Inherited Neuropathy Consortium Rare Disease Clinical Research Consortium (INC-RDCRC)
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ABSTRACT:
PROVIDER: PRJNA994668 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Inherited Neuropathy Consortium Rare Disease Clinical Research Consortium (INC-RDCRC)
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Project description:Lung Genomics Research Consortium
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Project description:Phosphatase and tensin homolog (PTEN) is a tumour suppressor gene associated with inherited tumour susceptibility conditions, macrocephaly, autism, ataxia, tremor and epilepsy. Functional implications of this protein have been investigated in Parkinson’s and Alzheimer’s diseases. We describe the first patient presented with multifocal demyelinating motor neuropathy in association with a de novo PTEN mutation. The pathogenicity of the mutation was supported by altered expression of several proteins involved in tumorigenesis and fibroblasts showed a reversible defect in catalytic activity of PTEN against the secondary substrate, phosphatidylinositol 3,4,-trisphosphate, suggesting a novel and potentially treatable mechanism for multi-focal demyelinating motor neuropathy.
2018-10-22 | PXD008014 | Pride
Project description:These subjects were diagnosed as being controls or having interstitial lung disease (ILD) or chronic obstructive pulmonary disease (COPD) as determined by clinical history, CT scan, and surgical pathology. There was no intervention, these are cross-sectional data. All samples are from the Lung Tissue Research Consortium (LTRC) and are indexed by their LTRC tissue label.
2015-09-18 | GSE72967 | GEO
Project description:INC-Seq: Accurate single molecule reads using nanopore sequencing
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Project description:This SuperSeries is composed of the SubSeries listed below. Consortium contacts: Maria Pedersen: mpedersen@nygenome.org Hemali Phatnani: hphatnani@nygenome.org NYGC ALS Consortium: cgndhelp@nygenome.org
2019-09-20 | GSE137810 | GEO
Project description:These subjects were diagnosed as being controls or having interstitial lung disease (ILD) or chronic obstructive pulmonary disease (COPD) as determined by clinical history, CT scan, and surgical pathology. There was no intervention, these are cross-sectional data. All samples are from the Lung Tissue Research Consortium (LTRC) and are indexed by their LTRC tissue label. These are 319 total subjects, 183 have ILD and 136 have COPD, who went for surgery for the investigation of a nodule and have no chronic lung disease by CT or pathology. Each sample is total RNA extracted from flash frozen human whole lung homogenate. Between the two platforms were analyzed. Samples are titled by source (LT=LTRC), 6-digit tissue label, lobe of extraction, and major disease state.
2015-09-18 | E-GEOD-72967 | biostudies-arrayexpress
Project description:NHGRI GREGoR Consortium: Genomics Research to Elucidate the Genetics of Rare Disease
| PRJNA875549 | ENA
Project description:NHGRI GREGoR Consortium: Genomics Research to Elucidate the Genetics of Rare Disease
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Project description:Performing GWAS on multiple myeloma in relation to the development of the toxicity neuropathy. This set was used as validation set. We performed a genome-wide association study using Affymetrix HD-SNP arrays 6.0 to identify risk variants for developing bortezomib-induced peripheral neuropathy (BiPN) in 469 multiple myeloma (MM) patients who received bortezomib-dexamethasone therapy prior to autologous stem-cell transplantation and conducted validation in an independent cohort of 116 MM patients. We identified one previously unreported BiPN risk locus at 21q22.3 (rs2839629, PKNOX1; OR = 0.53, 95% CI: [0.40-0.69]). PKNOX1 is known to regulate MCP-1, a potent mediator of chemotherapy-induced peripheral neuropathy. rs2839629 is in strong linkage disequilibrium ( r2 = 0.87) with rs915854, localized 6.5kb centromeric to CBS encoding endogenous H2S-producing enzyme. CBS-H2S signalling pathway is implicated in the pathogenesis of a variety of neurodegenerative and inflammatory disorders, and specifically in neuropathy models. Our data provide conclusive evidence for genetic susceptibility to BiPN in MM and new potential targets in neuro-protective strategies of treatment. Each patient of both IFM and HOVON cohorts was genotyped using the Affymetrix SNP6.0 Human DNA chip (Affymetrix, Santa Clara, CA) according to manufacturerâs instructions (Affymetrix, Santa Clara, CA). The HOVON65 samples were genotyped using CRLMM v2 resulting in a call rate higher than 95%. Unannotated SNPs according to the hg19 na32 SNP6 Affymetrix annotations (n= 130) along with SNPs from MT and sexual chromosomes (n= 37,326) were not considered in the study. To perform GWAS in the IFM cohort, we used stringent criteria to select a total of 370,605 SNPs from the 872,166 SNPs available onto the array. A SNP was analysed if an AA or BB genotype was present in more than 5% of patients, if its genotype was determined in at least 95% of the patients and if the Hardy-Weinberg rule was not rejected. Statistical analyses were performed using SNPTEST v2.5.11. Firstly, we compared 370,605 genotypes from 155 IFM patients with neuropathy (grade >= 2) after bortezomib exposure to 314 control patients treated with bortezomib who did not develop neuropathy (grade 0-1). Secondly, we performed a validation in the HOVON 65/GMMG-HD4cohort for the highest associated SNPs as identified in the discovery cohort. We compared 41 bortezomib-treated patients with neuropathy (grade >= 2) with 75 bortezomib-treated controls who did not develop neuropathy. We applied a one-sided logistic regression with 10,000 label swapping permutations to correct for multiple testing in order to confirm BiPN association in this independent cohort. This set was used as a validation set. An independent dataset was used for discovery [GSE65777].
2016-06-01 | E-GEOD-66903 | biostudies-arrayexpress