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• March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001958

• March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001959

• Comparison of protocols for deriving pancreatic progenitors from hPSCs (ATAC-seq)

  This dataset contains 27 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared ATAC-seq libraries for the 27 samples, and sequenced them on Illumina HiSeq4000.

  Dataset EGAD00001004824

• Reference exome data for Australian Aboriginal populations from Western Australia and the Northern Territory

  Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. The data is provided as 2 VCF files, one for the WA population and one for the NT population.

  Dataset EGAD00001005189

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Multi-Ethnic Study of Atherosclerosis (MESA)

  Cohort Description The Multi-Ethnic Study of Atherosclerosis (MESA) is a study of the characteristics of subclinical cardiovascular disease (CVD) and the risk factors that predict progression to clinically overt CVD or progression of the subclinical disease. MESA researchers study a diverse, population-based sample of 6,814 asymptomatic men and women aged 45-84. Participants were recruited from six field centers across the United States: Wake Forest University, Columbia University, Johns Hopkins University, University of Minnesota, Northwestern University and University of California - Los Angeles. Participants of this study are limited to MESA Classic participants. MESA Family and MESA Air Pollution cohorts are excluded from C4R. Data Being Submitted Wave 1 questionnaire data includes 397 variables for up to 3119 MESA participants in C4R. Wave 2 questionnaire data includes 448 variables for up to 1933 MESA participants in C4R. Dried Blood Spot/Serosurvey data includes 7 variables for up to 1058 MESA participants in C4R. Derived data includes 43 variables for up to 3283 MESA participants in C4R. Phenotype data includes 113 variables for up to 3136 MESA participants in C4R.

  Study phs003017

• Resequencing (MIPS) of candidate genes for Keratoconus (2020)

  In this study, we selected 34 candidate genes for KC based on previous Whole Exome Sequencing (WES) and the literature, and resequenced them in 745 KC patients and 810 ethnically matched controls. Data analysis was performed using the single variant association test as well as gene-based mutation burden and variance components tests. In our study, we detected enrichment of genetic variation across multiple gene-based tests for the genes COL2A1, COL5A1, TNXB, ZEB1 and ZNF469. The top hit in the Fisher’s exact test was obtained for a common variant in the COL12A1 gene. Interestingly, COL5A1, TNXB, ZNF469 and COL12A1 are all known Ehlers-Danlos Syndrome (EDS) genes. Though the co-occurrence of KC and EDS has been reported previously, this study is the first to demonstrate a consistent role of genetic variants in EDS genes in the etiology of KC. In conclusion, our data show a shared genetic etiology between KC and EDS, and clearly confirm the currently disputed role of ZNF469 in disease susceptibility for KC. Besides the role for EDS genes, we also confirm the previously reported involvement of genetic variation in ZEB1 in KC.

  Study EGAS00001004267

• Compilation of Aggregate Genomic Data for General Research Use

  This study contains all authorized aggregate genomic data from datasets currently in dbGaP that are approved for general research use (GRU) and have no further limitations beyond those outlined in model Data Use Certification Agreement. Access to this study will be granted for one year and any additional authorized aggregate GRU datasets that become available during this one-year period. This study does not include individual-level data.

  Study phs000501

• Meta-analysis of Genome-Wide-Association Sudies for plasma Factor XI

  Coagulation factor XI (FXI) has become increasingly interesting for its role in pathogenesis of thrombosis. We performed a genome-wide association study (GWAS) for plasma FXI levels, using novel data imputed to the 1000 Genomes reference panel. Individual GWAS analyses, including a total of 16,169 European individuals from the ARIC, GHS, MARTHA and PROCARDIS studies, were meta-analyzed, and results are presented here.

  Study EGAS00001002123

• Immunological hallmarks for clinical response to BCG in bladder cancer

  Intravesical Bacillus Calmette-Guerin (BCG) is an effective immunotherapy for non-muscle invasive bladder cancer (NMIBC). However, recurrence and progression remain frequent warranting deeper insights into its mechanism. We herein comprehensively profiled blood and tissues obtained from NMIBC patients before, during and after BCG treatment using cytometry by time-of-flight (CyTOF) and RNA sequencing to identify the key immune subsets crucial for anti-tumour activity.

  Study EGAS00001004764

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  Dataset EGAD00001000159