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• Reference epigenome CKD24_C_Podo_mRNA-Seq data generated from KEP study

  A CKD24_C_Podo_mRNA-Seq paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003482

• Reference epigenome OB57_D_PreA_smRNA-Seq data generated from KEP study

  A OB57_D_PreA_smRNA-Seq single end data for Preadipocyte(fat)

  Dataset EGAD00001003496

• McGill EMC Release 4 in tissue "Brodmann (1909) area 11"

  McGill EMC Release 4 in tissue "Brodmann (1909) area 11"

  Dataset EGAD00001001284

• Reference epigenome CKD24_C_Podo_smRNA-Seq data generated from KEP study

  A CKD24_C_Podo_smRNA-Seq single end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003498

• ONGOING CHROMOSOMAL INSTABILITY ACROSS ANEUPLOID SUBTYPES OF CHILDHOOD B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA ASSOCIATES WITH DISEASE PROGRESSION

  This is the DAC for the scDNA data on the c-B-ALL datasets

  Dac EGAC50000000005

• Access to shallow whole genome sequencing data from DETECT

  Access to this dataset is subject to aceptance of the terms and conditions. Please summarise your project and sign the following document:

  Dac EGAC50000000553

• RNA-Seq for academic use only

  RNA-Seq transcriptome data is only for academic use.

  Dataset EGAD00001009675

• Next Generation Sequencing in an IBD Pedigree Exome Data

  The aim is to find rare variants of intermediate penetrance in those at risk of Crohn's disease

  Dataset EGAD00001000423

• Nanopore sequencing enables allelic phasing of FLG loss-of-function variants, intragenic copy number variation and methylation status in atopic dermatitis and ichthyosis vulgaris

  Loss-of-function (LoF) variants in the FLG gene are associated with ichthyosis vulgaris (IV) and atopic dermatitis (AD). IV and AD patients with two FLG LoF variants are reported to have a more severe disease course. However, subsets of compound heterozygous patients display phenotypic heterogeneity despite a prediction of a severe phenotype from their genotype. The underlying genetic mechanism of this phenotypic variability is unknown. One possibility is that two LoF FLG variants could be located in cis (on the same allele), thus altering the predicted gene dosage. To investigate the allelic contribution of compound heterozygous FLG LoF mutations to IV phenotypic variability, we employ long reads from Oxford Nanopore Technologies, utilising two methodologies to phase the entire coding region of FLG into parental alleles: an amplicon-sequencing approach and an adaptive-sampling strategy. We investigated the allelic phasing of FLG LoF variants and intragenic-repeat copy-number variations (CNV) of 21 subjects with known compound heterozygous genotypes and mixed IV severity. Our results suggest that IV severity is not linked to the presence of cis variants in our IV patient cohort. Nanopore reads enabled detection and accurate phasing of CNVs and LoF variants into parental alleles, providing a framework for future in-depth genetic analysis. These results highlight the usefulness of utilising long reads for interrogating the FLG gene and other highly repetitive genes for genetic stratification related to clinical phenotypes.

  Study EGAS50000000166

• Genomic Predictors of Combat Stress Vulnerability and Resilience

  The Genomic Predictors of Combat Stress Vulnerability and Resilience Study was designed to probe the likely hereditary basis for risk or resilience to develop PTSD and other trauma spectrum disorders. The overall guiding hypothesis was that genomic variation gives rise to risk/susceptibility traits that, when actuated by traumatic environmental stimuli, such as combat, give rise to PTSD and other stress-related phenotypes. Two studies designed to identify risk and resilience factors for combat-induced, stress-related symptoms are being conducted by our group: The Marine Resiliency Study (MRS) is a prospective PTSD study with longitudinal follow-up (pre- and post-exposure to combat stress) of US Marines bound for deployment to Iraq or Afghanistan. Extensive phenotyping includes 3 domains: Psychosocial, Psychophysiologic, and Biophysiologic. The biological and physiological measures collected were chosen in part due to their potential to serve as intermediate phenotypes for stress-related disorders. A second, cross-sectional study involves a cohort of combat-exposed active duty or previously deployed service members (CAVC), including PTSD cases and controls with comparable psychosocial and clinical phenotypes. Little information is available about the factors that explain why some trauma survivors develop stress disorders and some do not. It is hoped that the insights gained from this approach will improve understanding of the genetic contributors to PTSD, and potentially provide novel diagnostic tests and therapeutic approaches to this currently enigmatic and difficult-to-manage condition.

  Study phs000864