16476 results for "sec+and+unspecified+malignant+neoplasm"

in 31.46 milliseconds.

• WGS short read and 10X linked read sequencing of HR Deficient breast cancers

  A set of tumor/normal paired sequencing experiments, performed in short read WGS and 10X linked read whole genomes. BAM files aligned to hg19 are provided. Sample Alias number and Subject ID reflects patient of origin. T/N distinction discriminates between tumor and normal (peripheral blood) tissue.

  Dataset EGAD00001010326

• Single-cell RNA sequencing on 11,138 single T cells from 12 colon and rectal cancer (CRC) patients

  Deep single-cell RNA sequencing data for 11,138 T cells from tumour, adjacent normal tissue and peripheral blood of treatment-naive CRC patients. The DATA ACCESS AGREEMENT is provided at https://github.com/zhangyybio/single-T-cell-data-access. Applicants can request access to the data by directly downloading it or by sending an email to cancerpku@pku.edu.cn. The process that is used to approve an application includes verifying the institution, participants and research purposes of the application. In general this process will take about two weeks. In principal, any academic research institutions complying with the laws and bioethic regulation policies of China will be approved.

  Dataset EGAD00001003910

• Genomic alterations in MM - BAM

  Tumor DNA was extracted from 100 bone marrow aspirate samples where CD138+ selection had been performed to enrich plasma cells from patients with multiple myeloma. Patient matched control DNA from either peripheral blood leukocytes or CD34+ stem cell harvests was also isolated. Both tumor and control DNA underwent library preparation using the Hyperplus kit (KAPA Biosystems) and were hybridized to baits for a targeted SeqCap myeloma panel (Nimblegen) encompassing 129 genes, regions for SNPs for copy number determination, and the IGH, IGK, IGL loci, as well as approximately 5 Mb surrounding the MYC locus. Samples were sequenced on a HiSeq2500 using 100 bp paired end reads. Resulting BAM files were returned along with annotations for somatic events including single nucleotide mutations, indels and structural rearrangements.

  Dataset EGAD00001004117

• Whole Genome Sequencing of Liver Cancers

  Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers.

  Dataset EGAD00001003281

• Identifying autosomal recessive mutations causing neurological disorders

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

  Dataset EGAD00001000340

• Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Project 1: KARE

  T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. Table 1. T2D-GENES Whole Exome Sequencing Studies Ancestry Study Countries of Origin # Cases # Controls African American Jackson Heart Study US 502 527 African American Wake Forest School of Medicine Study US 518 532 East Asian Korea Association Research Project Korea 526 561 East Asian Singapore Diabetes Cohort Study; Singapore Prospective Study Program Singapore (Chinese) 486 592 European Ashkenazi US, Israel 506 352 European Metabolic Syndrome in Men Study (METSIM) Finland 484 498 European Finland-United States Investigation of NIDDM Genetics (FUSION) Study Finland 472 476 European Kooperative Gesundheitsforschung in der Region Augsburg (KORA) Germany 97 90 European UK Type 2 Diabetes Genetics Consortium (UKT2D) UK 322 320 European Malmö-Botnia Study Finland, Sweden 478 443 Hispanic San Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component US 272 219 Hispanic Starr County, Texas US 749 704 South Asian London Life Sciences Population Study (LOLIPOP) UK (Indian Asian) 530 538 South Asian Singapore Indian Eye Study Singapore (Indian Asian) 563 585 The Korea Association Research Project (KARE) studies contributed 526 cases and 561 controls to T2D-GENES Project 1.

  Study phs001096

• Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Project 1: Ashkenazi

  T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. Table 1. T2D-GENES Whole Exome Sequencing Studies Ancestry Study Countries of Origin # Cases # Controls African American Jackson Heart Study US 502 527 African American Wake Forest School of Medicine Study US 518 532 East Asian Korea Association Research Project Korea 526 561 East Asian Singapore Diabetes Cohort Study; Singapore Prospective Study Program Singapore (Chinese) 486 592 European Ashkenazi US, Israel 506 352 European Metabolic Syndrome in Men Study (METSIM) Finland 484 498 European Finland-United States Investigation of NIDDM Genetics (FUSION) Study Finland 472 476 European Kooperative Gesundheitsforschung in der Region Augsburg (KORA) Germany 97 90 European UK Type 2 Diabetes Genetics Consortium (UKT2D) UK 322 320 European Malmö-Botnia Study Finland, Sweden 478 443 Hispanic San Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component US 272 219 Hispanic Starr County, Texas US 749 704 South Asian London Life Sciences Population Study (LOLIPOP) UK (Indian Asian) 530 538 South Asian Singapore Indian Eye Study Singapore (Indian Asian) 563 585 The Ashkenazi study contributed 506 cases and 352 controls to T2D-GENES Project 1.

  Study phs001095

• Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Project 1: Singapore

  T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. Table 1. T2D-GENES Whole Exome Sequencing Studies Ancestry Study Countries of Origin # Cases # Controls African American Jackson Heart Study US 502 527 African American Wake Forest School of Medicine Study US 518 532 East Asian Korea Association Research Project Korea 526 561 East Asian Singapore Diabetes Cohort Study; Singapore Prospective Study Program Singapore (Chinese) 486 592 European Ashkenazi US, Israel 506 352 European Metabolic Syndrome in Men Study (METSIM) Finland 484 498 European Finland-United States Investigation of NIDDM Genetics (FUSION) Study Finland 472 476 European Kooperative Gesundheitsforschung in der Region Augsburg (KORA) Germany 97 90 European UK Type 2 Diabetes Genetics Consortium (UKT2D) UK 322 320 European Malmö-Botnia Study Finland, Sweden 478 443 Hispanic San Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component US 272 219 Hispanic Starr County, Texas US 749 704 South Asian London Life Sciences Population Study (LOLIPOP) UK (Indian Asian) 530 538 South Asian Singapore Indian Eye Study Singapore (Indian Asian) 563 585 The Singapore studies contributed 1049 cases and 1177 controls to T2D-GENES Project 1.

  Study phs001097

• Type 2 Diabetes Genetic Exploration by Next-generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Project 1: London Life Sciences Population Study (LOLIPOP) UK South Asian

  T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups. The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP. Table 1. T2D-GENES Whole Exome Sequencing Studies Ancestry Study Countries of Origin # Cases # Controls African American Jackson Heart Study US 502 527 African American Wake Forest School of Medicine Study US 518 532 East Asian Korea Association Research Project Korea 526 561 East Asian Singapore Diabetes Cohort Study; Singapore Prospective Study Program Singapore (Chinese) 486 592 European Ashkenazi US, Israel 506 352 European Metabolic Syndrome in Men Study (METSIM) Finland 484 498 European Finland-United States Investigation of NIDDM Genetics (FUSION) Study Finland 472 476 European Kooperative Gesundheitsforschung in der Region Augsburg (KORA) Germany 97 90 European UK Type 2 Diabetes Genetics Consortium (UKT2D) UK 322 320 European Malmö-Botnia Study Finland, Sweden 478 443 Hispanic San Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component US 272 219 Hispanic Starr County, Texas US 749 704 South Asian London Life Sciences Population Study (LOLIPOP) UK (Indian Asian) 530 538 South Asian Singapore Indian Eye Study Singapore (Indian Asian) 563 585 The London Life Sciences Population Study (LOLIPOP) contributed 530 cases and 538 controls to T2D-GENES Project 1.

  Study phs001093

• Rare Genetic Steroid Disease Consortium (GSD) Apparent Mineralocorticoid Excess (AME) Syndrome Natural History Clinical Protocol

  The objective of this project is to observe the natural history of apparent mineralocorticoid excess (AME). AME is a rare monogenic hypertensive disease first described by the Principal Investigator, Dr. Maria I. New, in 1977 [1], for which the first mutation in the causative HSD11B2 gene was reported by her group in 1995. [2] Little is known about the progression of this rare hypertensive disorder, which is defined by the presence of hypertension in conjunction with low renin, low to absent levels of the mineralocorticoid aldosterone, elevated urinary cortisol/cortisone metabolite ratio 5β-tetrahydrocortisol (THF) + allo-THF/ tetrahydrocortisone (THE) (i.e., THF+αTHF/THE) and the presence of mutations in the HSD11B2 gene on both alleles. The range of symptoms reflecting progressive end-organ damage is wide in the small number of affected individuals studied to date. It is important to develop accurate information on the longitudinal pattern of progression (natural history) of AME not only because it may improve the care of affected individuals, but also because it may serve as a platform for understanding the role of mineralocorticoid excess in other forms of low-renin hypertension, which constitute 40% of all forms of hypertension. In this study, we will recruit as widely as possible through the Rare Diseases Clinical Research Network (RDCRN) to identify individuals with the triad of low renin, low aldosterone, and elevated urinary THF+αTHF/THE and confirm their disorder as AME by molecular genetic testing of the HSD11B2 gene. We will gather clinical and biochemical data yearly for the duration of the grant. We will describe phenotype and genotype at diagnosis and follow the progression or regression of symptoms over time under standard treatment, with rigorous review of end organs potentially damaged by chronic hypertension. Finally, we will study the natural history of the carriers of HSD11B2 mutations, i.e., the heterozygote relatives of the probands, in order to ascertain evidence of existing or developing hypertension and resulting end-organ damage. This will be the first rigorous study of AME heterozygotes. The participant accrual for AME-affected patients and the carriers of HSD11B2 mutations will be at least two years, but as long as seven years.

  Study phs000603

• Genetic Causes of Congenital Anosmia

  The Genetic Causes of Congenital Anosmia study was designed to provide a list of candidate genes that are potentially causal for isolated congenital anosmia (ICA), a rare inherited disorder where individuals lack a sense of smell from birth in the absence of a known genetic syndrome (i.e. Kallman's syndrome). This study includes 193 participants from 18-87 years of age, divided into two cohorts: family and non-family. Genetic data from the family cohort was analyzed in a case-control family design to generate a list of 162 candidate genes for ICA. A targeted search for variants in this list of genes was then conducted in the non-family cohort to create a prioritized list of genes for further study. Ten unrelated families were recruited for the family cohort for a total of 52 participants, 25 of which had anosmia. The non-family cohort consisted of 141 anosmic individuals. 3 additional normosmic participants from incomplete families were collected, one of whom has a participating family member in the non-family cohort, and so has data provided here. Data collection was conducted remotely, resulting in 146 participants recruited from the United States, and 48 recruited internationally from ten different countries. Participants were interviewed for their anosmia status and to confirm that they had no known genetic syndromes. Participants also completed the University of Pennsylvania Brief Smell Identification Test (BSIT; Doty et al., 1984) to confirm their anosmic/normosmic status and provided a saliva sample for whole exome sequencing (WES). Participants who had family members with anosmia provided pedigree information via interview. Data submitted to dbGap include whole exome sequences from 194 individuals (163 anosmic) conducted with Illumina HiSeq2500 and Illumina NovaSeq next generation sequencing technologies. Family pedigree information for the 10 participating families and all participants in the non-family cohort who have non-participating anosmic family members was also included. Our goal was to provide a resource for further research into the genetics of isolated congenital anosmia and to aide in the understanding of this disorder, as well as human olfaction, in general. The WES data provided could be further analyzed for polygenic interactions, additional non-targeted analysis on the non-family cohort, or combined into databases of other anosmic populations for further gene targeting or selection.

  Study phs003328

• All you need to know about the new Submitter Portal

  In September we launched new services for all EGA users, including a new version of the former Submitter Portal. Our main objective with this Portal is to transform the metadata submission in a simplified and user-friendly method. Although it is possible to find documentation about the Submitter Portal on our website, we wanted to highlight the new features in this article. Enjoy! Credentials: who needs to create a new user to access the Submitter Portal and who doesn't? Users with an old submission account (ega-box) can already access the new Submitter Portal. If it is the first time that you want to access, it is time to request a submitter role linked to the EGA User. In the form, it is mandatory to explain which type of data you want to deposit, the size of your submission, add any comment you’d like us to read, and manage the EGA Data Processing Agreement (DPA) document. This document should be checked by the legal department of your institution and signed by a person with authority to sign contracts on behalf of the institution. Note that we provide a DPA template for new Users; it can be found and downloaded in the Submitter Request section. With the DPA signed and the Submitter Request sent, it is time to wait for our Helpdesk team to validate the request. Metadata submission now can be collaborative It is possible to add collaborator(s) to your submissions. Only registered EGA Users will appear on the search bar. When adding a collaborator, it is mandatory to define the permission granted: Read only: collaborators with this permission can check if the information of the submission is correct but cannot modify anything. Read & write: collaborators with this label can register new objects and modify the registered ones. We wanted to save time for submitters that usually rely on the same collaborators. For that, we have implemented the possibility of adding the same collaborators from previous submissions; all you need to do is to search the submission, and the exact set of EGA users will have access to your submission. You can check the collaborators and their permissions at any point of the submission by going to the collaborators section. Even adding more people to complete the submission is allowed by following the same steps: looking for the EGA User and defining the permission granted (please, note that during the submission it is not possible to add collaborators from previous submissions). Use external links to complement the study information When filling the information about the study we recommend users to enrich the submission with complementary fields such as PubMeds IDs, custom tags and external links. External links are used to connect a study to an external repository. We have implemented an external link to Euro-Bioimaging for a European Project (EuCanImage). Now, we are looking forward to keeping increasing the list of external repositories! Choose the expected release date for your metadata to be searchable on our website Once all the metadata objects are registered it is time to finalise the submission so that the Helpdesk team can approve it. In the new version of the Submitter Portal users can choose the expected release date for the metadata to be searchable on the EGA website. Please, note that the selected date will have a minimum of one week margin from the day of finalisation. This time is necessary for your files to be archived and for the submission to be validated by the Helpdesk Team. Are you looking for the Array submission within the Submitter Portal? Our Submitter Portal does not support array submissions. The submission of Array-based metadata must be done using the EGA programmatic submission. You will find our Array-based format template and all the necessary information on our website, and you can find all the steps in our submission quickguide! More information about the submission process at the EGA Our Team has developed an extended documentation related to metadata submission. A good first step is to take a closer look at the Submission FAQ. To have a general overview of all the metadata submission process we recommend taking a glimpse of our take-the-tour or watching the tutorial available on our YouTube Channel. Don't miss our section on EGA Schemas, to learn more about how the EGA is built. It can be useful to fully ensure that your submissions comply with the EGA's standards and contribute to a valuable and accessible genomic resource.

  Blog new-submitter-portal

• Molecular_characterization_of_invasive_lobular_carcinoma

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

  Study EGAS00001000292

• GCAT| WGS Imputation Panel V1

  This dataset includes the .hap, .legend and .sample files from the GCAT|Panel (Iberian reference panel), built from 785 samples, after QC, from the 808 WGS GCAT cohort, including 30.3M SNVs, 5M Indels and 89K SVs. This resource has been generated using Shapeit4 and WhatsHap software. Technology used HiSeq 4000, read length 150 bp, inner mate disatance 300 bp.

  Dataset EGAD00010002153

• Expression array

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains expression array data for 32 patients of the screening cohort with 8 of them having paired normal tissue plus an additional relapse tumor/normal pair of one of those 8 patients and a patient only with normal tissue. Data was generated on a HumanHT-12 v4 Bead Array (Illumina) and is stored in IDAT file format.

  Dataset EGAD00010002596

• Whole genome sequencing of Sinonasal hemangiopericytoma and patient derived cell line model

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1 using whole genome sequencing.

  Study EGAS50000000025

• RNA-Sequencing of cervical cancers

  We used RNA sequencing of 81 cervical cancer specimens to developed an immune-based gene expression signature to predict distant metastasis in cervical cancer patients treated with RT/cisplatin. Our 55-gene risk score, validated across independent cohorts, was strongly linked to higher rates of metastasis and lower survival. The score also correlated with higher copy-number alteration and a less immune-responsive tumor microenvironment, indicating its potential in identifying high-risk patients and informing targeted therapies.

  Dataset EGAD50000000120

• Single-cell RNA-seq of immune cell subsets isolated from human tumors (Kaptein et al., 2024)

  Single-cell RNA-seq profiling of effector (KLRG1+ PD1-), transitional (KLRG1+ PD1-intermediate), dysfunctional (CD39+ PD1+) and memory (IL7Rα+) CD8 T cells isolated from 4 human tumors (1 melanoma, 1 renal carcinoma and 2 ovarian carcinoma). Respective cell populations were identified and isolated using FACS. FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on individual CD8 T cell subsets across the 4 different samples.

  Dataset EGAD50000000376

• Brigham and Women's Hospital Multiple Sclerosis Genetic Collection

  The main objective of this GWA study is to identify Multiple Sclerosis (MS) susceptibility loci. Whole-genome association analysis was performed on 924 individuals genotyped on the Affymetrix 6.0 Genechip. The cohort consisted of 860 clinically diagnosed MS patients and 64 control subjects.

  Study phs000275

• Phase 2 Study of Pembrolizumab in Combination with Gemcitabine and Cisplatin as Neoadjuvant Therapy

  The purpose of the clinical trial (NCT02690558) is to evaluate whether adding pembrolizumab (Keytruda) to the combination of gemcitabine and cisplatin will improve shrinkage of the tumor before having a cystectomy, for people with muscle-invasive bladder cancer (MIBC).

  Study phs003452

• Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

  Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycaemic traits. However, little is known about the function of the zinc finger transcription factor Ras-responsive element binding protein 1 (RREB1) in glucose homeostasis or how changes in its expression and/or function influence diabetes risk.

  Dataset EGAD50000000515

• Diagnostic yield and clinical utility of whole-exome sequencing in pediatric patients with rare and undiagnosed diseases in the Czech Republic

  In our single-center study, we have launched a pilot program for pediatric patients with undiagnosed diseases in the second-largest university hospital in the Czech Republic. WES was implemented as a first-line test after inclusion in the study as part of the diagnostic workflow. This study was prospectively conducted at the Department of Pediatrics at University Hospital Brno between 2020 and 2023.

  Dataset EGAD50000000640

• WES profiles from the CheckMate-142 clinical trial.

  The dataset contains WES profiles of 59 patients from the CheckMate-142 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. Baseline tumor tissue and matched whole -blood samples were processed using the Agilent SureSelect Human All Exon V5 in-solution hybrid capture panel and underwent subsequent next-generation sequencing (NGS) on the Illumina NovaSeq platform. Fastq files are included.

  Dataset EGAD50000000610

• High-grade serous ovarian carcinoma tumour exome sequencing variants

  Tumour variants (in VCF format) from exome sequencing (using Agilent SureSelect and TWIST library preparation systems followed by sequencing on Illumina HiSeq and NovaSeq platforms) of 108 high-grade serous ovarian tumour samples. Germline variants from EGAD00001006030 for these individuals were used to call somatic and tumour-only variants separately, creating two VCF files per sample (except for one sample without paired germline data- somatic variant file only provided). The dataset comprises 215 VCF variant files.

  Dataset EGAD50000001132

• Determinants of DNA methylation patterning in human placental development and trophoblast stem cell models.

  To assess whether the DNA methylation landscape of human trophoblast stem cells resembles an in vivo cell type, we used post-bisulfite adaptor-tag sequencing to measure genome-wide DNA methylation of preimplantation human trophectoderm and sorted first trimester cytotrophoblast.

  Study EGAS50000000661

• WES analysis of DMD-ASD, DMD-ID and DMD-Control individuals for de novo and rare risk variants analysis

  This project generated a whole-exome sequencing (WES) dataset of 83 boys with a pathogenic variant in the DMD gene, along with WES data from the parents of 38 of them, totaling 159 samples. In addition to DMD, 12 boys also had ID (12 DMD-ID samples), 36 boys had ASD (DMD-ASD samples) and 35 did not present ID or ASD diagnosis (DMD-Control samples).

  Dataset EGAD50000001113

• Human brain development single cell sequencing additional samples

  69 tissue samples from various parts of the developing human embryo brain were dissociated and single cells were collected and processed without bias for mRNA-seq using 10X chromium 3' protocol. Libraries were sequenced on Illumina NovaSeq and reads aligned against the human GRCh38 genome. This is an addition to EGAD00001006049 Human development single cell sequencing, consisting of samples added after the original submission to EGA, but included in final paper.

  Dataset EGAD50000001295

• RNA-seq libraries from FFPE samples using Illumina Ribo-Zero Plus kit

  RNA was extracted from FFPE human tissue samples and used to prepare RNA-seq libraries with the Illumina Stranded Total RNA Prep Ligation kit with Ribo-Zero Plus. cDNA synthesis was performed starting from 100 ng of DNA-free RNA. Libraries were amplified with 16 PCR cycles and sequenced in paired-end mode (2×150 bp) on the Illumina NextSeq 550 platform. Library quality was assessed with Bioanalyzer and Qubit.

  Dataset EGAD50000001553

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established a kind of lung cancer tumoroids derived from a mucus-producing solid pulmonary adenocarcinoma patient. We performed whole exome sequencing and RNA sequencing to analyze genetic background of the tumoroids.

  Study JGAS000664

• Comprehensive survey for the construction of an integrated database of food, gut microbiome, and health information (the "Sukoyaka Health Survey")

  We conducted a cohort-based study to investigate the association between the genetic background and diet/lifestyle in 59 healthy Japanese. We analyzed some participants living in Nagasaki. Shotgun metagenomic sequencing of fecal microbiome were analyzed.

  Study JGAS000681

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established a kind of lung cancer tumoroids derived from a mucus-producing solid pulmonary adenocarcinoma patient. We performed whole exome sequencing and RNA sequencing to analyze genetic background of the tumoroids.

  Study JGAS000653

• Dataset of Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  This dataset is made of 166 samples extracted from 1) FFPE blocks of the most recent biopsy (metastasis when applicable or primary tumor) of the breast tumor 2) Plasma samples and blood samples at baseline, at Day 1 Cycle2, Day 1 Cycle 3 and at progression or treatment discontinuation. Target sequencing has been perfomed using GREAT_A_v3 panel

  Dataset EGAD50000001665

• Dynamics of checkpoint receptors in γδ T cell subsets are associated with clinical responses during anti-PD-1 immunotherapies

  scRNA-seq data from circulating gamma delta T cells derived from healthy donors and patients with stage IV melanoma that either responded or did not respond to anti-PD-1 monotherapy or anti-PD-1 and anti-CTLA-4 combination therapy. This dataset includes paired samples from these patients before and 3 months after the start of immunotherapy.

  Dataset EGAD50000001812

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - RNA validation cohort

  This reposiroty contains bulk RNA data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001212

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - WGS validation cohort

  This reposiroty contains bulk WGS data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001211

• Single cell data from TB patients

  The dataset comprises single-cell RNA sequencing (scRNA-seq) data derived from around 60,000 PBMCs collected from donors across different severity groups of extrapulmonary tuberculosis (EPTB) and healthy controls (3 healthy, 3 mild, 3 intermediate, 3 severe). The data include both transcriptomic and surface protein expression profiles obtained using the BD Rhapsody Single-Cell Multiomics System. Libraries were prepared for whole transcriptome analysis (WTA), AbSeq, and sample tagging, with sequencing performed on a NovaSeq 6000 system.

  Dataset EGAD50000001118

• Tapestri Sequencing Data of PDAC Autopsy Samples

  This dataset comprises single-cell DNA sequencing data for selected pancreatic ductal adenocarcinoma (PDAC) autopsy samples. It employs a targeted gene panel to identify single nucleotide variants (SNVs) and copy number variations (CNVs) using the Mission Bio Tapestri platform. The samples encompass primary and metastatic tissue from selected PDAC patients. This dataset includes 74 sample-level BAM files and 24 patient-level H5 files, generated by the MissionBio pipeline.

  Dataset EGAD50000001936

• Targeted sequencing data of regulatory regions in 200 Spanish ASD trios

  This dataset consists of genomic sequencing data obtained through targeted sequencing of regulatory regions ( 85,394 human cCREs from ENCODE v2, version 2, https://screenv2.wenglab.org/) in 200 ASD (Autism Spectrum Disorder) trios (father and mother unaffected and proband affected)(600 samples total). Sequencing was carried out at the Centre for Genomic Regulation (CRG), Barcelona, Spain. Uploaded files are .vcf (600 samples). The goals of our study were to detect de novo and inherited variants in ASD probands. Sequencing data were obtained in an Illumina NovaSeq6000 instrument.

  Dac EGAC50000000695

• Transcriptome sequencing, DNA methylation analysis, and SNP array analysis of acute lymphoblastic leukemia in Down syndrome

  Pathogenesis of acute lymphoblastic leukemia in Down syndrome (DS-ALL) is poorly understood. To investigate molecular basis of DS-ALL, we performed whole transcriptome sequencing, DNA methylation array, and SNP array analysis in 43 cases of DS-ALL.

  Study JGAS000147

• RNAseq of organoid and fibroblast co-cultures

  The dataset includes whole transcriptome RNAseq BAM files of both organoids and fibroblast mono- and co-cultures with have been processed by Picard markdups. The experiment featured 6 fibroblast cell lines derived from 5 different early CRC biobank patients (pt10, pt12, pt15, pt19, pt22) as well as from different regions within those samples (normal tissue, core or invasive front). The organoids were generated from patient pt5 carcinoma samples.

  Dataset EGAD50000002202

• Long read whole genome sequencing data from brain postmortem tissue

  Dataset consisting of 172 whole genome sequencing runs from healthy controls and Parkinson's disease patients. The data was sequenced on Oxford Nanopore (PromethION) platform. The data has been mapped to T2T-CHM13v2.0 reference genome. The data processing pipeline is available on the following link: [https://zenodo.org/records/13385065](https://zenodo.org/records/13385065). The data is in CRAM format and subet of donors also have information on C (hydroxy)methylation (MM and ML tag). The reads are also phased (HP tag).

  Dataset EGAD50000001349

• WGS data of paediatric ETV6::RUNX1 B cell acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of five ETV6::RUNX1 ALL patients (ALLT-380, ALLK-114, ALLT-388, ALLT-392, ALLT-394). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002285

• Oxford Nanopore Adaptive Sampling WGS

  Eight samples were analyzed on an Oxford Nanopore MinION flow-cell, and to evaluate multiplexing, four samples were run together on one flow-cell on the P2 Solo device. Using adaptive sampling, we targeted 10 regions of different structural variant types, including deletions, translocations and complex rearrangements. MinION sequencing resulted in between 14.1-18.3 Gb of data per flow cell, with mean autosomal on-target coverage of 28.4x and off-target read depth coverage of 5.3x.

  Dataset EGAD50000001821

• Single‑nucleus multiome data of human fetal livers

  Single‑nucleus multiome data of 53 human fetal liver hematopoiesis spanning 5-18 post-conception-weeks. Nuclei were isolated after tissue dissociation and sorting live CD45+CD235- cells, and processed according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Manual specifications. Sequencing data was processed with CellRanger Arc v2.0.2 and aligned to GRCh38-2020-A-2.0.0.

  Dataset EGAD50000002337

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of eight hyperdiploid ALL patients (ALLT-364, ALLT-367, ALLT-368, ALLT-371, ALLT-377, ALLK-111, ALLT-382, ALLT-395). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002427

• Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH

  Initially IDH1 mutant gliomas are shown to have IDH1 is deletions or amplifications at recurrence yielding a higher-grade tumor with a reprogrammed epigenome. We also report systematic selection for cells with IDH1 CNA in vitro and in vivo.

  Study EGAS00001002618

• RNA sequencing of untreated and treated KRAS-mutated metastatic colorectal cancer PDX-derived organoids.

  RNA sequencing was performed on patient-derived xenograft (PDX)-derived organoid models of metastatic colorectal cancer (mCRC). The aim of this study was to characterize the transcriptional landscape of KRAS-mutant mCRC cells in response to therapeutic strategies targeting the EGFR and KRAS signaling pathways. Transcriptomic profiling was conducted following drug treatments to investigate molecular changes associated with single and combination therapies. A total of 24 samples were analyzed.

  Dataset EGAD50000002443

• WTCCC2 Reading and Mathematics (RM) samples

  A WTCCC2 project genome-wide association study for reading and mathematics ability in 3665 12-year-old individuals from the UK, genotyped on the Affymetrix 6.0 array. Details of the WTCCC2 analysis can be found in Davis et al. [Nat. Commun. 2014 July;5:4204]

  Study EGAS00001000886

• BLUEPRINT RNA-seq data for rare cells in the haematopoietic lineages, from adult and cord blood samples.

  RNA-seq data for rare cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001000284

• The genomic landscape of germinal center derived B-cell lymphomas other than follicular, diffuse-large B-cell and Burkitt lymphom

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing and RNA sequencing of germinal center derived B-cell lymphoma. Analyses were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002422