NGS zwc practice
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ABSTRACT:
PROVIDER: PRJEB28063 | ENA |
REPOSITORIES: ENA
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Project description:Practice Programmatic Submission
| PRJEB26575 | ENA
Project description:Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is believed to be the counterpart to stress response and is characterized by decreased oxygen consumption, increased exhaled nitric oxide, and reduced psychological distress. Individuals experiencing chronic psychological stress have the opposite pattern of physiology and a characteristic transcriptional profile. We hypothesized that consistent, long-term practice of RR techniques results in characteristic changes in gene expression. We tested this hypothesis by assessing the transcriptional profile of whole blood in healthy, long-term practitioners of daily RR practice (group M) in comparison to healthy controls (group N1). The signature obtained has been validated on new subject data. Experiment Overall Design: In the study, the gene expression profiling was performed on individuals with a long-term RR practice (group M; n=19) or those with no prior RR experience; novice (group N1; n=19). Group N1 novices, furthermore, underwent 8-weeks of RR training (Group N2; n=20) for the prospective analysis.As a validation of results , we developed an independent validation sets that includes gene expression profiling on 4 N1, 4 N2 and 6 M subjects.
2008-10-21 | E-GEOD-10041 | biostudies-arrayexpress
Project description:Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is believed to be the counterpart to stress response and is characterized by decreased oxygen consumption, increased exhaled nitric oxide, and reduced psychological distress. Individuals experiencing chronic psychological stress have the opposite pattern of physiology and a characteristic transcriptional profile. We hypothesized that consistent, long-term practice of RR techniques results in characteristic changes in gene expression. We tested this hypothesis by assessing the transcriptional profile of whole blood in healthy, long-term practitioners of daily RR practice (group M) in comparison to healthy controls (group N1). The signature obtained has been validated on new subject data. Keywords: time course
2008-07-05 | GSE10041 | GEO
Project description:Genomic Grade Index (GGI) is a 97-gene signature that improves histologic grade (HG) classification in invasive breast carcinoma. In this prospective study we sought to evaluate the feasibility of performing GGI in routine clinical practice and its impact on treatment recommendations. Patients with pT1pT2 or operable pT3, N0-3 invasive breast carcinoma were recruited from 8 centers in Belgium. Fresh surgical samples were sent at room temperature in the MapQuant DxM-bM-^DM-" PathKit for centralized genomic analysis. Genomic profiles were determined using Affymetrix U133 Plus 2.0 and GGI calculated using the MapQuant DxM-bM-^DM-" protocol, which defines tumors as low or high Genomic Grade (GG-1 and GG-3 respectively). 180 pts were recruited and 155 were eligible. The MapQuant test was performed in 142 cases and GGI was obtained in 78% of cases (n=111). Reasons for failures were 15 samples with <30% of invasive tumor cells (11%), 15 with insufficient RNA quality (10%), and 1 failed hybridization (<1%). For tumors with an available representative sample (M-bM-^IM-% 30% inv. tumor cells) (n=127), the success rate was 87.5 %. GGI reclassified 69% of the 54 HG2 tumors as GG-1 (54%) or GG-3 (46%). Changes in treatment recommendations occurred mainly in the subset of HG2 tumors reclassified into GG-3, with increased use of chemotherapy in this subset. The use of GGI is feasible in routine clinical practice and impacts treatment decisions in early-stage breast cancer. Total RNA was extracted from fresh tumor tissues comprising M-bM-^IM-%30% invasive tumor cells and hybridized on Affymetrix microarrays if the RIN was M-bM-^IM-% 7.
2013-06-03 | E-GEOD-43365 | biostudies-arrayexpress
Project description:Human Podocytes Develop “Names” to Practice Self-Avoidance
| PRJNA939188 | ENA
Project description:Genomic Grade Index (GGI) is a 97-gene signature that improves histologic grade (HG) classification in invasive breast carcinoma. In this prospective study we sought to evaluate the feasibility of performing GGI in routine clinical practice and its impact on treatment recommendations. Patients with pT1pT2 or operable pT3, N0-3 invasive breast carcinoma were recruited from 8 centers in Belgium. Fresh surgical samples were sent at room temperature in the MapQuant Dx™ PathKit for centralized genomic analysis. Genomic profiles were determined using Affymetrix U133 Plus 2.0 and GGI calculated using the MapQuant Dx™ protocol, which defines tumors as low or high Genomic Grade (GG-1 and GG-3 respectively). 180 pts were recruited and 155 were eligible. The MapQuant test was performed in 142 cases and GGI was obtained in 78% of cases (n=111). Reasons for failures were 15 samples with <30% of invasive tumor cells (11%), 15 with insufficient RNA quality (10%), and 1 failed hybridization (<1%). For tumors with an available representative sample (≥ 30% inv. tumor cells) (n=127), the success rate was 87.5 %. GGI reclassified 69% of the 54 HG2 tumors as GG-1 (54%) or GG-3 (46%). Changes in treatment recommendations occurred mainly in the subset of HG2 tumors reclassified into GG-3, with increased use of chemotherapy in this subset. The use of GGI is feasible in routine clinical practice and impacts treatment decisions in early-stage breast cancer.
2013-06-03 | GSE43365 | GEO
Project description:Background: One of the main fields of lung cancer research is identifying patients who are at high risk of post-resection recurrence. Individual recurrence risk evaluation by accurate but simple and reproducible method is needed for the clinical practice. Results: The log-rank test and further selection by our criteria of assayability generated 87 genes from microarray data with significant level 5%. Of these, by PTQ-PCR, the expression of most significant 18 genes was obtained. Using these gene expression information and clinical parameters, by stepwise variable selection method, the recurrence prediction model, which composed of 6 genes (CALB1, MMP7, SLC1A7, GSTA1, CCL19, IFI44) and pStage and cell differentiation, were developed. Validation into the two independent cohorts showed good results of the proposed model (p=0.0314, 0.0305, respectively). The predicted median recurrence-free survival times for each patient were reflected real ones well. Conclusions: Our method of individualized recurrence risk prediction is accurate, technically simple and reproducible to be used in clinical practice. Therefore, it would be useful in customizing the lung cancer management strategies. Keywords: Recurrence Free Survival Analysis
2007-11-20 | GSE8894 | GEO
Project description:eMERGE: A Multi-Center Pilot of Pharmacogenetic Sequencing in Clinical Practice
| PRJNA282562 | ENA
Project description:Case report: Next Generation Sequencing in clinical practice – a real tool for ending the protracted diagnostic odyssey
| PRJEB48104 | ENA
Project description:Podocyte effacement and loss characterizes glomerulopathies such as diabetic nephropathy, lupus, and glomerular toxicity. Human primary podocyte-like epithelial cells cultured from urine (ECU) were characterized as a window to understand podocyte regeneration in these glomerulopathies. Cytokines TNF, and VEGF stimulated regrowth, whereas FGF-1 and IL1 inhibited growth, consistent with other podocyte or parietal epithelial cell models. Review of published micrographs indicated that podocyte foot processes in rodent kidneys interdigitated exclusively with foot processes from other cells, suggesting podocytes practice self-avoidance. In culture, ECU avoided close interactions with other cells arising from the same clone, until enough cells grew for the culture to become confluent. In contrast, ECU derived from multiple clones associated actively to form contiguous monolayers. Gene expression profiling of eight clonal ECU colonies using RNA sequencing revealed that each colony expressed a highly variable profile of the 53 Protocadherin genes. Variable combinations of the 53 Protocadherin PCDHA-, PCDHB-, and PCDHG- gene products are known to act homophilically to direct self-avoidance interactions in human neurons, so PCDH- genes are postulated to govern self-avoidance similarly in podocytes. Such protocadherin profiles could be considered cell names. Transcriptional profiles of ECUs suggest they may represent intermediate stages of Parietal Epithelial Cells (PECs) differentiating into podocytes. They further suggest that each podocyte practices self-avoidance, interdigitating selectively with other cells in the glomerulus. To enable further investigation of multi-clonal podocyte interactions, five podocyte clones were immortalized using temperature-sensitive SV40 Large T antigen. These results suggest that non-self interdigitation of new podocytes with remnant podocytes may facilitate replacement of dying podocytes and re-establishment of a functional filtration barrier.
2024-02-24 | GSE226224 | GEO