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• Whole exome sequencing of Congenital Cataract

  Whole exome sequencing to identify potentially relevant mutations of congenital cataract in a Chinese girl. The novel PAX6 mutation (c.221G>A) is associated with congenital cataract, and the WFS1 mutation (c.2070_2079del) interactively aggravates this process.

  Study EGAS00001005673

• Rare Diseases Clinical Research Network (RDCRN) Vasculitis Clinical Research Consortium (VCRC) Longitudinal Protocol for Polyarteritis Nodosa

  The development and validation of accurate biological markers and predictors of disease activity and outcome in Polyarteritis Nodosa (PAN), a form a idiopathic vasculitis, would have a major positive impact on the clinical care of patients with this rare disease, be an important advance in the design of clinical trials and feasibility of new drug development, and provide important insight into the pathogenesis of this condition. Current measures of disease activity, including erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP), while helpful in selected settings, are mostly considered highly flawed and markers whose poor correlation with disease flares makes them inadequate to help guide therapy. Similarly, ESR and CRP are clearly unhelpful as diagnostic tests for vasculitis. The current state of clinical investigation for vasculitis relies heavily upon determination of disease status solely by clinical presentation and investigator opinion. Thus, discovery and validation of more precise markers that quantifiably measure activity, predict disease course, and correlate with an important biological process, would be of great importance. Knowledge to be gained from this study could potentially be highly important. Discovery of effective biomarkers of vasculitis and assessment of long term disease course and complications by the collection of clinical and diagnostic imaging studies proposed could lead to better care and less toxic treatment regimens. Furthermore, insight into the pathophysiology of vasculitis could be gained and this might lead to better treatments and improved outcomes in terms of reduction of vascular and treatment related complications. Ideally, excellent biomarkers reflect a sophisticated understanding of the pathophysiology of a disease.

  Study phs000590

• Searching for rare/low frequency variants in rheumatoid arthritis by exome sequencing

  Rheumatoid arthritis (RA) is a multifactorial and systemic autoimmune disease and characterized by synovial inflammation and hyperplasia, autoantibody production, cartilage and bone destruction and systemic features including cardiovascular, pulmonary, psychological and skeletal disorders. Although the causality of RA is not completely understood, genetic factors contribute to the onset. About 60% of the RA risk is genetic. To identify causative- or susceptible- rare/low-frequency variants in RA, exome sequencing of 39 patients with RA was conducted. We also conducted genotyping of pooled healthy men and women exome-sequencing data.

  Study JGAS000035

• Transcriptomic response of miRNAs of monocytes to bacterial and viral stimuli assessed by RNA-seq in Africans and Europeans

  The dataset includes raw RNA-seq data (fastq files) for miRNAs of monocytes before and after 6-hour exposure to four different immune stimuli, measured in 200 African- and European-descent healthy donors from Belgium. The stimuli include ligands for TLR4 (LPS), TLR1/2 (Pam3CSK4) and TLR7/8 (R848) and to a human seasonal influenza A virus (IAV).

  Dataset EGAD00001006181

• Somatic Mutational Analysis by Exome Sequencing Endometrial Carcinosarcomas

  The purpose of this study was to identify somatic (tumor-specific) mutations in endometrial carcinosarcoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 14 de-identified primary tumor DNAs and matched non-tumor DNAs.

  Study phs001152

• Spatial Profiling of Patient-Matched HER2 Positive Gastric Cancer Reveals Resistance Mechanisms to Trastuzumab and Trastuzumab Deruxtecan Sequencing

  HER2-positive gastric cancer (HER2+ GC) exhibits significant intra-tumoral heterogeneity and frequent development of resistance to HER2-targeted therapies. This study aimed to characterize the spatial tumor microenvironment (TME) and identify mechanisms of resistance to HER2 blockade including trastuzumab and trastuzumab deruxtecan (T-DXd) in HER2+ GC, with the goal of informing novel therapeutic strategies. We performed spatial transcriptomics on pre- and post-treatment samples from patients with HER2+ metastatic GC who received trastuzumab-based therapy.

  Study EGAS50000000636

• Whole-Exome Sequencing analyses in tamoxifen-associated endometrial cancer

  An increased incidence of endometrial cancer has been described for patients that have received tamoxifen to treat breast cancer. Using samples from endometrial tumors, isolated from surgivcal specimens of patients who previously received tamoxifen treatment for breast cancer, we aimed to identify whether there are specific somatic mutations enriched in this population, relative to endometrial tumors from the general population. For this, WES was performed on matched endometrial tumors and healthy tissue (n=21).

  Study EGAS00001006453

• The polarity and specificity of antiviral T lymphocyte responses determine susceptibility to SARS-CoV-2 infection in cancer patients and healthy individuals.

  The goal of this study was to identify immune correlates of clinical protection against SARS-CoV-2 infection.

  Study EGAS00001005985

• Identification_of_synthetic_lethal_genes_by_CRISPR_Cas9_library

  Sequencing is performed on PCR products from the amplification of gRNA segments introduced into cell lines (some are commercial, some are derived by collaborators, as described in HMDMC 13/076). Cellular DNA or RNA are not sequenced. This data is defined as "Other Biological/Biochemical Assay Data" under the WTSI datasharing guidelines and consequently will be released at the time of publication and/or through faculty websites. SEQUENCING DETAILS: in October 2016 3 DNA samples will be submitted for PCR amplification and purification through CGP pipeline using Thompson's custom primer set and PCR settings and sequencing with Hiseq using a custom protocol (with 3 forward reads to read sgRNA1, sgRNA2 and the index, optimized with Illumina Bespoke Sanger team); read length 50bp. The following set of samples will be submitted in later 2016 and ealry 2017 as cell pellet to be processed through CGP Cas9 pipeline (Thompson's oligos and protocols) and sequences on Hiseq (same custom sequencing protocol described above) We are utilizing a custom CRISPR/Cas9 library to identify synthetic lethal gene pairs. Cells will be transduced with LV expressing Cas9, then infected with LV expressign the library of 42'000 sgRNA pairs. Cell pellet will be collected from the cell population at different timepoints. The samples will be processed by CGP pipeline customized for the specific protocol and then sequenced to identify the 19bp of the sgRNA and quantify their representation.

  Study EGAS00001002117

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the feature of age-associated helper T (ThA) cells and its contribution to autoimmune diseases, single-cell RNA-sequencing analysis of peripheral blood CD4+ T cells from healthy control, CD4+ T cells in muscles and bronchoalveolar lavage fluid (BALF) from patients with idiopathic inflammatory myopathy were conducted.

  Study JGAS000648