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

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• Whole genome sequencing of pancreatic cystic fluid for early detection and diagnosis of pancreatic cancer

  Pancreatic cancer (PC) is a leading cause of cancer-related deaths globally. Accurate PC detection at early or premalignant stage, when surgery is effective, would increase survival rates and prevent unnecessary surgery or surveillance. Molecular diagnostic attempts using PCy fluid (PCyF), as a liquid biopsy, to analyze common mutations associated with PC development are yet to contribute to early diagnosis. Whole genome sequencing (WGS) is utilized in various cancers, PC inclusive, for detecting genetic changes associated with carcinogenesis, but not in PCyF due to technical limitations, including isolated DNA purity. The goal of the study was to achieve high quality of WGS from PCyF from 9 patients to enable development of signatures of malignancy. The WGS was performed using Illumina sequencing. Experimental design was at a 50x depth.

  Dataset EGAD50000000869

• Cas9-targeted-based long-read sequencing for genetic screening of RPE65 locus

  In order to compare sequencing performance of different technologies in a specific locus, we sequenced blood samples of five inherited retinal dystrophies (IRD) patients harboring a monoallelic variant in RPE65 that remained uncharacterized with: 1) Clinical exome targeted sequencing (CES), 2) whole genome sequencing (WGS), and 3) Long-read sequencing on a MinION platform where CRISPR-Cas9 guide RNA probes were designed to target a 31 kb region including the entire RPE65 locus.

  Study EGAS50000000596

• CIDR: Molecular Pathological Epidemiology of Colorectal Cancer

  Colorectal cancer, the second most commonly diagnosed cancer is a biologically heterogeneous disease. To characterize the molecular attributes of colorectal tumors, we conducted targeted sequencing at the Center for Inherited Disease Research (CIDR) on 4,518 tumor and matched normal DNA samples from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colon Cancer Family Registry (CCFR). These consortia are based on cohort and population-based case-control studies.

  Study phs001905

• Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [scRNAseq]

  Single-cell RNA-sequencing of brain organoids at day 120 grown in four distinct growth protocols designed to generate dorsal (D) and ventral (V) forebrain, midbrain (M) and striatum (S) tissue using eight different pluripotent stem cell lines. Per per cell line-protocol combination two organoids (biological replicates) were grown. For cell line 176 the experiment was conducted in two independent biological replicates (repititions E1 and E2).

  Study EGAS50000000662

• Single-cell RNA sequencing of human IL-18R supported CAR T cells targeting oncofetal Tenascin C

  C.TNC-CAR.Zip18R CAR-T cells are from 2 donors and multiplexed 10x Genomics scRNA-seq were performed with a hashtag to label each sample. For tumor and CAR-T cell cocluture samples, CAR-T cells were extracted from 3 time points. The raw data are fastq format for total 20 samples considering sequencing lanes. The multiplexing information, CAR and Zip18R sequences are deposited in analyses.

  Study EGAS50000000772

• Whole Exome Sequencing of controls performed at the Broad Institute on a cohort from Bristol, UK

  These data were generated as part of a collaboration between University of Bristol, UK and the Stanley Center at the Broad Institute. This project sequenced and analysed the whole exomes of 2969 samples from the Avon Longitudinal Study of Parents and Children (ALSPAC). ALSPAC is a population-based pregnancy cohort with participants acting as ‘controls’ for this project. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina NovaSeq 6000 machines producing CRAM files. ALSPAC recruited pregnant women in the Avon County of south-west England between 1991 and 1992. Of the 15,447 pregnancies, 14,901 children were alive at 1 year of age.  DNA was extracted from child blood samples taken between ages 7 and 24.

  Dataset EGAD50000000716

• Whole-genome sequences of Korean populations generated by using long- and short-read sequencing technologies.

  We newly sequenced whole-genome of Korean participants by using long- and short-read sequencing platforms (n = 3 and n = 100 for long- and short-read sequencing, respectively). With these data, generated by Sequel II HiFi system (Pacific Bioscience) and DNBSEQ-T7 (MGI) sequencers, we identified a set of structural variations common in Korean population as well as the genetic features distinct from other ethnicities.

  Study EGAS50000000375

• Patient-derived models of primary breast cancer for preclinical development of novel neoadjuvant therapies

  Generation of the first large-scale cohort of mouse intraductal patient-derived xenograft (MIND-PDX) models of primary invasive breast cancer (IBC) and a collection of matched PDX-derived organoids (PDXO) representing all molecular subtypes of IBC, including estrogen receptor (ER-) positive breast cancer. Furthermore, we show that our IBC-MIND cohort can serve as a platform to test experimental neoadjuvant treatment options in different molecular subtypes of breast cancer.

  Study EGAS50000000398

• Matched_breast_cancer_fusion_gene_study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from 40 breast cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000031

• Measurement of the Male Germline Mutation Rate Using Sequential Sperm Samples

  We recalled 23 sperm donors with prior banked samples to provide a new sperm sample. The old and new sequential sperm samples were then profiled by high-fidelity duplex sequencing to measure individual-specific mutation rates and patterns. We also performed deep whole-genome sequencing of sequential sperm samples from two individuals followed by targeted validation, which measured remarkably stable mosaicism of clonal mutations that likely arose during embryonic and germline development.

  Study phs003716