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• Non Dystrophic Myotonias: Genotype-Phenotype Correlation and Longitudinal

  NMD are rare ion channel disorders. The optimal management and treatment of these disorders are not known. This multi-center proposal will allow the prospective collection of standardized data from a critical number of patients to help better define the clinical features of NDM. The data will also be used to establish clinically relevant endpoints for use in therapeutic trials. The identification and genetic characterization of patients will facilitate recruitment of participants for future therapeutic trials. Ultimately, the information gained will lead to the improvements in the treatment and management of NMD with an associated reduction in morbidity and improvement in patient quality of life.

  Study phs000578

• Single-cell atlas of penile cancer reveals TP53 mutations as driver for an aggressive phenotype, irrespective of HPV status, and provides clues for treatment personalization

  Our aim was to identify molecular differences in the microenvironment of penile squamous cell carcinoma (PSCC) stratified by TP53 loss-of-function (TP53LOF) mutations and HPV-status. Hence, we present a first single-cell transcriptomic atlas of PSCC. Stratification based on TP53 and HPV-status uncovered differences in CSS and underlying molecular pathways. Our data indicate that TP53LOF tumors are characterized by worse biological behavior regardless of HPV-status. These findings and further research are essential for trial design in PSCC, allowing us to move away from the current one-size-fits-all approach.

  Study EGAS50000000217

• Evolutionary Pressures Shape Undifferentiated Pleomorphic Sarcoma Development and Radiotherapy Response

  To study tumor evolution during tumorigenesis and in response to radiotherapy, we performed whole exome sequencing of 120 spatially distinct tumor regions and matched germline DNA from 20 patients with undifferentiated pleomorphic sarcoma. This data was utilized to generate personalized capture probes for targeted resequencing of the tumor and normal samples along with 17 matched plasma samples for circulating tumor DNA analysis. We found evidence of subclonal selection prior to treatment that was increased after radiotherapy. In addition, circulating tumor DNA analysis was able to measure the abundance of subclones before, during, and after treatment. This dbGaP submission includes whole exome sequencing and targeted resequencing from the study.

  Study phs003830

• Targeted DNA sequencing and mRNA sequencing data from patients with peritoneal metastasis from colorectal cancer

  Patients with peritoneal metastasis from colorectal cancer (PM-CRC) have inferior prognosis and respond particularly poorly to chemotherapy. This study aims to identify the molecular explanation for the observed clinical behavior and suggest novel treatment strategies in PM-CRC. Tumor samples (230) from a Norwegian national cohort undergoing surgery and hyperthermic intraperitoneal chemotherapy (HIPEC) with mitomycin C (MMC) for PM-CRC were subjected to targeted DNA sequencing, and associations with clinical data were analyzed. mRNA sequencing was conducted on a subset of 30 samples to compare gene expression in tumors harboring BRAF or KRAS mutations and wild-type tumors.

  Study EGAS50000000404

• RNA seq of intestinal biopsies and blood cells from patients with celiac disease and controls

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Study EGAS50000001104

• Population whole-genome bisulfite sequencing across two tissues highlights environment as principal source of human methylome variation

  The study includes whole-genome bisulfite sequencing (WGBS) on 34 adipose(7 MZ pairs, 6 DZ pairs and 8 singletons) and 27 blood (7 MZ pairs, 6 DZpairs and 1 singleton) DNA samples derived from a total of 43 female twinsbelonging to the MuTHER/TwinsUK cohort. We generated 11.5 billion 100bppaired-end reads covering 2.3 Tera-basepairs (Tbp) ofsequence using the Illumina HiSeq2000 or 2500 systems. Applying standardalignment methods and filters we obtain a mean genome coverage of 6.3-fold(range: 1.0- to 12.9-fold) for adipose and 8.7-fold (range: 0.7- to29.0-fold) for blood.

  Study EGAS00001001569

• Neutrophils infected with Leishmania donovani

  In the context of studying visceral leishmaniasis, neutrophils infected with Leishmania donovani have been compared to uninfected neutrophils. Compared time points are 0, 6 and 24 hours post infection. Neutrophils of three human donors have been used. Overall 6 samples for infected neutrophils at time point 6 hours and 6 samples for infected neutrophils at time point 24 hours exist, including three biological samples and two technical samples. Uninfected neutrophils represent 3 samples at time point 0 hours, 3 samples at time point 6 hours and 3 samples at time point 24 hours. Transcriptome of Leishmania donovani culture has been assessed in two replicates.

  Study EGAS00001004912

• GWAS Results from Danjou et al, Nature Genetics 2015

  We report genome-wide association study results for the levels of A1, A2 and fetal hemoglobins, analyzed for the first time concurrently. Integrating high-density array genotyping and whole-genome sequencing in a large general population cohort from Sardinia, we detected 23 associations at 10 loci. Five signals are due to variants at previously undetected loci: MPHOSPH9, PLTP-PCIF1, ZFPM1 (FOG1), NFIX and CCND3. Among the signals at known loci, ten are new lead variants and four are new independent signals. Half of all variants also showed pleiotropic associations with different hemoglobins, which further corroborated some of the detected associations and identified features of coordinated hemoglobin species production.

  Study EGAS00001003645

• Whole-genome sequencing of rare disease patients in a national healthcare system

  Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and mediating genes for more than half such disorders remain to be discovered. We implemented whole-genome sequencing (WGS) in a national healthcare system to streamline diagnosis and to discover unknown aetiological variants, in the coding and non-coding regions of the genome. In a pilot study for the 100,000 Genomes Project, we generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 patients with detailed phenotypic data. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed aetiological. Using WGS of UK Biobank1, we showed that rare alleles can explain the presence of some individuals in the tails of a quantitative red blood cell (RBC) trait. Finally, we reported 4 novel non-coding variants which cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

  Dataset EGAD00001006065

• August 2021 data update (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.

  August 2021 data update (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 EGAD00001008101