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• Whole_genome_sequencing_of_100_DDD_trios_with_suspected_noncoding_causal_mutations

  We would like to whole-genome sequence 100 trios (300 individuals) from the DDD project in which we suspect the proband has a pathogenic noncoding mutation, to 30X coverage. These have been carefully selected to maximise the chances of finding pathogenic noncoding mutations. Specifically, we have selected probands who have no likely causal mutation within the coding region but who have a heterozygous loss-of-function mutation inherited from one parent in a known recessive developmental disorder gene, and whose phenotype is a good match for the typical phenotype caused by recessive variants in that gene. We suspect that these probands may have a heterozygous noncoding mutation on the other allele which reduces expression of the gene so that, together, these two mutations are effectively equivalent to a homozygous loss-of-function mutation. About a quarter of the probands have affected siblings and, if those siblings have been exome sequenced, we have checked that they are identical-by-descent in the region of the gene. We propose to search in the promoter region, intronic and annotated regulatory regions around these genes of interest for rare variants inherited from the other parent (i.e. not the one who transmitted the loss-of-function variant), or de novo variants. If we find such variants, and demonstrate an enrichment of this compound heterozygous LoF noncoding mechanism above that expected by chance, we intend to follow up specific candidates by RNAseq and potentially CRISPR/Cas9 experiments. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002452

• Genomic Studies of Bipolar Disorder in a Large Cohort from The Netherlands

  The transcriptomes of whole blood samples of a large cohort of individuals from the Netherlands were assayed using RNA-seq. These whole blood samples included patients diagnosed with schizophrenia or bipolar disorder, family members of patients, and healthy controls. Within the whole blood dataset, about 600 of the samples were sequenced to an average of 13.9 million mapped reads per sample, while about 2,000 were sequenced to an average of 5.9 million mapped reads per sample, in order to assess changes in power to detect eQTLs based on sample size. We find that expression, defined as the log transcripts per million reads (TPMs), is highly correlated when comparing the moderate (13.9M) and lower (5.9M) coverage datasets. Additionally, a subset of about 150 individuals provided fibroblast cell lines which were assessed for the levels of gene expression using RNA-seq at an average of 50 million mapped reads per sample. We use downsampling techniques to generate synthetic datasets derived from this real fibroblast RNA-Seq data to explore the relationship between coverage and number individuals in an eQTL analysis. Corresponding individual-level genotypes for the samples included in the expression matrix are also made available. The genotypes were derived from multiple other project cohorts, each using different genotyping platforms including OmniExpress Exome, Global Screening Array, Illumina550, and PsychChip. A Plink file set of these cohorts is provided here after merging the separate project file sets and extracting only the individuals who have expression data also provided here; quality control for SNP-missingness is recommended. We demonstrate in this study that given a fixed budget, eQTL discovery power can be increased by lowering the sequencing depth per sample to allow for an a greater number of individuals sequenced. 

  Study phs002856

• PROstate Cancer Medically Optimized Genome Enhanced ThErapy (PROMOTE) of Castration Resistant Prostate Cancer (CRPC) Patients Treated with Abiraterone Acetate

  The Prostate Cancer Medically Optimized Genome-Enhanced Therapy (PROMOTE) study uses genetic clues in castration-resistant prostate cancer that may identify an individualized treatment approach for men with the disease. Understanding the molecular biology behind castration-resistant prostate cancer has led to more treatment options, but there are still no definite conclusions about which specific drug best treats patients - maximum suppression of cancer growth while minimizing side effects. The PROMOTE study explores the genetic characteristics of each tumor to predict these treatment paradigms for the future, resulting in more effective and less toxic options for patients. Our long-term goal is to improve treatments for men with advanced prostate cancer by using genomic sequencing to increase life span and quality of life. We also will uncover novel vulnerable targets in the cancer genome that may provide new drug therapies. PARTICIPATION Eligible participants are men: With castration-resistant prostate cancer or prostate cancer not responding to hormone treatments About to begin abiraterone acetate therapy Agreeable to undergoing two tumor biopsies During the study, participants travel to Mayo Clinic for an initial biopsy (before beginning abiraterone acetate) and a second biopsy approximately three months later. The cell tissue collected is analyzed to identify gene alterations in the tumor that could eventually be targeted with treatments. Tissue is preserved for future research. Participants can continue to be treated by their local cancer care team during this period and beyond. In addition, the Mayo team carefully monitors participants' cancer via follow-up studies and the genetic signature of tumors that were biopsied so that patients may benefit from future treatments.

  Study phs001141

• Intraductal transplantation models of human pancreatic ductal adenocarcinoma reveal progressive transition of molecular subtypes

  Pancreatic ductal adenocarcinoma (PDAC) is the most lethal common malignancy, with little improvement in patient outcomes over the past few decades. Recently, subtypes of pancreatic cancer with different prognoses have been elaborated. However, the inability to model these subtypes has precluded mechanistic investigation of their origins. Here, we present an orthotopic xenotransplantation model of human patient-derived PDAC organoids in which organoids are grafted via direct injection into the pancreatic duct of immunocompromised (NSG) mice. Tumors that arise from these intraductally grafted organoids (IGOs) enable the distinction of the two main PDAC subtypes: intraepithelial neoplasms from this model progress in an indolent or invasive manner representing the classical or basal-like subtypes of PDAC, respectively, depending on which organoid they originate from. RNA-sequencing was used to characterize the tumors that resulted from IGO xenografts, and to compare the fast- and slow-progressing IGO tumors. Tumors generated using a traditional orthotopic xenograft model, in which organoids are injected into the parenchyma of the pancreas (i.e. orthotopically grafted organoids, or OGOs), were also sequenced for comparison with the IGO tumors. To further characterize the model, laser-capture microdissection followed by RNA-sequencing was used to compare intraductal to invasive lesions resulting from IGOs. To better understand the connection between KRAS signaling and the fast-progressing phenotype, RNA-sequencing was used to compare cultured organoids in which oncogenic KRAS (GeneID: 3845) was hyperactivated to control organoids, and to compare laser-capture microdissected lesions derived from IGOs of KRAS-hyperactivated organoids to lesions derived from control organoids. To ascertain copy number, low-coverage, whole genome DNA-sequencing was performed on organoids cultured in vitro, and on laser-capture microdissected lesions derived from IGO tumors.

  Study phs002045

• Human Gene Expression Patterns Associated with Experimental P. falciparum Infection

  Description: Experimental exposure to malaria parasites can lead to development of protective immunity, providing a foothold for the development of a malaria vaccine. The goal of this study is to investigate immune transcriptional profiles associated with malaria protective immune responses induced by experimental Chemo-Prophylaxis and Sporozoites (CPS) immunization of P. falciparum-naive human volunteers. Samples for this study were obtained from a CPS-immunization study conducted in 2011 (ClinicalTrials.gov Identifier: NCT01218893), where healthy volunteers received CPS-immunization with bites from different numbers of P. falciparum-infected mosquitoes (three times 15 (n=5), 10 (n=9) or 5 (n=10)). Five control subjects received uninfected mosquito bites under chloroquine prophylaxis. Fifteen weeks after discontinuation of chloroquine prophylaxis, all volunteers were challenged by exposure to infected mosquito bites. Study Design: A maximum of 30 volunteers were divided into four groups. All volunteers received weekly chloroquine prophylaxis for a period of 13 weeks (91 days). During these 13 weeks, on days 8, 36 and 64 they were exposed to the bites of 15 mosquitoes. Group 1 (n=5, positive control) received three CPS immunizations by 15 mosquitoes infected with P. falciparum sporozoites. Group 2 (n=10) received three times 10 bites from infected mosquitoes and 5 bites from uninfected mosquitoes. Group 3 (n=10) received three times 5 bites from infected mosquitoes and 10 bites from uninfected mosquitoes. Group 4 (n=5), the negative control, received three placebo immunizations with 15 bites of uninfected mosquitoes. Fifteen weeks after discontinuation of chloroquine prophylaxis, all 30 volunteers were challenged at day 196 by the bites of 5 infectious mosquitoes and followed for 21 days. All subjects were treated with chloroquine 21 days after challenge or whenever they had a positive thick smear during that period.

  Study phs001346

• A Population Genomics Study Using a Disease-Targeted Cell model: Integration of

  The common genetic variants associated with complex traits typically lie in non-coding DNA and may alter gene regulation in a cell type-specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an expression quantitative trait loci (eQTL) study of primary human osteoblasts (HOb) derived from 95 unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. We combined our data with publicly available information from a genome-wide association study (GWAS) of bone mineral density (BMD). The top 2000 BMD-associated SNPs were tested for cis-association of gene expression in HObs and in lymphoblastoid cell lines (LCLs) using publicly available data and showed that HObs have a significantly greater enrichment (threefold) of converging cis-eQTLs as compared to LCLs. The top 10 BMD loci with SNPs showing strong cis-effects on gene expression in HObs were selected for further validation using a staged design in two cohorts of Caucasian male subjects. All 10 variants were tested in the Swedish MrOS Cohort (n = 3014), providing evidence for two novel BMD loci (SRR and MSH3). These variants were then tested in the Rotterdam Study (n = 2090), yielding converging evidence for BMD association at the 17p13.3 SRR locus. The cis-regulatory effect was further fine-mapped to the proximal promoter of the SRR gene (rs3744270). Our results suggest that primary cells relevant to disease phenotypes complement traditional approaches for prioritization and validation of GWAS hits for follow-up studies. Reprinted from Grundberg E, Kwan T, Ge B et al., Genome Res Nov 2009, with permission from Genome Research, Cold Spring Harbor Press, PMID:19654370.

  Study phs000225

• ChiLDReN/BA: Genetic Studies of Biliary Atresia in the Childhood Liver Disease Research Network

  Biliary atresia (BA) is a progressive necroinflammatory process initially involving the extra-hepatic biliary tree. Little is known about the factors that cause BA or the factors that influence disease progression. A variety of genetic, autoimmune, and environmental influences have been hypothesized to be important. Most studies to date have focused on the neonate and young child with BA, yet the older surviving child with BA can provide important information about genetics as well as natural history.The Childhood Liver Disease Research Network (ChiLDReN) conducts two longitudinal and observational studies that include BA patients: Biliary Atresia Study in Infants and Children (BASIC) and A Prospective Database of Infants with Cholestasis (PROBE). Using samples from participants in these two protocols, we have formed the largest known data set of biliary atresia patients in the world. ChiLDReN is performing a series of genomic analyses, with subsequent analyses being released as subsequent versions of this registration, phs003356. Version 1 concerns PKD1L1.About the PKD1L1 Analysis (phs003356.v1): While multiple factors have been implicated in the perinatal biliary injuries that characterize BA, a definitive etiology has not yet been established. This study is part of a larger project to characterize the largest cohort of pediatric BA patients through whole-exome sequencing (WES). In this analysis, we examine the WES of those with various laterality defects to determine whether genetic factors could be identified to explicate the etiopathogenesis of BA in biliary atresia splenic malformation (BASM) syndrome. We specifically explored variations in the PKD1L1 gene, which recently has been identified in mouse models as playing a role in laterality.

  Study phs003356

• Genetic Investigations of Attention-Deficit/Hyperactivity Disorder

  Design and Aims:We conducted whole-exome DNA sequencing on 152 parent-child trios (456 individuals total) that included a child meeting DSM-IV or DSM-5 criteria for ADHD along with both biological parents to identify rare de novo damaging DNA variants associated with ADHD risk. Mutation rates were compared between 147 ADHD trios and 780 unaffected control trios. We aimed to identify specific ADHD risk genes by combining the de novo trio data with rare variant data from an independent case-control cohort.Population Information:ADHD trios were collected from four sites. The 780 control trios were unaffected siblings from the Simons Simplex Collection who scored in the normal range on the Child Behavior Checklist (CBCL) or Adult Behavior Checklist (ABCL) ADHD subscale.Molecular Technologies:Whole-exome DNA sequencing was performed on the ADHD trios using the IDT xGen V1 or Agilent SureSelect All Exon V7 capture and the Illumina NovaSeq6000 sequencer. Control trios were previously sequenced with the NimbleGen SeqCap EzExomeV2 capture and Illumina HiSeq 2000 sequencer. Joint variant calling was performed for all trios. Rare de novo variants with allele frequency Principal Findings:We found a 1.67-fold enrichment of rare de novo damaging variants and a 1.93-fold enrichment of ultra-rare de novo damaging variants in ADHD cases vs controls. By integrating the de novo data with an independent case-control cohort, KDM5B was identified as a high-confidence ADHD risk gene (FDR=0.04). Three potential risk genes were also identified. Twenty-three genes with ultra-rare damaging de novo variants in ADHD overlapped with previously reported risk genes for other neuropsychiatric conditions. Exploratory analyses showed enrichment of these genes in early neurodevelopmental pathways.

  Study phs003647

• Analysis of CD20 loss in patients treated with Mosunetuzumab

  CD20 is an established therapeutic target in B-cell malignancies. The CD20xCD3 bispecific antibody mosunetuzumab has significant efficacy in B-cell non-Hodgkin lymphomas (NHL). Since target antigen loss is a recognized mechanism of resistance, we evaluated the contribution of CD20 expression to clinical response in patients with relapsed and/or refractory NHL in the phase 1/2 GO29781 trial (ClinicalTrials.gov: NCT02500407) investigating mosunetuzumab monotherapy. CD20 was studied using immunohistochemistry (IHC), RNA sequencing, and whole-exome sequencing performed centrally in biopsies collected prior to treatment, or as paired samples at pre-dose and on-treatment, or at-progression. Prior to treatment, most patients exhibited a high proportion of tumor cells expressing CD20; however, the proportion of CD20+ tumor cells in 14/293 (6%) patients was <10%. Analyses of paired biopsies from patients during treatment revealed that CD20 levels were maintained in 29/30 (97%), vs patients with samples at-progression, in which 11/32 (34%) showed CD20 loss. Reduced transcription or acquisition of truncating mutations explained most but not all cases of CD20 loss. In vitro modeling confirmed the effect of CD20 variants identified in clinical samples on reduction of CD20 expression and confirmed missense mutations in the extracellular domain that could block mosunetuzumab binding. This study expands knowledge about the occurrence of target antigen loss after anti-CD20 therapeutics to CD20-targeting bispecific antibodies and elucidates the underlying mechanisms for reduced CD20 expression at disease progression that may be generalizable to other anti-CD20 targeting agents. These results also establish the utility of readily-available IHC staining for CD20 as a tool to inform clinical decisions.

  Study EGAS50000000151

• Repeat expansions with small TTTCA insertions in MARCHF6 cause Familial Adult Myoclonus without Epilepsy

  Familial Adult Myoclonic Epilepsy (FAME) is a rare autosomal dominant disorder characterized by cortical tremulous myoclonus and generalized tonic clonic (GTCS) or myoclonic seizures. Intrafamilial variability regarding the prevalence of seizure has been reported. Despite apparent genetic heterogeneity, FAME is caused by the same TTTTA/TTTCA pentanucleotide repeat expansion in introns of seven different genes with no common function. Expansions containing only TTTTA repeats are benign, and only expansions including a TTTCA expansion insertion, which can be located 3' to the TTTTA expansion or in the middle of the TTTTA repeats, are pathogenic. We aimed to identify the underlying genetic cause of dominant cortical myoclonus without GTCS in two unrelated families. We used a combination of repeat-primed PCR, long-range PCR and nanopore sequencing to detect and characterize expansions at known FAME loci. We report a novel configuration of the FAME3 repeat expansion in MARCHF6 segregating with cortical myoclonus without epilepsy GTCS in both families. This expansion predominantly comprises elongated TTTTA repeats, ranging from 388 to 454 repeats, with the presence of only 5-11 TTTCA repeats at its 3' terminus (i.e., 5’-(TTTTA)~388-454(TTTCA)5-11-3’). This configuration exhibits greater stability upon meiotic transmission but somatic variability in TTTCA repeat number was detected at low level in blood. We observed an inverse correlation between the number of TTTCA repeats and the age at myoclonus onset. This study shows that as little as five TTTCA juxtaposed with expanded TTTTA expansions is sufficient to cause cortical myoclonus without GTCS. This finding has implications regarding possible pathophysiological mechanisms leading to FAME.

  Study EGAS50000000570

• EGA account management

  How to manage your EGA account Welcome to the documentation page for creating an EGA user. The European Genome-Phenome Archive (EGA) is a platform for archiving, managing, and sharing human genomic and phenotypic data. To submit, access, and manage requests for the data hosted on the EGA platform, users are required to register for an account. This documentation page provides step-by-step instructions for creating an EGA user account, as well as information on the different types of EGA user accounts and their associated privileges. You can check the EGA data flow for a better understanding. Manage EGA account step-by-step guide Contact Information Public Keys Password Authenticator Federated Identity Sessions Request an EGA account step-by-step guide Fill in this form.You cannot use a generic email account (e.g., Gmail). Make sure you use your institutional email account.Your email is by default your username.The criteria for a strong password is: It should contain between 8 and 32 charactersIt should contain at least one uppercase letterIt should contain at least one numberIt should contain at least one special characterYou will need to wait for the Helpdesk team to check your identity. Please allow two business days for this step.After the Helpdesk validation step, you will receive an email with a link to validate your institutional email.Click the link to verify your email. It will redirect you to the EGA website.As soon as your account has been validated, you will be able to start adding more information to your EGA profile. For that, you first need to log in using your credentials from step 1. Manage EGA account step-by-step guide As a logged-in user, go to your profile by clicking on Welcome > My Profile. To modify it, click the Edit button.You will see the following options: Contact Information In this section, you can modify the personal information of your EGA account. Public Keys Adding a public key is necessary for downloading data via Live Outbox distribution. If you don’t know how to generate your key, you can follow the instructions available on How do I create a key? Password In the Password tab, you can change your password anytime to ensure the security of your account. However, if you receive an email notifying you that your password was modified and you did not initiate the change, it could be a sign that your account has been compromised. In this case, you should immediately contact our Helpdesk team to report the issue and receive assistance in restoring your account security. Authenticator You can set your two-factor authentication (2FA) system for your EGA account as an identity and access management security method that requires two forms of identification to access resources and data. To obtain your code, please follow the instructions below, also available in the Authenticator tab in your profile. Sessions The Sessions tab displays a list of all devices where you are currently logged in as an EGA user. This includes any open sessions you have on your computer, phone, or other devices. By reviewing the list of active sessions, you can monitor the devices that have access to your account and ensure that there are no unauthorised logins. If you notice any suspicious activity, you can close the sessions from this page to immediately terminate access to your account from the unauthorised device.

  Documentation how-to-manage-your-account

• Genesis of Two Most Prevalent Variants Causing Combined Pituitary Hormone Deficiency in 21 Populations

  Two variants (c.[301_302delAG];[301_302delAG] and c.[150delA];[150delA]) in the PROP1 gene are the most common genetic causes of recessively inherited combined pituitary hormones deficiency (CPHD). Our objective was to analyze in detail the origin of the two most prevalent variants. In the multicentric study were included 237 patients with CPHD and their 15 relatives carrying c.[301_302delAG];[301_302delAG] or c.[150delA];[150delA] or c.[301_302delAG];[ 150delA]. They originated from 21 different countries worldwide. We genotyped 21 single nucleotide variant markers flanking the 9.6Mb region around the PROP1 gene that are not in mutual linkage disequilibrium in the general populations - a finding of a common haplotype would be indicative of ancestral origin of the variant. Haplotypes were reconstructed by Phase and Haploview software, and the variant age was estimated using an allelic association method. We demonstrated ancestral origin of both variants: c.[301_302delAG] was carried on 0.2Mb-long haplotype in a majority of European patients arising approximately 101 generations ago (confidence interval 90.1-116.4). Patients from the Iberian Peninsula displayed a different haplotype which was estimated to have emerged 23.3 (20.1-29.1) generations ago. Subsequently, the data indicated that both haplotypes were transmitted to Latin American patients approximately 13.8 (12.2-17.0) and 16.4 (14.4-20.1) generations ago, respectively. The c.[150delA] variant that was carried on a haplotype spanning about 0.3Mb was estimated to appear 43.7 (38.4-52.7) generations ago. We present strong evidence that the most frequent variants in the PROP1 gene are not a consequence of variant hot-spots as previously assumed, but are founder variants.

  Study EGAS00001001165

• Whole genome sequencing of a breast cancer cohort with known functional homologous recombination status

  Optimal patient selection for PARP inhibitors and double strand break (DSB) inducing chemotherapy is of great clinical importance. In principle, the use of these therapies can be extended beyond germline BRCA1/2 mutated cancers. Although several methods for detection of BRCA-like tumors have been developed, a golden standard is lacking. We have developed the RECAP test, a functional HR assay exploiting the formation of RAD51 foci in proliferating cells after ex vivo irradiation of fresh primary breast cancer (BrC) tissue. The RECAP test seems robust and has an advantage over genetic tests, due to its functional character for exploring the HR phenotype. Another type of HRD test is the BRCAness classifier, which is based on specific genomic patterns derived from copy number data of BRCA1/2 mutated BrCs that also occur in sporadic cancers. The BRCAness classifier is a robust test that is easily applicable in the clinic and has also been validated to predict in vivo response to high dose chemotherapy in clinical trials. More recently, a new HRD test based on genomic signatures which can be extracted from whole genome sequencing has been published, HRDetect. Studies comparing these different HRD tests within the same cohort of patients do not yet exist. Here, we have the unique opportunity to compare three HRD tests within the same cohort. We aim to compare three different HRD tests (RECAP, BRCAness classifier and HRDetect) within the same cohort of primary BrCs (n=41). As a secondary aim, we will analyze additional genetic alterations in HRD tumors (both BRCA-deficient and BRCA-proficient HRD tumors).

  Study EGAS00001005572

• Single_cell_measurements_to_characterise_B_cell_repopulation_in_SLE_after_rituximab_therapy__a_pilot_study

  Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterised by autoantibodies against DNA and nuclear proteins. Kidney involvement (lupus nephritis) is one of the most serious manifestations and is the leading determinant of long-term prognosis. Therapies targeting B cells (e.g. rituximab) are used in the treatment of severe lupus, including lupus nephritis. Rituximab is a monoclonal antibody that targets the CD20 surface protein on the surface of B cells. Following rituximab treatment, there is near complete depletion of B cells in peripheral blood. Peripheral blood B cells slowly return over a period of months. The speed of repopulation varies but typically B cells have returned to baseline levels between 9 and 12 months post rituximab therapy. Return of B cells may be associated with increased disease activity, but this is not always the case. For example, some patients remain in clinical remission for several years following one cycle of rituximab, despite B cell repopulation, whilst others relapse as soon as the B cell number reaches the normal range. The reasons for the different response remain unclear. The B cell subpopulations that return following B cell depleting therapy have been previously studied using flow cytometry but have never been characterised using single cell -omic technologies and thus no data on their molecular signatures are available. Previous studies have shown that naïve B cells were the predominant repopulating B-cells, indicating de novo production of B cells. Obtaining an integrated understanding of the molecular programs of these cells at the single cell level will enhance our ability to predict disease outcome, to identify patients with poorer B-cell drug responses, understand disease heterogeneity and design more effective B-cell targeted therapies approach.

  Study EGAS00001006798

• Analysis of T-cell receptor clonotypes in tumor micro-environment identifies shared cancer type-specific signatures

  Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias towards the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T-cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus- driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T-cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (ie viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer, but in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific motifs that were unique to each cancer type, suggesting they may be enriched for specificity to common antigens found in the tumor microenvironment. The identification of shared TCRs in infiltrating tumor T-cells not only adds to our understanding of the tumor adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.

  Study EGAS00001005480

• A catalog of the genetic causes of Hereditary Angioedema in the Canary Islands (Spain)

  Hereditary angioedema (HAE) is a rare disease where known causes involve C1 inhibitor dysfunction or dysregulation of the kinin cascade. The updated HAE management guidelines recommend performing genetic tests to reach a precise diagnosis. Unfortunately, genetic tests are still uncommon in the diagnosis routine. Here, we characterized for the first time the genetic causes of HAE in affected families from the Canary Islands (Spain). Whole-exome sequencing data was obtained from 41 affected patients and unaffected relatives from 29 unrelated families identified in the archipelago. The Hereditary Angioedema Database Annotation (HADA) tool was used for pathogenicity classification and causal variant prioritization among the genes known to cause HAE. Manual reclassification of prioritized variants was used in those families lacking known causal variants. We detected a total of eight different variants causing HAE in this patient series, affecting essentially SERPING1 and F12 genes, one of them being a novel SERPING1 variant (c.686-12A>G) with a predicted splicing effect which was reclassified as likely pathogenic in one family. Altogether, the diagnostic yield by assessing previously reported causal genes and considering variant reclassifications according to the American College of Medical Genetics guidelines reached 66.7% (95% Confidence Interval [CI]: 30.1-91.0) in families with more than one affected member and 10.0% (95% CI: 1.8-33.1) among cases without family information for the disease. Despite the genetic causes of many patients remain to be identified, our results reinforce the need of genetic tests as first-tier diagnostic tool in this disease, as recommended by the international WAO/EAACI guidelines for the management of HAE.

  Study EGAS00001006547

• Gene expression and Cancer

  Dac EGAC00001001727

• CHIP and LOY in AD

  Dac EGAC00001003606

• Genomewide Association Study of Inflammatory Bowel Disease

  WTCCC genome-wide case-control association study for Inflammatory Bowel Disease (IBD) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000006

• WTCCC case-control study for Rheumatoid Arthritis

  WTCCC genome-wide case-control association study for Rheumatoid Arthritis (RA) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000011

• WTCCC case-control study for Type 1 Diabetes

  WTCCC genome-wide case-control association study for Type 1 Diabetes (T1D) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000014

• WTCCC case-control study for Type 2 Diabetes

  WTCCC genome-wide case-control association study for Type 2 Diabetes (T2D) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000016

• WTCCC case-control study for Coronary Artery Disease

  WTCCC genome-wide case-control association study for Bipolar disorder (CAD) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000003

• EGAD00010000766

  We have established a mechanism for the collection of postal DNA samples from consenting National Joint Registry for England and Wales (NJR) patients and have carried out genotyping genome-wide in 903 patients with the condition Developmental Dysplasia of the Hip (DDH) on the Illumina CoreExome array

  Dataset EGAD00010000766

• Evaluation of size selection on cancer specific sequencing libraries

  A couple of previously characterized and sequenced libraries will be repeated using a couple of differing size selection criteria and skim sequenced using an Illumina HiSeq. The resulting sequence will be analyzed to determine the optimal DNA library size for our specific downstream analysis.

  Dataset EGAD00001000301

• Paroxysmal Neurological Disorders - rare epilepsies

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Dataset EGAD00001000647

• COLONOMICS small RNA sequencing

  This dataset consists of SOLiD small RNA-seq of 250 colorectal samples: 100 tumor tissue samples, 100 normal tissue samples (adjacent to tumor sites) and 50 matched control samples of healthy individuals. CSfasta and qual files converted to single fastq files prior to uploading.

  Dataset EGAD00001004827

• Exome sequencing for heterogeneity and evolution of DNA mutation rates

  Dataset comprising 27 pairs of high-depth (300x) WES results obtained from 54 PDXs derived from primary CRCs resected synchronously with their corresponding metastases. These exoms sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Dataset EGAD50000000208

• INCLIVA-CC-WES

  This dataset consists of WES NGS paired-end raw data (FASTQ R1, R2 and UMI sequence) obtained from 25 localised colon cancer patients. Specifically, we have 25 primary tumor tissue samples, 17 metastatic tissues, 25 white blood cell samples, 25 plasma samples collected at relapse, 12 baseline plasma samples and 15 plasma samples post-surgery.

  Dataset EGAD50000000293

• Whole exome sequencing of preneoplasia lung adenocarcinoma

  Multi-region exome sequencing of 271 pulmonary nodules and matched adjacent lung tissue including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=49), adenocarcinoma in situ (AIS, N=42), minimally invasive adenocarcinoma (MIA, N=37), invasive lung adenocarcinoma (ADC, N=86) and adjacent lung tissues (Normal, N=57).

  Dataset EGAD50000000397

• Human Brain Small Extracellular Vesicles Contain Selectively-Packaged, Full-Length mRNA

  sEVs were isolated from postmortem human brain tissue. RNA was extracted from the source brain tissue and the sEVs and prepared for RNA sequencing. cDNA was sequenced on the Illumina HiSeq using a 2x150 paired-end read configuration.

  Dataset EGAD50000000042

• Genetic Heterogeneity of Diffuse Large B Cell Lymphoma

  We sequenced exomes of 94 DLBCL tumors and cell lines. 34 of the tumors had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in DLBCL.

  Study phs000573

• ctDNA diva aggregate data

  ctDNA biomarker and relevant clinical data for divarasib phase I GO42144 study, including tumor type, KRAS G12C mutation detectability in plasma at baseline, baseline SLD, sites of metastasis, lines of therapy, best response, confirmed best response, PFS, ctDNA tumor fraction and KRAS G12C VAF at baseline/C1D15/C3D1.

  Dataset EGAD50000000454

• Haukeland University Hospital Data Access Committee for ParkOme-1 datasets archvied in Federated EGA Norway

  Data Access Committee appointed by Haukeland University Hospital for omics datasets for Parkinson's disease and related disorders, generated in studies under the ParkOme-1 project. Omics datasets of different types are generated from fresh frozen brain tissue from individuals with neurodegenerative parkinsonisms and neurologically healthy controls.

  Dac EGAC50000000193

• The evolution of ovarian high grade serous carcinoma from STIC lesions

  We performed shallow whole genome sequencing of normal fallopian tube, stroma, p53 signatures, STIL/STIC, invasive and metastasis carcinoma from 5 high grade serous carcinoma cases.

  Study EGAS50000000360

• ERa ChIP-seq in breast healthy, primary cancer and metastatic tissues

  ChIP-seq has been perfomed on fresh-frozen tissue derived from healthy breast (HB), primary breast cancer (PB), BCa-derived liver metastasis (LM). Immunoprecipitation has been performed for ERa (sc-542, SantaCruz). Raw paired-end fastq.gz files are provided for both immunoprecipitated DNA and input samples.

  Dataset EGAD50000000642

• Prognostic whole-genome and transcriptome signatures in colorectal cancers

  This dataset consists of RNA-seq CRAM raw-data files of 1063 primary colorectal cancer and 120 adjacent normal tissue samples. The expression profiles for these samples can be found at the ArrayExpress with accession number E-MTAB-12862.

  Dataset EGAD50000000169

• Dataset for acute myeloid leukemia samples

  This dataset contains RNA, ATAC and WGS sequencing data of 9 acute myeloid leukemia samples. Sequencing was performed on Illumina HiSeq 2000, HiSeq 4000, NovaSeq 6000 and HiSeq X Ten. The sequencing was always paired.

  Dataset EGAD50000000175

• snRNA and snATAC analysis of human cocaine use disorder in caudate nucleus

  The dataset contains raw data from 10x Multiome derived single-nuclei RNA and single-nuclei ATAC sequencing in the same cells

  Dataset EGAD50000000691

• DAC-2020-03-26-Lemola (DAC-039))

  This is only the location. For the raw data and any check if the dataset may be relevant please refer to the Harvard Dataverse (https://dataverse.harvard.edu/dataverse/lemola).

  Study EGAS50000000635

• LRS - episignature samples

  This dataset contains 22 long-read WGS fastq.gz files sequenced ONT PromethION. In total the dataset includes 20 individuals, for all of them sequencing starting from blood was performed, and for one of the samples sequencing from urine and from the buccal swab was also included. In all the samples methylation calls are included in the fastq file.

  Dataset EGAD50000001000

• Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms

  To elucidate the heterogeneity of tumour immune cell infiltration, we performed single cell RNAseq sequencing on CD45+ cells enriched from matched fresh tumour tissue following surgical resection of 12 treatment-naïve patients and matched PBMCs.

  Dataset EGAD50000001008

• Saliva Microbiota of Finnish children from the PANIC study

  Saliva Microbiota of Finnish children aged between 6-8 yrs in the PANIC study. Baseline data. Studied for various lifestyle conditions and oral diseases (without caries/with caries).

  Study EGAS50000000708

• Sant Joan de Déu Research Institute (IRSJD)

  Sant Joan de Déu Research Institute (IRSJD) institutional Data Access Committee. The objective of the DAC is to manage, review and assess datasets access requests. The DAC is managed by the Knowledge Management Unit, and an adhoc committee per dataset will be formed to take into consideration each access request. Contact the Knowledge Management Unit at gestio.coneixement@sjd.es

  Dac EGAC50000000253

• Single-cell RNA-sequencing data of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons, to define the molecular response of astrocytes to misfolded alpha-synuclein.

  Samples were derived from an human iPSC-derived astrocyte line, both alone and in co-culture with neurons +/- alpha-synuclein oligomer treatment.

  Dataset EGAD50000001110

• Sahel Data Access Committee

  Genome-wide genotype array data of Fulani populations presented in Fortes-Lima et al. 2025. Citation: Population History and Admixture of the Fulani People from the Sahel. Cesar A. Fortes-Lima, Mame Y. Diallo, Václav Janoušek, Viktor Černý, and Carina M. Schlebusch. American Journal of Human Genetics 112(2), February 6, 2025. doi: https://doi.org/10.1016/j.ajhg.2024.12.015

  Dac EGAC50000000290

• Whole exome sequencing of ETV::RUNX1 positive acute lymphoblastic leukemia

  This dataset contains whole exome sequencing of ETV::RUNX1 positive acute lymphoblastic leukemia. Germline and leukemia samples were sequenced in pairs. A total of 94 samples were sequenced and reads were aligned to hg19 genome reference. Aligned bam files are provided in this data set.

  Dataset EGAD50000001184

• Paired RNA sequencing of Thymic epithelial tumors - Additional Dataset

  Paired RNA sequencing of additional samples of Thymic epithelial tumors. Uploaded are the paired fastq files, sequencers were Illumina HiSeq 2500, HiSeq 4000, NovaSeq 6000 and HiSeq X Ten. The kits used were Illumina Truseq RNA and Illumina Truseq stranded mRNA.

  Dataset EGAD50000000324

• Tumor Profiler Project - OV scDNA data

  The dataset contains 10x Chromium single-cell DNA sequencing data from 42 samples from 38 different patients with ovarian cancer. 35 samples were collected from the tumor, and 7 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000001291

• CHIP panel sequencing of rheumatoid arthritis patients

  Targeted NGS sequencing data (bam and index files aligned to hg38) a total of 573 newly diagnosed, untreated RA patients and 163 healthy controls. The sequencing panel included 65 genes recurrently mutated in myeloid malignancies, to capture clonal hematopoiesis of indeterminate potential (CHIP) mutations. The median target coverage was 1700x across samples.

  Dataset EGAD50000001300