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• A Dormant TIL Phenotype Defines Non-Small Cell Lung Carcinomas Sensitive to Immune Checkpoint Blockers

  The biological determinants of sensitivity and resistance to immune checkpoint inhibitors are not completely understood. To elucidate the role of intratumoral T-cells and its association with the tumor genomic landscape, we perform paired whole exome DNA sequencing and multiplexed quantitative immunofluorescence (QIF) in pre-treatment samples from non-small cell lung carcinoma patients treated with PD-1 axis blockers. QIF was used to simultaneously measure the level of CD3+ tumor infiltrating lymphocytes (TILs), in situ T-cell proliferation (Ki-67 in CD3) and effector capacity (Granzyme-B in CD3). Whole exome sequencing reported in the number/type of mutations and predicted class I and class II mutant neoantigens.

  Study phs001618

• SJCRH pediatric HGG sequencing data

  A DAC to manage access to sequencing data derived from primary patient tumors and associated models, e.g. xenografts and cell lines.

  Dac EGAC50000000101

• Pseudogene_RNAseq

  RNA sequencing to validate findings of somatic pseudogenes acquired during cancer development

  Study EGAS00001000606

• Low_input_LC__ISC_

  R&D project to develop low input library construction methods.

  Study EGAS00001001856

• Infant_Spindle_Tumour_Study

  We aim to describe the transcriptomic landscape of infant spindle cell tumours.

  Study EGAS00001002935

• Settlement of Polynesia

  Genotypes used to reconstruct the settlement timings and paths of Polynesia.

  Study EGAS00001005362

• HCA_Muscle_Adult_Wellcome_RNA_Managed_Access

  Transcriptomic analysis of skeletal muscle, to understand the mechanisms of muscle ageing.

  Study EGAS00001007495

• Identification of Structural Variants Relevant to Autism by Pacific Biosciences HiFi Whole-Genome Sequencing

  The purpose of this research study was to perform long-read whole-genome sequencing on a family with autism. This family had no known genetic cause based on clinical array and whole-exome sequencing analysis. Utilizing PacBio HiFi long-read whole-genome sequencing, we identified a relevant missense variant in the KCNC2 gene. This variant was likely to be a germline mosaic in the paternal germline.

  Study phs002698

• Autosomal Recessive PGM3 Mutations Link Glycosylation Defects to Atopy, Immune Deficiency, Autoimmunity, and Neurocognitive Impairment

  To define a genetic syndrome of severe atopy, elevated serum IgE, immune deficiency, autoimmunity, and motor and neurocognitive impairment, eight patients from two families who had similar syndromic features were studied. Whole exome sequencing was performed to identify disease-causing mutations. A disease segregated with a novel autosomal recessive mutations in a single gene, phosphoglucomutase 3 (PGM3). The result defines a new Congenital Disorder of Glycosylation.

  Study phs000809

• Possible DNA damage after paternal exposure to ionizing radiation in radar technicians

  Effects of accidental and prolonged radiation exposure on the human germline remain a topic of medical interest. Transgenerational signatures of ionizing radiation exposure are primarily implicated to be clustered de-novo mutations (cDNMs, multiple de-novo mutations within 20bp). We sequenced the whole genome of 110 children from 70 families (Radar cohort). The father in this cohort were exposed to 0-353mSv of ionizing radiation and serve as exposed samples.

  Study EGAS00001007321