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• A Case Controlled Etiologic Study of Sarcoidosis (ACCESS-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. Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from (ACCESS) include Bronchial Lavage, DNA, Peripheral Blood Mononuclear Cells, and Plasma. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: To determine the etiology of sarcoidosis by establishing a case control, multi-center study. In addition to etiology, this study also sought to examine socioeconomic variables and the clinical course of patients with sarcoidosis, including quality of life.Background: Sarcoidosis is a chronic granulomatous disorder of unknown cause that is characterized by activation of T-lymphocytes and macrophages. For many years, sarcoidosis was presumed to be an atypical manifestation of tuberculosis because of the similarity between the inflammatory responses of the two diseases. However, as culture techniques became more widely employed to diagnose tuberculosis and it became less common, it became clear that sarcoidosis was not simply a variation of tuberculosis. Data on the etiology of sarcoidosis have come from diverse sources: in clinical investigations, alveolitis has been found to precede granulomatous inflammation; in case control studies, familial aggregation has been identified; and in case reports, recurrence of granulomatous inflammation has been observed after lung transplantation. The cause may not prove to be a single, known exposure. Interactions of exposures with genetic dispositions could have important implications for our understanding of immune responses as well as the pathogenesis of sarcoidosis.Participants: 736 participants with sarcoidosis enrolled within 6 months of diagnosis from 10 clinical centers in the U.S. Using the ACCESS sarcoidosis assessment system, organ involvement was determined for the whole group and for subgroups differentiated by sex, race, and age (Conclusions: The initial presentation of sarcoidosis is related to sex, race and age, and it tends to remain stable over two years in the majority of patients. The etiology is probably multifactoral with both genetic and environmental factors contributing.Specimen Details: The PBMC for this study are pelleted and suspended in guanidinium-based solution and are nonviable.

  Study phs004276

• Molecular_characterization_of_invasive_lobular_carcinoma

  Invasive lobular carcinoma (ILC) is the second most common histological subtype of breast cancer accounting for 10-15% of cases. ILC differs from invasive ductal carcinoma (IDC)with respect to epidemiology, histology, and clinical presentation. Moreover, ILC is lesssensitive to chemotherapy, more frequently bilateral, and more prone to form gastrointestinal, peritoneal, and ovarian metastases than IDCs. In contrast to IDC, the prognostic value ofhistological grade (HG) in ILC is controversial. One of the three major components of histological grading (tubule formation) is missing in ILC which hinders the process of gradingin this histological subtype and results in the classification of approximately two thirds of ILC as HG 2.Over the last decade, a number of gene expression signatures have shed light onto breast cancer classification, allowing breast cancer care to become more personalized. Withrespect to the management of estrogen receptor (ER)-positive breast cancer, several gene expression signatures provide prognostic and/or predictive information beyond what is possible with current classical clinico-pathological parameters alone. Nevertheless, most studies using gene expression signature have not considered different histologic subtypesseparately. Recently, a comprehensive research program has elucidated some of the biological underpinnings of invasive lobular carcinoma. Genetic material extracted from 200 ILC tumor samples were studied using gene expression profiling and identified ILCmolecular subtypes. These proliferation-driven gene signatures of ILC appear to have prognostic significance. In particular, the Genomic Grade (GG) gene signature improved upon HG in ILC and added prognostic value to classic clinico-pathologic factors. In addition this study demonstrated that most ILC are molecularly characterized as luminal-A (~75%)followed by luminal-B (~20%) and HER2-positve tumors (~5%). Moreover, we investigated the prognostic value of known gene signatures/ gene modules in the same cohort of ILC. As a second step within the scope of this project, we aim to investigate the interactionsbetween somatic ILC tumor mutations to observed transcriptome findings. To this end, we aim to perform somatic mutation analysis for the ILC tumors for which Affymetrix gene expression profiling is available. To this end, we will use a gene screen assay, which specifically interrogates the mutational status of a few hundreds of cancer genes. We believe that this pioneering effort will be fundamental for a tailored treatment of ILC withimprovement in patients' outcome.

  Study EGAS00001000292

• Single cell transcriptomes of of primary tumors and normal endometrial derived organoids treated with DBZ

  Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed single cell sequencing on endometrial and ovarian tumours, and on organoids both treated with DBZ and normal and found both secretory-like and ciliated-like tumour cells.

  Dataset EGAD00001006280

• Longitudinal study of whole blood gene expression in Kenyan children exposed to malaria

  We have collected RNA samples from whole blood of Kenyan children exposed to malaria in the Kilifi region of Kenya. Collections were performed each year from 2015 until 2018. This is a follow-up study to that described in Bediako et al. (in preparation). The SIMS consortium is seeking to identifying the underlying reasons why some children are more susceptible to malaria than others. In this study we hope to track changes in children’s immune systems over time which relate to the number of malaria episodes they experience. 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/

  Dataset EGAD00001015405

• Identifying autosomal recessive mutations causing neurological disorders

  The objective of this study is to resequence of targeted intervals containing autosomal recessive variants causing neurological disorders in consanguineous pedigrees. Using homozygosity mapping, three intervals of very different sizes have previously been unambiguously mapped for three different neurological diseases: 2.4Mb, 8Mb and 14.3Mb in size, for Microlissencephaly, Severe Mental Retardation and Complicated hereditary spastic paraplegia respectively. This study is a pilot to assess how well custom targeted resequencing performs across a broad size range of intervals. The study design is to use a different custom capture probe set for each interval, pulldown from a single patient from each family, and sequence 1 lane using Illumina paired-reads for each sample. Candidate variants will be followed up in the families themselves, and in patients with similar phenotypes from outbred populations

  Dataset EGAD00001000340

• Serrated Colorectal Cancer: An Emerging Disease Subtype

  This dataset represents two combined study populations. Serrated Colorectal Cancer: An Emerging Disease Subtype (called the Advanced Colorectal Cancer of Serrated Subtype Study or ACCESS Study) was a grant awarded to investigate a newly-recognized, biologically-distinct subtype of colorectal cancer (CRC) called “serrated CRC.” The objective of this project was to characterize factors related to the genetic predisposition, clinical presentation, and prognosis of serrated CRC. The study recruited incident invasive CRC cases diagnosed between April 2016 and December 2018, aged 20-74 years at diagnosis. Cases were identified through the Surveillance, Epidemiology and End Results (SEER) cancer registry serving 13 counties in western Washington State. Eligibility for all individuals was limited to those who were English-speaking and could consent. Participation included completing a baseline epidemiologic questionnaire shortly after diagnosis, optional donation of a saliva sample for genetic analysis, and optional consent to release of medical records and tissue specimens related to their diagnosis. Tumor specimens were tested for serrated CRC-defining molecular characteristics. Further, we have vital status on all participants and cause of death on those that have died since enrollment. Hormones and Colon Cancer: Epigenetic Subtypes, Risks, and Survival (called the Post-Menopausal Hormones Study or PMH Study) was a grant awarded to investigate the impact of post-menopausal hormone use on colon cancer risk, tumor molecular characteristics, and outcomes. Eligible cases were females, newly diagnosed with invasive colorectal adenocarcinoma between October 1998 and February 2002, aged 50 to 74 years. Cases were residents of 10 out of the 13 counties in western Washington State served by the Surveillance, Epidemiology and End Results (SEER) cancer registry. Eligibility for all individuals was limited to those who were English-speaking with available telephone numbers, in which they could be contacted. Unrelated population-based controls were randomly selected according to age distribution (in 5-year age intervals) of the eligible cases by using lists of licensed drivers from the Washington State Department of Licensing (for individuals aged 50 to 64 years) and rosters from the Health Care Financing Administration (now the Centers for Medicare and Medicaid, for individuals older than 64 years). Participation included completing a baseline epidemiologic questionnaire, optional donation of a saliva sample for genetic analysis, and (for cases only) optional consent to release of medical records and tissue specimens related to their diagnosis. Tumor specimens were tested for epigenetic and other molecular characteristics. The ACCESS study was supported by funding from the National Cancer Institute of the National Institutes of Health (NCI/NIH) (R01CA196337, PI: Newcomb, PA), as was the PMH Study (R01CA076366, PI: Newcomb, PA). Additional support for the PMH Study came from the Seattle site of the Colon Cancer Family Registry (SCCFR) (U01CA167551, PI: Jenkins, M, and U01/U24CA074794, PI: Newcomb, PA). Additional support for case ascertainment was provided by the Cancer Surveillance System of the Fred Hutchinson Cancer Center, which is funded by Contract Number HHSN261201300012I; NCI Control Number: N01 PC-2013-00012; Contract Number HHSN261201800004I; and NCI Control Number: N01 PC-2018-00004 from the Surveillance, Epidemiology and End Results (SEER) Program of the National Cancer Institute with additional support from the Fred Hutchinson Cancer Center and the State of Washington. This research was also supported by the Genomics and Bioinformatics, Comparative Medicine, Specialized Pathology, Collaborative Data Services, and Experimental Histopathology Shared Resources of the Fred Hutch/University of Washington Cancer Consortium (P30 CA015704).Tumor marker testing was performed using formalin-fixed paraffin-embedded diagnostic tumor tissue specimens, and DNA extracted from those specimens. Testing for microsatellite instability (MSI) was based on either a 10-gene panel (BAT25, BAT26, BAT40, MYCL, D5S346, D17S250, ACTC, D18S55, D10S197, BAT34C4) or a 4-marker immunohistochemistry panel of DNA mismatch repair proteins (MLH1, MSH2, MSH6, PMS2). CpG island methylator phenotype (CIMP) testing was based on a validated quantitative DNA methylation assay using a five-gene panel (CACNA1G, IGF2, NEUROG1, RUNX3, SOCS1) or eight-gene panel (CACNA1G, IGF2, NEUROG1, RUNX3, SOCS1, MLH1, CRABP1, CDKN2A). Somatic p.V600E BRAF mutation status was tested for using a fluorescent allele-specific PCR assay. KRAS mutations in codons 12 and 13 were also assessed through forward and reverse sequencing of amplified tumor DNA. DNA was extracted from blood/saliva samples using conventional methods. The genotyping panel completed was the Build37 OncoArray500K-C, including 1%-6% blinded duplicates to monitor the quality of the genotyping. Quality control procedures were performed to 1) make sure that there were no patterns of missing data by batch, study, or plate, 2) check for gender discrepancies and kinship, 3) complete Principal Component Analysis, and 4) test for Hardy-Weinberg equilibrium (HWE). Samples were excluded based on call rate, heterozygosity, unexpected duplicates, gender discrepancy, and unexpectedly high identity-by-descent or unexpected genotypic concordance (>65%) with another individual. In addition, variants were excluded based on call rate (98%), lack of HWE in controls (P

  Study phs002171

• FEGA FAQs: a summary of the Q+A session from the FEGA workshop at ELIXIR AHM 2024

  The ELIXIR All Hands Meeting (AHM) was held in Uppsala, Sweden this June. We at EGA always look forward to this meeting as a chance to see many of our partners and colleagues face-to-face. The Federated EGA (FEGA) is one initiative that always benefits from the AHM, and this year FEGA was in the spotlight, with several questions related to the advances we've made recently. We held this year's FEGA workshop a little differently, with most time for discussions on various “hot topics”. Organised in different breakouts, over 2 rounds, participants could choose which session they wanted to attend. One breakout was a general Q+A about FEGA and the path to join. We had a diverse range of participants, including experts from Central EGA (CEGA) and FEGA inaugural nodes, people from up and coming nodes at various stages of readiness, as well as participants not directly a part of FEGA but curious to learn more. It made for a great discussion! In this blog post, we highlight some of the questions for those who didn’t have a chance to be there. What is the FEGA Collaboration Agreement? It is a legal agreement between the node and Central EGA (CEGA) where both parties agree to certain responsibilities, like what services will be provided, sharing of public metadata with CEGA, interoperable technologies and more. The agreement is for 4 years, with the expectation of long-term sustainability. If a node is made up of multiple institutes, one institute must be the signatory. This could require a legal agreement within the node. CEGA is composed of CRG and EMBL-EBI (EGA itself has its own legal agreement between these institutes) Check the FEGA Collaboration Agreement What about purely medical data? Is this accepted in FEGA? CEGA only accepts data approved for secondary research use. We do accept medical data collected in this context, as do some nodes. Nodes are able to accept any data they like, as long as it is sensitive, thus in need of controlled access. What about other data types other than genomics? Like proteomics or images? They can be accepted, although CEGA is currently not designed with those formats in mind, so they might not fit with precision in the data model. The FEGA nodes are welcome to accept any data they want. Proteomic studies generating sensitive data are increasing, and specific work will likely be developed in the near future to adress this need. Does CEGA require a certain amount or type of data to be shared by the node? No, we do not and it's up to each node to decide what specific data types they accept and in what format. Nonetheless, a FEGA node has the duty to be open to data submission from any institution of their country, and can't be limited by design to a single or limited data source. Does CEGA and FEGA require a certain amount or type of details and description on the data to be submitted to the node? Data description (technical and biological), usually called metadata in this field, is crucial for the findability of the submitted data. Thus, we highly recommend including as much information as available to maximise the discoverability of the data. Specifical minimal metadata is defined in the submission schema, and thresholds are specified by the nodes. We are currently working towards a unified FEGA metadata model. What are the geographical borders of FEGA? FEGA should make the E for Everyone, because any institute worldwide could join and we indeed do have countries and use-cases worldwide. Some of them are very close to officially joining the federation. What are the main differences between FEGA and GDI? The two networks have a lot in common and also some critical differences. You can read all about this in one of our latest blog post. If you have more questions, please consider having a look at the FEGA onboarding webpage and, of course, don't miss our workshop at the ELIXIR AHM next year!

  Blog fega-faqs-elixir-ahm-2024

• Global Microbiome Conservancy Sequence Data

  The human body is a complex ecosystem, hosting tens of billions of bacteria, primarily in the gut. This community, known as the 'gut microbiome', is vital to human health, affecting functions ranging from metabolism, immunity, and development, to behavior. Conversely, reduced microbiome diversity and other imbalances of the gut community (dysbiosis) are associated with many diseases of the industrialized world, such as metabolic syndrome, asthma, and inflammatory bowel diseases among others. Microbiome-based interventions thus hold the potential to revolutionize our understanding of, and therapeutic approaches to, many aspects of human health and disease. Despite many advances, current understanding of the human microbiome is largely limited to majority ethnic groups in industrialized nations, and does not reflect the full diversity of human commensal microbiota. In addition to the scientific ramifications of minority underrepresentation, there are significant translational and ethical implications as well: first, failing to capture the full diversity of healthy human microbiota may limit our ability to understand and generate effective therapeutics for many microbiome-associated diseases. Second, underrepresented groups are less likely to benefit from microbiome-based medical advances tailored to well-studied populations, propagating healthcare inequities.  Human gut microbial diversity is diminishing around the globe, due to the spread of industrialized diets and lifestyles, which are associated with reduced microbiome biodiversity. The Global Microbiome Conservancy (GMbC) is a non-profit collaboration between scientists and communities around the world that aims to 1) preserve the full biodiversity of the human gut microbiome, 2) characterize its evolution across populations and host lifestyles and 3) investigate its interactions with the human host. We are collecting gut microbiome and human DNA samples from diverse populations around the world, from isolated groups to urbanized populations, to culture and study this essential biodiversity and to preserve it in a living "seed bank" of bacterial isolates as a long-term safeguard against future extinctions. Human genetic data for the samples sequenced in this study can be found in phs002205.

  Study phs002235

• Genetic Associations in Idiopathic Talipes Equinovarus (Clubfoot) - GAIT

  Isolated clubfoot or idiopathic talipes equinovarus (ITEV) is one of the five most common birth defects, affecting approximately 4,000 newborns each year in the US. While the orthopedic care of these children has improved, long-term problems persist and the health care costs are significant. Studies suggest that clubfoot is a complex disorder with segregation analyses and family studies indicating that genetic factors play an important etiologic role in the development of clubfoot. Only one environmental factor, maternal smoking during pregnancy, has been implicated. We postulate that a small number of genes account for a substantial fraction of clubfoot and that these genes can be identified in a defined population. The challenge now is to identify the genetic loci and, later, the effect of environmental exposures. To accomplish this task, it is important to have a well-defined population and the methodology to detect linkage with and without association. Towards these goals, we have identified and characterized multiplex clubfoot families, including two large clubfoot families, a resource which is among the largest ITEV populations in existence. We will perform a high-density SNP genome scan (GWAS) on our clubfoot dataset to identify chromosomal regions that may harbor clubfoot genes with subsequent interrogation of these regions and candidate genes. We are in a position with our unique clubfoot population and with the methodology in place to undertake this study. The study phases are: 1) continued ascertainment of multiplex and simplex families and 2) GWAS and characterization of identified chromosomal regions and candidate genes. The results of this study will provide data essential to the identification of the gene(s) contributing to the clubfoot phenotype. Identification of high-risk genotypes can lead to the development of prevention programs in selected populations and may suggest gene-based prevention strategies.

  Study phs000314

• Identifying novel DNA damage response genes in radiosensitive individuals

  Ionizing radiation is an effective therapeutic agent for cancer treatment as well as a potent carcinogen. Sensitivity to the cell-killing effects of radiation can vary across human population with a subset of individuals displaying extreme hypersensitivity. It is usually attributable to inherited defects in DNA damage response pathways. The present study was designed to elucidate the genetic basis of variation in hypersensitivity to radiation exposure through exome sequencing of radiosensitive individuals, with the ultimate goal of identifying genes with the most significant effects on cellular DNA damage responses. The study participants included subjects referred for clinical testing for Ataxia-telangiectasia (A-T), Nijmegen Breakage Syndrome (NBS) or Ligase IV Syndrome. These are rare, recessive genetic disorders and hypersensitivity to radiation exposure is a common phenotype among individuals affected by all the three disorders. The study participants exhibited phenotypic characteristics similar to individuals with A-T, NBS or Ligase IV Syndrome, but lacked the causative mutations in ATM (GeneID:472) or NBN (GeneID:4683) genes. For further validation of the radiation sensitivity phenotype among the enrolled subjects, B-lymphoblastoid cells lines were established for each subject from peripheral blood lymphocytes. Each cell line was evaluated for displaying impaired survival rates relative to normal controls after exposure to ionizing radiation. 53 subjects with validated phenotype were finally included in the study and DNA extracted from their B-lymphoblastoid cell lines was used for exome sequencing. This sequencing data for radiation sensitive subjects is being made available in the dbGaP. It is hoped that this resource will be beneficial for researchers who wish to further investigate components of human cellular DNA damage response pathways and/or genetic architecture underlying radiation hypersensitivity. This data may also aid in the rational design of new radiosensitizing or radioprotective agents.

  Study phs001911