14676 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Whole-exome sequencing profiling of patients with metastatic prostate cancer at VHIO

  Metastatic prostate cancer (mPC) is enriched for homologous recombination repair (HRR) gene alterations, which have prognostic and predictive value. Routine clinical implementation of next-generation sequencing (NGS) is still limited. We investigated the association between genomic and functional loss of HRR, using NGS and a RAD51 immunofluorescence (RAD51-IF) iprimary or metastatic biopsies from patients with stage IV prostate cancer. Whole-exome sequencing was pursued for paired tumor-normal samples.

  Study EGAS50000000736

• RNA sequencing of serial samples from patients enrolled in the NA-PHER2 trial

  Improved outcomes in HER2+ breast cancer have resulted from chemotherapy and anti-HER2 therapies. However, HER2+ER+ cancers exhibit lower response rates. The NA-PHER2 trial investigated chemo-free preoperative HER2 and CDK4/6 blockade with or without endocrine therapy in HER2+ER+ breast cancer. Through RNA sequencing and tumour infiltrating lymphocytes (TIL) assessment in serial biopsies we identified predictive biomarkers of pCR, Day 14 Ki67 response, and unveiled treatment-induced molecular changes.

  Study EGAS50000000248

• MOSAIC - Multi-Omics Spatial Atlas In Cancer

  MOSAIC is a collaborative initiative founded by Owkin, Lausanne University Hospital (CHUV), Charité Universitätsmedizin Berlin, University Hospital Erlangen (UKER), Gustave Roussy Institute in Paris, and University of Pittsburgh. The goal of MOSAIC is to build the largest collection of spatial omics data in cancer. By integrating comprehensive high quality clinical annotations with advanced deep profiling techniques, MOSAIC aims to uncover novel cancer subtypes and identify key drug targets and biomarkers within them.

  Study EGAS50000000689

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  99 FFPE derived tumor tissue DNA, 9 circulating tumor DNA samples and 38 paired germline DNA were used. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) at the National Genomic Analysis Center (CNAG, Barcelona, Spain) was performed.

  Study EGAS50000000371

• Targeted Sequencing of 52 Genes for Severe COVID-19

  This dataset comprises targeted sequencing data of 52 genes previously implicated in severe COVID-19 outcomes. The study includes samples from 764 individuals with severe COVID-19 and 3,939 population-based controls from the GCAT cohort (Spain). Molecular Inversion Probes (MIPs) were utilized for cost-effective and precise sequencing of the selected genes. The targeted genes include: Inflammasome/IL-1/TNF Pathway: NLRP3, CASP1, CASP8, IL1B, TNF, RIPK1, RIPK3, MYD88, TNFRSF13B SARS-CoV-2 Entry/Replication: ACE2, TMPRSS2, FURIN, SLC6A20, DDX1, DDX58, TLR4, FYCO1, CTSB, CTSL, ADAM17 Complement System: MBL2, CFH, CFI, CFB, ADAM10, CD46 Interferon Signaling: TLR3, IFIH1, IFITM3, TBK1, TLR7, IL10RB, IFNAR1, IFNAR2, SIGLEC1, MYD88, IFNGR1 Chemokine Receptor Signaling: CCR1, CCR3, CCR2, CCR9, IL8, CXCL3, CXCL10, CXCR6, XCR1, CCL2, CCL20 Immunodeficiency Genes: CASP8, CD46, CFB, CFH, CFI, IFNAR1, IFNAR2, IFNGR1, IFIH1, MYD88, NLRP3, RIPK1, TBK1, TLR3, TLR7

  Dataset EGAD50000001378

• Indonesian Microbiome Ecology and Evolution v1 (raw data)

  This dataset comprises 124 human faecal samples collected across Indonesia between 2015 and 2021, together with 6 controls. It was collected to study patterns of human microbiome variation across Indonesia’s diverse geography and lifestyles, and to generate the Indonesian Microbiome Ecology and Evolution (IndoMEE) metagenome-assembled genome (MAG) reference database. The dataset consists of 250 bp paired-end metagenomic reads from 124 faecal samples acquired from 116 individuals, at ca. 10.6 Gb / sample, together with 2 positive controls (ZymoBIOMICS Microbial Community DNA Standard by Zymo Research Cat# D6305), and 4 negative controls (for sampling: Blank, for extraction: Buffer EB by Qiagen Cat# 19086, for library prep: Nuclease Free Water by Ambion-Invitrogen Cat# AM9937). Library preparation was carried out using Illumina's TruSeq DNA Nano DNA kit, and sequencing was performed on the Illumina NovaSeq 6000 platform.

  Dataset EGAD50000001399

• Single-cell transcriptomic analyses of peripheral blood mononuclear cells, peritoneal fluid, and peritoneal metastases from patients with colorectal cancer

  The data published here contains single-cell RNA- sequencing (scRNAseq) on peripheral blood mononuclear cells (PBMC), peritoneal fluid (PF), and peritoneal metastases (PM). PBMC, PF and, where possible, PM was acquired from patients with colorectal cancer (CRC) and subjected to 3' scRNAseq using the 10X Genomics (Chromium Single Cell 3’ Reagent). Sequencing was performed in a paired-ended fashion on either the HiSeq4000 or the NovaSeq6000.

  Study EGAS50000000173

• Single-cell RNA-sequencing and cellular indexing of transcriptomes and epitopes of peripheral blood mononuclear cells and peritoneal fluid from patients with achalasia

  The data published here contains cellular indexing of transcriptomes and epitopes (CITE-seq) and single-cell RNA- sequencing (scRNAseq) data on patients with achalasia. Paired PBMC and PF were subjected to 3' scRNAseq and CITE-seq, respectively. All single-cell data was generated using the 10X Genomics (Chromium Single Cell 3’ Reagent) and sequenced in a paired-ended fashion on the NovaSeq6000.

  Study EGAS50000000174

• Skin Microbiome of Monogenic Skin Disorder

  Ichthyosis introduces multiple sources of disturbance to the skin, including the direct biochemical consequences of the genotype, the phenotypic changes in skin physiology, and an altered skin microbiome. The association between changes in the skin microbiome and the disease's genotypic and phenotypic effects are historically obscured. Here we characterize the skin microbiome of healthy participants and ichthyosis patients, before assessing the association between these microbiome features and the ichthyosis genotype and phenotype while adjusting for contextual host covariables.

  Study phs003799

• Long-read whole genome sequencing as a tool for variant detection in inherited retinal dystrophies

  Advances in whole-genome sequencing (WGS) have significantly enhanced our ability to detect genomic variants underlying inherited diseases. In this study, we performed long-read WGS on 24 patients with inherited retinal dystrophies (IRDs) to validate the utility of nanopore sequencing in detecting genomic variations. We confirmed the presence of all previously detected variants and demonstrated that this approach allows for precise refinement of structural variants (SVs). Furthermore, we could perform genotype phasing by sequencing only the probands, confirming variants were inherited in trans. Moreover, nanopore sequencing enabled the detection of complex variants, such as transposon insertions and structural rearrangements. This comprehensive assessment illustrates the power of long-read sequencing in capturing diverse forms of genomic variation and in improving diagnostic accuracy in IRDs.

  Dataset EGAD50000001238