14388 results for ""Pennsylvania+German"+ACS+study+'Socius'+open+access"

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• Identification of new molecular targets with profiling of malignant mesothelioma

  Aims: Malignant mesothelioma which is associated with asbestos exposure is highly aggressive and refractory to conventional therapeutic modalities. The aim of this study is identification of new targets for molecular target therapy by next generation sequencing and application of the genomic data to new diagnostic and therapeutic strategies for malignant mesothelioma patients. Methods: We extracted genomic DNAs from surgical specimens or established mesothelioma cell lines from Japanese malignant mesothelioma patients. We also extracted control DNAs from peripheral blood of the same patients. We performed whole exome sequencing using these DNAs.

  Study JGAS000062

• Nanopore whole-genome sequencing of sample RK067 and variant-call data (SNVs and intermediate-sized deletions) of 174 Japanese samples.

  We performed whole-genome sequencing of a human samples using Oxford Nanopore MinION sequencer, so as to be able to establish methods to detect and identify structural variations in Japanese individuals. Intermediate-sized deletions were identified from 174 Japanese samples��� short-reads whole-genome sequencing data. Variant call information of these intermediate-sized deletions were joined with SNVs identified in a previous study (Fujimoto, A et al., Nat Genet, 2016) to create a reference panel for use in imputation.

  Study JGAS000180

• Establishment of an integrated database for clinical and genomic data in cancer

  In this study, to clarify the genomic varieties of MM in Asian population, we planned to investigate the genomic features in Japanese population, represented as an Asian cohort, and preformed the comprehensive genomic analysis of MM cells with newly diagnosed multiple myeloma (NDMM) by means of targeted capture sequencing (TCS) method. In our TCS assay, MM cells are subjected to the detection of following genomic abnormalities; IG rearrangements, IG associated translocations, CNAs, and somatic mutations from 340 genes related to the pathogenesis and therapeutic agent of MM.

  Study JGAS000206

• ChIP sequencing for β-catenin and histone modifications in HCC cell lines and organoids with CTNNB1 mutations

  CTNNB1 mutation is a major driver of HCC, particularly in metabolic-associated subtype. This study utilized patient-derived tumour organoids and cell lines harbouring various endogenous CTNNB1 mutations to comprehensively map the transcriptional repertoire regulated by mutant β-catenin through ChIP-seq under normal and fatty conditions. Genome-wide binding patterns of β-catenin were integrated with ChIP-seq data for histone modifications H3K27ac and H3K27me3 to assess active and repressive chromatin states. Oleic acid treatment was used to model fatty conditions.

  Study EGAS50000001274

• ctDNA Quantification in Blood Plasma Using Deep Learning Based Fragle Tool

  The project aims to develop an easy to use software named Fragle that can quantify ctDNA in blood plasma. This can help in cancer screening and progress monitoring from simple blood test without any need for tumor biopsy. We aim to make Fragle usable for both low pass whole genome sequencing and targeted sequencing data of cell free DNA. Fragle can work directly on the raw bam files mapped to hg19/GRCh37. We are uploading the bam files used in this study for Fragle evaluation.

  Study EGAS50000000122

• Prime-seq of human term placenta-derived trophoblast organoids

  To study the one of the mechanisms through which obesity could affect placental cells, we used a novel microfluidic organs-on-a-chip device fabricated for co-culturing adipose spheroids and trophoblast organoids. The organoids were derived from the term placenta of a over-weight women. The adipose spheorids were derived from the white adipose tissue of a woman. And we sequenced the RNAs from the trophoblast organoids. The RNA extracted were subjective to Prime-seq library preparation protocol and being sequenced on Illumina NovaSeq 6000 at Novogene.

  Study EGAS50000000833

• Discordant_Monozygotic_Twins_ALS(Genetics)

  Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Regarding genetic factors, pathogenetic mutations in more than 35 genes have been identified as playing a role in disease pathogenesis. However, a substantial portion of ALS heritability remains unaccounted for, pointing to the potential involvement of additional genetic and epigenetic factors. For this reason, we conducted a multi-omics study on a monozygotic twin pair discordant for amyotrophic lateral sclerosis, performing whole exome sequencing, transcriptomic and epigenetic analyses to gain crucial insights into underlying pathogenetic disease mechanisms. Here, we share genetic data.

  Study EGAS50000000908

• Whole-genome sequencing of cell-free DNA from pancreatic and breast cancer cohorts for fragmentomic and tumor fraction analysis

  This project provides whole-genome sequencing data from cell-free DNA collected from patients with pancreatic ductal adenocarcinoma and breast cancer, alongside healthy and benign controls. The study aims to identify novel liquid biopsy biomarkers by exploring the relationship between per-base quality scores and fragmentomic signals like end-motifs and fragment length. Furthermore, the data supports the development of Bayesian deep learning frameworks for the uncertainty-aware estimation of tumor fraction and ploidy in low-concentration clinical samples.

  Study EGAS50000001620

• Sequencing data for Clinical Trial

  This study is a tri-institutional Phase 1/randomized Phase 2 trial, bevacizumab-naïve rHGA patients were randomized to either LITT (laser interstitial thermal therapy) plus pembrolizumab (LITT+PEM) or non-LITT surgery plus pembrolizumab (NLS+PEM). Randomization ceased after 21 patients when emerging data showed limited adjuvant ICI (immune checkpoint inhibitors) benefit, and the next 24 patients all received LITT+PEM. The goal of the trial is to use LITT, a minimally invasive cytoreductive approach, to prime these “cold” tumors for enhanced ICI response. rHGA= high-grade astrocytoma

  Study EGAS50000001144

• Single-nucleus RNA-seq of human fetal liver hematopoiesis

  The fetal liver is the primary haematopoietic organ during early human development, yet the timing and regulatory mechanisms governing blood formation remain incompletely understood. To define the cellular, transcriptional, and epigenetic changes underlying human fetal liver hematopoiesis over development, we generated a high-resolution, time-resolved single-nucleus multiome atlas of human fetal liver spanning 5–18 post-conception weeks (PCW) for CD45+CD235- cells. In total, 308,021 high-quality nuclei from 53 donors were profiled using paired chromatin accessibility and transcriptomic modalities. This study is for the gene expression.

  Study EGAS50000001631