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• Upper cortical layer-driven network impairment in schizophrenia

  Schizophrenia is one of the most wide-spread and complex mental disorders. To characterize the impact of schizophrenia, we performed single nucleus RNA sequencing (snRNA-seq) of >220,000 neurons from the dorsolateral prefrontal cortex of patients with schizophrenia and matched controls. Additionally, >115,000 neurons were analyzed topographically by immunohistochemistry. Compositional analysis of snRNA-seq data revealed a reduction in abundance of GABAergic neurons and a concomitant increase in principal neurons, most pronounced for upper cortical layer subtypes, which was substantiated by histological analysis. Many neuronal subtypes showed extensive transcriptomic changes, the most dramatic - in upper layer GABAergic neurons, including downregulation in energy metabolism and upregulation in neurotransmission. Transcription factor network analysis demonstrated a developmental origin of transcriptomic changes. Finally, Visium spatial transcriptomics further corroborated upper layer neuron vulnerability in schizophrenia. Overall, our results point towards general network impairment within upper cortical layers as a core substrate associated with schizophrenia symptomatology. Study is available on bioRxiv (https://doi.org/10.1101/2020.11.17.386458) and in upcoming publication.

  Study EGAS00001006495

• Human Developmental Cell Atlas_HDCA - WGS (2019-04-11)

  Single cell + bulk genomics study for immune and hematopoietic organs during human fetal development . This dataset contains all the data available for this study on 2019-04-11.

  Dataset EGAD00001004953

• V4 Colorectal panel test (2018-03-07)

  Targeted gene screen of cell line tumours for testing the new V4 Colorectal gene panel. . This dataset contains all the data available for this study on 2018-03-07.

  Dataset EGAD00001004000

• Framingham Heart Study-Cohort (FHS-Cohort) - 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. Related Studies Other Framingham data available include: Imaging studies (Framingham Heart Study-Cohort (FHS-Cohort)-Imaging, phs003593), Genetics and genomics (Framingham Cohort, phs000007), Collaborative Cohort of Cohorts for COVID-19 Research (C4R): (Framingham Heart Study, phs002911), and as a component of the Sleep Heart Health Study (SHHS-BioLINCC, phs003637). Available Data Original cohort: data now include examination data from the first 32 clinical exams, selected ancillary data, and event follow-up through 2018. Offspring/Omni1 cohort: Data available include Framingham Offspring examination data from the first 9 clinical exams and selected ancillary data and event follow-up through 2019. Also included are the first 4 exams from the OMNI 1 cohort. Third Generation/Omni2/New Offspring Cohort: Data available include Framingham Generation 3 examination data from the first 3 clinical exams, selected ancillary data and event follow-up through 2019. Also included are the OMNI 2 and New Offspring (NOS) cohorts. A genetic pedigree is not provided for the Framingham phenotype only data. Objectives The objectives of the Framingham Study are to study the incidence and prevalence of cardiovascular disease (CVD) and its risk factors, trends in CVD incidence and its risk factors over time, and familial patterns of CVD and risk factors. Other important objectives include the estimation of incidence rates of disease and description of the natural history of cardiovascular disease, including the sequence of clinical signs and systems that precede the clinically recognizable syndrome and the consequences and course of clinically manifest disease. Background Original cohort: The original cohort of the Framingham Study began in 1948 under the U.S. Public Health Service and was transferred under the direct operations of the new National Heart Institute, NIH, in 1949. Participants were sampled from Framingham, Massachusetts, including both men and women. This was the first prospective study of cardiovascular disease and identified the concept of risk factors and their joint effects. Offspring/Omni1 cohort: With the aging of the Framingham cohort and with interest in familiar aggregation and heritability, a new cohort consisting of the offspring of the original cohort was sampled. Spouses of offspring were also included. This new sample, began enrollment in 1971 and constituted a second generation of participants, permitting new assessment of risk factors and outcomes, and provided a resource for the genetic analyses which were yet to come. The Offspring participants have had repeated examinations, though at typically longer intervals than the original cohort. Third Generation/Omni2/New Offspring Cohort: Thirty-one years after enrollment began for the second generation of the Framingham Heart Study (Framingham Offspring Study), Framingham investigators began enrolling adults with at least one parent enrolled in the Offspring study into the Framingham Generation 3 cohort. The addition of the third generation was expected to facilitate investigation of secular trends in risk factors and indicators of health and disease within families, to enhance statistical power to detect genetic and environmental determinants of complex diseases, and to clarify how subclinical cardiovascular disease predicts occurrence of overt clinical events. Participants Original cohort: At entry to the study in 1948-1952, the study recruited 5,209 men and women, ages 28-62 years, living in Framingham, MA. Offspring/Omni1 cohort: 5,124 men and women, ages 5-70 years at entry consisting of offspring of the original Framingham cohort (and spouses of the offspring). In 1994, the Omni Cohort 1 enrolled 507 men and women of African-American, Hispanic, Asian, Indian, Pacific Islander and Native American origins, who at the time of enrollment were residents of Framingham and the surrounding towns. Third Generation/Omni2/New Offspring Cohort: 4095 men and women, almost all who self reported their ethnicity as white, ages 19+ years at entry, with at least one parent in the Framingham Offspring study, participated in the Gen III cohort. The New Offspring Cohort enrolled spouses of Offspring participants that were not otherwise enrolled and had at least two biological children participating in Gen III. 103 New Offspring Spouses (47 men and 56 women) participated. The OMNI 2 cohort enrolled additional ethnically diverse participants, including many individuals related to the participants of Omni Cohort 1 and also individuals unrelated to Omni Cohort 1 members for a total of 410 new participants. Design The cardiovascular disease conditions under investigation include coronary heart disease (angina pectoris, myocardial infarction, coronary insufficiency and sudden and non-sudden death), stroke, hypertension, peripheral arterial disease and congestive heart failure. Original cohort: The Framingham Study is a longitudinal investigation of constitutional and environmental factors influencing the development of CVD in men and women. Examination of participants has taken place every two years and the cohort has been followed for morbidity and mortality over that time period. Offspring/Omni1 cohort: By 1975, a sample of 5,124 men and women, consisting of offspring of the original Framingham cohort (and spouses of the offspring) had participated in the study. Additional studies of these subjects have continued under research contracts. Third Generation/Omni2/New Offspring Cohort: The children of Offspring Cohort participants were initially identified who would be 20 years of age or older by the end of the enrollment period. A higher priority for recruitment was assigned to individuals who belonged to large extended families, in order to complement phenotypic and genotypic information already obtained from prior generations. The baseline examination was begun in 2002 and completed in 2005.

  Study phs003594

• Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer

  This randomized phase II trial studies how well paclitaxel with or without carboplatin and/or bevacizumab followed by doxorubicin and cyclophosphamide works in treating patients with breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, carboplatin, doxorubicin, and cyclophosphamide, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Bevacizumab may stop the growth of tumor cells by blocking blood flow to the tumor. Giving chemotherapy together with bevacizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed. All participants in this study were female.

  Study phs001863

• Clinical Outcomes of 344 Diffuse Large B-Cell Lymphoma patients

  This study examines clinical outcomes of patients with diffuse large B-cell lymphoma (DLBCL). We analyzed a cohort of 344 patients from the German High-Grade Non-Hodgkin Lymphoma Study Group (DSHNHL). To protect patient confidentiality, all samples were pseudonymized. The dataset includes clinical key characteristics, such as patient age at diagnosis, sex, ECOG performance status, disease stage, serum lactate dehydrogenase levels, bulky disease, bone marrow involvement, extranodal involvement, and B-symptoms. We used these data alongside proteomic and transcriptomic profiles to explore relationships between clinical features and molecular signatures, reconstructing regulatory networks. Insights from this integrative analysis aim to identify key pathological drivers and biomarkers of DLBCL progression, ultimately informing improved risk stratification and targeted therapeutic approaches.

  Study EGAS50000001054

• Genome-Wide Assessment of DNA Methylation in Systemic Lupus Erythematosus-Related Autoantibodies

  Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that can have debilitating effects on multiple organ systems. In SLE, the pivotal immunologic disturbance is the formation of autoantibodies directed against nuclear and cellular antigens. These autoantibodies are associated with specific organ manifestations. Our previous work has shown that certain single nucleotide polymorphisms (SNPs) are associated with the production of SLE-related autoantibodies. However, these genetic associations do not completely explain autoantibody development in SLE. Therefore, we examined whether epigenetic factors such as DNA methylation may be associated with the development of SLE-related autoantibodies. In this study, we examined whether differential DNA methylation is associated with anti-dsDNA, anti-SSA/Ro, anti-Smith, and anti-RNP autoantibodies. Using the Illumina HumanMethylation450 Beadchip, over 450,000 DNA methylation sites were characterized in 325 female SLE cases of European descent. Using a multivariable regression analyses, the methylation status of 16 CpG sites in 11 genes was found to be associated with the SLE-related autoantibodies under study. This study shows that epigenetic factors are associated with autoimmune disease phenotypes, and epigenetic studies are a complementary method to genetic association studies for understanding the biologic mechanisms contributing to autoimmune disease.

  Study phs000947

• Single cell phenotypic profiling of 27 DLBCL cases reveals marked inter- and intra-tumoral heterogeneity

  Diffuse large B-cell lymphoma (DLBCL) is the most common histologic subtype of non-Hodgkin lymphoma and is notorious for its clinical heterogeneity. Patient outcomes can be predicted by cell-of-origin (COO) classification, demonstrating that the underlying transcriptional signature of malignant B-cells informs biological behavior in the context of standard combination chemotherapy regimens. In the current study, we used mass cytometry (CyTOF) to examine tumor phenotypes at the protein level with single cell resolution in a collection of 27 diagnostic DLBCL biopsy specimens from treatment naïve patients. We found that malignant B-cells from each patient occupied unique regions in 37-dimensional phenotypic space with no apparent clustering of samples into discrete subtypes. Interestingly, variable MHC class II expression was found to be the greatest contributor to phenotypic diversity. Within individual tumors, a subset of cases showed multiple phenotypic subpopulations, and in one case we were able to demonstrate direct correspondence between protein-level phenotypic subsets and DNA mutation-defined subclones. In summary, CyTOF analysis can resolve both inter- and intra-tumoral heterogeneity among primary samples, and reveals that each case of DLBCL is unique and may be comprised of multiple, genetically distinct subclones.

  Study EGAS00001003860

• Study of Women's Health Across the Nation (SWAN) Repository

  The Study of Womens Health Across the Nation (SWAN) is an active multi-site, multi-disciplinary, longitudinal study of women's health. Initially funded in 1994 by the National Institute on Aging (NIA), the National Institute of Nursing Research (NINR), and the Office of Research on Women's Health (ORWH), the overall goal of SWAN is to describe the natural history of the menopausal transition and the post menopause including biological, behavioral, and psychosocial characteristics. SWAN focuses on the impact of menopause on age-related chronic diseases, such as diabetes, cardiovascular disease, depression, bone loss and osteoporosis, as well as physical and cognitive functioning. SWAN has seven clinical study sites located in six states, two in California, and one each in Chicago, Boston, Detroit area, northern New Jersey and Pittsburgh. The SWAN cohort was recruited from these areas and consists of 3,302 African American, Caucasian, Chinese American, Hispanic and Japanese American women. SWAN participants were enrolled in 1996-1997 and have been seen annually or bi-annually for clinic visits, which include interviews, measurements, and the collection of blood and urine samples. SWAN participants have now been seen for the baseline and 15 follow-up visits.

  Study phs001470

• Comparison Between qPCR and RNA-Seq Reveals Challenges of Quantifying HLA Expression

  Human leukocyte antigen (HLA) class I and HLA class II loci are essential elements of innate and acquired immunity. Their exceptional influence on disease outcome is well documented by GWAS and candidate gene studies. The impact of HLA allelic variation on human disease through allele-specific presentation of antigenic peptides to T cells has been the main focus to determine HLA effects on disease susceptibility/pathogenesis. However, HLA expression levels have also been implicated in disease, adding another dimension to the extreme diversity of HLA that impacts variability in immune responses across individuals. HLA expression levels routinely rely on quantitative PCR (qPCR). An alternative is adoption of high throughput technologies such as RNA-Seq. This provides the opportunity to quantify HLA expression in large datasets, but also allows comparison between RNA-Seq and qPCR. In this study, we analyze expression data for HLA Class I genes for a matched set of individuals (N = 96) by RNA-Seq, qPCR and cell surface expression. Samples were obtained from the Research Donor Program (NCI-Frederick). We observed a moderate correlation between RNA-Seq and qPCR. We suggest technical and biological factors that might contribute to differences in the techniques.

  Study phs003177

• P647 Targeted resequencing project

  In collaboration with Dr Robert Semple we have identified a family harbouring an autosomal dominant variant, which leads to severe insulin resistance (SIR), short stature and facial dysmorphism. This family is unique within the SIR cohort in having normal lipid profiles, preserved adiponectin and normal INSR expression and phosphorylation. DNA is available for 7 affected and 7 unaffected family members across 3 generations. All 14 samples have been genotyped using microsatellites and the Affymetrix 6.0 SNP chip. Linkage analysis identified an 18.8Mb haplotype on chromosome 19 as a possible location of the causative variant. However, Exome sequencing of 3 affected and 1 unaffected family members has not identified the causative variant suggesting the possibility of an intronic or intergenic variant in this region or elsewhere in the genome. We propose to conduct whole genome sequencing of 5 members of the pedigree at a depth of 20X. The chosen samples are two sets of parents plus one member of an unaffected branch of the pedigree who shares the risk haplotype on chromosome 19. Sequencing of the two sets of parents will be used along with the genome-wide SNP data to impute 4 affected children giving an effect sample size of 6 affected individuals.

  Dataset EGAD00001000383

• Transcriptomic Analysis of HIV-Infected Cells

  Defining the attributes of rare CD4 T cells that harbor latent HIV under therapy with anti-retroviral agents has been challenging due to difficulties in identifying and isolating these cells. These cells represent an important barrier to cure, and characterizing them would aid the design and development of novel HIV cure strategies. In this study, we addressed this challenge using a custom microfluidic technology named Focused Interrogation of cells by Nucleic acid Detection and Sequencing (FIND-seq) that isolates HIV-infected cell transcriptomes, based on HIV DNA detection. We applied this method to HIV DNA+ memory CD4 T cells isolated from blood from five persons with HIV who were receiving anti-retroviral agents. After curating samples based on data quality, we proceeded with bioinformatics analysis from three persons. This analysis identified six transcriptomic pathways that were inhibited in HIV DNA+ cells compared to HIV DNA- cells. These included death receptor signaling, necroptosis signaling, and anti-proliferative G-alpha12/13 signaling. Furthermore, we identified two gene clusters, including 60 and 85 genes, that were significantly associated with HIV DNA+ cells identified by co-expression network analysis. These genes included negative regulators of HIV transcription that were higher in HIV DNA+ cells, positive regulators of HIV transcription that were lower in HIV DNA+ cells, and other genes involved in the negative regulation of mRNA translation, additional RNA processing functions, and the regulation of cellular state and fate. We further examined these signatures in transcriptomic data from CD4 T cell subsets sorted by flow cytometry from nine persons with HIV. We found a partial similarity between the smaller cluster of genes and the signature of CCR6- peripheral TFH cells. Raw sequencing data from all eleven human participant samples included in the study are available. These include samples from two participants who were studied only by FIND-seq, three participants who were studied by both FIND-seq and flow cytometry and six participants who were studied only by flow cytometry.

  Study phs003095

• Integrated genomic, transcriptional and epigenomic analyses in germinal center-cell lymphomas link the mutation landscape with differential DNA methylation in Burkitt lymphoma

  Biologically and clinically diverse B-cell neoplasms, including Burkitt, follicular and diffuse large B-cell lymphoma, show features of germinal center (GC) B-cells. Here we present a comprehensive analysis of the epigenetic landscape of GC-B-cell lymphomas using whole genome bisulfite sequencing paired with genome and transcriptome sequencing from 29 primary tumor samples and four normal GC-B-cell samples. All lymphomas studied showed extensive genome-wide methylation losses as well as intragenic regions where DNA methylation levels were strongly correlated with expression of associated genes. Pathway analysis revealed that these intragenic regions were enriched in signaling networks differentially activated in Burkitt and follicular lymphomas and affected regulatory mechanisms deregulated by recurrent mutations in a large fraction of Burkitt lymphomas (including the ID3/TCF3 complex, the SWI/SNF remodeling complex and the inhibitory GI signaling pathway). Taken together, these results provide a global picture of Burkitt lymphoma pathomechanism and demonstrate a tight connection between epigenetic regulation and other levels of regulatory control in these tumors.

  Study EGAS00001001067

• Combined MEK and BCL-2/XL inhibition is effective in high-grade serous ovarian cancer patient-derived xenograft models and BIM levels are predictive of responsiveness

  Most patients with late stage high-grade serous ovarian cancer (HGSOC) initially respond to chemotherapy but inevitably relapse and develop resistance, highlighting the need for novel therapies to improve patient outcomes. The MEK/ERK pathway is activated in a large subset of HGSOC, thus making it an attractive therapeutic target. Here, we systematically evaluated the extent of MEK/ERK pathway activation and efficacy of pathway inhibition in a large panel of well-annotated HGSOC patient-derived xenograft (PDX) models. The vast majority of models were nonresponsive to the MEK inhibitor cobimetinib (GDC-0973) despite effective pathway inhibition. Proteomic analyses of adaptive responses to GDC-0973 revealed that GDC-0973 upregulated the pro-apoptotic protein BIM, thus priming the cells for apoptosis regulated by BCL2-family proteins. Indeed, combination of both MEK inhibitor and dual BCL-2/XL inhibitor (ABT-263) significantly reduced cell number, increased cell death and displayed synergy in vitro in most models. In vivo, the GDC-0973 and ABT-263 combination was well tolerated and resulted in greater tumor growth inhibition than single agents. Detailed proteomic and correlation analyses identified two subsets of responsive models – those with high BIM at baseline that was increased with MEK inhibition and those with low basal Bim and high pERK levels. Models with low BIM and low pERK were non-responsive. Our findings demonstrate that combined MEK and BCL-2/XL inhibition has therapeutic activity in HGSOC models and provide a mechanistic rationale for clinical evaluation of this drug combination as well as the assessment of the extent to which BIM and/or pERK levels predict drug combination effectiveness in chemoresistant HGSOC.

  Dataset EGAD00001005111

• Whole genome sequencing and mutation rate analysis of Vietnamese trios with paternal dioxin exposure

  2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) or dioxin, is commonly considered the most toxic man-made substance, and from 1962 to 1971, more than 19 million gallons of Agent Orange (AO) and other toxic chemicals contaminated with dioxin were sprayed in South of Vietnam. Dioxin exposure impacts human health and diseases, and birth defects and teratogenesis were frequently observed in children of persons who have been exposed to dioxin in Vietnam. However, the impact of dioxin on human mutation rate has not yet been analyzed. To identify and characterize the genetic alterations in the individuals exposed to dioxin, we perfomed whole genome sequencing of nine Vietnamese trios whose fathers were exposed to dioxin.

  Study JGAS000137

• University of Michigan Clinical Sequencing Exploratory Research (CSER)

  Overview. The personalization of therapy for cancer will require molecular characterization of unique and shared genetic aberrations. In particular, patients who have a sarcoma or other rare cancers and are candidates for clinical trials could potentially benefit by identifying eligibility for "targeted" drugs based on the "actionable" genes in their specific tumor. Growing technological advances in genomic sequencing has now made it possible to consider the use of sequence data in a clinical setting. For instance, comprehensive testing that includes whole exome and transcriptome sequencing may identify biomarkers for predictive or prognostic purposes and thereby inform treatment choices and prevention strategies. Thus, the translation of high throughput next generation sequencing would support a "personalized" strategy for cancer. However, the translation of clinical sequencing bears unique challenges including identifying patients who could benefit, developing informed consent and human subjects protections, outlining measurable outcomes, interpreting what results should be reported and validated, and how results should be reported. In addition, we know very little about how patients and clinicians will respond to the potentially confusing and overwhelming amount of information generated by genomic sequencing, and we lack model processes for clinically evaluating and presenting these data. For the promise of our innovative biotechnologies to be realized, "translational genomics" research that evaluates genomic applications within real-world clinical settings will be required. This proposal brings together expertise at the University of Michigan including clinical oncology, cancer genetics, genomic science/bioinformatics, clinical pathology, social and behavioral sciences, and bioethics in order to implement this clinical cancer sequencing project. Three integrated Projects have the following themes: Project 1) "Clinical Genomic Study" will identify patients with a rare cancer (i.e., 15 out of 100,000 individuals per year) who are eligible for clinical trials, consent them to the study, obtain biospecimens (tumor tissue, germline tissue), store clinical data, and assemble a multi-disciplinary Sequencing Tumor Board to deliberate on return of actionable or incidental genomic results; Project 2) "Sequencing & Analysis" will process biospecimens and perform comprehensive sequencing and analysis of tumors to identify point mutations, copy number changes, rearrangements/gene fusions, and aberrant gene expression; Project 3) "Ethics & Psychosocial Analysis" will observe the expert review process for evaluating sequence results and will examine the clinician and patient response to the informed consent process, delivery of genomic sequence results, and use of genomic results.

  Study phs000673

• Research Study into The Molecular Genetics of Hereditary Neuropathies

  Identification of genes implicated in inherited neuropathy through collecting and sequencing multiple generation families with inherited neuropathy. Patients in this study have been evaluated for demyelinating peripheral neuropathy as determined by decreased motor nerve conduction velocities in the sural nerve. Patients have also been screened for mutations in all genes implicated in demyelinating peripheral neuropathy and are expected to have previously unidentified mutations. Exome (WES) sequencing for two patients affected with inherited neuropathy. VCF files with called variants for each de-identified patient have been submitted.

  Study phs001351

• UK_ReplicationChip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC Replicationchip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper.

  Dataset EGAD00010002118

• Whole genome sequencing of Cas9 repaired cystic fibrosis organoids description

  Three SpCas9-ABE (R785X/R785X) and three xCas9-ABE-repaired organoid clones (F508del/R553X) and their respective unrepaired control organoids were paired-end whole genome sequenced using Illumina Novaseq 6000 system. The reads were mapped to hg19 genome assembly and data is provided as BAM files.

  Dataset EGAD00001005427

• WGS of human colorectal cancer organoid exposed to genotoxic pks+ E. coli

  Organoid cultures were exposed to two different E.Coli strains and a dye control with three biological duplicates. Their original culture was harvested as a control. In total 10 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.

  Dataset EGAD00001005416

• Genome-Wide Association Studies of Prematurity and Its Complications (African American)

  Preterm delivery resulting in the birth of a premature infant is a complex problem with a devastating impact on individuals, families and society. The prevalence of preterm birth has increased steadily in developed countries over the last 20 years and more than three million children die of preterm birth worldwide each year. Despite the importance of the problem and its disproportionate occurrence in poor and minority populations, the underlying causes have been difficult to identify. Spontaneous preterm labor has as its suspected triggers infection, stress, poor nutrition and inherited factors. The single best predictor for preterm delivery is a previous preterm birth. Studies of twins and of recurrences within families provide evidence that genetic factors underlie a substantive component of the risk for prematurity. One major challenge in studying genetic factors in prematurity is that the risk case is not truly established. The genetic risk could reside either in the mother and her uterus or in the infant/placenta. Identification of genetic factors in the mother and/or infant could provide insights into identifying relevant environmental covariates that may be more amenable to rapid interventions but difficult to find using standard epidemiology alone. A comprehensive genome-wide association study (GWAS) is the ideal way to identify those genes that would not be suspected based on our current understanding of the biology of parturition. We are using 2200 African American samples with term or preterm labor. A subset of these (~800) are infant samples recruited by the Neonatal Research Network as part of a study on cytokines and infection in extremely low birth weight infants (Schelonka RL, et al., 2011. PMID: 21145756). Therefore, this group consists of infants <1,000 grams with clinical outcome data for the infant allowing study of the genetic contributors for not only preterm birth but also the complications that often accompany preterm birth. The result will enable a better understanding of the biology of parturition and suggest environmental modifications that can prolong gestations to improve neonatal and adult outcomes. This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to preterm birth through large-scale genome-wide association studies of African-American cases and controls from multiple sites in the United States. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington.

  Study phs000353

• Biological Determinants of Peritoneal Dialysis Outcomes

  Peritoneal Dialysis (PD) is a technique for treating kidney failure where fluid is instilled into the body's peritoneal cavity. Fluid and solutes travel across the peritoneum, and this is critical to successful PD. Studies have shown that certain demographic and clinical variables explain a small part of the variability in baseline peritoneal solute transfer rate and water transfer function across the peritoneum. This study sought to identify the common genetic variants associated with the baseline peritoneal function in patients starting treatment with PD and change in function upon treatment with PD. This study has two specific aims: Aim 1: To identify and validate genetic loci that influence the peritoneal solute transfer rate (PSTR) at start of PD. Aim 2: To identify and validate genetic loci in pre-specified biologic pathways with change in peritoneal ultrafiltration capacity. This study incorporates data from participants' peritoneal solute transfer rate in their first ever peritoneal equilibrium test (PET) and changes in the transfer of water across the peritoneal membrane over time in a sub-group of participants, demographic information, and results from laboratory analysis of DNA, blood, and dialysate. This study comprises patient populations from pre-existing biorepositories in Europe, and prospectively enrolled participants in United States, Canada, United Kingdom, and Australia. Clinical data related to the participants' peritoneal solute transfer rate from their first ever Peritoneal Equilibrium Test (PET), demographic information, and change in ultrafiltration capacity over time, are correlated with various genetic markers of interest. For individuals enrolled prospectively, blood and dialysate were collected at the first study visit. Annually, subjects either underwent a PET as standard of care or perform an additional 4-hour dwell as part of the study. These subsequent measures were utilized to determine change in ultrafiltration capacity over time. Inclusion criteria included adults over the age of 20 who are able to provide consent and had a record of a PET within 6 months of starting PD. Subjects with missing outcome data and that did not pass genotyping QC were excluded. Genotyping was performed in two batches using the Illumina InfiniumOmni2-5-8v1-3_A1 array with 2,372,784 single nucleotide variants (SNVs) in the first batch (n=1957). The second genotyping batch (n=1053) was on the InfiniumOmni2-5-8v1-4_A1 array with 2,382,209 SNVs. Imputation was performed using the Michigan Imputation Server and the HRC1.1 genotype reference. The Institutional Review Board of the University of Washington has “dbGaP-certified” the consent forms used to enroll participants in Australia, Canada, and United States and the genotype-phenotype data from the participants (n=827) deposited in the public repository. Furthermore, it has been determined that under the EU-GDPR regulations, depositing data of participants enrolled in UK, Belgium, and Sweden (n=2,023) into dbGaP “serves no lawful purpose” as the consent form used for enrolling participants did not obtain explicit permission for depositing data in a public repository.

  Study phs002996

• High Resolution Analysis of Spatial Interactions of Hundreds of Promoters in HeLa Cells

  In this study we developed a new hybridisation-based promoter Capture-C protocol that makes use of biotinylated dsDNA probes and allows high-resolution promoter interactome description. Experiments aimed to describe spatial interactions of set of 861 promoters were performed in HeLa cells. We have found that enrichment efficiency and quality of final libraries in our study is on a par with established promoter Capture-C protocols. Meanwhile, our version of the probe preparation protocol is reasonably simple and makes Capture-C experiments more affordable and flexible.

  Study phs002014

• Celiac disease meta-analysis

  Celiac disease (CeD) is a common immune-mediated disease of the small intestine that is triggered by exposure to dietary gluten. While the HLA locus plays a major role in disease susceptibility, 39 non-HLA loci were also identified in a study of 24,269 individuals. We now build on this earlier study by adding 4,125 additional Caucasian samples including an Argentinian cohort genotyped on the Immunochip. In doing so, we not only confirm the previous associations, we also identify two novel independent genome-wide significant associations.

  Study EGAS00001003805

• Genome-wide search to find the genetic elements underlying visual contour perception

  Contour integration is a key function of the visual system to deal with occlusion and discontinuity in natural scenes. The current study is the first one to investigate the genetic basis of this visual function in humans. A total of 2619 normal participants were tested on their ability to detect continuous contours embedded in a cluttered background with a standard psychophysical protocol. Multi-level genomic analysis was performed, involving heritability estimation based on single nucleotide polymorphism (SNP) and association testing at SNP and gene levels.

  Study EGAS00001003639