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• Reference epigenome IPS04_X_Fibroblast_mRNA-Seq data generated from KEP study

  A IPS04_X_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4)

  Dataset EGAD00001003491

• Reference epigenome OB57_D_PreA_WGBS data generated from KEP study

  A OB57_D_PreA_WGBS paired end data for Preadipocyte(fat)

  Dataset EGAD00001003480

• Reference epigenome IPS01_N_Fibroblast_mRNA-Seq data generated from KEP study

  A IPS01_N_Fibroblast_mRNA-Seq paired end data for iPSC(Oct4)

  Dataset EGAD00001003488

• Reference epigenome IPS04_X_Fibroblast_smRNA-Seq data generated from KEP study

  A IPS04_X_Fibroblast_smRNA-Seq single end data for iPSC(Oct4)

  Dataset EGAD00001003504

• University of Miami Study on Genetics of Autism and Related Disorders (AutismDisorders)

  Autism spectrum disorders (ASD) are neurodevelopmental in origin and characterized by impairments in reciprocal social interaction and communication accompanied by restricted and repetitive patterns of interest or behavior. With improved surveillance and a broadening of the diagnostic criteria, the most recent prevalence studies suggest that ASD may affect as many as 1/166 children in the US. Treatments are limited resulting in little impact on the profound morbidity. Little is known about the etiology of ASD, but there is a strong genetic component. Genetic studies over the past decade have failed to identify definitive ASD genes, but have clearly shown that the underlying genetics are more complex than anticipated with the likelihood that multiple genes are acting independently and/or interactively. With this realization the field of ASD genetics is at a critical juncture. To move forward we must embrace new and creative paradigms to successfully dissect the genetic etiology of this disease. Specifically the current study will: Extend our ascertainment to the full range of ASD. We will increase our ASD dataset by collecting 600 families who meet clinical diagnostic criteria for the three most common ASDs: autism (AUT), Asperger disorder (ASP) and Pervasive Developmental Disorder-NOS (PDD-NOS). Phenotype assessment will be expanded to include the Social Responsiveness Scale (SRS) and detailed seizure data. Ascertainment will focus on parent-child trios. Further characterize the ASD-associated variations in the Gamma-Aminobutyric Acid (GABA) receptor (GABR) subunits. We will complete our GABR subunit variant analysis, including coding, UTR, regulatory, and conserved intronic sequence, concentrating on GABRA4 and GABRB1. We will also investigate the role of variation in other GABR subunits. All AUT specific findings will be examined in the entire ASD dataset. Identify the chromosome 19p ASD gene. Multiple genome-wide screens have provided significant evidence for linkage to Chromosome 19p and we have found evidence for significant association in the linked families within an ~3 Mb region. We will genotype 768 SNPs spaced at ~4 kb to refine the candidate region and delineate specific candidate genes for further testing. We will screen the strongest associated candidate genes for additional variants and evaluate evidence for association in the entire ASD dataset (SA5). Develop and apply the Phenotypic Homogeneity Distinction (PHD) algorithm for identification of the phenotypic signature of linkage and/or association signals. The PHD algorithm identifies phenotypic covariates that discriminate a target sample subset (e.g. the positively linked families or families carrying the associated risk allele) from its complement. The resulting PHD discriminators will define a homogeneous subset from our newly-ascertained ASD dataset to use, as a confirmatory dataset and for localization within genes under study in our other aims. Test for gene-gene interactions. To fully explain the spectrum of autism risk, we will test for interactions between genetic variations associated with ASD (such as those in GABR subunit genes). We will build upon our experience using the MDR method and extend our analyses across biological pathways using the entire ASD data set.

  Study phs000436

• SEARCH for Diabetes in Youth Study - Genetic Risk Score

  Genetic risk scores (GRS) quantify polygenic disease risk into a single measure and can aid in disease classification. GRS studies have focused primarily on adult populations of recent European ancestry. We aimed to assess the utility of GRS in classification of diabetes type among racially/ethnically diverse youth in the United States. We used data from SEARCH baseline visits and follow up visits for which key data elements were available. 2260 participants are included. Phenotypic Data to be submitted here include: Self-reported sex, race and ethnicity Diabetes type determined by provider Etiologic diabetes type T1D (antibody positive, or antibody negative/missing and insulin sensitive) T2D (antibody negative and insulin resistant) Diabetes duration (years) Age at diagnosis (years) Measures from baseline, SEARCH 3 (follow-up) and SEARCH 4 (follow-up): Age Height Weight Waist circumference HbA1c Fasting/non-fasting glucose C-peptide Triglycerides HDL LDL Systolic Blood Pressure Diastolic Blood Pressure Measures from SEARCH 3 and 4:Arterial stiffness as characterized by PWVRetinopathy Measures from SEARCH 4 only: LV structure and diastolic function measurements from echocardiogram GAD autoantibody IAD autoantibody ZnT8 autoantibody We performed genotyping using the Illumina Multi-Ethnic Global Array (MEGA) array with 1,697,069 genotyped variants including 748,291 with minor allele frequency <0.01. Genotyping and preliminary quality control checks were performed at the Colorado Center for Personalized Medicine. After additional quality control, 2,238 samples and 900,743 variants remained for analyses. Samples genotyped on the MEGA array were categorized using SEARCH etiologic type and consisted of predominantly type 1 diabetes cases (n=2,051) but also those with other diabetes (n=133 type 2 diabetes, n=52 other diabetes including monogenic diabetes; genetic confirmation with either a genetic clinical test or test performed as an ancillary study to SEARCH). The median reported age at DNA collection was 11.2 years (interquartile range 7.6 – 14.1) with a minimum age of 1.9 years and maximum of 21.9 years. We used additional data genotyped on the Affymetrix 500K imputation scaffold chip with 239,279 genotyped variants. This cohort consisted of predominantly type 2 diabetes cases (n=417) but also those with type 1 (n=104), and other diabetes types (n=16). After additional quality control, 537 samples and 235,967 variants remained. The median reported age at collection was 11.2 years (quartile range 8.1 – 14.2) with a minimum of 2.0 years and a maximum of 21.1 years. About 100 type 2 diabetes cases were also genotyped using the MEGA chip to ensure concordance between the data sets and facilitate strand alignment between the two chips before genotypic imputation. The data sets had n=230,228 genotyped variants in common and concordance between the genotypes was high (mean correlation r2 for SNPs used in GRS=0.95). We used the 1000 Genomes reference panel to impute each data set separately, resulting in a total of 34.5M and 27.8M well-imputed variants (r2>0.8) for the MEGA and Affymetrix data sets respectively. We combined high quality imputed variants for analysis.

  Study phs002703

• Resuscitation Outcomes Consortium Trial of Continuous Compressions Versus Standard CPR in Patients With out-of-Hospital Cardiac Arrest (ROC CCC-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To compare the rate of survival to hospital discharge after continuous chest compressions versus standard American Heart Association recommended cardiopulmonary resuscitation with interrupted chest compressions in patients with out-of-hospital cardiac arrest.Background: Standard cardiopulmonary resuscitation (CPR) consists of manual chest compressions to maintain blood flow and positive-pressure ventilation to maintain oxygenation until spontaneous circulation is restored. Chest compressions during standard CPR are interrupted frequently by ventilations. These interruptions reduce blood flow and potentially reduce the effectiveness of CPR. In animals with cardiac arrest, the interruption of chest compressions has been associated with decreased survival. Observational studies involving humans with out-of-hospital cardiac arrest of presumed cardiac cause have suggested that continuous compressions are associated with higher rates of survival than interrupted compressions.Participants: Of 35,904 patients with out-of-hospital cardiac arrest who were screened, 26,148 were eligible for participation in the trial and were enrolled in the trial during either the run-in phase or the active-enrollment phase. The active-enrollment phase included 23,711 patients, of whom 12,653 were assigned to the intervention group and 11,058 to the control group.Design: There were 114 participating EMS agencies across the eight participating Resuscitation Outcomes Consortium (ROC) sites, which were grouped into 47 clusters. Clusters of agencies were randomly assigned, in a 1:1 ratio, to perform continuous chest compressions or interrupted chest compressions during all the out-of-hospital cardiac arrests to which they responded. Each cluster was required to begin enrolling patients in a run-in phase to demonstrate adherence to the protocol before entering the active-enrollment phase of the trial. Twice per year, each cluster was crossed over to the other resuscitation strategy.Patients assigned to the group that received continuous chest compressions (intervention group) were to receive continuous chest compressions at a rate of 100 compressions per minute, with asynchronous positive-pressure ventilations delivered at a rate of 10 ventilations per minute. Patients assigned to the group that received interrupted chest compressions (control group) were to receive compressions that were interrupted for ventilations at a ratio of 30 compressions to two ventilations; ventilations were to be given with positive pressure during a pause in compressions of less than 5 seconds in duration. The primary outcome was the rate of survival to hospital discharge. Secondary outcomes included neurologic function at discharge, which was measured with the use of the modified Rankin scale, and adverse events. Conclusions: During the active-enrollment phase, 1129 of 12,613 patients in the continuous chest compression group and 1072 of 11,035 patients in the interrupted chest compressions group survived to hospital discharge.In patients with out-of-hospital cardiac arrest, continuous chest compressions during CPR performed by EMS providers did not result in significantly higher rates of survival or favorable neurologic function than did interrupted chest compressions.

  Study phs003901

• Weighing Risks and Benefits of Laparoscopic Anti-Reflux Surgery in Patients With Idiopathic Pulmonary Fibrosis (WRAP-IPF-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: To determine if the reduction of abnormal gastro-esophageal reflux (GER) with laparoscopic anti-reflux surgery will slow the progression of idiopathic pulmonary fibrosis (IPF) as measured by forced vital capacity (FVC).Background: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease of unknown cause and increasing prevalence in the United States. Aside from lung transplantation, which approximately only 1% of participants will receive, there is no FDA-approved therapy. Abnormal acid gastro-esophageal reflux (GER) has been well described in participants with IPF and is thought to play a role in the progression of the disease. The several retrospective cohort studies that have assessed the association of anti-acid therapies for GER with clinical outcomes in IPF have had inconsistent results.Participants: A total of 58 participants were enrolled.Design: The WRAP-IPF trial was a multicenter, unblinded randomized clinical trial with participants randomized to either laparoscopic anti-reflux surgery or no surgery. Participants in the no-surgery group had the option of receiving laparoscopic anti-reflux surgery from 24 weeks after randomization if their clinician deemed it medically necessary. Medications for acid GER were allowed in both groups if the clinician felt it was necessary.Participants were followed up from time of randomization to 52 weeks. All participants had study visits at baseline, 12, 24, 36, and 48 weeks, during which spirometry, 6-min walk testing, and participant-related outcome assessments were done. Participants in the surgery group had clinical visits for preoperative evaluation, laparoscopic anti-reflux surgery, and postoperative management as clinically indicated. Surgery participants additionally underwent repeat 24-hour pH testing at 24 weeks to assess the efficacy of the surgery. All participants were contacted by telephone for safety assessments at weeks 4, 8, 16, 20, 28, 32, 40, 44, and 52. All participants completed an exploratory questionnaire on reflux symptoms at baseline and 48 weeks. The primary endpoint was change in FVC from randomization (baseline) to 48 weeks. Secondary endpoints included acute exacerbation, non-elective hospitalization (both all-cause and respiratory-related), death, change in cough severity, change in dyspnea severity, change in health-related quality of life, change in 6-min walk distance, and time to selected event-driven composite endpoints of disease progression. Conclusions: In participants with IPF and abnormal acid GER, laparoscopic anti-reflux surgery is safe and well tolerated but did not significantly slow the rate of FVC decline. Further research is needed, particularly with a larger study in order to achieve sufficient statistical power, regarding the possible benefits of anti-reflux surgery in this population.Raghu G, Pellegrini CA, Yow E, et al. Laparoscopic anti-reflux surgery for the treatment of idiopathic pulmonary fibrosis (WRAP-IPF): a multicentre, randomised, controlled phase 2 trial. Reference: Raghu, et al., 2018; PMID: 30100404.

  Study phs003968

• Transcriptomic analysis of liver CD8+ T cells

  Sorted single CD8+T cells expressing CD14 from human liver for SMARTSeq2. Livers processed: Kucykowicz et al STAR Prot 2022:pubmed.ncbi.nlm.nih.gov/35516846/ Published: Pallett et al Nature 2022 Tissue CD14+CD8+T-cells are reprogrammed by myeloid cells and modulated by LPS The liver is bathed in bacterial products including LPS transported from the intestinal portal vasculature, but maintains a state of tolerance exploited by persistent pathogens and tumours1,2,3,4. The cellular basis mediating this tolerance, yet allowing a switch to immunity or immunopathology, needs to be better understood for successful immunotherapy of liver diseases. Here we show that a variable proportion of CD8+T-cells compartmentalised in the human liver co-stain for CD14 and other prototypic myeloid membrane proteins; CD14+CD8+T-cells preferentially accumulate within the donor pool in liver allografts, amongst hepatic virus-specific and tumour-infiltrating responses, and in cirrhotic ascites. CD14+CD8+T-cells exhibit increased turnover, activation and constitutive immunomodulatory features with high homeostatic IL-10/IL-2 production directly ex vivo, and an enhanced capacity to rapidly produce antiviral/anti-tumour cytokines upon TCR engagement. This CD14+CD8+T-cell profile can be recapitulated by acquisition of membrane proteins, including the LPS receptor complex, from mononuclear phagocytes, resulting in augmented tumour killing by TCR-redirected T-cells in vitro. CD14+CD8+T-cells express integrins and chemokine receptors favouring interactions with the local stroma, which can promote their induction through CXCL12. LPS can also increase the frequency of CD14+CD8+T-cells in vitro and in vivo, and skew their function towards the production of chemotactic and regenerative cytokines. Thus, bacterial products in the gut-liver axis and tissue stromal factors can tune liver immunity by driving myeloid instruction of CD8+T-cells with immunomodulatory capacity. For the analysis of the single cell transcriptome two intrahepatic perfusate samples were isolated and frozen at -80 'C for storage prior to transportation to Newcastle, UK. Once thawed in pre-warmed HBSS containing 0.001% DNaseI, intrahepatic leukocytes were sorted by FACS to index classical mononuclear phagocytes (MNP) defined as Singlets, CD3-CD56-CD19-CD14hiHLA-DR+ or CD14± CD8+T-cells as follows: Singlets, CD3+CD56-CD19-CD4-CD8+V7.2- and split in to CD14± based on an isotype control. Single cells were sorted into 96-well skirted LoBind plates (Eppendorf) containing 5 µL lysis buffer (TCL buffer [Qiagen], supplemented with 1% b-mercaptoethanol [Sigma Aldrich; Merck]) on a BD Bioscience FACSFusion. The sorted plates were subsequently immediately sealed, centrifuged, and placed on dry ice to flash-freeze the cell lysate and stored at -80 'C. A modified SMART-seq2 protocol57 was performed on the single flow cytometry sorted-cells as previously described58. After cDNA generation, libraries were prepared (384 cells per library) using the Illumina Nextera XT kit (Illumina). Each library was sequenced to achieve a minimum depth of 1-2 million raw reads per cell using an Illumina HiSeq 4000 using v. 4 SBS chemistry to generate 75-bp paired-end reads.

  Study EGAS00001006885

• A Genome-Wide Association Study in Patients Experiencing Breast Events While Receiving Adjuvant Aromatase Inhibitors for Early Breast Cancer on NCIC CTG Trial MA.27

  Source of patients:The source of the patients for this genome-wide case-control study was MA.27, which was conducted as a multi-cooperative group effort under the auspices of the NCI Breast Cancer Intergroup of North America. The NCIC Clinical Trials Group (CTG) serves as the coordinating group, with participation by the NCI-sponsored North Central Cancer Treatment Group, Eastern Cooperative Oncology Group (ECOG), Southwest Oncology Group, and Cancer and Leukemia Group B (CALGB). MA.27 involved postmenopausal women with histologically confirmed and completely resected invasive breast cancer with surgical margins clear of invasive carcinoma in the following TMN categories (AJCC Version 6): pT1, pT2, pT3; pNx, pN0, pN1, pN2, pN3 (only when the sole basis is presence of 10 or more involved axillary nodes); MO. The primary tumor must have been estrogen receptor (ER) and/or progesterone receptor positive. Patients were stratified by lymph node status at diagnosis, prior adjuvant chemotherapy, and trastuzumab use and were randomized to 5 years of adjuvant therapy with anastrozole or exemestane. The trial was activated on May 26, 2003, and reached its accrual objectives on July 31, 2008, after the randomization of 6827 North American patients, with the majority (79%) providing DNA and consent for genetic testing. Non-North American patients were also entered by the International Breast Cancer Study Group but they did not contribute DNA. From 2003 to December 21, 2004, patients also underwent a second randomization to celecoxib 400 mg twice daily or placebo but, after the entry of 1,622 patients, this treatment was discontinued because of reports of increased cardiovascular risk associated with celecoxib. The final results of this study have been published, see Goss et al., 2013 (23358971). The patients in this analysis came from three cohorts: Cohort 1 consisted of 870 patients genotyped on the Illumina Human610-Quad BeadChip studied in a GWAS with the phenotype of musculoskeletal adverse event, see Ingle et al., 2010 (20876420), Cohort 2 consisted of 882 patients genotyped on the Illumina OmniExpress platform studied in a GWAS with the phenotype of fragility fractures, see Liu et al., 2014 (25148458), and the remaining 2913 patients were genotyped with the Illumina OmniExpressExome platform.

  Study phs001043