity and facilitate lineage tracing.

  Study EGAS00001008056

• Assessing the suitability of formalin-fixed paraffin-embedded (FFPE) tissue for genome-wide association studies (GWAS)

  This study evaluates the feasibility of conducting genome-wide association studies (GWAS) using DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue. Genotyping results from paired FFPE and blood samples were compared using both microarray technology and low-coverage whole-genome sequencing (lcWGS). The analysis demonstrated high concordance between FFPE- and blood-derived genotypes. Although both platforms performed well, microarrays achieved significantly higher recall and precision and currently offer greater cost-effectiveness and computational efficiency. These findings support the suitability of FFPE-derived DNA for GWAS, with microarrays representing the preferred approach at present. However, the broader variant detection enabled by lcWGS may represent an additional advantage to be explored in future studies, particularly in diverse populations.

  Study EGAS00001008103

• Identifying autosomal recessive mutations causing neurological disorders

  The objective of this study is to resequence of targeted intervals containing autosomal recessive variants causing neurological disorders in consanguineous pedigrees. Using homozygosity mapping, three intervals of very different sizes have previously been unambiguously mapped for three different neurological diseases: 2.4Mb, 8Mb and 14.3Mb in size, for Microlissencephaly, Severe Mental Retardation and Complicated hereditary spastic paraplegia respectively. This study is a pilot to assess how well custom targeted resequencing performs across a broad size range of intervals. The study design is to use a different custom capture probe set for each interval, pulldown from a single patient from each family, and sequence 1 lane using Illumina paired-reads for each sample. Candidate variants will be followed up in the families themselves, and in patients with similar phenotypes from outbred populations.

  Study EGAS00001000023

• Recording physiological history of cells with chemical labeling.

  Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G-protein-coupled receptor activation and elevations in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogenous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.

  Study EGAS50000000056

• Clonal heterogeneity leads to secondary resistance in a melanoma patient after adoptive cell therapy with tumor-infiltrating lymphocytes

  Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TIL) is effective in melanoma patients, although long-term responses seem restricted to patients with complete remissions. Many patients develop secondary resistance to TIL-ACT but involved mechanisms are unclear. Here, we describe a case of secondary resistance to TIL-ACT likely due to intratumoral heterogeneity and selection of a resistant tumor cell clone via transferred T cells. This is the first case of clonal selection of a pre-existing non-dominant tumor cell clone and demonstrates a new mechanism involved in secondary resistance to TIL-ACT and could potentially change current clinical practice, because it advocates for T cell collection from different tumor sites and analysis of tumor heterogeneity before the treatment with TIL-ACT.

  Study EGAS50000000279

• Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells

  Resolving causal genes for type 2 diabetes at loci implicated by genome-wide association studies (GWAS) requires integrating functional genomic data from relevant cell types. Chromatin features in endocrine cells of the pancreatic islet are particularly informative and recent studies leveraging chromosome conformation capture (3C) with Hi-C based methods have elucidated regulatory mechanisms in human islets. However, these genome-wide approaches are less sensitive and afford lower resolution than methods that target specific loci. Methods: To gauge the extent to which targeted 3C further resolves chromatin-mediated regulatory mechanisms at GWAS loci, we generated interaction profiles at 23 loci using next-generation (NG) capture-C in a human beta cell model (EndoC-βH1) and contrasted these maps with Hi-C maps in EndoC-βH1 cells and human islets and a promoter capture Hi-C map in human islets. Results: We found improvements in assay sensitivity of up to 33-fold and resolved ~3.6X more chromatin interactions. At a subset of 18 loci with 25 co-localised GWAS and eQTL signals, NG Capture-C interactions implicated effector transcripts at five additional genetic signals relative to promoter capture Hi-C through physical contact with gene promoters. Conclusions: High resolution chromatin interaction profiles at selectively targeted loci can complement genome- and promoter-wide maps.

  Dataset EGAD50000000517