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• Molecular profiling for a patient with lipoblastoma-like tumor of the vulva

  Lipoblastoma-like tumors of the vulva (LLTVs) are exceptionally rare indolent adipocytic mesenchymal tumors arising in adults. Only total 19 cases have been reported previously and has just been categorized as mesenchymal tumours of the lower genital tract on the latest WHO classification of tumours, 5th edition. This is the first case of LLTV assessed for RNA-seq, WES, and WGS by next generation sequencing.

  Study JGAS000529

• 120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  Study EGAS00001001733

• NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)

  This is a case pharmacogenetic study of bronchodilator drug response (Albuterol) among racially admixed Latino children with asthma between the ages of 8-40. Lung function testing was performed using the KoKo PFT system and each participant was administered albuterol dependent on age. Participants under 16 years of age, were administered 2 puffs of albuterol from a standard metered dose inhaler and 4 puffs for participants over 16 years old. The overall goal is to identify genetic factors which are predictive of drug response in children with asthma. The principal tools include a questionnaire and biological specimen collection. Participants with asthma have physician-diagnosed asthma, symptoms and medications.

  Study phs001542

• IDH1 Somatic Mutation Profile in Intrahepatic Cholangiocarcinoma

  The objective of this study is to identify somatic IDH1 mutations in intrahepatic cholangiocarcinoma samples.

  Study EGAS50000001638

• Genetic Studies of Chronic Kidney Disease (CKD)

  The Genetic Studies of Chronic Kidney Disease (CKD) is an ongoing genetic research and biobanking protocol which aims to elucidate the genetic basis CKD. The study recruits patients seen at the Columbia University Medical Center (CUMC) Nephrology Division for the evaluation and care of CKD. All patients clinically diagnosed with CKD are eligible to participate; there are no inclusion or exclusion criteria related to age, sex/gender, and/or race/ethnicity. In addition to office visits, patients are recruited in contexts including perinatal care and nonprofit events for patients with various forms of CKD; recruitment tools include bilingual informational brochures, flyers, and consent forms. All individuals provide informed consent; for minors, signature of the parent/guardian is required. Consent includes: use of biosamples given for genetic studies, and the request to be re-contacted if medically actionable genetic findings are identified. In the case of the latter, such research-level findings are first validated in a clinically certified (CLIA) laboratory environment, using a second sample given by the individual at the time of re-contact; following CLIA validation, the individual is once again re-contacted, and, assuming he or she still desires return of these results, they can then be returned. Following the above consent process to participate in the study, individuals provide a single biosample (generally, a venous blood sample), from which DNA is extracted using standard protocols and used for genetic studies, such as exome sequencing. Basic clinical and demographic data, including sex/gender, age, and race/ethnicity are also collected. All data collected is stored in a secure computerized database, with patient samples anonymized using numerical identifiers; the relation of this identifier to patients' names is kept in a locked computer file in a centralized database. Electronic data complies with all HIPAA and other privacy and security regulations, and resides on a firewall server maintained by the CUMC IT department.

  Study phs001828

• Genome Variation among HIV-Resistant People with Hemophilia

  Rare individuals are highly resistant to infection with human immunodeficiency virus (HIV). Studies of candidate genes resulted in the discovery of a 32bp deletion in the CC-chemokine receptor 5 gene (CCR5Δ32), which rendered this critical co-receptor for primary HIV infection to be non-functional. Pharmacologic and vaccine-induced blockade of CCR5 is being pursued to treat and prevent HIV infection and other conditions. The allele frequency of CCR5Δ32 among persons of European ancestry is approximately 10%. CCR5Δ32/Δ32 homozygotes are almost totally resistant to HIV infection. People with severe hemophilia A require frequent replacement with clotting Factor VIII (FVIII) to control hemorrhage. Prior to the discovery of HIV in 1984 and licensure of recombinant FVIII in the late 1980s, people with severe hemophilia A were treated with plasma-derived FVIII and thus were intensively exposed to HIV. Only 5% of such patients were not infected with HIV. Of these, approximately 1/3 were CCR5Δ32/Δ32 homozygotes. The remaining 2/3 of these people who were highly resistant to HIV remain unexplained. This project seeks to discover genome variations among people who are highly resistant to HIV infection. Such variation is likely to serve as a target for reducing the morbidity and incidence of HIV.

  Study phs000445

• Diverse_outcomes_of_controlled_human_malaria_infection_originate_from_host_intrinsic_immune_variation_and_not_var_gene_switching

  Falciparum malaria is clinically heterogeneous and the relative contribution of parasite and host factors in shaping disease severity remains unclear. We set out to explore the interaction between host inflammation and parasite variant surface antigen (VSA) expression, asking whether this relationship underpins the variation observed in controlled human malaria infection. We uncovered marked heterogeneity in the response of naive hosts to blood challenge with some volunteers maintaining a state of immune quiescence, others triggering interferon-stimulated inflammation and a small group showing transcriptional evidence of myeloid cell suppression. Significantly, only inflammatory volunteers experienced hallmark symptoms of clinical malaria. When we then tracked temporal changes in parasite VSA expression to ask whether variants associated with severe disease preferentially expand in naive hosts (as predicted by current theory) we found that var gene profiles were essentially unchanged after 10-days of blood-stage infection. These data therefore show that the diverse clinical outcomes of CHMI largely originate from host-intrinsic variation and there is no evidence for switching or selection of var genes in naïve hosts. 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 EGAS00001003766

• Longitudinal Multi-Omic Immune Resource Reveals Dynamic Responses in Healthy Human Aging

  The generation and maintenance of protective immunity is a dynamic interplay between host and environment that is impacted by age. Understanding fundamental changes in the healthy immune system that occur over a lifespan is critical in developing interventions for age-related susceptibility to infections and diseases. Here, we use multi-omic profiling (scRNA-seq, proteomics, flow cytometry) to examine human peripheral immunity in over 300 healthy adults, with 96 young and older adults followed over two years with yearly vaccination. The resulting resource includes scRNA-seq datasets of >16 million PBMCs, interrogating 71 immune cell subsets from our new Immune Health Atlas. This study allows unique insights into the composition and transcriptional state of immune cells at homeostasis, with vaccine perturbation, under Cytomegalovirus (CMV) infection and across age. We find that T cells specifically accumulate age-related transcriptional changes more than other immune cells, independent from inflammation and chronic perturbation. Moreover, impaired memory B cell responses to vaccination are linked to a Th2-like state shift in older adults' memory CD4 T cells, revealing possible mechanisms of immune dysregulation during healthy human aging. This extensive resource is provided with a suite of exploration tools at https://apps.allenimmunology.org/aifi/insights/dynamics-imm-health-age/ to enhance data accessibility and further the understanding of immune health across age. Please note that the Sound Life Cohort raw data are spread across three dbGap submissions: phs003841.v1 (this study), phs003944.v1, and phs003400.v1.

  Study phs003841

• eMERGE Genome-Wide Association Studies of Obesity (Metabochip)

  The Geisinger eMERGE Genome Wide Association Studies of Obesity (Metabochip) Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery. Roux-en-Y gastric bypass (RYGB) surgery, in which intestinal anatomy is altered, dramatically ameliorates and/or eliminates Type 2 diabetes mellitus (T2D) in 50-80% of patients within hours to days following surgery, well before significant weight loss, in contrast to other types of bariatric surgeries, such as gastric banding, that attenuate insulin resistance as a result of substantial weight loss that occurs over months to years. The molecular mechanism by which RYGB exerts this clinical phenomenon is not known. The goal of this project was to conduct a genome wide association study (GWAS) to identify genetic variants associated with amelioration in T2D defined by medication independence. Identifying genetic variants that influence the dramatic resolution of T2D from RYGB may identify novel targets for pharmacological T2D therapies and/or identify patients in whom RYGB may not be effective.

  Study phs000380

• eMERGE Genome-Wide Association Studies of Obesity

  The Geisinger eMERGE Genome-Wide Association Studies of Obesity Project is a genetic study of a cohort of primarily Caucasian patients with extreme obesity who have undergone bariatric surgery. Roux-en-Y gastric bypass (RYGB) surgery, in which intestinal anatomy is altered, dramatically ameliorates and/or eliminates Type 2 diabetes mellitus (T2D) in 50-80% of patients within hours to days following surgery, well before significant weight loss, in contrast to other types of bariatric surgeries, such as gastric banding, that attenuate insulin resistance as a result of substantial weight loss that occurs over months to years. The molecular mechanism by which RYGB exerts this clinical phenomenon occurs is not known. The goal of this project was to conduct a genome-wide association study (GWAS) to identify genetic variants associated with amelioration in T2D defined by medication independence. Identifying genetic variants that influence the dramatic resolution of T2D from RYGB may identify novel targets for pharmacological T2D therapies and/or identify patients in whom RYGB may not be effective.

  Study phs000408

• Helse Bergen HF Data Access Committee for the MetBreCS trial dataset submitted to Federated EGA Norway

  This Data Access Committee is appointed by Helse Bergen HF to administer access requests for the MetBreCS trial dataset submitted to Federated EGA Norway.

  Dac EGAC50000000523

• ICR Centre for Paediatric Experimental Medicine

  This is the DAC for granting access to consented patient data generated in association with the Centre for Paediatric Experimental Medicine at ICR. Data access can be granted by bioinformatician Claire Lynn: claire.lynn@icr.ac.uk

  Dac EGAC50000000362

• Genomic and transcriptomic profiling of signalling networks in follicular lymphoma

  This dataset is composed of sequencing data from 16 patients diagnosed with follicular lymphoma, who developed transformed disease and for whom representative frozen tumor biopsy samples were available. For 14 patients there is paired material from both disease stages. DNA and RNA libraries were constructed and captured with a kinome bait library (Agilent Technologies), before sequencing on an Illumina platform.

  Study EGAS00001002175

• Genome-Wide Scan for Genetic Variants Associated with Early-Onset Prostate Cancer

  This is a genome-wide association scan of 931 early-onset prostate cancer cases of European ancestry. The samples were selected from prostate cancer studies at the University of Michigan. Controls were previously genotyped individuals selected from the Cancer Genetics Markers of Susceptibility (CGEMS) and Illumina's iControlDB database.

  Study phs001185

• Analysis_of_genomic_integrity_of_disease_corrected_human_induced_pluripotent_stem_cells_by_exome_sequencing

  Induced pluripotent stem (iPS) cells hold great promise for autologous cell transplantation. In order to apply this therapy to monogenic disorder, disease-causing mutations must be corrected prior to transplantation. We generated iPS cells from patients with alpha-1 antitrypsin deficiency, which is caused by homozygous non-synonymous mutation in the SERPINA1 gene. In vitro differentiation of patient-derived iPS cells to hepatocytes showed recapitulation of the disease phenotype. We corrected the mutations by gene targeting using zinc finger nuclease (ZFN) and piggyBac transposon technologies. Our mutation correction is highly accurate. There is no exogenous sequence left behind at the targeted site. The corrected iPS cell-derived hepatocytes were indistinguishable from healthy hepatocyte, suggesting that the corrected gene was fully functional. The genomic integrity was also analyzed by CGH and SNP array, showing no genomic alterations. These are important points to ensure clinical safety as well as functional restoration of the corrected gene. One remaining question is if these corrected iPS cells are clinically safe at the single base-pair level. Recent publications suggested that cancer-related mutations are significantly accumulated during iPS cell propagation. We aim to assess the clinical safety of the corrected iPS cells by using exome sequencing. Outcome from this project would bring iPS cell technology one step closer to clinical applications.

  Study EGAS00001000055

• MutWPX__CRUK_Grand_Challenge_Mutographs_of_Cancer__Effects_of_Chemotherapy_on_the_Somatic_Mutational_Landscape_in_Normal_Human_Tissue___Matched_Normals

  This study is investigating the effects of chemotherapy drugs used in cancer treatment on the somatic mutational landscape in normal human tissues. The samples used in this study have been taken from rapid autopsies of patients who have undergone chemotherapy using drugs thought to cause mutations in the DNA. Structures from a variety of tissues will be dissected using LCM and whole genome sequences will be produced in order to assess mutational burdens and signatures. This study contains the samples used as matched normals for each patient to remove germline mutations.

  Study EGAS00001004957

• Genome-wide NanoRCS sequencing of cfDNA and ctDNA from liquid biopsies of healthy individuals and cancer patients

  Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant molecules, extremely sensitive sequencing methods are required. We developed a new technique, NanoRCS, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule for genome-wide sequencing, and applied this to plasma of healthy individuals, Esophageal cancer patients and Granulosa cell tumor patients and ascites of Ovarian cancer patients. We also sequenced these samples on Illumina Novaseq, to compare the two techniques.

  Study EGAS50000000154

• Construction of endoscopic biopsy banking for understanding the intestinal environment in colorectal diseases and exploratory studies using these banking systems.

  Colorectal cancer is the most common type of cancer in Japan. Although some colorectal cancers have a genetic background, most colorectal cancers are sporadic. Known risk factors for colorectal cancer include smoking, obesity, lack of exercise, and red and processed meat. Furthermore, although it has been suggested that changes in the intestinal environment due to changes in diet and lifestyle may be involved in the increased incidence of colorectal cancer in Japan, the molecular mechanism has not yet been fully elucidated. The main objective of this study is to elucidate the changes in the intestinal environment that cause colorectal tumors, and also to contribute to the establishment of colorectal mucosal tissue banking in Japan.

  Study JGAS000655

• How mitochondrial DNA research can benefit from data reuse through EGA?

  Mitochondria are the only cellular organelles harbouring their own DNA, which encodes for proteins essentials in its respiration process. Despite its discovery in 1960, Mitochondrial DNA is often overlooked compared to nuclear DNA. Indeed, not all sequencing technologies capture a good representation of mtDNA (mitochondrial DNA). Recently, Ed Reznik's team (The Ed Reznik Lab | Memorial Sloan Kettering Cancer Center) carried out a massive analysis and reanalysis of single cells WGS (whole genome sequencing) produced with an amplification-free protocol (Direct library prep, DLP). As they demonstrated in the paper Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes - PMC, DLP is more effective in catching mtDNA compared to classical single-cell sequencing. These data allowed the team to unravel mtDNA dynamics in tumoral and normal samples, highlighting how mtDNA and nuclear DNA are co-regulated and their ratio is critical for phenotype. Data reuse to achieve the greatest results For this project, Reznik's team re-used data from 3 studies stored at the European Genome-phenome Archive (EGAS00001006343, EGAS00001004448 and EGAS00001003190) that comprised a total of 602 datasets. All of them were initially produced by the teams of Sam Aparicio and Sohrab P. Shah at the Memorial Sloan Kettering Cancer Centre, where Ed Reznik is a promising group leader. This demonstrates, once again, that networking, collaboration and data sharing can achieve the greatest results when coupled with innovative and smart ideas. At the EGA we are proud to provide the scientific community with an infrastructure to enable all those very smart ideas out there to find the right data to be tested.

  Blog mitochondrial-dna-research

• PRDM9_loss_of_function_follow_up_from_Born_in_Bradford_Autozygosity_sequencing

  In the autozygosity exome sequencing of Born-in-Bradford samples of Pakistani origin thereis a mother who is homozygous for an apparent truncating stop codon in PRDM9, the generesponsible for localising recombination during meiosis. We plan to deep sequence motherand child with X10, and physically phase the mother with PacBio sequencing.We will use this data to identify recombination locations, and test whether these areconsistent with the known fine scale recombination map.

  Study EGAS00001001301

• Comprehensive Analysis of Structural Variants in Breast Cancer Genomes Using Single Molecule Sequencing

  This study used the SKBR3 breast cell line and tumor/normal organoids derived from breast tissue to explore the utility of long read sequencing for detecting structural variants in complex samples. Three technologies were used to characterize the samples: Illumina/10X, Pacific Biosciences, and Oxford Nanopore. Methylation results were derived from the Oxford Nanopore data. It is hoped that this resource will better help researchers better understand the utility of long read sequencing in cancer samples.

  Study phs002210

• The_British_Autozygosity_Populations_BioResource

  This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes. 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 EGAS00001002742

• exploration of biomarkers discriminating squamous cell carcinoma from other lung cancers

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. The most effective regimen in lung cancers is different between squamous cell carcinoma (SCC) and adenocarcinoma (AD). Therefore a precise diagnosis is crucial, but this has been difficult, particularly for poorly differentiated SCC (PDSCC) and AD without a lepidic growth component (non-lepidic AD). Biomarkers enabling a precise diagnosis are therefore urgently needed. To achieve this goal, we initially performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 97 frozen tissues from surgically resected lung cancers (22 SCC and 75 AD). We furhter expanded the transcriptome profiling to cover additional 48 malignant neoplasm of bronchus and lung, including mesothelioma and metastatic lung cancers derived from other tissues.

  Study JGAS000488

• Effect of Crohn's Disease Risk Alleles on Enteric Microbiota

  This UH2/UH3 demonstration project entitled "Effects of Crohn's disease risk alleles on enteric microbiota" is focused on characterizing intestinal associated microbiota in patients with ileal Crohn's disease (ileal CD), ulcerative colitis (UC) and control patients without inflammatory bowel diseases (non-IBD). We hypothesize that genetic factors that affect Paneth cell function, contribute to compositional changes in intestinal microbiota. These changes in microbiota may lead to reduction of protective commensal organisms and increased numbers of aggressive organisms that incite intestinal inflammation. This hypothesis is being tested by high throughput 16S rRNA sequence analysis of de-identified ileal and colonic tissues that have been archived at Washington University St. Louis, University of North Carolina, Mount Sinai Hospital and the Cleveland Clinic. Multivariate analysis of the metagenomic data will be conducted with genotyping metadata (highly reproducible CD risk alleles, including NOD2 and ATG16L1) and phenotyping metadata (e.g. age, gender, race, body mass index, medications and smoking.) Shotgun sequencing will be performed on selected fecal specimens linked to ileal tissues to identify additional, or auxiliary, or synergistic pathogenic factors or other functional changes in the microbiome. Because members of this research team have observed that a chronic viral infection is required for the Paneth cell defect in Atg16l1 hypomorphic mice, a major focus of these studies will be towards identifying potential viral triggers for the defective Paneth cell phenotype in individuals harboring the ATG16L1 risk allele. Novel genetic probes for protective and aggressive organisms will be developed by mining bacterial genome and shotgun sequencing data. Genomic sequences will be produced for candidate protective and aggressive strains (e.g. adherent-invasive strains of E. coli) isolated from human intestinal tissues where there is limited existing genome information. Quantitative qPCR assays using the novel as well as established genetic probes will be conducted to test the hypothesis that an imbalance between protective and aggressive organisms is associated with genetic factors that affect Paneth cell function. Our combined expertise in multiple disciplines across multiple institutions, our demonstrated ability to collect a large number of well-phenotyped samples with longitudinal clinical information that will be linked to host response and morphologic studies, and our consortium's capacity for high-throughput sequencing will be used to investigate how alterations in human microbiome relate to CD risk alleles and CD pathogenesis.

  Study phs000255

• Creatine in Huntington's Disease (HD) (CREST-E)

  This is a multi-center, randomized, double-blind, placebo-controlled trial of creatine monohydrate involving 553 ambulatory subjects with HD who are not requiring skilled care or institutionalization. Eligible subjects were randomized to receive up to 40 grams daily of creatine monohydrate or matching placebo. Randomization will be followed by a Titration Phase, a Maintenance Phase, an Optional Extended Maintenance Phase, and Washout. During the Titration Phase, which may last up to six months, study drug will be initially escalated in 5-gram increments starting at 5 g/day until the 40 g/day target dose is reached. Should subjects be unable to reach or stay at the maximum dose during the Titration Phase, they will remain on the highest tolerated dose (HTD) for which they have no significant side effects. During the Maintenance Phase, subjects will be followed prospectively and systematically. Subjects completing 36 months of follow-up on study drug will be eligible to continue in the study for an additional twelve months of follow-up in the Extended Maintenance Phase. The primary measure of efficacy is the annualized rate of change in TFC. The primary hypothesis of the study is that chronic treatment of early-stage HD subjects with creatine monohydrate will slow the progressive functional decline of HD.

  Study phs001488