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• Epigenomics of Neurocognitive Function in Breast Cancer

  This study harnessed the data and biospecimens from the Exercise Program in Cancer and Cognition (EPICC) study (parent study) that collected data on cognitive function, demographics, other symptoms and biospecimens at two time points (T1: enrollment, T2: six months later) within the context of a six-month randomized controlled trial of a moderate intensity aerobic exercise intervention. This study collected genome wide DNA methylation data from T1 and T2 and conducted epigenome-wide association-based analyses to find genes and biological pathways explaining variability in cognitive function and explaining how exercise mitigates cognitive decline. Our initial findings identified cg10331779 near CTNND2 (p-value=9.65×10-9) associated with processing speed and cg25906741 in MLIP (p-value=2.01×10-8) associated with subjectively measured cognitive function. Additionally, differentially methylated regions were identified near SLC6A11, PRKG1/CSTF2T, and FAM3B for processing speed and near PI4KB and SGCE/PEG10 for mental flexibility.

  Study phs003959

• High-depth whole genome sequencing of paired ductal carcinoma in-situ (DCIS) and germline control samples from 51 individuals.

  Deposited here are whole-genome sequencing data for 51 paired breast cancer DCIS and matched-normal samples taken from the same individual. Average sequence depth is 110x for DCIS samples and 39x for matched-normals. Matched-normals are from blood (n=14) or adjacent normal breast (n=37). Sequencing was performed on Illumina HIseqX (n=70) or Illumina Novoseq (n=32). They are a part of a broader project that uses high-depth WGS to investigate the somatic mutation genomic landscape of DCIS in order to uncover biological insights into breast cancer progression as well as possible methods to stratify DCIS patients for individualised therapy or disease monitoring.

  Dataset EGAD50000002071

• Single Cell Analysis of Sporadic Human Basal Cell Carcinomas

  To explore tumor heterogeneity in sporadic human basal cell carcinoma tumors, we profiled three individual patient tumors by scRNA-Seq and scATAC-Seq. Basal cell carcinomas (BCCs) are driven by hedgehog signaling with GLI1 representing the key downstream transcription factor that drives tumor growth. GLI1 as such is a readout of active hedgehog signaling. We identified that LY6D can mark squamous populations such as in squamous cell carcinomas (SCCs) that are negative for GIL1 and hedgehog signaling. As such, both GLI1 and LY6D can be used as biomarkers of BCCs and SCCs and their related states.

  Study phs003103

• Merkel Cell Carcinoma Tissue and Data Repository

  Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine skin cancer with increasing incidence in the United States. In this study we performed the first whole genome sequencing of three Merkel cell carcinomas with their matched normal tissues for somatic variant calling. From these data we describe the likely mechanism of Merkel cell polyomavirus integration and focal host genomic amplifications in two tumors and the dominance of UV-mediated mutagenesis in a virus-negative tumor. We also performed poly-A RNA sequencing on a total of six Merkel cell carcinomas to address expression differences between virus-positive and virus-negative MCC.

  Study phs002189

• Joint Addiction, Aging, and Mental Health Data Access Committee General Research Use Datasets (GSR Restricted) Collection

  This collection contains the Joint Addiction, Aging, and Mental Health Data Access Committee's authorized individual-level genomic datasets currently in dbGaP that are approved for General Research Use (GRU) and have no further limitations beyond those outlined in the model Data Use Certification Agreement. The public posting of Genomic Summary Results are not allowed. Access to this study collection will include additional authorized individual-level GRU datasets that become available. Renewal of this study collection is required annually. To request access to this study collection, select phs003421 in the dbGaP Authorized Access System.

  Study phs003421

• Spatiotemporal single-cell roadmap of human skin wound healing

  Wound healing is vital for human health, yet the details of cellular dynamics and coordination in human wound repair remain largely unexplored. To address this, we conducted single-cell and spatial transcriptomics analyses on human skin and acute wound tissues through inflammation, proliferation, and remodeling phases of wound repair from the same individuals, monitoring the cellular and molecular dynamics of human skin wound healing at an unprecedented spatiotemporal resolution. Comparison with single-cell data from venous and diabetic foot ulcers uncovers a link between failed keratinocyte migration and impaired inflammatory response in chronic wounds.

  Study EGAS50000000571

• Single B cell analysis in pemphigus patients

  pemphigus is caused by autoantibodies that target cell-cell adhesion molecules, desmoglein(Dsg). Clinical effect of anti-CD20 antibody therapy suggtests that Dsg-specific memory B cell, the precursor of autoantigen secreting plasmablast, may play an important role of disease activity. This study aimed to isolate Dsg-specific memory B cell using recombinant labeled Dsg proteins and performed single cell RNA-sequence to detect autoimmune B cell specific gene expression. For control, we also isolate non-Dsg specific memory B cells from same patients, or forein antigen (Flu HA) specific memory B cells from vaccinated healthy volunteers.

  Study JGAS000281

• HipSci___RNAseq___Rare_BBS

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001318

• Single cell transcriptomic and genomic profiling of carcinogenesis in patients with familial adenomatous polyposis

  Familial Adenomatous Polyposis (FAP) is characterized by hundreds to thousands of adenocarcinomas at different evolutional stages in the colon and rectum. Much effort has been made to illuminate the key genomic alterations that facilitate the transition from adenoma to carcinoma. However, the strong heterogeneity of the tumors may hamper these efforts. Here, by sequencing matched adjacent normal tissues, adenomas at different stages and carcinomas from the same patient, we precisely traced the process of colorectal carcinogenesis. Our study offers an accurate genomic landscape during the initiation and progression of carcinogenesis, especially for the transition between adenomas and carcinomas.

  Study EGAS00001003598

• Methylation_changes_in_OA_patients_with_chronic_exposure_to_cobalt_and_chromium

  We have whole blood from a population of 70 patients, half exposed chronically to an excessof metals cobalt and chromium. The 2 groups are age, sex, and OA diagnosis matched. The2 groups have systemic differences in bone mass and turnover, and other systemicdifferences.We will type the cohort of 70 individuals on the Illumina 450k methylation array and willcompare between the two groups.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001180