2197 results for "盛和资源+机构评级+2026年3月最新"

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• Single cell RNA-sequencing of treatment naïve PDAC patient samples

  Single cell RNA-sequencing of treatment naïve PDAC patient samples. We have 10 samples, sequenced using the 10X genomics chromium platform with 3 prime chemistry. We are submitting FASTQ files representing the index files (I1), Read1 (R1) and Read2 (R2).

  Dataset EGAD00001008961

• GELATO clinical trial RNA-Seq data (primary tumors and local recurrences)

  RNA-Seq data of 10 lobular breast cancer primary tumors and 3 local recurrences obtained from 11 unique patients from GELATO clinical trial. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material.

  Dataset EGAD00001009835

• Differential methylation positions

  This dataset includes an analyzed DMP file that provide the information about differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. Of the five lung cancer cases, 3 are adenocarcinoma and 2 are squamous carcinoma.

  Dataset EGAD00001010147

• Peripheral Blood Leukocytes 10x Genomics scRNA-seq

  This dataset contains 10x Genomics Single Cell 3’ Solution (version 2) scRNA-seq data from peripheral blood leukocytes of a single healthy donor. Data from 20939 cells were collected over 8 lanes and 2 sequencing runs.

  Dataset EGAD00001008590

• Single-cell short-read transcriptomes from CH, MDS and AML patients with splicing factor mutations

  Single-cell RNA sequencing from CH (n = 2), MDS (n = 6, MDS02 in 2 replicates) and AML (n = 1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8, U2AF1 n = 1). cDNA from 10x Genomics 3' V3.

  Dataset EGAD00001011283

• Whole exome sequencing of patient derived cell lines

  Whole exome sequencing of 3 patients derived cell lines and patient blood (N = 6 samples), performed using Agillent SureSelect All Exon V5 and Illumina HiSeq 4000. Data is in raw fastq format (N = 10 fastq pairs, 20 files total), as some samples were split between two lanes.

  Dataset EGAD00001007738

• Bulk RNA-sequencing of AML blasts pre and post culture

  This dataset contains 18 Fastq files from 9 samples (pre-culture (n=3), post culture in standard (n=4) or niche-llike (n=2) conditions) from 4 patients.They correspond to bulk RNA sequencing on Illumina instrument of libraries prepared using SMARTer Universal Low Input RNA Kit.

  Dataset EGAD00001008773

• bulk RNA-Seq samples of CRC patients

  The dataset contains samples of 30 CRC patients (3 samples for each patient, tumor and 2 normal adjacent tissue sites, 90 samples in total). Dataset is composed by fastq file (paired end) type from bulk RNA-Seq.

  Dataset EGAD00001009635

• Exome sequencing of a novel cervical cancer cell line

  In this work, we establish and characterized a low-passage cervix cancer cell line from a Brazilian patient with squamous cell carcinoma. The dataset contains three samples from the same patient (blood, tumor tissue and the primary cell line). The technology used was exome sequencing and the file type available is fastq files.

  Dataset EGAD00001004480

• RNA-seq data of 370 high grade ovarian tumors from the ICON7 trial

  Collection of RNA-seq, Illumina, paired-end fastq files for 370 archival tissues from a subset of patients with high grade serous ovarian carcinoma enrolled in the phase 3 ICON7 trial. Clinical data and digital pathology information for CD8 is also available.

  Dataset EGAD00001004988

• Exome sequencing of serially transplanted genetically marked IC-enriched primary PDAC cultures.

  In order to elucidate whether newly acquired genetic alterations during serial transplantation of patient derived primary pancreatic cancer cultures contribute to the observed clonal dynamics in vivo, all coding genes of two patient derived primary cultures and derived genetically marked serial xenografts (1°/2°/3°) were sequenced.

  Dataset EGAD00001000884

• IBD WES trio data-ALPI-P2

  This project focused on identifying rare coding variation that substantially increases risk of VEOIBD by exome sequencing of VEOIBD patients and some of their family members. Here you can find BAM files from an affected proband (P2) and his unaffected parents. In this study ALPI mutations were identified as a likely cause of the disease.

  Dataset EGAD00001004485

• Cancerous Adaptive Dosing Melanoma WGS Dataset

  Illumina NovaSeq 6000 30x WGS of 26 samples, each with up to 5 matched timepoints. Timepoints A,B,C,D,and E correspond to Pretreatment, Week 3, Week 6, Week 9, and Week 12 after treatment, respectively. Additional sample metadata (sample recurrence, treatment course, age, sex, comorbidities, etc.) are present in sample description.

  Dataset EGAD00001010926

• Human Hi-C

  This dataset contains 2 human tumor-derived cell lines and 1 human tumor Hi-C samples. The raw fastq files and the processed .hic file is provided for each sample.

  Dataset EGAD00001009050

• Osteosarcoma whole genome rearrangement screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Dataset EGAD00001000368

• Whole genome sequencing of patient IPSCs and tumors (organoids)

  This dataset contains whole genome sequencing data of a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) . This dataset further contains whole genome sequencing data of two tumors showing CNLOH. Tumors were isolated from organoids grown using the patient IPS cell line (Patient 1 TSC2+/- iPSCs )

  Dataset EGAD00001006333

• HPS1 patient monocyte-derived macrophage and control macrophage RNAseq with and without infection

  4 HPS1 patient monocyte-derived macrophages and 4 controls were RNA sequenced at baseline and after Salmonella Typhimurium infection. We used paired end sequencing on an Illumina HiSeq 4000. Each sample was run on 3 lanes for sequencing depth, which we combined for our analysis.

  Dataset EGAD00001006978

• Mutation of FOXL2 in granulosa cell tumors of the ovary

  We generated paired-end RNA-Seq data using the Illumina Genome Analyzer II platform for four adult granulosa cell tumours (GCTs) of the ovary (1 primary, 3 recurrent). We screened this data for the presence of GCT specific sequence variants and detected a non-synonymous mutation in the FOXL2 gene that was found to be recurrent in 97% of 89 additional GCTs. To measure genomic stability of the four index cases, we generated Affmetrix SNP 6.0 data and analysed these data for copy number changes. Raw sequence reads as well as Affymetrix CEL files are available to applicants.

  Study EGAS00000000040

• Test Study for EGA using data from 1000 Genomes Project - Big CRAM, BAM, VCF and BCF files used for testing

  This is a test study for EGA using data from 1000 Genomes Project, specifically created to add more diversity to the existing dataset EGAD00001003338. This Test Study should NOT be confused with the real study of 1000 Genomes Project - Phase 3. Specifically, this study encompasses 4 CRAM, 4 BAM, 2 VCF and 2 BCF files, of different sizes (all above 1 GB), used for testing downloads and monitoring services. It also contains their respective indexes: crai for crams, bai for bams, tbi for vcfs and csi for bcfs.

  Study EGAS00001006718

• Gene Expression and Epigenetic Analyses of Human Myocytes From Different Muscles

  The study contains expression and DNA methylation data of in vitro cultured myoblasts derived from biopsies of control, FSHD1 and FSHD2 patients from the tibialis anterior, quadricep, bicep and deltoid. Expression data is from bulk RNA-seq using the SmartSeq2 protocol for days 0 and 5 of in vitro differentiation of primary myocytes from the bicep and deltoid of FSHD1 patients. DNA methylation data was produced using the TruSeq Methyl Capture EPIC kit (Illumina) for days 0, 3 and 12 of in vitro differentiation of primary myocytes from the tibialis anterior and quadricep of healthy individuals and FSHD2 patients.

  Study phs002554

• Transcriptomic Profiling of Patient Derived Alternative Lengthening of Telomeres (ALT) and Non-MYCN-Amplified Neuroblastoma Cell Lines

  Patient derived neuroblastoma cell lines are excellent tools to study biology of the disease. While many previous studies sequenced neuroblastoma cell lines, there are very few ALT and non-MYCN-amplified neuroblastoma cell lines that were sequenced previously. Here, we present raw RNA sequencing data for 3 ALT (CHLA-90, SK-N-FI, COG-N-515) and 8 non-MYCN-amplified telomerase positive (CHLA-171, Felix, COG-N-579h, COG-N-615, COG-N-618h, COG-N-619h, COG-N-708h, COG-N-709) neuroblastoma cell lines. Additionally, gene expression data are provided as a supplement files.

  Study phs002421

• Genomics from LCCC1525: A Priming Dose of Cyclophosphamide Prior to Pembrolizumab to Treat mTNBC

  This phase II, single-arm, multicenter study will evaluate pembrolizumab therapy, 200 mg IV, given every 3 weeks (Q3W), following a single priming dose of cyclophosphamide, 300 mg/m2 IV, in patients with advanced triple-negative breast cancer (TNBC) who have received at least one prior line of therapy. Data uploaded consists of FASTQ sequencing data from tumor RNASeq (pre-pembrolizumab), tumor and normal tissue WES, and sequencing for targeted T and B cell chains (TRB, IGK, IGL, IGH) from peripheral blood at various timepoints: pre-, post-, and during pembrolizumab therapy.

  Study phs002659

• Whole Exome Sequencing of Uveal Melanoma

  Uveal melanoma is a rare form of melanoma that occurs in the eye and has no effective treatment once metastatic. To further characterize the genomic events driving uveal melanoma, whole exome sequencing was performed on 61 primary tumors derived from enucleations, 3 liver metasases, and paired normal DNA. Recurrent somatic genetic alterations including point mutations, small insertions and deletions, as well as copy number variations were identified. In addition, RNA sequencing of uveal melanoma cell lines expressing shRNAs was performed from total RNA as well as polysome-associated mRNA in order to identify transcripts regulated by EIF1AX at the level of translation.

  Study phs001370

• Multiregion Sequencing of Localized Prostate Cancer

  Ten patients with treatment-naïve, locally advanced or localized prostate cancer underwent radical prostatectomy. Pathological stage ranged from T2aN0 to T3bN1, and Gleason scores from 3+4 to 4+5. Tumor foci were mapped, and DNA was extracted from multiple (5-9) regions from a single, contiguous index focus. Whole exome sequencing was performed to identify single nucleotide variants and indels, and low coverage whole genome sequencing was performed to estimate copy number variation. Phylogenetic relationships between foci was determined, and alterations associated with advanced disease or response to targeted therapy were identified.

  Study phs001465

• Whole Exome Sequencing Identifies

  Combined Immunodeficiency with Multiple Intestinal Atresias (CID-MIA) is a rare genetic disorder with the cause previously unknown. Symptoms of CID-MIA include atresias in the small and/or large intestine, as well as immunodeficiency. In this study, we sequenced the whole exome of 5 unrelated CID-MIA patients as well as their healthy family members, and identified deleterious homozygous or compound heterozygous mutations in the gene TTC7A in all the 5 patients, as well as in 3 additional patients with Sanger sequencing. Our findings strongly indicate TTC7A dysfunction to be the cause for CID-MIA.

  Study phs000641

• The UC San Diego Chronic Lymphocytic Leukemia (CLL) Study

  The UC San Diego Chronic Lymphocytic Leukemia Study is designed to identify genetic, epigenetic, and transcriptional changes important for CLL. This data release consists of samples collected to 1) identify genomic changes associated with CLL progression using serially collected tumor samples; 2) characterize the transcriptional consequences of SF3B1 mutation through RNA-seq; and 3) characterize the expression profiles of ROR1+ vs. ROR1- tumors. The samples were collected from participants at the University of California, San Diego Moores Cancer Center and the data was generated at UC San Diego or in collaboration with the BC Cancer Agency Genome Sciences Centre.

  Study phs000767

• Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions

  Chromosomal inversions (INV) are particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage sensitive genes in cis. Short-read genome sequencing (srGS) can only resolve ~70% of cytogenetically visible inversions referred to clinical diagnostic laboratories, likely due to breakpoints in repetitive regions. Here we study twelve inversions by srGS (n=3) or long read genome sequencing (lrGS) (n=9)

  Study EGAS50000000436

• RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

  Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect.

  Study EGAS50000000667

• Comparison of transcriptomics profile of stem cell-derived beta cells from HUES8 and RC9

  Stem cell-derived islet cells have a potential to be used to restore endogenous insulin production in people with diabetes. The goal of this experiment is to compare the transcriptomics profile of stem-cell derived beta cells from two different cell lines: HUES8 (non-clinical grade) and RC9 (clinical grade) in terms of beta cell identity and maturity. Stem cell-derived islets were produced using differentiation protocol detailed in Rajaei et al. 2025 (manuscript approved in Science Translational Medicine, pending pubmed ID). Single cell transcriptomics data were generated using 10x Genomics 3' Single Cell Gene Expression kit.

  Study EGAS50000000905

• Transcriptomic profiles studies CAREs group - IDIBGI

  The purpose of this DAC document is to outline the principles and procedures governing access to the transcriptomic data generated from endothelial progenitor cells, or any biological origin from patients. Data Access Policy: 1) Access to this dataset is restricted and subject to approval by the DAC to ensure ethical and legal compliance. 2) The DAC reserves the right to evaluate all applications for access based on: 2.1) The scientific validity and merit of the proposed research. 2.2) The ethical considerations and adherence to data protection regulations, including GDPR. 2.3) The qualifications and affiliations of the applicants. 3) Applicants must submit a detailed research proposal, including objectives, methods, and anticipated outcomes. 4) Data usage is limited to the specified research project approved by the DAC. Any secondary use of the data requires additional approval. Confidentiality: All applicants must agree to maintain the confidentiality of the dataset. Personal identifiers have been pseudonymized to protect patient privacy. Application Process: 1) Researchers must complete the application form provided by the DAC. 2) Submit proof of ethical approval and relevant certifications for their research project. 3) Provide a signed agreement affirming adherence to the DAC's terms and conditions.

  Dac EGAC50000000607

• Transcriptional characterization of human innate lymphoid cells (ILCs) and natural killer (NK) cells from fresh umbilical cord blood

  The heterogenicity of cord blood ILCs (ILC1, ILC2, ILC3) and NK cells in humans has so far not been assessed. In this study, we sorted from fresh cord blood the respective cell types from 3 donors and performed single-cell transcriptome analysis. To achieve high resoluation, each sorted population was labelled individually via multiplexing antibodies and subsequent Abseq staining before pooling. To determine single-cell transcriptomes the BD Rhapsody pipeline was performed. This is the first data set to characterize human ILCs and NK cells at such depth.

  Study EGAS50000001204

• Primary breast tumor heterogeneity through therapy

  We performed whole-exome sequencing on multiple regions (n=2-3) from four primary untreated breast tumors (n=1 HER2+, n=2 ER+/HER2-, n=1 triple-negative), as well as matched normal. We also performed whole-exome sequencing on one region from the pre-treatment diagnostic core biopsy and multiple regions (n=2-6) from the post-treatment surgical specimen for five HER2+ primary breast tumors, as well as matched normal; all were treated with combination chemotherapy and trastuzumab. Analysis of these specimens allows characterization of breast tumor heterogeneity and clonal evolution.

  Study EGAS00001003168

• Single-cell transcriptomic data from tumor samples

  Extramedullary multiple myeloma is an aggressive form of multiple myeloma where the myeloma cells escape BM microenvironment and infiltrate distant tissues.We analyse using single cell techniques, the composition and functional state of major immune cells in EMM tumor microenvironment, T and NK cells. This dataset contains the singlecell RNAseq data used in the publication. It includes scRNAseq data from tumor samples across extramedullary multiple myeloma soft tissue (EMM) (n=5; 3 additional samples in the study are under accession numbers mentioned in the publication), EMM bone marrow (EMM_BM) (n=5), and relapsed/refractory multiple myeloma (RRMM_BM) BM (n=6).

  Study EGAS50000001038

• RNA-seq analysis of megakaryocytes and granulocytes in Quebec platelet disorder

  Quebec Platelet disorder (QPD) is a unique bleeding disorder that markedly increases urokinase plasminogen activator (uPA) in megakaryocytes and platelets but not in plasma or urine. The cause is tandem duplication of a 77 kb region of chromosome 10 containing PLAU and C10orf55. Blood cells and cultured megakaryocytes from donors (7 QPD, 10 control subjects) were prepared for total and allele-specific, quantitative reverse transcription polymerase chain reaction, immunoassays, Western blots and RNA-seq. Transcriptomes for cultured megakaryocytes and peripheral blood granulocytes from 4 control and 3 QPD individuals were analyzed using mRNA-seq.

  Study EGAS00001001840

• Adult-type Granulosa Cell Tumour of the Ovary RNA Sequencing

  We analyzed 34 AGCTs (19 primary and 15 recurrent) and the KGN cell line by RNA-Seq. Our cohort comprised of 3 AGCTs WT for FOXL2, 28 heterozygous and 3 homo/hemizygous for the pathogenic variant. Fresh-frozen AGCTs were selected from OVCARE’s Gynecological Tissue Bank in Vancouver, Canada for bulk RNA-seq. RNA was extracted from frozen tissue and sections adjacent to the scrolls submitted for RNA-seq were stained with hematoxylin and eosin (H&E) to evaluate tumour cell purity. Cases with >80% tumour cell purity were selected for sequencing with the majority of cases (29 of 34 patients) containing >90% tumour cells. Ribodepleted RNA libraries were constructed and paired-end sequencing (125 base pair reads) was performed.

  Dataset EGAD00001007812

• Methylome profiling of Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) and a 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 the twist human methylome panel.

  Dataset EGAD50000000040

• Short-read single-cell RNA-sequencing of the human brain in neurodegenerative diseases

  Nuclei were isolated from postmortem human brain tissue, and single-nucleus barcoded cDNA libraries were generated using the 10X Genomics 3' v3.1 kit. Samples were sequenced on an Illumina NovaSeq 6000 to an average of 343 million reads per sample and 52,000 reads per cell.

  Dataset EGAD50000000178

• WGS of Newly Diagnosed and Refractory/Relapsed Multiple Myeloma

  This dataset includes paired tumor and non-tumor WGS data from patients diagnosed with newly diagnosed (n = 6), refractory/relapsed multiple myeloma (n = 3) or plasma cell leukemia (n = 1). These samples presented >95% tumor PCs in bone marrow aspirates. Plasma cells and T cells (non-tumor cells) were isolated from bone marrow aspirates using a magnetic approach.

  Dataset EGAD50000001177

• MDACC Lymphoma & Myeloma WGS of Tumor and Non-tumor Cells in Multiple Myeloma

  FastQ files from paired tumor and non-tumor WGS data from patients diagnosed with newly diagnosed (n = 6), refractory/relapsed multiple myeloma (n = 3) or plasma cell leukemia (n = 1). These samples presented >95% tumor PCs in bone marrow aspirates. Plasma cells and T cells (non-tumor cells) were isolated from bone marrow aspirates using a magnetic approach.

  Dac EGAC50000000282

• Mutational Profile in Newly Diagnosed Diffuse Large B-Cell Lymphoma: Insights from the GAINED Study

  The GAINED study (NCT01659099) is a randomized phase 3 trial comparing obinutuzumab (G) to rituximab (R) in combination with ACVBP or CHOP14 induction, followed by PET-guided consolidation. This post-hoc analysis focuses on primary mediastinal B-cell lymphoma (PMBL) patients, confirmed through expert pathological review and characterized using gene-expression profiling (GEP) and Next-Generation Sequencing (NGS).

  Dac EGAC50000000540

• Citeseq of human bone marrow

  CITE-seq dataset of human bone marrow from four healthy donors. Single-cell RNA sequencing was performed using the 10x Genomics 3’ v3 platform. Approximately 7,000–10,000 cells were loaded in each 10x channel, after which the single-cell libraries were prepared according to manufacturer’s instructions, except for the added CITE-seq steps. Demultiplexed FASTQ files are provided.

  Dataset EGAD50000001211

• DNA methylation changes associated with hyperglycemia in type 1 diabetes

  This dataset includes DNA methylation profiles from 112 young with Type 1 Diabetes (T1D) at T1D diagnosis, who were longitudinally monitored for hyperglycemia over an average duration of 3 years. These datasets were generated using whole-genome bisulfite sequencing. It includes 1872 fastq files (i.e. 936 paired-end fastq files) generated through 150 bp paired-end sequencing on Illumina HiSeqX.

  Dac EGAC50000000237

• APP p.V742L and control fibroblasts RNA-seq

  This dataset consists of 16 FASTQ file pairs containing 3` RNA-sequencing data of patient-derived fibroblasts and three age- and sex-matched control fibroblast lines (CTR1, CTR2, and CTR3). The patient and CTR1 fibroblast lines have three biological replicates, while CTR2 and CTR3 lines both have one sample. Each sample has two lanes.

  Dataset EGAD50000001825

• human placenta snRNA-seq (n=12)

  This dataset include the snRNA-seq raw sequencing files from the placentas of 4 normal weight control and 8 obese individuals. The files are paired-end fastq files. The snRNA-seq libraries were generated with Chromium Single Cell 3’ kit v3.1 (10X Genomics) and sequenced on Illumina NovaSeq 6000 at Novogene, UK.

  Dataset EGAD50000001222

• Lymphoma_primary_patient_drug_perturbed_RNASeq_samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET-762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dac EGAC50000000578

• Single-nucleus Isoforms of Down Syndrome Brains (long-read)

  16 DS and Control brains samples were prepared using the 10X Genomics Single Cell 3' v3 kit. Pre-fragmented cDNA libraries were loaded onto a Pacific Biosciences Sequel II to sequence single-nucleus isoforms.

  Dataset EGAD00001008286

• Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

  RNA seq of iPSC-derived cardiomyocytes cultured in lipid-enriched maturation medium (MM), in MM on nanopattern-surfaces (NP) and under the influence of MM, NP and electrical Stimulation (ES, 2Hz, 14 days). 9 Samples from 3 Independent batches/differentiations of cardiomyocytes from 2 different iPSC-lines (iWTD2.1 and isWT7.22).

  Dataset EGAD00001011289

• Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections

  Advamced Visium Spatial Gene Expression assay for FFPE tissues with human and SARS-CoV-2 whole transcriptome (WT) information at a 55 µm resolution. The dataset consists of 13 tissue sections from 5 patient lung tissue samples, 3 from COVID-19 patients and 2 from control patients.

  Dataset EGAD00001008701

• Bulk ATAC data

  Bulk ATAC libraries were generated for patient samples A.1, A.3, A.5, A.6, A.7, A.11, A.12, A.13 and A.15. For each patient a library of CD3- cells (myeloid cells, considered tumor cells) and CD3+ cells (T cells, considered healthy) were generated.

  Dataset EGAD00001010188

• Transcriptome/Exome for glioblastoma intra-tumoral heterogeneity

  Total of 49 tumor specimens from 20 patients were subjected for whole-exome and/or whole-transcriptome sequencing including matched normal/blood. Tumor samples are acquired based on 4 categories; 1) locally adjacent tumors, 2) multifocal/multicentric tumors, 3) 5-ALA (+/-) tumors and 4) Longitudinal tumors.

  Dataset EGAD00001002248

• SPATC1L variants associated with age-related and hereditary hearing loss.

  The dataset contains three BAM files that include SPATC1L variants identified in Italian patients affected by hearing loss (both hereditary and age-related hearing loss). Data have been produced by whole exome sequencing and targeted re-sequencing, using Ion Proton and Ion Torrent PGM platforms respectively.

  Dataset EGAD00001004147

• NHLBI GO-ESP Family Studies: Idiopathic Bronchiectasis of unknown etiology that is not related to cystic fibrosis or classic primary ciliary dyskinesia or immune deficiency or any other known causes

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. The major goal of this project is to apply next generation resequencing technology to identify disease-causing variants that cause bronchiectasis of unknown etiology (e.g. non cystic fibrosis (CF), classic primary ciliary dyskinesia (PCD), immune deficiency, or any other known cause of bronchiectasis), i.e., "idiopathic bronchiectasis." As part of our ongoing efforts to define the genetic cause of rare lung diseases, we have also studied families in whom diagnosis of PCD or other known etiologies could not be confirmed. We have systematically collected and stored the DNA and phenotypic data on each of the families in our cohort. The phenotypic data includes age, gender, ethnicity information, clinical data pertaining to the airways disease, including neonatal respiratory distress, otitis media, sinusitis and bronchiectasis, ciliary ultrastructure analysis, and microbial colonization (status of nontuberculosis mycobacterium). During the course of our study, we have acquired 98 unrelated patients in whom bronchiectasis seemed to be of unknown causes. We will be using 11 unrelated patients, 5 unrelated affected sib-pairs, and 3 affected sibs from a family from this cohort, based on 1) development of bronchiectasis in the absence of smoking, 2) a good family pedigree with available DNA, and 3) a family history of bronchiectasis and/or occurrence of airways disease in a sibling. Classic CF, PCD and immune deficiency were ruled out, based on the tests described above. Alpha-1 antiprotease deficiency work up was negative and none of the patients were tobacco users or smokers.

  Study phs000518

• Genetic Epidemiology of COPD (COPDGene) Funded by the National Heart, Lung, and Blood Institute

  Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States and the only leading cause of death that is steadily increasing in frequency. This project will establish a racially diverse cohort that is sufficiently large and appropriately designed for genome-wide association analysis of COPD. A total of 10,000 subjects will be recruited, including control smokers, definite COPD cases (GOLD Stage 2 to 4), and subjects not included in either group (GOLD 1 or GOLD-Unclassified). This cohort will be used for cross-sectional analysis, although long-term longitudinal follow-up will be a future goal. The primary focus of the study will be genome-wide association analysis to identify the genetic risk factors that determine susceptibility for COPD and COPD-related phenotypes. Detailed phenotyping of both cases and controls, including chest CT scan assessment of emphysema and airway disease, will allow identification of genetic determinants for the heterogeneous components of the COPD syndrome. The hypotheses to be studied are: 1) Precise phenotypic characterization of COPD subjects using computed tomography, as well as clinical and physiological measures, will provide data that will enable the broad COPD syndrome to be decomposed into clinically significant subtypes. 2) Genome-wide association studies will identify genetic determinants for COPD susceptibility that will provide insight into clinically relevant COPD subtypes. 3) Distinct genetic determinants influence the development of emphysema and airway disease. The initial phase of genome-wide association analysis included 500 COPD cases and 500 control subjects (all non-Hispanic White) genotyped with the Illumina Omni-1 chip. The second phase genotyped the entire study cohort using the Illumina Omni-Express chip. Unique aspects of the study include: 1) Inclusion of large numbers of African American subjects (approximately 1/3 of the cohort); 2) Obtaining chest CT scans (including inspiratory and expiratory images); and 3) Inclusion of the full range of disease severity. The COPDGene_v6 Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs000179 COPDGene_v6 Cohort. phs000296 ESP LungGO COPDGene phs000765 COPDGene_Geno

  Study phs000179

• Cellular Indexing of Transcriptomes and Epitopes Sequencing (CITE-Seq) Analysis to Investigate the Impact of Granulocyte-Colony Stimulating Factor on CRISPR/Cas9 Gene Edited Human Hematopoietic Stem Cell Function

  Our research using in-vivo preclinical xenograft mouse models demonstrated that G-CSF impedes engraftment of CRISPR-Cas9 gene edited human hematopoietic stem cells (HSCs). In this CITE-seq study, we sought to investigate the mechanisms by which G-CSF negatively impacts long-term repopulating functions of CRISPR-Cas9 gene edited human HSCs. Accordingly, human CD34+ cells were obtained from a healthy volunteer and edited with Cas9 alone (Cas9 group), Cas9+AAVS1-targeting gRNA (RNP group), or Cas9+AAVS1-targeting gRNA+GSE56 (RNP/GSE56 group). Then, these edited cells were transplanted into busulfan-conditioned NSG mice, and these mice subsequently received 3 days of phosphate buffered saline (PBS) or G-CSF. Each mouse was subsequently euthanized and harvested for bone marrow cells and human CD34+cells were isolated using immunomagnetic beads. Isolated CD34+ cells from a total of 6 mice were individually stained with Total seq B CITE-seq antibodies (CD38, CD45RA, CD90, CD49f) + hashtag oligo antibodies 1, 2, 3, 4, 5 and 6. Fluorescence activated cell sorting (FACS) was used to purify ~2,500 cells from each group that were subsequently pooled for CITE-seq library preparation and sequencing. Seurat was used to demultiplex data into 6 individual groups and differential gene expression analysis was performed to evaluate the impact of G-CSF within Cas9, RNP and RNP/GSE56 groups.

  Study phs003277

• Identification_of_synthetic_lethal_genes_by_CRISPR_Cas9_library

  Sequencing is performed on PCR products from the amplification of gRNA segments introduced into cell lines (some are commercial, some are derived by collaborators, as described in HMDMC 13/076). Cellular DNA or RNA are not sequenced. This data is defined as "Other Biological/Biochemical Assay Data" under the WTSI datasharing guidelines and consequently will be released at the time of publication and/or through faculty websites. SEQUENCING DETAILS: in October 2016 3 DNA samples will be submitted for PCR amplification and purification through CGP pipeline using Thompson's custom primer set and PCR settings and sequencing with Hiseq using a custom protocol (with 3 forward reads to read sgRNA1, sgRNA2 and the index, optimized with Illumina Bespoke Sanger team); read length 50bp. The following set of samples will be submitted in later 2016 and ealry 2017 as cell pellet to be processed through CGP Cas9 pipeline (Thompson's oligos and protocols) and sequences on Hiseq (same custom sequencing protocol described above) We are utilizing a custom CRISPR/Cas9 library to identify synthetic lethal gene pairs. Cells will be transduced with LV expressing Cas9, then infected with LV expressign the library of 42'000 sgRNA pairs. Cell pellet will be collected from the cell population at different timepoints. The samples will be processed by CGP pipeline customized for the specific protocol and then sequenced to identify the 19bp of the sgRNA and quantify their representation.

  Study EGAS00001002117

• InterPregGen-GWAS-UZB-3

  GWAS genotype data for maternal and fetal (baby) cases of preeclampsia and controls from Uzbekistan. This dataset is a component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium members in Tashkent, Uzbekistan at the Institute of Immunology, Uzbek Academy of Sciences and at the Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology

  Dataset EGAD00010001919

• PARK7/DJ-1 deficiency modulates microglial activation in response to LPS-induced inflammation

  Starting point is one patient from which iPSC cells are created, some received a genome correction to be called iCtrl from those two batches (DJ1 and iCtrl). 3 independent differentiation to Microglia cells were done, named R1, R2 and R3. On top, growing conditions were either untreated or LPS, leading to the 12 samples.

  Dataset EGAD50000000291

• Whole-genome sequencing of tumour, germline and plasma samples from a BRCA1-mutant breast cancer patient

  This data set contains the fastq files from whole-genome sequencing of temporally matched tumour (fresh frozen biopsies), blood germline and plasma samples collected from a BRCA1-mutant breast cancer patient to directly compare mutation signature analysis using gold-standard tumour-germline paired variant calling with a novel ctDNA-based method (MisMatchFinder).

  Dataset EGAD50000000811

• CAYA glioma sequencing data

  Low pass WGS and targeted glioma panel sequencing of low and high-grade gliomas in children, adolescent, and young adult patients.. File type is paired-read fastq files (2 per sample). Sequencing was performed on Illumina NextSex instruments. Genes covered on panel: TP53, H3F3A, HIST1H3B, HIST1H3C, IDH1, IDH2, KRAS, PIK3CA, TERT promoter, PTPN11, FGFR1/2/3, MYB, BRAF, MYBL1, EGFR, PDGFRA, MYCN, MYC, CDKN2A.

  Dataset EGAD50000000560

• Single-cell RNA sequencing of 16 NPM1 mutated AML patients

  This dataset contains paired-end fastq files for single-cell RNA-seq of 16 NPM1 mutated AML patients. 19 fastq pairs are included, with two samples split into two lanes and a second (technical) replicate for one patient. Libraries were constructed using 10x Genomics Chromium Next GEM Single cell 3’ v3.1 and sequencing was performed using Illumina NovaSeq6000.

  Dataset EGAD50000000478

• ChIP seq samples

  Dataset contains 12 ChIP-Seq samples sequenced on the Illumina NextSeq500 sequencer. 3 samples are control samples (HcAct-Chip 1,HcAct-Chip 2,HcAct-Imput 2) 9 samples are case samples (HcAct2DG-Chip 1,HcAct2DG-Chip 2,HcAct2DG-Imput 1,JIAAct-Chip1,JIAAct-Chip2,JIAAct-Imput2,JIAAct2DG-Chip1,JIAAct2DG-Chip2,JIAAct2DG-Imput2)

  Dataset EGAD50000001188

• MB_COMICS_Methylome

  Medulloblastoma (MB) is the most common malignant brain tumor in children. It is a neuroectodermal tumor located in the cerebellum. International consensus recognizes four distinct subgroups of MBs including Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4) with distinct molecular characteristics, prognoses, and mortality rates in patients. Here, we have compiled and evaluated a large international MB cohort for which we generated methylome data for 369 primary MB patient samples.

  Dataset EGAD00010002669

• TenK10K Phase 1: scRNA-seq AnnData objects

  Single cell RNA-sequencing data for PBMCs from the Tenk10k Phase 1 cohort (1925 individuals post-QC). Libraries were prepared using the 10x Genomics 3’ Chromium Next GEM Single Cell HT V3.1 kit and sequenced on the NovaSeq 6000 platform. Reads were mapped to the GRCh38 reference genome with Cellranger, and count matrices were preprocessed using Scanpy.

  Dataset EGAD50000002379

• Single-cell atlas of the human healthy airways

  Single cell atlas of human airways from 10 healthy volunteers by 10X Genomics 3’ RNA-seq profiling. 77,969 cells were collected by bronchoscopy at 35 distinct locations, from the nose to the 12th division of the airway tree, either by forceps (46,791 cells), or brush biopsies (31,178 cells).

  Dataset EGAD00001005714

• WXS Tumor Samples Javelin head and neck 100

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the phase 3 randomized, double-blinded, placebo-controlled study in patients with locally advanced squamous cell carcinoma of the head and neck JAVELIN Head and Neck 100 (NCT02952586). There are 471 WXS Tumor samples and 346 RNASeq tumor samples. All tumor samples have matching normal samples.

  Dataset EGAD00001011680

• analysis of the off target effect after Prime editing in IPSC line KCNQ2 R201C. Comparison of parental KCNQ2 R201C with two corrected clonal lines.

  Short read whole genome sequencing analysis of the off target effect after Prime editing in IPSC line KCNQ2 R201C. Comparison of parental KCNQ2 R201C with two corrected clonal lines (3samples in total). Dataset contains CRAM files and VCF files for the respective samples.

  Dataset EGAD00001010904

• 10x genomics RNAseq of an isogenic human iPSC model of SMA

  10x genomics single-cell RNAseq of an isogenic human iPSC model for SMA and control. The transcriptomic analysis was performed at 3 timepoints, day 4, day 20 and day 40. The analysis of this dataset was reported in the manuscript "An isogenic human iPSC model unravels neurodevelopmental abnormalities in SMA" from Grass et al.:

  Dataset EGAD00001011259

• Javelin head and neck 100

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the phase 3 randomized, double-blinded, placebo-controlled study in patients with locally advanced squamous cell carcinoma of the head and neck JAVELIN Head and Neck 100 (NCT02952586). There are 471 WXS Tumor samples and 346 RNASeq tumor samples. All tumor samples have matching normal samples.

  Dataset EGAD00001011290

• scRNA-seq from brain metastasis micorenvironment and cerebrospinal fluid

  A total of 9 brain metastasis were sequenced. For 6/9 a matched cerebrospinal fluid sample, prior to surgery and in two cases after surgery (+1 month from surgery) and after treatment (+3 month) were collected. Single-cell gene expression was produced using the Chromium Single Cell 5’ Library and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD00001006452

• Genetic Basis of Hepatosplenic T Cell Lymphoma (HSTL)

  Whole exome sequencing of hepatosplenic T cell lymphoma (HSTL) tumors, paired normals, and cell lines, including (1) 68 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL tumor samples, (2) 20 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL paired normal samples, and (3) 2 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL cell lines.

  Dataset EGAD00001003246

• Whole genome sequencing of adult glioblastoma nuclei

  Three primary adult glioblastoma specimens were dissociated and nuclei were extracted. A portion of the nuclei was used for single-cell ATAC seq and the remainder were submitted for whole genome sequencing, to provide orthogonal validation of copy number variations in the samples compared to single-cell ATAC seq. Samples were sequenced on the Illumina NovaSeq 6000 in paired-end mode.

  Dataset EGAD00001007651

• Exome sequencing and RNAseq data

  Whole Exome Sequencing of 9 Colorectal Cancer (CRC) samples performed on Illumina HiSeq4000 consisting of aligned paired reads. RNAseq data sequenced on Illumina NextSeq500 consisting of FASTQ single reads from 3 CRC colon samples. A total of 12 samples from five patients (we matched normal tissue or pbmc and tumors) were sequenced on Illumina NextSeq500.

  Dataset EGAD00001003788

• Genomic Analysis of Anaplastic Thyroid Carcinoma

  This dataset includes WGS & WTS alignment data generated from 1 ATC tumor, its matched peripheral blood specimen and 3 authenticated ATC cell lines, THJ-16T, THJ-21T and THJ-29T. In addition, it includes WTS data from extra 4 unique anaplastic cell lines, ACT-1, C643, HTh7 and T238.

  Dataset EGAD00001001321

• Human tumor scMultiome

  We profile 10 high-grade gliomas patient brain tumor samples by single-cell multiome ATAC + gene expression, using the 10X Chromium technology. 3 sets of fastq are provided for each samples: R1 and R2 for gene expression, R1 and R2 for ATAC-seq as well as index1 and index2 for ATAC-seq.

  Dataset EGAD00001008349

• A Single-Cell Atlas of the Multicellular Ecosystem of Primary and Metastatic Hepatocellular Carcinoma

  Single-cell transcriptomes for 10 hepatocellular carcinoma (HCC) patients from 21 sample of four relevant sites: primary tumor (T), portal vein tumor thrombus (P), metastatic lymph node (L) and non-tumor liver (N). Single cells were sequenced using Chromium Single Cell 3’ Library (10x Genomics).

  Dataset EGAD00001006190

• scTCR-seq from brain metastasis micorenvironment and cerebrospinal fluid

  A total of 9 brain metastasis were sequenced. For 6/9 a matched cerebrospinal fluid sample, prior to surgery and in two cases after surgery (+1 month from surgery) and after treatment (+3 month) were collected. Single-cell T cell receptor clonotypes were produced using the Chromium Single Cell 5’ Library and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD00001006451

• HSC_population_dynamics___KX004_samples___WGS

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003768

• HSC_population_dynamics___CB002_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003743

• HSC_population_dynamics___KX007_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004193

• HSC_population_dynamics___KX008_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004490

• HSC_population_dynamics_CBD_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003091

• HSC_population_dynamics___KX003_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003550

• HSC_population_dynamics___TG001_2_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001003688

• Phase I Study of the Oral PI3kinase Inhibitor BKM120 or BYL719 and the Oral PARP Inhibitor Olaparib in Patients with Recurrent Triple Negative Breast Cancer or High Grade Serous Ovarian Cancer

  We analyzed massive parallel sequence data from patients with breast and ovarian cancer and identified single base substitution mutational signature 3 (Sig3) - extracted using SigMA - as a biomarker of homologous recombination deficiency (HRD) and predictive for response to PARP inhibitors. Participants were patients enrolled in clinical trials as 2 independent datasets: (1) high-grade serous ovarian cancer and triple-negative breast cancer (TNBC) from a Phase 1b trial of the PARP inhibitor olaparib in combination with the PI3K inhibitor buparlisib (BKM120) (NCT01623349), and (2) TNBC patients who received neoadjuvant olaparib in the Phase II PETREMAC trial (NCT02624973).

  Study phs003019

• Copy Number Variation in Congenital Kidney Malformations

  We report a study of large rare, copy number variants (CNVs) in 192 patients with renal hypodysplasia (RHD). Congenital malformations of the kidney and urinary tract are present in 3 to 7 per 1,000 births, accounting for 16% of birth defects. These malformations account for 40-50% of pediatric and 7% of adult end-stage renal disease worldwide. Among these malformations, RHD represents a severe forms of disease with profound impact on long-term renal survival. We found that a significant fraction of RHD patients have a molecular diagnosis attributable to a genomic disorder, suggesting kidney malformations as a sentinel manifestation of pathogenic genomic imbalances.

  Study phs000565

• BIRC5 Upregulation Enhances DNMT3A-Mutant T-ALL Cell Survival and Pathogenesis

  The goal of this study was to determine how patients with T-ALL who have DNA methyltransferase 3 alpha (DNMT3A) mutations develop resistance to therapy. Since DNMT3A is a methyltransferase, we examined the effect of those mutations on epigenetic regulation using whole genome bisulfite sequencing (WGBS). We also assessed any changes in gene expression using RNA-sequencing. We found that T-ALL patients with DNMT3A mutations are resistant to apoptosis and some chemotherapies. WGBS showed that DNMT3A mutated patients clustered together by their epigenetic profile, which was associated with hypomethylation at TERT and HOX genes. RNA sequencing identified differences in JAK/STAT signaling.

  Study phs003623

• Systematic immune cell dysregulation and molecular subtypes revealed by single cell RNA-seq of subjects with type 1 diabetes

  Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes and has the potential to guide non-invasive test development and patient stratification.

  Study EGAS50000000231

• HSC_population_dynamics___PX001_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004146

• HSC_population_dynamics___KX009_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004580

• HSC_population_dynamics___KX010_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004581

• Understanding Rare Variant Contributions to autism: Lessons from Dystrofin-Deficient Model

  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. Pathogenic DMD variants, besides causing dystrophinopathies, are also known risk factors for neurodevelopmental disorders (NDDs). However, the low penetrance of NDDs in individuals with dystrophinopathies suggests that additional factors contribute to their manifestation. This study aimed to: (1) characterize ASD in males with dystrophinopathies; (2) determine the relevance of additional de novo and inherited rare risk variants for their neurodevelopmental phenotype; and (3) clinically and functionally characterize the identified risk variants.

  Study EGAS50000000754

• Investigating immunopathological signatures associated with COVID-19 severity post Omicron

  The aim of this study was to investigate the type and duration of protective immunity alongside immunopathological signatures associated with COVID-19 severity. RNA sequencing was performed using the Illumina Stranded mRNA Prep Ligation kit to investigate the protein coding transcriptome of PBMC cells. T cell receptor (TCR) repertoire profiling was performed with the TakaraBio SMART-Seq Human TCR (with UMIs) on PBMC cells to investigate the depth and persistence of SARS-CoV-2 targeting TCRs. The cohort (n=20) consisted of 10 non-hospitalised and 10 Hospitalised individuals with samples analysed 3 months post positive SARS-CoV-2 PCR.

  Study EGAS50000000926

• NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)

  The CHIRAH project was a community-based study of the factors associated with asthma morbidity in the African American population. CHIRAH evaluated the role of various variables (biologic/environmental, psychologic/behavioral, and socioeconomic) on asthma morbidity and the function of changes in these variables on asthma morbidity in a longitudinal fashion. This involved collection of a cohort-based on school screening which was sampled to include similar numbers of underprivileged and non-underprivileged subjects which roughly equally represented self-reported African Americans and self-reported non-African Americans. Subjects were followed up every 3 months of this cohort over the course of 2 years.

  Study phs001605

• HSC_population_dynamics_KSP_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001002762

• Amplicon sequencing of melanoma samples

  The types of biomarkers for skin tumors have been 1) biochemical markers in blood, urine, and body fluid, 2) histopathological markers, 3) genetic examination of tumor tissue, 4) tumor-susceptibility assessed by germ_x0002_line genetic examination. Biomarkers in a blood are frequently used in the treatment of cutaneous malignancies, but are not suitable for early detection of malignancies. Research on circulating tumor cells, cell free DNA, exosomes has been promoted in recent years, but clinical application is halfway. Based on these circumstances, the purpose of this study is to search for biomarkers for diagnosis, therapeutic effect, and follow-up of skin tumors, and to verify their usefulness.

  Study JGAS000351

• Study for establishment for effective screening and diagnosis of Lynch syndrome

  The purpose of this study is to establish efficient diagnostic procedure of the Lynch syndrome in Japan and to determine the MMR gene mutation spectrum and clinicopathologic characteristics.The person who is suspected Lynch Syndrome and gives informed consent for participation in this study .To carry out the project ?Construction of clinical and genetic integral information database to help Lynch syndrome management?, the following three are required. 1) screening for Lynch syndrome-suspected cases, 2) genetic testing to define Lynch syndrome, 3) integration of detailed clinical data of Lynch syndrome, and 4) The case which has not been diagnosed Lynch syndrome, is investigated causing gene.

  Study JGAS000638

• ISCAPE V(D)J libraries from HA-specific single memory B cells and personalized IGM, IGK, IGL V(D)J repertoire sequencing of four Influenza A exposed individuals

  Peripheral blood mononuclear cells were used to produce paired, full-length IGM, IGK and IGL V(D)J libraries from HA-binding single memory B cells using the ISCAPE (Individualized Single Cell Analysis of Paired Expressed antigen receptors) technique. Locus-specific multiplexed nested PCR with 5’ leader IGHV/IGKV/IGLV and 3’ constant IGG/IGK/IGL primer mixtures was performed before well and plate indexing and paired chain sequencing with an Illumina MiSeq instrument. Expressed total IGM, IGK and IGL V(D)J libraries from each donor were generated to define personalized IG allele content.

  Study EGAS50000001390

• Rapid response of APC/TP53/KRAS mutated stage IV colorectal cancer under FOLFIRI + Bevacizumab detected by liquid biopsy: a case report

  In our non-interventional liquid biopsy study, a male patient in his fifties diagnosed with stage IV colorectal cancer and polytope liver metastases rapidly progressed after completing chemotherapy and deceased 8 months after diagnosis. Retrospective cell free DNA testing showed that the APC/TP53/KRAS major clone responded quickly after 3 cycles of FOLFIRI + Bevacizumab. Retrospective exome sequencing of pre-chemotherapy and post-chemotherapy tissue samples including metastases confirmed that the APC/TP53/KRAS and other major clonal mutations (GPR50, SLC5A, ZIC3, SF3A1 and others) were present in all samples. After the last chemotherapy cycle,

  Study EGAS00001004088

• HSC_population_dynamics___LEUK4_samples

  My research project aims to use the clonal dynamics of spontaneously occurring somatic mutations to answer fundamental questions about human haematopoietic stem cell (HSC) biology. The four major questions I will address are: 1. How do age and aging affect normal human HSC dynamics in vivo? 2. How do in vivo perturbations, particularly chemotherapy and increased levels of reactive oxygen species, affect HSC population dynamics? 3. Is response to in vitro perturbation heritable and/or correlated with other features such as age of individual and contribution of the lineage to peripheral blood? 4. How are HSC dynamics altered in people with early driver mutations (clonal haematopoiesis)?

  Study EGAS00001004247

• Reconstruction of complex rearrangement patterns causing the initiation of clear cell renal cell carcinoma.

  The genomic hallmark of clear cell renal cell carcinoma is the loss of the short arm of chromosome three. This appears to be the earliest genomic event in the formation of these cancers. Often chromosome 3 is lost at the same time as part of chromosome 5 is duplicated via an unbalanced translocation, often with features consistent with focal chromothripsis. In this study, we sought to reconstruct the chromothriptic event that underlies the initiation of kidney cancer. We used long read sequencing (promethION, Oxford Nanopore Technologies) of patient tumour-derived DNA to elucidate how a single cell division error can generate cancer genome complexity.

  Study EGAS00001004015