12277 results for ""statistically+reactive"+taxa+in+microbial+community"

in 16.33 milliseconds.

• Genomic gain of EBV's LMP-1 in NKTCL

  The study found a high recurrence of genomic gain of LMP1 locus within EBV-associated NKTCL. The pilot data set and extended dataset of 77 WGS NKTCLs found 18/77 tumoral genomes to harbour genomic gain of LMP-1 locus within the EBV viral genomes within NKTCL tumoral sequencing data. The study also found 1/10 NKTCL cell lines to be positive for LMP-1 locus gain within EBV genomes too. This dataset includes solely the confirmatory WGS data of LMP-1 gain from NKYS cell lines using Oxford Nanopore long-read sequencing technology.

  Study EGAS50000000260

• Profiles of extracellular miRNA in cerebrospinal fluid and serum from patients with Alzheimer's or Parkinson's disease correlate with disease status and features of pathology

  We profiled the miRNA contents from cerebrospinal fluid and serum (using next generation sequencing) from postmortem patients diagnosed with Alzheimer's or Parkinson's disease, and neurologically normal controls. All biofluids were cell-free and patient matched, there was one cerebrospinal fluid and one serum sample from each of 70 patients with Alzheimer's disease, 67 patients with Parkinson's disease and 78 age-similar controls. We correlated the miRNA changes with measurements of neuropathology such as plaques, tangles and Lewy bodies.

  Study phs000727

• A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk

  Identification of the genes and processes mediating genetic association signals for complex diseases represents a major challenge. As many of the genetic signals for type 2 diabetes (T2D) exert their effects through pancreatic islet-cell dysfunction, we performed a genome-wide pooled CRISPR loss-of-function screen in a human pancreatic beta cell line. We assessed the regulation of insulin content as a disease-relevant readout of beta cell function and identified 580 genes influencing this phenotype. Integration with genetic and genomic data provided experimental support for 20 candidate T2D effector transcripts including the autophagy receptor CALCOCO2. Loss of CALCOCO2 was associated with distorted mitochondria, less proinsulin-containing immature granules and accumulation of autophagosomes upon inhibition of late-stage autophagy. Carriers of T2D-associated variants at the CALCOCO2 locus further displayed altered insulin secretion. Our study highlights how cellular screens can augment existing multi-omic efforts to support mechanistic understanding and provide evidence for causal effects at genome-wide association studies loci.

  Dataset EGAD50000000518

• Immune signature of malignant melanoma in pregnancy

  Melanoma is a highly immunogenic malignancy and there is a deep-rooted notion among clinicians that a probable systemic immunosuppressed state during pregnancy would negatively influence melanoma related prognosis. To test this hypothesis on a more fundamental level, we collected a unique set of melanoma tumor samples and performed RNAseq to draw comparisons between the immune cell infiltrate of pregnant patients and non-pregnant matched controls. We found that there is indeed no differential expression of any immune cell subset. This underscores the notion that the supposed immunosuppressive state of pregnancy does not hamper the anti-tumor immune response.

  Study EGAS50000000492

• Gabriella Miller Kids First Pediatric Research Program in Bladder Exstrophy, Epispadias, Complex (BEEC)

  Urogenital anomalies account for 20-30% of prenatally detected structural defects. Bladder Exstrophy Epispadias Complex (BEEC) describes a subset of anomalies with a spectrum of developmental defects ranging from a mild form of epispadias, to classic bladder exstrophy, to omphalocele, exstrophy, imperforate anus, spinal anomalies (OEIS) complex. Patients with BEEC suffer substantial morbidity and mortality due to impaired genito-urinary dysfunction. The etiology of BEEC is largely unknown. Elucidating the underlying genetic component is critical to gaining a better understanding of the developmental signaling pathways and is likely the first step to developing targeted therapy.

  Study phs002173

• A non-canonical lymphoblast in refractory childhood T-cell leukaemia

  Refractory cancers may arise either through the acquisition of resistance mechanisms by cancer cells or represent distinct diseases. The origin of childhood T-cell acute lymphoblastic leukaemia (T-ALL) that does not respond to initial treatment, i.e. refractory disease, is unknown. Refractory T-ALL carries a poor prognosis and cannot be predicted at diagnosis. Here, we performed single cell mRNA sequencing of T-ALL from children who did or did not respond to initial treatment. We identified a transcriptionally distinctive blast population, exhibiting features of innate-like lymphocytes, as the major source of refractory disease.

  Study EGAS50000000767

• Single B cell analysis in pemphigus patients

  pemphigus is caused by autoantibodies that target cell-cell adhesion molecules, desmoglein(Dsg). Clinical effect of anti-CD20 antibody therapy suggtests that Dsg-specific memory B cell, the precursor of autoantigen secreting plasmablast, may play an important role of disease activity. This study aimed to isolate Dsg-specific memory B cell using recombinant labeled Dsg proteins and performed single cell RNA-sequence to detect autoimmune B cell specific gene expression. For control, we also isolate non-Dsg specific memory B cells from same patients, or forein antigen (Flu HA) specific memory B cells from vaccinated healthy volunteers.

  Study JGAS000281

• Stage-specific gene and transcript dynamics in human male germ cells

  The testis is one of the most transcriptionallyactive organs, however how germ cell differentiation is controlled at the molecular level remains largely unknown. To study global transcriptional dynamics during human spermatogenesis we sequenced total RNA of human testicular biopsies with 5 specific histological phenotypes: Sertoli cell-only (SCO, n=3), spermatogenic arrests at the spermatogonial (SPG, n=4), spermatocyte (SPC, n=3), and spermatid (SPD, n=3) level, as well as normal spermatogenesis (Normal, n=3). To our knowledge, this work provides the most complete capture of the transcriptome and its dynamics during human spermatogenesis to date.

  Study EGAS00001006135

• Leucocyte eQTLs in autoimmune disease and health

  Peripheral blood was taken from healthy controls and patients with active autoimmune disease. CD4 T cells, CD8 T cells, monocytes, neutrophils, and B cells were separated using magnetic-activated cell sorting. RNA and genomic DNA was extracted from cell lysates using Qiagen Allprep kits. Genotyping of healthy controls and patients with inflammatory bowel disease was performed using the Illumina Human OmniExpress12v1.0 BeadChip at the Wellcome Trust Sanger Institute. 200 ng RNA was processed for hybridization onto Affymetrix Human Gene ST 1.1 microarrays. Gene expression and genotyping data was used to perform eQTL mapping.

  Study EGAS00001001251

• Longitudinal analysis of treatment induced genomic alterations in gliomas

  Here, we report the longitudinal whole exome sequencing analysis of a patient with a primary GBM and two recurrences, demonstrating the heterogeneity caused by the therapy induced molecular changes and their implications for clinical decision-making. This analysis revealed the impact of temporal evolution for tumors under the pressure of treatment. We presented that while targeted treatments eliminated some sensitive clones, there were clones that were enriched leading to resistance. This study demonstrates the importance of longitudinal genomic profiling to adjust to the dynamic nature of therapy induced molecular changes to improve the outcomes of precision therapies.

  Study EGAS00001002168