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• CATHeterization GENetics (CATHGEN)

  The CATHGEN biorepository consists of biological samples collected on 9334 sequential consenting individuals undergoing cardiac catheterization at Duke University Medical Center between 2001 and 2010 inclusive. The Institutional Review Board informed consent allowed for 50 mL of blood to be collected from fasting patients through the femoral arterial sheath during the catheterization procedure. Three 7.5 mL EDTA tubes for DNA extraction are stored at -80°C. The Duke Database for Cardiovascular Disease (DDCD) provides the bulk of the clinical data used for analysis. Follow-up includes mortality information gleaned from the National Death Index and Social Security Death Index plus follow-up phone calls and written questionnaires regarding MI, stroke, re-hospitalization, coronary re-vascularization procedures, smoking, exercise, and medication use.

  Study phs000703

• Exploring germline and somatic mutagenesis in the extended family with germline pathogenic variant in POLD1

  This study aimed to estimate the influence of POLD1 L474P on somatic and germline mutagenesis. We studied the mutation rate and spectra in germline and soma in an extended family harboring the POLD1 c.1421T>C p.(Leu474Pro) pathogenic variant. The study includes WGS data for DNA extracted from blood, fibroblasts or buccal swabs from the 16 family members, from DNA obtained single-cell derived colonies obtained from immortalized fibroblasts for 8 of 16 family members and from the same single-cell derived immortalized fibroblasts after approximately 40 passages for 6 out of 8 family members. Additionaly, study includes WXS sequencing for 1 tumor FFPE sample and adjacent normal tissue from the individual from one family member.

  Study EGAS00001006434

• Fixation effects on variant-calling in a clinical resequencing panel

  Formalin fixation is the standard method for preservation of tissue for diagnostic purposes, including pathological review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic tests. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade laboratory-developed targeted resequencing assay. We examined and quantified several parameters relating to sequencing quality and variant-calling from tumor and normal colon epithelial tissues. We identify one alterative fixative, Sakura Universal Molecular Fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathological review.

  Study EGAS00001003507

• single-cell RNA-seq Case-Control study of children progressing to Type1 diabetes

  Single-cell RNA sequencing was carried out on four selected PBMC samples of Finnish children at risk of developing Type 1 diabetes and their gender age and HLA matched control children using 10X genomic platform. All four Case children were positive for multiple islet specific autoantibodies and two of them also progressed to clinical disease during the follow up whereas the control children remain negative for all autoantibodies. Age at seroconversion for Case 2, 3, 5, and 9 children is 12, 18, 24, and 18 months, respectively. Age at sampling, in months, for the pairs was as follows (Case/Control): pair 2:24/24; pair 3: 12/18; pair 5: 12/12; pair 9:24/18.

  Study EGAS00001004070

• Data access committee for white blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer

  Dac EGAC00001001435

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000162

• WGS DATA FILES FOR SJCBF

  DATA FILES FOR SJCBF

  Dataset EGAD00001000268

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000853

• CGMH data access committee for the CGMH-OCCC-WES data

  CGMH data access committee for the CGMH-OCCC-WES data

  Dac EGAC50000000028

• The data access committee for Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

  Dac EGAC50000000588