15136 results for "cancer studies using rna-seq"

in 24.96 milliseconds.

• 300BCG study ATAC-seq data: human population variation of trained immunity

  ATAC-seq dataset for the paper: Title Multi-omics analysis of human population variation in immune function and in vivo response to BCG vaccination Abstract Immune responses are tightly regulated, yet highly variable between individuals. To investigate human population variation of trained immunity, we immunized healthy individuals with Bacillus Calmette-Guérin (BCG). This live attenuated vaccine induces not only an adaptive immune response against tu-berculosis, but also triggers innate immune activation and memory. We established personal immune profiles and chromatin accessibility maps over a time course of BCG vaccination in 323 individuals. This large resource uncovered genetic and epigenetic predictors of baseline immunity and BCG vaccine response. We found that BCG vaccination enhances the innate immune response only in individuals with dormant immune states at baseline, suggesting that exogeneous induction of trained immunity is not a universal booster of innate immunity, but specifically elevates weak innate immune responses. This study advances our understanding of BCG’s heterologous immune-stimulatory effects and trained immunity in humans. Moreover, our results highlight the value of epigenetic cell states as an “endo-phenotype” that connects immune function with genotype and the environment.

  Dataset EGAD50000000123

• Feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric brain tumors for classification

  Array-based DNA methylation profiling is the gold standard for molecular classification of brain tumors. However, it relies on significant amount of input DNA extracted from surgical tissue, thus limiting its use for tumors where biopsy is challenging or limited in quantity. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) presents alternative opportunities for brain tumor diagnosis and disease monitoring following treatment. Novel enzymatic DNA methylation sequencing (EM-seq) methods may allow us to overcome input DNA limitations and accurately quantify methylation from cfDNA for tumor classification.

  Study EGAS50000000871

• Ibrutinib induces a global chromatin reorganisation in chronic lymphocytic leukaemia

  Chronic lymphocytic leukaemia (CLL) is the most common haematological malignancy in developed countries. Ibrutinib (PCI-32765), a specific and irreversible inhibitor of Bruton's Tyrosine Kinase (BTK) represents a major step forward in the treatment of CLL. We have undertaken a detailed analysis of the changes happening to the chromatin structure in CLL cells from patients continuously receiving oral doses of ibrutinib. ChIP-seq has been performed for H3K4me3, H3K27ac, H3K27me3 and EZH2 . We observed that Ibrutinib-dependent lymphocytosis correlates with a global and transient recruitment of EZH2 to active cis-regulatory elements and increased H3K27me3.

  Study EGAS00001002827

• Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging

  In this study we characterised the consequences of DNMT3A- and TET2-mutations in human clonal haematopoiesis. We screened 195 bone marrow samples for mutations by targeted DNA sequencing, and sequenced 99 paired peripheral blood samples to compare mutation detection between bone marrow and blood. We performed single-cell analysis with TARGET-seq+ on 13 samples (4 controls and 9 clonal haematopoiesis samples), which combines single-cell genotyping for targeted mutations with whole transcriptome sequencing on FACS sorted cells. Single-cell genotyping and transcriptomes were sequenced separately and linked by common single-cell identifiers.

  Study EGAS00001007358

• LCLF1.0 Data

  In this study, we investigated ad libitum food intake of 20 healthy adult volunteers who each completed a 4-week stay at the National Institutes of Health (NIH). During their stay, they consumed a low-carbohydrate, high-fat (LCHF) diet and a low-fat, high-carbohydrate (LFHC) diet for 2 weeks each, in random order. We collected information about energy intake and metabolic changes in response to the two test diets. The test diets were presented to subjects in amounts exceeding their daily energy requirements, and subjects were instructed to eat as much or as little of each diet as desired. This study implemented 7-day rotating menus for each test diet. The diets were matched for presented calories and protein, but the LCHF diet was low in carbohydrate (~10% of calories) and high in fat (~75% of calories) whereas the LFHC diet was high in carbohydrates (~75% of calories) and low in fat (~10% of calories). The two test diets had a common foundation of vegetables with low amounts of digestible carbohydrates such as lettuce, spinach, kale, cabbage, cauliflower, zucchini, tomato, asparagus, broccoli, peppers, brussels sprouts, and green beans. The LCHF diet included meat, poultry, fish, eggs, dairy, and nuts. The LFHC diet included legumes, rice, root vegetables, soy products, corn, lentils, peas, whole grains, bread, and fruit. The test diets were designed using a standard computerized nutrition database, and blood samples were collected from the subjects.

  Study phs003187

• Identification of RNA biomarkers in Parkinson's disease patients

  Parkinson?s disease (PD) is an age-related, chronic and progressive neurodegenerative disorder characterized by a loss of dopaminergic neurons and subsequent motor symptoms. These overt motor symptoms are often preceded by prodromal non-motor symptoms. Though a number of genetic and environmental factors have been identified to play a role in PD, more exact methods for both diagnosing and assessing prognosis are yet to be discovered. By analyzing the transcriptome of early-stage PD patients, this study aims to identify genes (including important non-coding RNAs) and pathways altered at disease onset that may be used as novel biomarkers for PD diagnosis as well as potential new drug targets. The study consists of three main sources of data: first year blood transcriptomes, second year blood transcriptome and matched neural stem cell (NSC)/neuron transcriptomes. All transcriptome libraries were synthesized and sequenced using no-amplification non-tagging cap analysis of gene expression (nAnT-iCAGE) on the Illumina HiSeq 2500 platform. Resulting data was mapped to the human genome annotation (hg38), processed CAGE tags were clustered ready for differential expression analyses. First year blood sequencing consisted of 22 PD patients and 10 healthy controls across four lanes. In the second year, a further four lanes were sequenced containing 17 PD patients (12 patients from the first year and 5 new patients) along with 10 healthy controls and 5 first year blood samples matching the new second year patients.

  Study JGAS000119

• CALGB 80303:Genome-Wide Association Study of Advanced Pancreatic Cancer Patients - A Randomized Phase III trial of Gemcitabine Plus Bevacizumab versus Gemcitabine Plus Placebo in Patients with Advanced Pancreatic Cancer

  CALGB 80303 was a randomized, phase III study in advanced pancreatic cancer patients treated with Gemcitabine plus either Bevacizumab or placebo. No difference in overall survival (OS) was observed between the two arms. We prospectively collected germline DNA and conducted a genome-wide association study (GWAS).

  Study phs000250

• CAGEKID: Cancer Genomics of the Kidney

  The aim of CAGEKID is to carry out comprehensive detection of DNA markers for conventional (clear cell) renal carcinoma. The project includes complete analysis of somatic and constitutional DNA variation, methylation patterns and expression in a large number of constitutional/tumor pairs. CAGEKID is a part of the International Cancer Genome Consortium, ICGC.

  Study EGAS00001000083

• Identification of drug resistance genes in cancer cell lines by insertional mutagenesis

  Our aim is to identify genes involved in resistance to anti-cancer therapies. In order to do this we have taken advantage of a lentiviral vector (LV)-based insertional mutagen to mutagenize cancer cell lines. LV-transduced cell lines were then treated with anti-cancer therapies and the emergence of resistant clones scored. DNA from pools of resistant clones was collected, subjected to custom capture by baits designed against the LV sequence, and then sequenced to identify the LV-genomic junction. We hope that the identification of recurrently targeted genes in resistant cell population will allow us to identify genes that mediate drug resistance.

  Dataset EGAD00001002207

• AVENIO Expanded ctDNA panel sequence alignments (BAMs) from plasma DNA of BC, CRC and NSCLC patients

  The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.

  Dataset EGAD00001006301

• Feasibility and Clinical Utility of Whole Genome Profiling in Pediatric and Young Adult Cancers

  Comprehensive Whole Genome Sequencing and Whole Transcriptome (RNASeq) analyses from 114 pediatric patients at Memorial Sloan Kettering. This dataset was used as a prospective clinical utility and feasibility study. By using our Isabl infrastructure for precision medicine, we developed a 2-week end-to-end pipeline to analyze cfDNA, WGS and WTS, which we refer to as cWGTS.

  Study phs002620

• Myocardial Infarction Genetics Exome Sequencing Consortium: Ottawa Heart Study

  The Ottawa Heart Study is a cross-sectional case-control study designed to identify genes that predispose to angiographically defined coronary artery disease. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.

  Study phs000806

• Genetic Determinants of Susceptibility to Severe COVID-19 Infection

  The goal of the project is to identify genetic susceptibility variants associated with acute COVID-19 infection susceptibility and severity using whole genome sequencing. The target of the project will include WGS data from whole blood samples of up to approximately 2000 COVID-19 patients (including critical/severe patient subgroup, asymptomatic/mild subgroup) from domestic and international medical institutions.

  Study phs002245

• Whole-genome variant calling of individuals from the study of allergic diseases in the Canary Islands

  Research study of genetic susceptibility and analyses of polygenic risk scores in allergic diseases. This dataset consists of variant data derived from whole-genome sequencing in reference samples from one of the parental populations (i.e., North Africans). The dataset consist of 15 VCF files (and corresponding index files) with a total of 1.58 million variants called using GATK v4 and following the Broad Variant Calling Best Practices, from a set of unrelated individuals sequenced in paired-read mode 2x150 bp using an Illumina HiSeq 4000 sequencer.

  Dataset EGAD50000000429

• Mutational Profile in Newly Diagnosed Diffuse Large B-Cell Lymphoma: 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)

  Study EGAS50000000929

• The Genomic Map of Poland in Open Access

  The main goal is to prepare and share WGS/WES of Polish population In this project NGS (next generation sequencing) was performed using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner was used. Shared BAM and BAM.BAI files Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

  Study EGAS50000000091

• SECRETO Oral metagenome study

  The main goal of the project is to study the associations between the oral metagenome and young-onset cryptogenic ischemic stroke (CIS). The dataset includes information for n=329 participants who underwent saliva sampling. Participants for the SECRETO Oral study were enrolled between December 2013 and November 2019. Shotgun metagenomic sequencing was performed using the Illumina NovaSeq 6000 platform.

  Study EGAS00001007505

• MorphoITH: A Framework for Deconvolving Intra-Tumor Heterogeneity Using Tissue Morphology

  The ccRCC-ITH study WES dataset is derived from a morphology guided multi-regional sequencing dataset used to study the relationship between morphology and genetic evolution. It contains whole exome sequencing data of 18 tumor and 2 adjacent normal samples from 2 UTSW patients, who have consented to depositing their genomic data to public repository. Tumor samples come from different tumor sites, including primary tumor, thrombus and metastases. WES was performed using 75bp paired-end fragments at an average read depth > 50x on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA). The raw data is in fastq format.

  Dataset EGAD50000001550

• Reference Panel for Imputation Analysis Based on Whole Genome Sequencing Data of 3,256 Japanese Individuals(BioBank Japan genotype data)

  This reference panel was constructed using whole genome sequencing data from 3,256 Japanese individuals and the 1000 Genomes Project. It provides high accuracy and utility in analyzing genetic polymorphisms, while also reflecting the genetic diversity specific to the Japanese population. This dataset is expected to contribute to the advancement of genetic research and personalized medicine.

  Study JGAS000746

• CLUSTER Consortium RNAseq PBMC Dataset of pre-methotrexate UK JIA patients cohort

  This is the RNAseq PBMC dataset (paired FASTQ files, n = 82 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. Total PBMC were isolated from pre-treated blood of JIA patients and clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.

  Dataset EGAD50000001457

• CLUSTER Consortium RNAseq CD8 Dataset of pre-methotrexate UK JIA patients cohort

  This is the RNAseq CD8 dataset (paired FASTQ files, n = 85 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD8 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.

  Dataset EGAD50000001456

• CLUSTER Consortium RNAseq CD4 Dataset of pre-methotrexate UK JIA patients cohort

  This is the RNAseq CD4 dataset (paired FASTQ files, n = 86 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD4 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.

  Dataset EGAD50000001455

• CLUSTER Consortium RNAseq CD14 Dataset of pre-methotrexate UK JIA patients cohort

  This is the RNAseq CD14 dataset (paired FASTQ files, n = 80 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD14 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.

  Dataset EGAD50000001458

• CLUSTER Consortium RNAseq CD19 Dataset of pre-methotrexate UK JIA patients cohort

  This is the RNAseq CD19 dataset (paired FASTQ files, n = 83 paired files) generated from pre-methotrexate treatment JIA patients cohort samples. CD19 cells were sorted from isolated total PBMC by cell sorter (BD FACSAriaTM III, BD Biosciences). Clinical metadata is also included in this dataset. Samples were sequenced on the NovaSeq6000 instrument (Illumina, San Diego, US) at 300pM, using a 100bp paired read run with corresponding 8bp dual sample index and 5bp or 8bp unique molecular index reads. Run data were demultiplexed and converted to FASTQ files using Illumina’s BCL Convert Software v3.75.

  Dataset EGAD50000001459

• EstMB cohort participants sequenced with MGISEQ-2000 platform

  Ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms.

  Study EGAS50000001538

• Exome-sequencing of human B cell lymphoma cell lines

  26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x.

  Study EGAS00001001463

• Chromatin 3D interactions mediate genetic effects on gene expression

  Studying the genetic basis of gene expression and chromatin organization is key to characterize the effect of genetic variability on the function and structure of the human genome. Here, we unravel how genetic variation perturbs gene regulation using a dataset combining activity of regulatory elements, gene expression and genetic variants across 317 individuals and two cell types.

  Study EGAS00001003485

• Genetic_vulnerability_of_knockout_cancer_lines

  Genome-wide CRISPR/Cas9 library screen was performed in isogenic cell lines. Three biological replicates were used. Cells were harvested at initiation of screen and at specific time points following cell culture. Using this approach we aim to identify genes specifically important in cell survival in engineered cell lines. Please perform 72, instead of 36, PCR reactions as the screen performed at 200x coverage.

  Study EGAS00001002253

• Lothian Birth Cohort 1921 whole genome sequencing study

  297 members of the Lothian Birth Cohort 1921 (LBC1921) were sequenced using the Illumina HiSeq X platform. The LBC1921 are a relatively healthy cohort of 550 individuals who underwent cognitive and medical testing at a mean age of 79.1 (SD=0.6) years. They have since undergone four further waves of testing, approximately three years apart.

  Study EGAS00001003818

• Multiple esclerosis and mixed microbial infections

  This Project deals with the sequencing of ITS1 region, which is highly variable both in length and in nucleotide sequence for different yeast using yeast-specific primers ITS1 and ITS2. A total of 19 samples involving different brain regions from patients with different conditions were analysed. Of these, 10 are controls-healthy patients and 9 multiple sclerosis (MS) patients.

  Study EGAS00001002957

• Genomic landscape of signals of positive natural selection in North Eurasia

  We searched for the genomic signatures of positive selection in the genome-wide data of 432 people from eight different northern Russian populations (Russians from the Archangelsky and Vologdsky regions, Izhemski Komi, Priluzski Komi, Veps, Khanty, Mansi and Nenets) who were genotyped using microarrays for 700,000 SNPs (InfiniumOmniExpress-24v1-2_A1) through testing the extended haplotype homozigosity (EHH).

  Study EGAS00001003955

• Lothian Birth Cohort 1936 whole genome sequencing study

  1075 members of the Lothian Birth Cohort 1936 (LBC1936) were sequenced using the Illumina HiSeq X platform. The LBC1936 are a relatively healthy cohort of 1091 individuals who underwent cognitive and medical testing at a mean age of 69.5 (SD=0.8) years. They have since undergone four further waves of testing, approximately three years apart.

  Study EGAS00001003819

• Evolutionary analysis of pancreatic neoplastic cysts through whole-exome and targeted sequencing

  Intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs) are non-invasive neoplasms that are often observed in association with invasive pancreatic cancers, but their origins and evolutionary relationships are poorly understood. In this study, we analyzed 148 samples from IPMNs, MCNs, and small associated invasive carcinomas from 18 patients using whole exome or targeted sequencing.

  Study EGAS00001004473

• Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

  In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

  Study EGAS00001004925

• COVID-19 GWAS in Japanese

  The Japan COVID-19 Task Force (JCTF) was established in early 2020 as a nation-wide multicenter consortium to overcome the COVID-19 pandemic in Japan. We conducted a genome-wide association study (GWAS) involving 2,393 Japanese COVID-19 cases collected in initial pandemic waves with 3,289 controls. GWAS genotyping was performed using Infinium Asian Screening Array (Illumina, USA).

  Study EGAS00001006284

• Polymorphisms in the Mitochondrial Genome associated with Bullous Pemphigoid in Germans

  This study is the first to interrogate the whole mtDNA in BP patients and controls and to implicate multiple novel mtDNA variants in disease susceptibility. Whole mtDNA of German BP patients (n=180) and age- and sex-matched healthy controls (n=188) were sequenced using next generation sequencing (NGS) technology, followed by the replication study using Sanger sequencing of an additional independent BP (n=89) and control cohort (n=104). While the BP and control groups showed comparable mitochondrial haplogroup distributions, the haplogroup T exhibited a tendency of higher frequency in BP patients suffering from neurodegenerative diseases (ND) compared to BP patients without ND (p= 0.1448, Fisher’s exact test)

  Dataset EGAD00001005379

• Mutational analysis of an oligoprogressive sarcomatoid hepatocellular carcinoma treated with an immune checkpoint inhibitor.

  The dataset is composed of three sequenced tumor samples: (I) Meta-bone-557 (bone metastasis obtained from occipital lesion resection during treatment with Liposomal doxorubicin); (II) Meta-CNS-888 (brain metastasis obtained from surgical resection during treatment with Nivolumab); (III) Primary-liver-463 (primary hepatic tumor obtained from surgical resection during treatment with Nivolumab). Genomic DNA from tumor samples was extracted using GeneRead DNA FFPE kit (Qiagen), containing Uracyl-D Glycosylase, according to the manufacturer’s instructions. Whole-exome libraries were prepared using SureSelect XT Clinical Research Exome Target Enrichment kit (Agilent Technologies # 5190-7338). Sequences (150bp paired-end) were generated on a NextSeq 500 sequencing platform (Illumina).

  Dataset EGAD00001006982

• Whole genome sequencing of acute erythroid erythroid leukemia

  Briefly, twenty paired tumor and germline DNAs were extracted from patients’ BM and from buccal mucosa, respectively. Samples were subjected to massively parallel sequencing using the HiSeq 2000, HiSeq2500, HiSeq X Ten, and/or NovaSeq 6000 according to the manufacturer’s instructions. Sequencing reads were aligned to NCBI Human Reference Genome Build 37 (hg19) by Burrows−Wheeler Aligner, version 0.7.10, with default parameters (http://bio-bwa.sourceforge.net/). PCR duplicates were eliminated using Picard tools version 1.39 (GATK).

  Dataset EGAD00001008357

• Somatic mutations predict an aggressive phenotype in meningioma but do not drive grade progression

  A subset of meningiomas progress in histopathological grade and drivers of progression are poorly understood. We aimed to identify somatic mutations and copy number alterations (CNAs) associated with grade progression in a unique matched tumour dataset. This dataset consists of DNA sequencing from 10 individuals with meningiomas, where the meningiomas have underdone grade progression. 50 meningiomas were sequenced from the 10 individuals using the hybrid capture-based TruSight Oncology 500 (TSO500) Library Preparation Kit, and 13 of those meningiomas were also sequenced using Agilent SureSelect Clinical Research Exome V2. BAM files for the sequencing data are included in the dataset.

  Dataset EGAD00001009391

• C9orf72 region reads of 3001 samples

  This dataset includes cram files from 3,001 samples. These cram files include all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion. Additionally, these cram files also contain reads that are aligned to any of 29 pre-determined off target locations where the aligners are known to mis-align reads associated with this repeat expansion. These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner.

  Dataset EGAD00001004834

• Genetic background for cardio vascular disorders in the general Finnish population

  Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of approximately 30,300 samples and comprises 500 individuals of each gender in the extreme tail of high density lipoprotein (HDL) concentrations. Included individuals were between 25 and 65 years of age. Individuals with a diagnosis of diabetes or BMI>30 were excluded from the study.

  Dataset EGAD00001001251

• LCM_WES__Thyroid_

  Whole exome sequencing through the low-input DNA pipeline in thyroid samples. Tissue will be processed either from laser capture microdissection or directly from bulk frozen/fixed/paraffin-embedded tissue. Insights will be gained here directly from the sequencing but also from using the data as a matched normal in Exome Nanoseq. Thyroid samples will be obtained from patients with and without thyroid disease.

  Study EGAS00001007772

• Dr. Fatima Mechta-Grigoriou, PhD, DR1 Head of Stress and Cancer Laboratory Deputy Director Genetic and Biology of Cancer Dpt Institut Curie - Inserm U830

  Dac EGAC00001000581

• ICGC prostate cancer whole genome sequencing

  ICGC prostate cancer whole genome sequencing

  Dataset EGAD00001000306

• Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  Data access committe for the project: Converging and evolving immuno-genomic routes towards immune escape in breast cancer

  Dac EGAC50000000074

• Thoracic Patient-Derived Xenografts

  Targeted capture sequencing of 341 cancer associated genes in thoracic patient-derived xenografts.

  Study phs001192

• scRNAseq of ovarian cancer patient derived organoids

  scRNAseq of ovarian cancer patient derived organoids with or without estradiol

  Dataset EGAD50000002058

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumouroids

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008273

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008275

• Whole exome sequencing of 103 pairs BLCA-CN

  We sequenced 50M exomes of 103 pairs bladder cancer of chinese

  Study EGAS00001000677