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• RNASeq of OvCa

  RNAseq data relative to 56 primary and treatment-naive ovarian carcinomas, from independent donors.

  Dataset EGAD00001008547

• Strand-seq data of primary acute myeloid leukemia patient samples with complex karyotype

  In this study, we aimed to identify somatic structural variation of acute myeloid leukemia with complex karyotype (CK-AML) at the single-cell level and to investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of two patient-derived xenografts (PDXs).

  Dataset EGAD00001011172

• Sequencing data for oesophageal and related samples - Linossi et al

  Data supporting: "Utility of ctDNA assessment after six weeks of immunotherapy to predict radiological response in advanced oesophageal cancer" Linossi et al

  Dataset EGAD00001015434

• WGS Dataset of NGS based Aspergillus detection in liquid biopsies of immunocompromised patients

  The dataset comprises plasma and bronchoalveolar lavage (BAL) fluid samples from immunocompromised pediatric patients. Sequencing was performed on the NovaSeq 6000 platform, generating 2x150bp paired-end reads. The samples are provided as raw reads, post-demultiplexing, with no additional processing.

  Dataset EGAD00001015489

• RNA-seq from time-course experiment treating cells for 72h

  RNA sequencing from MSTO-211H cell line cultures treated for 72h with vehicle solution, palbociclib 250nM, or abemaciclib 250nM (N = 3, each). RNA-seq prepared using TruSeq Stranded mRNA libraries and sequenced with Illumina HiSeq 4000. Data is in raw fastq format, paired end. Some samples have been split in two lanes, with a final count of 24 fastq files.

  Dataset EGAD00001007737

• low pass WGS of patient from the CN300 cohort

  We copy number profiled 688 tumor regions from 300 patients presenting with advanced prostate cancer and prospectively followed-up (median, 7 years) in the control group of the STAMPEDE trial. Patients were categorised into four metastatic states, namely high-risk non-metastatic (with or without local lymph node involvement) or metastatic (low or high volume).

  Dataset EGAD00001008800

• Neuroblastoma WGS samples used for detection of seismic amplification

  Paired-end WGS data of 27 neuroblastoma patient samples (10 obtained at diagnosis, 6 at relapse and 11 matched blood samples as controls) used for detection of complex "seismic" amplification. Mean coverage is 24-55x per sample. The remaining patient samples of the dataset can be found under accession number EGAS00001001308.

  Dataset EGAD00001007807

• Digital tEchnology For Lung Cancer Treatment

  DEFLeCT metadata: 1) A table containing the mutational profile for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 2) A table containing the expression levels for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 3) A table containing the clinical, histology data and follow-ups of the cohort of 81 PROMOLE lung cancer patients.

  Dataset EGAD00001010838

• RNA-seq of cells cultured in vitro

  This dataset includes 90 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Normal human CD34+ cord blood (CB), bone marrow (BM), or post-natal thymus (PNT) cells were transduced with various combinations of T-ALL oncogenes and cultured in vitro.

  Dataset EGAD00001009750

• Follicular lymphoma at diagnosis, treated in first line with immunochemotherapy

  We performed targeted NGS in Follicular lymphoma samples at diagnosis. Explored clinico-genetic correlations and assessed four clinical or clinicogenetic risk models (FLIPI, FLIPI-2, PRIMA-IP or m7-FLIPI-molecular score) in patients with symptomatic FL who received frontline immunochemotherapy. Out of 191 patients with FL grade 1-3a, 109 were successfully genotyped. Treatment consisted on rituximab (R) plus CVP/CHOP (72.5%) or R-bendamustine (R-B) (27.5%).

  Dataset EGAD00001009647

• NCCS-NSCLC-ITH2-WES

  NCCS-NSCLC-ITH2 dataset of 185 sectors from 48 patients with early-stage non-small cell lung cancer diagnosed in National Cancer Centre Singapore; these are paired-end, whole-exome and bulk RNA sequencing data, sequenced by Illumina HiSeq 4000/2000.

  Dataset EGAD00001010158

• February 2021 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  February 2021 data update (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001007919

• Targeted DNA sequencing dataset for the study "Molecular profiling of EBV associated diffuse large B-cell lymphoma"

  We performed deep targeted DNA sequencing with a panel of 74 selected cancer-related genes previously identified to be recurrently mutated in EBV associated DLBCL. Sequencing was performed on a HiSeq platform (Illumina) with 250 bp paired-end reads. There are 68 FFPE samples in this targetedDNAseq-dataset with 46 unpaired tumors and 22 normals used as a panel of normals.

  Dataset EGAD00001009396

• Gut microbiome from melanoma patients

  Metagenomics shotgun sequencing was conducted on fecal samples from the Australian patients enrolled in the OpACIN-neo clinical trial (n = 38). Metagenomic shotgun sequencing was performed utilizing the same DNA from the same preparations as for the 16S rRNA gene analysis. Individual libraries were prepared using Nextera XT, and sequencing was performed on the Illumina NovaSeq 6000 S1 (2 x 150bp; Xp workflow).

  Dataset EGAD00001010028

• WGS

  Whole-genome sequencing of pancreatic cancer organoids and matched germline controls.

  Dataset EGAD00001010835

• RNA-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011819

• CUT&RUN/ChIP-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011821

• Reproducibility of variant calls in replicate next generation sequencing experiments

  To examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA, we performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. This data set contains 17 breast cancer samples that were sequenced in duplicate (n=14) or triplicate (n=3), in order to assess concordance of all calls and single nucleotide variant (SNV) calls.

  Dataset EGAD00001001209

• Whole genome bisulfite sequencing data of human monocyte sample 43_Hm01_BIMo_Ct from healthy male donor.

  Human monocytes from a healthy male blood donor were obtained after written informed consent and anonymised. Library preparation was performed essentially as described in the “Whole‐genome Bisulfite Sequencing for Methylation Analysis (WGBS)” protocol as released by Illumina. The library was sequenced on an Illumina HiSeq2500 using 101 bp paired-end sequencing. Read mapping was done with BWA.

  Dataset EGAD00001001390

• Colorectal Adenoma Gene Screen

  A pilot to establish the feasability of using a custom Agilent targeted pulldown of 110 genes implicated in colorectal tumourigensis to sequence for driver mutations in a set of 30 FFPE colorectal adenomas. If successful, we propose to sequence an additional 350 adenomas as part of a MRC research study in order to define the pattern of driver mutations across the spectrum of pathological subtypes including coventional adenomas, serrated adenomas and hyperplastic polyps

  Dataset EGAD00001001879

• Breast Cancer - immune clusters - RNA-seq

  In this study we use expression data from breast cancer tumors to define immune clusters in breast cancer. Immune clusters have gradual levels of immune infiltration. In the intermediate immune infiltration cluster, we found a worse prognosis which is independent of known clinicopathological features. We also found the immune clusters associated with treatment response. Further using gene expression data and deconvolution algorithms to dissect the immune contexture of the clusters.

  Dataset EGAD00001004985

• Smartseq2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This dataset is part of Smartseq2 data

  Dataset EGAD00001005960

• Lymphocyte LCM WGS (2020-02-20)

  Using whole genome sequencing of lymphocytes excised from human tissue using laser capture microscopy (LCM), we identify the mutations arising in these microenvironments. This work will contribute towards developing a catalogue of mutations present in tissue resident lymphocytes across a range of tissues, and will characterize the mutational signatures that result from each microenvironment. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005992

• Single-cell profiling maps the spectrum of crosstalk between glioma cells and tumor associated macrophages

  Tumor associated macrophages (TAMs) are a heterogeneous glioma infiltrate, implicated in cancer progression. We performed single-cell RNA-sequencing, to survey TAM response-patterns in glioma.

  Study EGAS00001002185

• Non-Coding Autoimmune Risk Variant Defines Role for ICOS in T Peripheral Helper Cell Development

  Our fine-mapping of 76 non-MHC loci associated with risk for rheumatoid arthritis (RA, 11,475 cases, 15,870 controls) has recently identified rs117701653, a non-coding single nucleotide polymorphism (SNP) in the CTLA4/CD28/ICOS locus, as the variant most likely to modulate RA risk within this region, with the minor allele C showing disease protection compared to the major allele A. We found that this SNP exhibits allele-specific protein binding and transcriptional modulation, further supporting its regulatory nature. Here, we aimed to determine whether the functional non-coding variant rs117701653 modulates the expression of genes within the CD28/CTLA4/ICOS locus. To address this question, we employed low-input RNA sequencing using the Illumina SmartSeq2 platform on resting total CD4+ T cells from the blood of 24 healthy subjects (8 AA, 8 AC, 8 CC) recruited based on genotype from the Mass General Brigham biobank. We performed a targeted cis-eQTL mapping analysis for protein coding genes with transcription start sites (TSS) within a 1MB window of SNP rs117701653. These genes included WDR12, NBEAL1, CYP20A1, ABI2, RAPH1, CD28, CTLA4, ICOS, and PARD3B. Surprisingly, allelic variation at rs117701653 correlated strongly with expression of ICOS. This suggests that individuals carrying the protective allele C at rs117701653 express lower levels of ICOS, implicating ICOS as a plausible target gene influenced by this protective allele. The raw sequence data from the 24 healthy individuals are available through dbGAP. Gene expression matrices have been deposited to GEO accession GSE235868.

  Study phs003448

• Genetic Modifiers of Duchenne Muscular Dystrophy

  The primary determinant of disease severity in patients with severe Duchenne muscular dystrophy (DMD) or milder Becker muscular dystrophy (BMD) is whether their dystrophin gene (DMD) mutation disrupts the mRNA reading frame or permits the expression of a partially functional protein. However, even in the complete absence of dystrophin, variability in disease severity is observed, with candidate gene studies implicating several genes as potential DMD modifiers. This study undertakes a comprehensive genome-wide search for modifier loci influencing disease severity in DMD patients. The availability of subjects for such studies remains limited, resulting in modest sample sizes that challenge the GWAS design. To address this, we have implemented measures to minimize heterogeneity within the dataset at the dystrophin (DMD) gene itself, adopting a conservative approach to DMD mutation classification to limit the possibility of residual dystrophin expression. Additionally, the study employed statistical methods that are well-suited to smaller sample sizes, including the use of a novel linear regression-like residual for time to ambulatory loss and the application of evidential statistics, specifically the Posterior Probability of Linkage Disequilibrium (PPLD), to assess trait-SNP associations in the GWAS framework. With a sample size of 419 patients, this study has identified multiple candidate genetic modifier loci. The molecular data available in dbGaP includes 2,562,265 directly genotyped variants in 419 people using the Illumina Infinium Omni2.5Exome-8 Beadchip assay, achieving a genotyping rate of 0.998. The phenotypic data comprises age at ambulatory loss, steroid status, DMD gene mutation, and the PPLD value from the time-to-event (TE) phenotype.

  Study phs003680

• Genetic Analysis of Normal Human Facial Variation

  The purpose of this project is to identify genes associated with normal human quantitative facial variation. The motivation for this project stems from the fact that very little is known about how variation in specific genes relates to the diversity of facial forms commonly observed in humans. Viable candidates for these morphogenes originate from a number of sources: tissue expression studies, animal models with targeted or spontaneous mutations, and genetic syndromes with craniofacial manifestations. Importantly, understanding the genetic basis for normal facial variation also has important implications for health-related research. For example, this work has the potential to shed light on the factors influencing liability to common craniofacial anomalies such as orofacial clefts. There is now ample evidence that certain facial features (e.g., increased midfacial retrusion) characterize individuals genetically at-risk for orofacial clefts (e.g., biological relatives of affected cases). While these predisposing facial features are statistically over-represented in at-risk groups, they are also common in the general population. Since many of the current candidate genes for clefting are thought to play a critical role in facial morphogenesis, variation in these genes may also underlie normal variation in these facial features. These candidate genes, however, probably represent only a small fraction of the total number of loci influencing normal human facial variation. Phenotypes for this project were obtained from over 3000 healthy Caucasian subjects recruited through three separate studies. The majority of the subjects were recruited as part of the 3D Facial Norms Project, which is described in extensive detail here: (https://www.facebase.org/facial_norms/notes). The provided dbGaP phenotypes include a series of anthropometric craniofacial measurements (linear distances) primarily derived from 3D photographic facial surface scans (see previous hyperlink). The specific genotyping requested is described elsewhere in this document. Our analysis team is pursuing a variety of different analytic approaches to derive genetically informative phenotypes, including various shape-based morphometric methods. For those interested in pursuing more advanced phenotypic approaches, the original 3D surface scans and additional phenotypic traits are available to researchers through the FaceBase Consortium. This dataset has the potential to facilitate the discovery of new genetic loci with an important role in both normal and abnormal facial development. It may also serve as a dataset to test hypotheses regarding specific SNP associations (e.g. as a replication dataset) or as part of a larger meta-analysis.

  Study phs000949

• Genetics of Human Inherited Retinal Diseases (GHIRD)

  The goal of this project is to identify novel mutations and genes involved in human retinal disorders, a stated priority of the National Eye Institute. To accomplish this, additional genes whose mutations cause inherited retinal diseases (IRD) will be identified by combining targeted gene panel sequencing, whole exome sequencing, and whole genome sequencing. We have collected about 1050 patient families around the world. In this proposal, we will identify the underlying mutations in these patients using a combination of targeted gene panel sequencing, whole exome sequencing, whole genome sequencing, bioinformatics, statistics, and functional studies. Genes targeted for gene panel sequencing are: ABCA4; ASIC2; JAG1; ABCC6; ARL3; ATP1B2; BBS1; BBS2; BBS4; OPN1SW; CAPN5; C21orf2; CA4; CACNA1F; CDH3; CHM; ERCC8; CLCN2; CLCN3; CLCN7; TPP1; CLN3; CLN5; CNGB1; CNGA1; CNGA3; COL2A1; COL9A1; COL11A1; CRX; VCAN; CTSD; TIMM8A; DMD; CLN8; ERCC6; EFEMP1; OPN1MW; GNAT1; GNAT2; GNGT1; GRM6; GUCA1A; GUCA1B; GUCY2F; GUCY2D; HARS; CFH; HK1; IDH3B; IMPDH1; IMPG1; KCNJ13; KIF11; LRP5; MAK; MITF; TRPM1; MTTP; MVK; MYO7A; NDP; NEK2; NEUROD1; NPHP1; NRL; OAT; OPA1; OTX2; PAX2; PAX6; PDCL; PCYT1A; PDE6A; PDE6C; PDE6G; PDE6H; PDE6B; PEX1; PEX6; PEX7; PEX10; PEX12; PEX13; PEX14; PFDN5; PGK1; PHYH; PIN1; PLA2G5; PPT1; PRKCZ; PEX19; PEX2; PEX5; RB1; RBP3; RBP4; OPN1LW; RDH5; PRPH2; RGR; RHO; GRK1; RLBP1; ROM1; RP9; RP1; RP2; RPGR; RPE65; RS1; SAG; ATXN7; CCL2; SLC6A6; ELOVL4; TEAD1; NR2F1; TIMP3; NR2E1; TTPA; TUB; TULP1; UCHL3; USH2A; CLRN1; VLDLR; BEST1; WFS1; ALMS1; MKKS; FZD4; OFD1; PEX3; CTSF; GBF1; ADAM9; RGS9; PEX11B; PROM1; UNC119; PRPF4; PRPF3; AIFM1; SLC24A1; LRAT; ASIC3; RAB28; PEX16; ITM2B; SLC4A7; IQCB1; CROCC; IFT140; DHX38; MFN2; NR2E3; USH1C; TOPORS; MERTK; FBLN5; CIB2; PRPF8; SDCCAG8; IFT27; TREX1; RRAS2; CEP164; ATF6; TRIM32; RIMS1; SNRNP200; CLUAP1; EMC1; ZNF423; TTLL5; AGTPBP1; RPGRIP1L; CRB1; TSPAN12; ARL2BP; AIPL1; PRPF6; FSCN2; ABHD12; PRPF31; TCTN3; IFT172; CNNM4; NPHP3; INVS; BBS9; FLVCR1; RDH8; IMPG2; WDPCP; RDH11; TMEM216; TMEM138; LZTFL1; CNGB3; AHI1; MKS1; CLN6; BBS7; POMGNT1; PEX26; SPATA7; KIZ; KLHL7; INPP5E; MDM1; CABP4; RPGRIP1; MCOLN1; CC2D2A; KIAA1549; SLC7A14; WDR19; NYX; CDH23; SEMA4A; MPP5; NMNAT1; TMEM237; PCDH15; C5orf42; GNPTAB; TMEM231; TCTN1; SRD5A3; BBS10; ZNF408; TTC21B; CSPP1; LPCAT1; DHDDS; PDZD7; PANK2; CEP290; OPA3; DNAJC5; PITPNM3; MFRP; HMCN1; ADGRV1; ARL6; FAM161A; TMEM126A; GNPTG; GJA10; RAX2; TUBGCP6; TMEM67; ACBD5; C12orf65; CDHR1; BBIP1; REEP6; CACNA2D4; RP1L1; CEP41; C1QTNF5; NXNL1; TTC8; USH1G; BBS5; ZNF513; RDH12; SLC38A8; C8orf37; VPS13B; NXNL2; BBS12; ADGRA3; LCA5; KCNV2; ADAMTS18; ARL13B; ATOH7; MFSD8; NPHP4; CCDC66; CYP4V2; CRB2; RD3; LRIT3; EYS; KIF7; CERKL; RGS9BP; C2orf71; GDF6; DTHD1; GPR179; CISD2; CCR2; PRCD; WHRN; ADGRA3. The current dbGaP study release makes available all sequencing-derived vcf data of study participants.

  Study phs001517

• Epilepsy Genetics Initiative

  The Epilepsy Genetics Initiative (EGI) was created in 2014 with the goal of amassing a database of clinically-generated exome sequence data for patients with epilepsy who have had diagnostic whole exome sequencing. Most of the subjects enrolled in the study did not receive a secure genetic diagnosis from their initial sequencing. Following participant/family consent, EGI transfers raw data from the respective clinical lab to the Institute for Genomic Medicine at Columbia University Medical Center. The strategy of the initiative has been to carry out systematic reanalysis of data to identify new diagnoses that were not possible or missed at the time of initial sequencing and to aid in novel gene discovery in epilepsy.

  Study phs001551

• Whole Exome Sequencing Analysis of Carfilzomib-Related Cardiotoxicity in Multiple Myeloma Patients

  This study investigated the contribution of germline genetic variants in protein-coding genes in carfilzomib-related cardiovascular adverse events among patients with multiple myeloma using whole-exome sequencing (WES) analysis. We analyzed 247 patients with multiple myeloma who had been treated with carfilzomib at the Moffitt Cancer Center. We identified a missense mutation in the TMSB10/TRABD2A locus that appeared to be associated with a higher risk for cardiovascular adverse events in these patients. In this submission, we will provide all the genotype data along with the phenotype data of whether or not a patient developed cardiovascular adverse events after carfilzomib treatment and all the covariates used in this analysis.

  Study phs003308

• Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

  Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. In version 1.0 of this study, we performed RNA-based next generation sequencing (mNGS) on 41 lower respiratory samples collected from 34 children. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Potential pathogens were detected in half of samples previously negative by clinical diagnostics. In version 2.0, we included an addition 278 samples from 229 pediatric stem cell transplant patients with pulmonary disease.

  Study phs001684

• Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients

  Our previous studies in mechanically ventilated Intensive Care Unit (ICU) patients with extrapulmonary sepsis revealed that pulmonary dysbiosis within 8 h from sepsis diagnosis was associated with ICU mortality. These observations offer promising options that could be technologically adapted to rapidly identify those patients at higher risk of death. However, they relied on 16S rRNA sequencing experiments which impedes deep characterization of the bacterial communities that could help to further substantiate the association. To further discern this association, here we assessed the pulmonary bacterial communities in these patients by leveraging metagenomics and evaluated if the presence of antibiotic resistance genes could explain the higher mortality of the patients.

  Study EGAS50000000384

• bulk RNAseq analysis of tumor from 3 non-muscle-invasive bladder cancer patients

  We performed screenings of patient-specific neo-epitopes by tumor-infiltrating CD8+ T lymphocytes of 4 non-muscle invasive bladder cancer patients. After the tumor resection, these patients went on to receive BCG treatment as they had high-risk disease. In order to select the neo-epitopes, we performed bulk RNAseq of the bladder tumor to select the mutated genes that were expressed in the tumor (TPM >1). For patient UC2, 3 different tumors were resected at the same time and RNA from these 3 tumors were sent separately for RNAseq. For patient UC4, no RNA was available, so this patient is not included in this study.

  Study EGAS50000001383

• Genetics of diffuse large B-cell lymphoma in Japan

  Diffuse large B-cell lymphoma (DLBCL) is a common hematological malignancy. Treatment with standard chemotherapy results in long-term remission in approximately 60% of patients. Whole-exome sequencing studies of large DLBCL cohorts revealed the biological diversity of tumors and facilitated the identification of genetic subtypes based on genetic alterations. Despite the progress facilitated by NGS, genetic classification is difficult to apply in clinical practice because of the complexity of the clustering algorithm. Furthermore, only a few reports included large Asian cohorts. Thus, a genetic overview of Japanese patients with DLBCL is still needed. Thus, in this study, we aimed to establish the clinical application of our simplified genetic classification algorithm in Japanese DLBCL.

  Study JGAS000307

• Exome sequencing to identify predisposition to Wilms tumour

  To identify new Wilms tumor predisposition genes, we performed whole-exome paired-end sequencing of lymphocyte DNA from 12 affected individuals from six unrelated, non-syndromic Wilms tumor families in which known causes had been excluded.We prepared DNA libraries from 1.5 mg blood-derived genomic DNA using the Paired-End DNA Sample Preparation Kit (Ilumina). DNAwas fragmented using Covaris technology and the libraries were prepared without gel size selection. We performed target enrichment using the TruSeq Exome Enrichment Kit (Illumina) by targeting 62 mb of the human genome. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers.Sequencing was performed with an Illumina HiSeq2000 generating 2?101 bp reads.

  Study EGAS00001000904

• Exome_sequencing_of_a_Novel_Primary_T_Cell_Immunodeficiency_Kindred

  Primary T cell immunodeficiency disorders are genetically heterogenous. Mutations in genes required for specific stages of T cell development within the thymus can lead to reduced numbers of circulating T cells. On the hand, T cells may not egress from the thymus normally leading to profound T cell lymphopenia. As a result, patients with these disorders succumb to a range of severe opportunisitic infections unless allogeneic transplantation is performed. We wish to whole exome sequence a Caucasian family in which the index case shows features of impaired T cell egress from the thymus. Importantly, known genes implicated in T cell immunodeficiency including CORO1A have been seqeuenced and found to normal in this individual.

  Study EGAS00001000099

• WES analysis in identifying additive genetic factors that may contribute to the occurrence of moyamoya in neurofibromatosis type 1

  Moyamoya is a progressive cerebral vasculopathy, for which genetic susceptibility factors were mainly identified in Asian populations. When associated with other medical conditions, such as neurofibromatosis type 1 (NF1), this vasculopathy is frequently reported as Moyamoya syndrome (MMS). Intriguingly, most cases of MMS-complicated NF1 have been described in Caucasians, inverting the population ratio for moyamoya vasculopathy observed in Asians, despite NF1 prevalence being constant worldwide. This study aims to investigate whether, among Caucasians, additive genetic factors may contribute to the occurrence of MMS in NF1. WES analysis has been carried out on an Italian family with co-occurrence of NF1 and MMS, as well as other cerebral vasculopathies.

  Study EGAS00001003053

• Whole exome sequencing of tumors from the Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

  Sequencing libraries were constructed according to standard procedures from 600 ng of tumor and paired constitutional DNA. WES was captured using Agilent SureSelect V5 (50 Mb), Clinical Research Exome (54 Mb) kit, SureSelect XT human All exon CRE version 1 or 2, or Twist Human Core Exome Enrichment System. Sequencing of subsequent libraries was performed using Illumina sequencers (Next-Seq 500 or Hiseq 2000/2500/4000) in 75 bp paired-end mode, aiming for a mean depth of coverage of 100x.

  Dataset EGAD00001010928

• Submitters and requesters Statistics

  EGA Statistics Bibliography Growth Community Archive Distribution Catalogue Here, we show the amount and global distribution of submitters and requesters Requester accounts created by country The below figure represents the number of requester accounts by country. In most of the cases cases, country was inferred from the requester email domain. Those requesters whose email domain could not be assigned to a country such as @gmail.com, are not included. Note that a requester is a user that has had a granted permission at some point in time. Requester Accounts Created by Country Download as PNG Download as JPG Download as WEBP Download as CSV map pie mapChart('requester-country', 'https://stats.ega-archive.org/requester/country') pieChart('requester-country-pie-chart', 'https://stats.ega-archive.org/requester/country','Requester accounts created by country') Requester accounts created by year The below figure represents the number of requester accounts by year. Note that a requester is a user that has had a granted permission at some point in time. Requester Accounts Created by Year Download as PNG Download as JPG Download as WEBP Download as CSV barChart('requester-year', 'https://stats.ega-archive.org/requester/year', ['Requester Accounts', 'Years'], true) Industry requester accounts The below figure represents the top 15 industry requesting companies. Industry Requester Accounts Download as PNG Download as JPG Download as WEBP Download as CSV pieChart('industry-requester-accounts', 'https://stats.ega-archive.org/industry/requester/accounts', 'Industry Requester Accounts') Submitter accounts created by country The below figure represents the number of submitter accounts by country. Location was infered from the requester email domain. Submitter Accounts Created by Country Download as PNG Download as JPG Download as WEBP Download as CSV map pie mapChart('submitter-accounts', 'https://stats.ega-archive.org/submitter/accounts/country') pieChart('submitter-accounts-pie-chart', 'https://stats.ega-archive.org/submitter/accounts/country','Submitter accounts created by country') Submitter accounts created by year The below figure represents the number of submitter accounts by year. Submitter Accounts Created by Year Download as PNG Download as JPG Download as WEBP Download as CSV barChart('submitter-users-year', 'https://stats.ega-archive.org/submitter/users/year', ['Submitter Accounts', 'Years'], true) DAC Members by Country The below figure represents the number of DAC members by country. DAC Members by Country Download as PNG Download as JPG Download as WEBP Download as CSV map pie mapChart('dac-members-by-country', 'https://stats.ega-archive.org/dac_member/country') pieChart('dac-members-by-country-pie-chart', 'https://stats.ega-archive.org/dac_member/country','DAC members by country')

  Documentation about/statistics/community

• The genomic architecture of mesothelioma

  The genome-wide landscape of somatically acquired mutations in mesothelioma has not been deeply characterised to date, but advances in DNA sequencing technology now allow this to be addressed comprehensively. Harnessing massively parallel DNA sequencing platforms, we will identify somatically acquired point mutations in all coding regions of the genome from patients with mesothelioma. In addition, using paired-end sequencing, we will map copy number changes and genomic rearrangements from the same patients.

  Dataset EGAD00001000360

• Molecular characterization of T-PLL by Next-Generation Sequencing

  Patients with T-cell prolymphocytic leukemia (T-PLL) were profiled with multiple OMICS approaches based on Next-Generation Sequencing (NGS). In total, data from RNA-Seq, Whole-Exome Sequencing, Whole-Genome Sequencing and amplicon panel analyses in 134 samples are available. All samples were processed as paired-end libraries on Illumina sequencing machines. The data are available as paired FastQ files.

  Dataset EGAD00001003825

• Arcagen – thoracic malignancies

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files from rare thoracic malignancies (n=102)

  Dataset EGAD50000000168

• RNA-Seq data from tumor samples collected from 12 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates differentially expressed genes associated with the progression of translocation renal cell carcinoma (tRCC) by analyzing RNA-Seq data from 23 tumor samples obtained from 12 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. RNA isolated from tumor samples was sequenced using the Illumina platform.

  Dataset EGAD50000000172

• RNAseq from 6 organotypic co-cultures (OC cells bulk/OCSC with or without TME)

  The dataset contains samples of 6 organotypic co-cultures, assembled with patient-derived material from ovarian cancer (OC) patients. Tumor cells, both as bulk and as cancer stem cells-enriched (OCSC) populations, are cultured or not with in vitro peritoneal TME (for details see Battistini C et al, Tumor microenvironment-induced FOXM1 regulates ovarian cancer stemness, CDDis 2024). Dataset is composed by fastq file (paired end) type from bulk RNA-Seq.

  Dataset EGAD50000000523

• scMultiomics of ARID1B+/+ (control) and ARID1B+/- human telencephalic organoids at D120

  This dataset contains scMultiomics (scRNAseq + scATACseq) data of human telencephalic organoids, at day 120, from 3 different sequencing runs (libraries), as follows (please see cell line clone nomenclature in original publication): 1. Library 233269(RNA)/235293(ATAC): Pat.1 ARID1B+/- clone 1a (9 pooled organoids). 2. Library 233270(RNA)/235294(ATAC): HD.1 ARID1B+/+ clone 3a (9 pooled organoids). 3. Library 233271(RNA)/235295(ATAC): HD.1 ARID1B+/- clone 3b (8 pooled organoids).

  Dataset EGAD50000000499

• RNAseq profiles from the CheckMate-274 clinical trial

  The dataset contains RNAseq profiles of 370 patients from the CA209-274 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNAseq libraries (75PE, 50M) were sequenced on Illumina NovaSeq 6000 at a plex-level appropriate to the coverage of 2 × 50 base pair (bp) paired end (PE) 50M reads. Fastq files are included.

  Dataset EGAD50000000793

• Transcriptome analysis of patient-derived Schwann cells isolated from human sural nerve biopsies

  This dataset contains the transcriptome analysis of human Schwann cell cultures obtained from sural nerve biopsies from six patients with polyneuropathies (N=3/patient, totalN=18) as well as the nerve fascicles from where they were isolated (N=1/patient, totalN=6). In addition, this dataset includes 8 samples out of commercial human Schwann cell cultures and one sample of a fibroblast culture, which serve as controls for further analysis.

  Dataset EGAD50000001021

• Transcriptomic analysis of metastatic colorectal cancer

  Metastatic colorectal cancer (mCRC) is the main cause of CRC mortality, with limited treatment options. Although immunotherapy has benefited some cancer patients, mCRC typically lacks the molecular features that respond to this treatment. However, recent studies indicate that the immune microenvironment of mCRC may be modified to enhance the effect of immune checkpoint inhibitors. This dataset was used to explore the metastatic immune microenvironment by comparing immune cell populations in colorectal liver (CLM), lung (mLu) and peritoneal (PM) metastases.

  Dataset EGAD50000000926

• Genotypic data of the individuals in HPP project

  Dataset contains imputed SNP genetics data for human phenotype project https://humanphenotypeproject.org/. The samples are genotypes of 8958 individuals that underwent genetic sequencing based on buccal swab.Sequencing is performed at Neogen GeneSeek Laboratories using Illumina Novaseq at low-pass, targeting coverage levels of 0.5× and 1×. Imputation was done using loimpute-v0.1.0 over the aligned reads. Imputation is done for the autosomal chromosomes (1-22) using The 1000 Genomes phase 3 haplotypes (1KGP3) as a reference panel. The samples are provided in merged PLINK 1 binaries (.bed/.bim/.fam)

  Dataset EGAD00010002714

• WHOLE GENOME SEQUENCING FOR THE CHARACTERIZATION OF CLEAR CELL RENAL CELL CARCINOMA IN VHL PATIENT

  To characterize clear cell Renal Cell Carcinoma (ccRCC), we set up a comprehensive multi-omics pilot study on a VHL-ccRCC-patient. Whole Genome Sequencing (WGS) was applied on six ccRCCs, four cysts and one blood DNA sample as germinal control. Raw-data were analyzed with GENomics-DRAGEN platform. We will upload WGS-Data for 11 samples (6 ccRCCs, 4 Cysts, 1 blood).

  Dataset EGAD50000000425