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• Serial TERT rearrangement breakpoint quantification in circulating tumor DNA enables minimal residual disease monitoring in patients with neuroblastoma

  Approximately 30% of high-risk neuroblastomas harbor genomic TERT rearrangements at diagnosis, resulting in high TERT transcript levels and active telomerase. Combined with mutations in the RAS/MAPK/ALK signaling transduction network, these patients have a dismal prognosis. Our objective was to establish a liquid biopsy-based monitoring strategy for this particularly vulnerable patient subgroup, for whom no in-time molecular diagnostic tools exist to date. Detection and quantification of TERT rearrangement breakpoints in cell-free tumor DNA circulating in peripheral blood and bone marrow plasma from patients with TERT-driven neuroblastoma improved minimal residual disease monitoring and early relapse detection in individual patients. TERT rearrangement breakpoints, as a single marker or combined with mutations in the RAS/MAPK/ALK signaling transduction network, can be reliably analyzed from 1ng DNA using droplet digital PCR assays fit for clinical routine use. TERT rearrangement breakpoints are reflected in cell-free tumor DNA and can serve as robust biomarkers for disease activity.

  Study EGAS00001007365

• WTCCC case-control study for Rheumatoid Arthritis - Combined Controls

  WTCCC genome-wide case-control association study for Rheumatoid Arthritis (RA) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000012

• WTCCC case-control study for Bipolar Disorder

  WTCCC genome-wide case-control association study for Bipolar disorder (BD) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000001

• RNA sequencing of baseline HCC PDX models

  To establish the baseline transcriptional profiles, we performed bulk RNA-seq for 36 of our HCC PDX models. 2-6 samples were collected for each model resulting in a total of 68 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000736

• BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 Full Summary Statistics

  BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 full summary statistics data include five molecular traits (eQTL, hQTL(H3K27ac), hQTL(H3K4me1), mQTL, and psiQTL) for three primary blood cells (Monocytes, Neutrophils, and T-cells). Each full summary statistics file contains the associations for all tested variants for each phenotype ID.

  Dataset EGAD00001005199

• Reference single cell SNP array dataset from Coriell for training and validation of method for accurate single cell genotyping

  This dataset contains DNA from B-lymphocytes from 2 Coriell families and 4 individuals hybridized to HumanKaryomap BeadChip Array. Single cells from subjects GM12878 and GM7228 were amplified using multiple displacement amplification (SureMDA) according to Infium Karyomapping Assay Guide. Bulk DNA was processed and hybridized to an array for subject GM12878, GM07224 and GM07225.

  Dataset EGAD00001006376

• BLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples

  BLLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001001596

• RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 10) or with vehicle (N = 10).

  Study EGAS00001006583

• WES and WGS data for HGSC patient derived cell lines and fresh frozen tumor samples from same patients

  Sequencing data for three HGSC patients with patient derived cell lines. WES data for two patient derived cell line samples and matched blood control samples. Fresh frozen tumor samples of two patients with WES or WGS sequencing data.

  Dataset EGAD00001009330

• Paired-end Whole Exome-seq analysis of multi-centric lower grade glioma

  This dataset includes Nimblegen SeqCap EZ Exome v3 data for each lesion of three patients with multicentric glioma. For two patients, each lesion was sequenced along with whole blood. For a third patient, 3 pieces from the right lesion and 4 pieces from the left were sequenced along with whole blood. In each case BAM files that have been aligned with BWA mem alignment are available.

  Dataset EGAD00001003795