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• DPY30_ChIP_seq

  H9 human embryonic stem cells (hESCs) were cultured in feeder-free chemically-defined conditions in medium containing 10ng/ml Activin A and 12ng/ml FGF2 (Vallier L. 2011, Methods in Molecular Biology, 690: 57–66). Chromatin immunoprecipitation was performed as described in Brown S. et al. 2011. Stem Cells 29: 1176–85 by using 5ug of anti-DPY30 antibody (Sigma, cat. number HPA043761). This protocol was performed in control hESCs (expressing a scrambled shRNA) and in hESCs stably expressing an shRNA against DPY30 (Sigma, clone n. TRCN0000131112).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 EGAS00001001132

• Cell motility and migration as determinants of stem cell efficacy

  Limited stem cell migration capacities and undirected homing hamper their therapeutic efficacy. We report here the novel technology to isolate stem cell subpopulations with high migration potential. Hereby, we identified podoplanin-dependent stem cell mobility as important mechanism for their in vivo homing capacities and therapeutic efficacy as validated in preclinical models of Alzheimer´s disease and mouse glioma. In vivo applications of highly migrating stem cells resulted in remarkable improvement of targeted homing and engraftment rates. Moreover, animals receiving highly migrating stem cells showed higher recovery rates compared to unselected stem cells. This novel technology provides useful tool to improve therapeutic efficacy of stem cells and give insights into stem cell subpopulations heterogeneity with the potential of general applicability for cellular therapies.

  Study EGAS00001002478

• TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism

  DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism/Seckel syndrome. We establish that TRAIP relocalizes to sites of DNA damage where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to UV irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a novel component of the DNA damage response to replication-blocking DNA lesions.

  Study EGAS00001001501

• PCa-LINES

  PCa-LINES: Ribo-minus RNA-seq of 4 patient samples and 2 PCa cell lines ---- Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data Youri Hoogstrate, Malgorzata A. Komor, René Böttcher, Job van Riet, Harmen J. G. van de Werken, Stef van Lieshout, Ralf Hoffmann, Evert van den Broek, Anne S. Bolijn, Natasja Dits, Daoud Sie, David van der Meer, Floor Pepers, Chris H. Bangma, Geert J. L. H. van Leenders, Marcel Smid, Pim French, John W.M. Martens, Wilbert van Workum, Peter J. van der Spek, Bart Janssen, Eric Caldenhoven, Christian Rausch, Mark de Jong, Andrew P. Stubbs, Gerrit A. Meijer, Remond J.A. Fijneman, Guido Jenster bioRxiv 2021.05.17.441778; doi: https://doi.org/10.1101/2021.05.17.441778 https://www.biorxiv.org/content/10.1101/2021.05.17.441778v1

  Study EGAS00001004613

• Determination of Cross-Reactive Immunological Material (CRIM) status and longitudinal follow-up of individuals with Pompe disease

  Infantile-onset Pompe disease is an inherited disorder that is normally diagnosed within the first months of life. It is caused by lack of or defect in an enzyme (a special protein that carries out normal chemical reactions within the body) called acid alpha-glucosidase (GAA). GAA normally breaks down glycogen (stored sugar) in lysosomes (the part of the cell that digests food and other chemicals). Pompe disease is one of many lysosomal storage diseases (LSDs). LSDs are diseases caused by the malfunction of the lysosome or one of their digestive enzymes. Patients with Pompe disease cannot break down lysosomal glycogen. This causes glycogen to build up and damage cells throughout the body, especially in the heart and muscles. Current treatment for Pompe disease involves enzyme replacement therapy (ERT). In this treatment, the drug alglucosidase alfa (Myozyme) is put into your blood. The drug provides a form of the GAA enzyme to replace the enzyme that is missing or not working properly in the patient's blood. This treatment has allowed babies to live longer and achieve developmental milestones. In this study, researchers will learn about the patient's ability to tolerate ERT. Cross-Reactive Immunological Material (CRIM) is a measurement of natural GAA production. A patient's CRIM status (either positive or negative) is an important factor that affects how he or she responds to ERT with Myozyme. Children who produce some natural GAA are classified as CRIM+, while children who do not produce any natural GAA are classified as CRIM-. Children who are CRIM+ generally tolerate ERT well. But, children who are CRIM-, and some children classified as CRIM+, have a poor response to ERT. Patients who have a poor response to ERT have complications because their body sees Myozyme as "foreign" and triggers an immune response to try to remove it from the body. Treatments are currently being developed to stop this immune response and prevent complications from ERT. We will enroll patients with Infantile Pompe disease in this longitudinal natural history (observational) study. The specific aims of this study are: To determine and correlate Cross-Reactive Immunological Material (CRIM) status with the GAA gene mutations found on these patients To validate an approach for determining CRIM status from whole blood sample, with the gold standard determination of CRIM status by skin fibroblasts and mutation analysis To explore the clinical treatment response and natural history of CRIM-positive and CRIM-negative Pompe disease patients with and without immune modulation To investigate the role of immune response to treatment

  Study phs001555

• ETMR_Nanostring

  Total RNA (100ng) from 21 ETMRs with C19MC structural alterations and 28 other PBTs was prepared with nCounter miRNA Sample Prep Kit according to standard protocol. miRNA expression profiling was conducted with human v1, v2, or v3 miRNA panel on nCounter miRNA expression platform (NanoString Technologies, Seattle, WA) according to manufacturer’s protocol. Signal normalization was done using nSolver Analysis and batch corrected using ComBat (Johnson et al. Biostatistics. 2007). 565 miRNAs overlapped between all three versions and was used for further analyses. Fold change and supervised t-test with FDR correction was calculated between the ETMRs and other PBTs.

  Dataset EGAD00010001701

• MassArray1-80

  234 samples genotyped at 40 loci using the MassArrayiPLEX genotyping assay using the iPLEX Gold genotyping kit (Agena Biosciences, cat. 10148-2) Gabriel et al. (2009) [Gabriel, S. , Ziaugra, L. and Tabbaa, D. (2009), SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform. Current Protocols in Human Genetics, 60: 2.12.1-2.12.18. doi:10.1002/0471142905.hg0212s60]). Products were detected on a MassArray mass spectrophotometer and data were acquired in real time with MassArray RT software 4.0.0.2 (Agena Biosciences). SNP clustering and validation was carried out with Typer 4.0.26.75 software (Agena Biosciences).

  Dataset EGAD00010001906

• MATISSE bulk RNA-sequencing data

  Tumor availability: Bulk RNA sequencing was performed on tumor biopsies of 48 patients at baseline and 45 patients across time points (baseline n=48, week 1 n=38, week 2 n=34, week 4 n=37), including lymph node metastasis that were sequenced in addition to the primary tumor. Tumor RNA was extracted from formalin-fixed paraffin-embedded (FFPE) primary tumor and lymph node metastasis sections containing at least 10% viable tumor cells present in the sample, except for on-treatment samples with a complete pathological response in which we isolated samples with at least 10% immune-infiltration with no viable tumor cells. A pathologist (LS) scored the tumor percentage and indicated the most tumor-dense region on a hematoxylin and eosin (H&E) stain slide for subsequent RNA isolation. According to the manufacturer's protocol, five to 10 FFPE slides (10 µm) were used for RNA isolation using the AllPrep DNA/RNA FFPE isolation kit (Qiagen, 80234) and the QIAcube. Genetic Diagnostics and Sequencing Services (CeGaT) performed RNA sequencing in Germany. Data processing: Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (v2.20). Adapters of the reads (Pico v2 SMART adapter, first three nucleotides of the second sequencing read) were trimmed with Skewer (v0.2.2), without quality trimming. RNA-sequencing data was aligned to GRCh38 (Ensembl v109) using STAR (v2.7.9) in 2-pass mode with default settings. Gene counts were generated with the HTSeq (v2.0.2). FastQC (v0.12.1) and MultiQC (v1.14) were used for assessing data quality, on FASTQ files and intermediate processing steps.

  Dataset EGAD50000001470

• Nala TAS-LRS PGx Study

  Sequencing was performed on the PromethION Flow Cell R10 (M version) using the P2 Solo Sequencer (MinION release 24.02.16). The library was divided into three portions and loaded in a tapered manner across three time points. At the first time point, the initial portion of the library was loaded, and sequencing began in whole-genome mode (without adaptive sampling), to monitor QC (N50 within the expected range). After one hour, adaptive sampling was activated. A custom BED file was used to define the target regions (N=326). Each region was extended by 20 kb upstream and downstream, and overlapping regions were merged into non-redundant intervals using bedtools43, covering a total of 1.3% of the human genome. At the second time point (20–24 hours after sequencing began, or when fewer than 2000 pores remained active), the flow cell was washed following ONT’s Flow Cell Wash Kit protocol, and the second portion of the library was loaded. At the third time point (40–48 hours), the second portion of the library was retrieved, and merged with the third portion. The flow cell was washed and reloaded with the mixed library. POD5 files were basecalled using Dorado v0.8.1 in super-accuracy (SUP) mode with the dna_r10.4.1_e8.2_400bps_SUP@v5.0.0. Reads from the initial 1 h Whole Genome Sequencing (WGS) and subsequent 72 h adaptive sampling were filtered for Q-scores >10. Passing reads were demultiplexed using Dorado’s demux function, then combined per sample and mapped to the GRCh38 reference genome using Minimap2 v2.22. Files were converted to CRAM using samtools.

  Dataset EGAD50000001609

• Population Architecture using Genomics and Epidemiology (PAGE): Causal Variants Across the Life Course (CALiCo): Strong Heart Study (SHS) and Strong Heart Family Study (SHFS)

  The SHS is a study of cardiovascular disease and its risk factors among American Indian men and women. Using standardized methodology, it was designed to estimate cardiovascular disease mortality and morbidity and the prevalence of known and suspected cardiovascular disease risk factors and to assess the significance of these risk factors in a longitudinal analysis. The study included 13 American Indian tribes and communities in three geographic areas: an area near Phoenix, Arizona, the southwestern area of Oklahoma, and western and central North and South Dakota. The SHS included three components: The first was a survey to determine cardiovascular disease mortality rates from 1984 to 1994 among tribal members aged 35-74 years of age residing in the 3 study areas (the community mortality study). The second was the clinical examination of 4,500 tribal members aged 45-74. The SHS has completed three clinical examinations of the original Cohort (Phase I: 1989-1991; Phase II: 1993-1995; Phase III: 1998- 1999, respectively). The third component is the morbidity and mortality (M&M) surveillance of these 4,500 participants. Yearly SHS surveillance has only 0.2% loss to follow-up. All deaths and all nonfatal CVD events are classified by standardized criteria, including details of stroke and HF. The Strong Heart Family Study (SHFS) is a genetic epidemiological study designed to investigate the heritability of CVD and its risk factors and to localize genes that contribute to CVD risk in American Indians. SHFS participants include 3,838 family members that were >/=15 years old, and ascertained through sibships of the original SHS, from 94 extended (large, multigenerational) families. Exams have occurred in a pilot Phase III (1998-1999, 900 SHFS participants), in Phase IV (2001-2003), and Phase V (2006-2009). SHFS morbidity and mortality surveillance has occurred throughout the study phases, with 0.3% lost to follow-up. Genetic data includes complete pedigree information, DNA samples from all family members, a 10cM-spaced microsatellite map used for IBD estimation and to perform linkage analysis, genotypes for more than 12,000 SNPs in candidate regions, and genotypes from commercially available SNP assays.

  Study phs000580