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• Tubulointerstitial fibrosis is the histological hallmark of chronic kidney disease (CKD). Hypoxia and inflammation (i.e., interleukin (IL)-1β signalling) are independent mediators of tubulointerstitial fibrosis. However, the physiological response of human kidney tubular cells to IL-1β/IL-1RI signalling under the hypoxic conditions of CKD is poorly understood and remains a clinical imperative for therapeutic targeting. This study reports that hypoxia and IL-1β act in synergy to trigger cell cycle arrest/cellular senescence of ex vivo patient-derived primary proximal tubular epithelial cells (PTECs).

  Hypoxia and interleukin (IL)-1β are independent mediators of tubulointerstitial fibrosis, the histological hallmark of chronic kidney disease (CKD). Here, we examine how hypoxia and IL-1β act in synergy to augment maladaptive proximal tubular epithelial cell (PTEC) repair in human CKD. Ex vivo patient-derived PTECs were cultured under normoxic (21% O2) or hypoxic (1% O2) conditions in the absence or presence of IL-1β and examined for maladaptive repair signatures. Hypoxic PTECs incubated with IL-1β displayed a discrete transcriptomic profile distinct from PTECs cultured under hypoxia alone, IL-1β alone or under normoxia. Hypoxia+IL-1β-treated PTECs had 692 ‘unique’ differentially expressed genes (DEGs) compared to normoxic PTECs, with ‘cell cycle’ the most significantly enriched KEGG pathway based on ‘unique’ down-regulated DEGs (including CCNA2, CCNB1 and CCNB2). Hypoxia+IL-1β-treated PTECs displayed signatures of cellular senescence, with reduced proliferation, G2/M cell cycle arrest, elevated senescence-associated β-galactosidase (SA-β-gal) activity and increased production of pro-inflammatory/fibrotic senescence-associated secretory phenotype (SASP) factors compared to normoxic conditions. Treatment of Hypoxia+IL-1β-treated PTECs with either a senolytic drug combination, quercetin+dasatinib, or a type I IL-1 receptor (IL-1RI) neutralizing antibody attenuated senescent cell burden. Our data identify a mechanism whereby hypoxia in combination with IL-1β/IL-1RI signalling trigger PTEC senescence, providing novel therapeutic and diagnostic check-points for restoring tubular regeneration in human CKD.

  Study EGAS00001007904

• Dynamics of circulating tumor DNA in acute myeloid leukemia (AML) patients who undergo allogeneic transplantation

  Allogeneic hematopoietic cell transplantation (allo-HCT) is the only curative option for many patients with acute myeloid leukemia (AML). With the increasing use of non-myeloablative conditioning regimens, it is widely assumed that the cytotoxic conditioning itself does not eradicate all leukemia cells. Instead, the donor-derived immune cells are believed to eliminate residual leukemia cells over time. This so-called graft-versus-leukemia (GvL) is postulated to be the primary mechanism by which allo-HCT achieves sustained remissions in patients with AML. However, the precise quantification of GvL effects and its contribution to leukemia eradication has not yet been demonstrated by sequential, highly sensitive measurements of residual disease at various time points following allo-HCT. In the current study, we employed a novel, highly sensitive and specific plasma-based assay to track mutations in the leukemia cells of 14 patients before and after allo-HCT. If the primary therapeutic benefit of allo-HCT is truly mediated through a GvL effect, we hypothesized that leukemia cells would persist following cytotoxic conditioning and would often be reduced after post-transplant immunosuppression was discontinued. In the majority of patients (11 of 14, 79%), the conditioning used for allo-HCT did not eradicate the leukemia cells. In seven of these 11 patients, the leukemia cells persisted until immunosuppression was discontinued, at which time the persistent leukemia cells were reduced or eradicated. These results demonstrate the feasibility of using circulating tumor DNA (ctDNA) as a dynamic marker of GvL as well as minimal residual disease for patients with AML undergoing alloHCT, and have substantial implications for their management.

  Study EGAS00001007969

• The Genomic Analysis of Medulloblastoma

  Medulloblastoma is a heterogenous disease made up of at least four distinct subtypes of disease which appear to exploit and disrupt naturally occurring developmental pathways of cellular growth and hindbrain development. To better understand the driver mutations of this disease, we performed whole genome sequencing of 37 medulloblastomas and the corresponding normal DNA of the 37 affected children treated at St. Jude Children's Research Hospital. We have found several novel mutations which appear subtype specific. These mutations were checked for frequency in a separate tumor cohort of 56 children with medulloblastoma, also treated on the St. Jude Medulloblastoma 2003 trial, and were tested in several animal models of medulloblastoma for proof of oncogenic potential.

  Study phs000409

• CADD/GADD centers on Antisocial Drug Dependence

  CADD (Center for Antisocial Drug Dependence): Funded through NIDA 011015 to study genetic influences on, and treatment of, antisocial drug dependence, studying both clinical probands and their families, and community samples of matched controls, twins, and participants in an ongoing longitudinal adoption study. A collaboration between three organizations at two campuses of the University of Colorado. Longitudinal with three waves of data collection completed. GADD (Genetics of Adolescent Antisocial Drug Dependence): Funded originally through NIDA 012845, s multisite collaboration including adolescent subjects at high-risk for antisocial drug dependence and their siblings, recruited in Denver, CO and San Diego, CA. Longitudinal with two waves of data collection completed, one in progress as of May, 2018.

  Study phs001841

• Whole genome sequencing of 25 South African individuals with myasthenia gravis

  This study investigated the genetic basis of an ophthalmoplegic subphenotype of MG (OP-MG) which occurs in a proportion of myasthenics with juvenile symptom onset and African genetic ancestry. This OP-MG subphenotype is characterised by treatment resistant weakness of the extraocular muscles (EOMs) and the pathogenetic mechanism(s) underlying its development is unknown. The aim of this study was to use a hypothesis-generating genome-wide case-control analysis to identify candidate OP-MG susceptibility genes and pathways. Whole genome sequencing (WGS) was performed on 25 AChR-antibody positive myasthenic individuals of African genetic ancestry sampled from the phenotypic extremes: 15 with OP-MG (cases) and 10 individuals with control MG (EOM treatment-responsive).

  Study EGAS00001003462

• Spatial transcriptomic data of breast cancer

  Fastq files from spatial transcriptomic of breast cancer coming from 8 Breast cancer sections. Sample preparation: frozen BC samples were chosen based on tissue structure and RNA quality (RIN > 8). The “Visium Spatial Tissue Optimization Slide and Reagent Kit” (10X Genomics; #PN-1000193) was then used to optimize permeabilization conditions for BC tissues. Briefly, sections were fixed, stained and then permeabilized at different time points to capture mRNA, and the reverse transcription was performed to generate fluorescently labeled cDNA. The permeabilization time that resulted in the highest fluorescence signal with the lowest background diffusion was chosen. The best permeabilization time for BC tissue was 18 min. Cryostat sections of 10 μm of thickness were cut and placed on Visium Spatial Gene Expression slides (10X Genomics, PN-1000184). The slide was incubated for 1 min at 37°C, then fixed with methanol for 30 min at -20°C followed by Hematoxylin and Eosin (H&E) staining and images were taken under a high-resolution microscope. After imaging, the coverslip was detached by holding the slide in water and the slide was mounted in a plastic slide cassette. The spatial gene expression process, including tissue permeabilization, second strand synthesis and cDNA amplification, was performed according to the manufacturer’s instructions (10X Genomics; #CG000239). cDNA quality was next assessed using Agilent High sensitivity DNA Kit (Agilent, #5067-4626). The spatial gene libraries were constructed using Visium Spatial Library Construction Kit (10X Genomics, PN-1000184).

  Dataset EGAD50000000322

• Alzheimer's Disease Sequencing Project (ADSP)

  NOTICE OF CHANGE IN LOCATION FOR ALZHEIMER'S DISEASE SEQUENCING PROJECT (ADSP) GENETIC AND PHENOTYPIC DATA: ADSP whole exome and whole genome sequence data that are shared through dbGaP were mapped to the Genome Reference Consortium human genome GRCh37 (build 37). These data are from the Discovery Phase of the project (described below) and will continue to be available at this site. Please see the ADSP Design page for the complete study description. All data that are mapped to GRCh38 (hg38) are being shared through the NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) Data Sharing Service (DSS). For instructions on how access the ADSP Build 38 data that are shared through NIAGADS DSS, visit the Application Instructions page. STUDY DESCRIPTION FOR dbGaP BUILD 37 ADSP DATA: The overarching goals of the Alzheimer's Disease Sequencing Project (ADSP) are to: (1) identify new genomic variants contributing to increased risk of developing Alzheimer's Disease (AD), (2) identify new genomic variants contributing to protection against developing AD, and (3) provide insight as to why individuals with known risk factor variants escape from developing AD. These factors will be studied in multi-ethnic populations in order to identify new pathways for disease prevention. Such a study of human genomic variation and its relationship to health and disease requires examination of a large number of study participants and needs to capture information about common and rare variants (both single nucleotide and copy number) in well phenotyped individuals. Using existing samples from NIH funded and other studies, three NHGRI funded Large Scale Sequencing and Analysis Centers (LSAC) - Broad, Baylor, and Washington University - produced the DNA sequence data. Variant call data are being made available to the scientific community through NIH-approved data repositories. Statistical analysis of the sequence data is anticipated to identify new genetic risk and protective factors. The ADSP will conduct and facilitate analysis of sequence data to extend previous discoveries that may ultimately result in new directions for AD therapeutics. Analysis of ADSP data will be done in two phases. The Discovery Phase analysis (2014-2018) is funded under PAR-12-183. The entire Discovery dataset contains whole-genome sequencing data on 584 subjects from 113 families, and pedigree data for > 4000 subjects; whole exome sequencing data on 5096 cases 4965 controls; and whole exome sequence data on an additional 853 (682 Cases [510 Non-Hispanic, 172 Hispanic]), and 171 Hispanic Control subjects from families that are multiply affected with AD. The Replication Phase (2016-2021) analysis will be funded under RFA-AG-16-001 and RFA-AG-16-002 and is expected to include a combination of genotyping and sequencing approaches on at least 30,000 subjects. Targeted sequencing will be done by the LSACs. GRCh37 Data Releases The first ADSP data release occurred on November 25, 2013. It included the whole-genome sequencing data in BAM file format on 410 individuals. The second ADSP data release occurred on March 31, 2014, and included the whole-genome sequencing data in BAM file format for an additional 168 individuals. The third ADSP data release occurred on November 03, 2014 and included whole-exome sequencing data in BAM file format for 10,939 individuals. The fourth ADSP data release occurred on February 13, 2015 and included revised ethnic data for subjects with whole-exome sequencing data. The fifth ADSP data release occurred on July 13, 2015 and included whole-genome genotypes and updated phenotypes as well as changes to pedigree structures and sample IDs. The sixth ADSP data release occurred on December 8, 2015, and included whole-exome genotypes and updated phenotypes as well as changes to subject IDs. This seventh ADSP data release on April 12, 2016 includes: (1) WES and WGS SNV VCF files (2) WES and WGS Indel PLINK files ADSP Data Available through dbGaP: ADSP - Whole Genome Sequencing ADSP - Whole Exome Sequencing Comments DNA-Seq (BAM) n=578 n=10913 Sequence data available (plus n=38 replications w/out genotype data) Concordant SNV Genotypes (PLINK format) N/A n=10913 QC'ed genotypes that are concordant between the Atlas (Baylor's) and GATK (Broad's) calling pipelines (a subset of the consensus genotype set) Consensus Genotypes (PLINK and VCF format) n=578 n=10913 QC'ed genotypes that are concordant between Atlas and GATK pipelines as well as those that that were called uniquely by Atlas or GATK Concordant Indel Genotypes (PLINK format) n=578 n=10913 QC'ed genotypes that are concordant between the Atlas and GATK calling pipelines Phenotype Data n=4735 n=10913 Data of n=53 phenotype variables available (plus administrative data), including APOE genotype. WGS phenotypes include data of connecting family members. Please use the release notes provided by dbGaP to obtain detailed information about study release updates. The ADSP data portal provides a customized interface for users to quickly identify and retrieve files by covariates, phenotypes, and data properties such as sequencing facility or coverage. For more information about the ADSP study and the data portal, please visit https://www.niagads.org/adsp/.

  Study phs000572

• Barcelona kids with melanoma

  This set of samples is composed of eight young people (7-16 years old) that have developed melanoma with first-degree relatives that have also developed cancer, which suggests a genetic component to their disease. Here we want to sequence these samples in order to find the causative mutations. As these samples do not carry any of the high-penetrance mutations known to date, finding the genes(s) responsible will offer new insights into the genetic mechanisms underlying predisposition to melanoma.

  Dataset EGAD00001002198

• Study of Osteoporotic Fractures (SOF)

  The Study of Osteoporotic Fractures (SOF) is a prospective multicenter study of risk factors for vertebral and non vertebral fractures. The cohort is comprised of 9704 community-dwelling women 65 years old or older recruited from populations-based listings in four U.S. areas: Baltimore, Maryland; Minneapolis, Minnesota; Portland, Oregon; and the Monongahela Valley, Pennsylvania. Women enrolled in the study were 99% Caucasian with African American women initially excluded from the study due to their low incidence of hip fractures. (A cohort of AA women was recruited at the 6th Visit.) The SOF participants were followed up every four months by postcard or telephone to ascertain the occurrence of falls, fractures and changes in address. To date, follow-up rates have exceeded 95% for vital status and fractures. All fractures are validated by x-ray reports or in the case of most hip fractures, a review of pre-operative radiographs. Blood samples were collected in 6795 women at their Year 2 exam (Visit 2) and with written consent for use of DNA in genetic studies. Of these, we have GWAS data on 3625 Caucasian participants. As a separate study, the SOF Osteoarthritis Project was funded separately to collect data about risk factors for osteoarthritis (OA) and analyze baseline hip and hand films for the presence and severity of OA. Raw GWAS data is housed at the study's coordinating center and not released as part of the dbGaP release. The raw data can be requested from the study's coordinating center. Only QC cleaned PLINK files are available at dbGaP. Auxiliary files are also available for duplicates and HapMap participants.

  Study phs000510

• The Breast and Prostate Cancer Cohort Consortium (BPC3) GWAS of Aggressive Prostate Cancer and ER- Breast Cancer

  The Breast and Prostate Cancer Cohort Consortium (BPC3) was established in 2003 to pool data and biospecimens from nine large prospective cohorts to conduct research on gene-environment interactions in cancer etiology. The BPC3 initially focused on the association of >70 candidate genes in the Steroid Hormone Metabolism and IGF pathways with risk of breast and prostate cancer. The Consortium's work expanded in 2007 to include genome-wide association studies of estrogen receptor negative (ER-) breast cancer and aggressive prostate cancer. ER- breast cancers have specific epidemiologic characteristics and greater lethality, suggesting ER- breast cancer has a different etiology than ER+ breast cancer. Similarly, aggressive forms of prostate cancer, characterized by extraprostatic extension (Stage C/D) or high histologic grade (Gleason score 8+), differ epidemiologically from the vastly more common indolent forms of prostate cancer and are of the greatest clinical importance. By restricting cases to these specific subtypes, the BPC3 GWAS increased power to detect loci associated with ER- and aggressive prostate cancer (Kraft P and Haiman CA, Nature Genetics 2010 Oct;42:819-20, PMID: 20877320 ). The BPC3 GWAS includes the following cohorts: the American Cancer Society Cancer Prevention Study-II (CPS-II); the European Prospective Investigation of Cancer (EPIC); the Physician's Health Study (PHS); the Nurses' Health Studies I and II (NHS and NHSII); the Health Professionals Follow-up Study (HPFS); the Multiethnic Cohort (MEC); the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial; and the Alpha-Tocopherol, Beta-Carotene (ATBC) Study. For the GWAS of ER- cancer, the BPC3 was expanded to include the Polish Breast Cancer Study (PBCS), a population-based case-control study.

  Study phs000812

• Genetic Epidemiology Network of Arteriopathy (GENOA)

  The Genetic Epidemiology Network of Arteriopathy (GENOA) is one of four networks in the NHLBI Family-Blood Pressure Program (FBPP). GENOA's long-term objective is to elucidate the genetics of target organ complications of hypertension, including both atherosclerotic and arteriolosclerotic complications involving the heart, brain, kidneys, and peripheral arteries. The longitudinal GENOA Study recruited European-American and African-American sibships with at least 2 individuals with clinically diagnosed essential hypertension before age 60 years. All other members of the sibship were invited to participate regardless of their hypertension status. Participants were diagnosed with hypertension if they had either 1) a previous clinical diagnosis of hypertension by a physician with current anti-hypertensive treatment, or 2) an average systolic blood pressure ≥ 140 mm Hg or diastolic blood pressure ≥ 90 mm Hg based on the second and third readings at the time of their clinic visit. The Family Blood Pressure Program (FBPP), GENOA's parent program, is an unprecedented collaboration to identify genes influencing blood pressure (BP) levels, hypertension, and its target-organ damage. This program has conducted over 21,000 physical examinations, assembled a shared database of several hundred BP and hypertension-related phenotypic measurements, completed genome-wide linkage analyses for BP, hypertension, and hypertension associated risk factors and complications, and published over 130 manuscripts on program findings. The FBPP emerged from what was initially funded as four independent networks of investigators (HyperGEN, GenNet, SAPPHIRe and GENOA) competing to identify genetic determinants of hypertension in multiple ethnic groups. Realizing the greater likelihood of success through collaboration, the investigators created a single confederation with program-wide and network-specific goals.

  Study phs001238

• Epigenetics of Cocaine and Nicotine Addiction

  This project characterizes DNA methylation and gene expression changes that occur in the human brain, specifically in neurons from the rostral striatum. Major advances from NIDA funded initiatives for noninvasive neuroimaging studies have made it possible to study neuroanatomical, neurochemical and functional changes in the human brain that contribute to the vulnerability to abuse drugs, together with the neurotoxic consequences of years of drug misuse. Animal models have been developed to explain the fundamental behavioral and biological mechanisms of addiction, including reward, tolerance and dependence. From these studies, we learned that cocaine abuse not only alters the epigenetic status of genes, but also induces particular epigenetic modifications depending on the frequency of the drug's administration. Certain genes are switched on by infrequent (short-term exposure) administration, while others are switched on only after chronic administration (addiction/dependence). Animal studies have also suggested that cocaine-seeking habits modeling chronic cocaine addiction in humans depend upon dopamine-dependent serial connectivity linking the ventral (nucleus accumbens) with the dorsal striatum (caudate nucleus). The primary goal of this study is to identify DNA methylation and gene expression changes that occur in the transition from recreational cocaine use to cocaine addiction. High throughput sequencing studies were designed to investigate unique postmortem human brain specimens from individuals that met criteria for cocaine dependence, as compared to unaffected age-matched controls. Brain biospecimens were available from the University of Miami Brain Endowment BankTM, from a collection of phenotypically well-characterized postmortem tissues sampled from chronic cocaine abusers that came to autopsy. This biobank of postmortem brain specimens and annotated genomic data serve as a research resource to support NIDA's scientific mission.

  Study phs001377

• NIDDK IBD Genetics Consortium Repository Exome Chip

  The Illumina Infinium HumanExome+ BeadChip contains putative functional exonic variants selected from individual exome and whole-genome sequences from diverse populations. It includes nonsynonymous variants, splice variants and stop-altering variants. It also includes tags for previous GWAS-identified loci, ancestry informative markers, markers designed for identity by descent analyses, synonymous variants, fingerprint SNPs common to major genotyping platforms, mitochondrial SNPs, chromosome Y SNPs, and HLA tag SNPs. For more information as well as a detailed description of the variant calling and QC procedures, see Li et al. (2016). Li, D., et al. (2016) A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition. Gastroenterology, 151, 1-9. PMID: 27492617.

  Study phs001723

• Exome sequencing of autosomal recessive progressive external ophthalmoplegia (arPEO)

  Progressive external ophthalmoplegia (PEO) is an inherited mitochondrial disease that follows either autosomal dominant or recessive forms of inheritance (adPEO or arPEO). AdPEO is a genetically heterogeneous disease and several genes including POLG1 and C10orf2/Twinkle have been identified as responsible genes. On the other hand, POLG1 was the only established gene causing arPEO with mitochondrial DNA deletions. We previously reported a case of PEO with unidentified genetic etiology. The patient was born of a first-cousin marriage. Therefore, the recessive form of inheritance was suspected. To identify the disease causing variant in this patient, we subjected the patient's DNA to whole-exome sequencing and narrowed down the candidate variants using public data and runs of homozygosity analysis.

  Study phs000392

• Prostate Cancer and Normal Adjacent Prostate RNA-seq samples, NGS-ProToCol

  The dataset "Prostate Cancer and Normal Adjacent Prostate RNA-seq samples, NGS-ProToCol" includes 41 Normal Adjacent Prostate and 51 ribo-depleted Prostate Cancer RNA-seq samples. ---- 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

  Study EGAS00001002816

• 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