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• Comprehensive miRNA Sequence Analysis Reveals Survival Differences in Diffuse Large B-cell Lymphoma Patients

  Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30-40% of patients failing to achieve complete responses to standard therapy. miRNAs are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue (FFPET) samples for validation.

  Study EGAS00001001025

• Genome- and epigenome-driven evolutionary dynamics of tumour-immune coevolution within primary colorectal cancers

  This data includes targeting sequencing of the immunopeptidome from 94 samples, usually individual laser microdissected cancer glands, from 11 cases of colorectal cancer. The data were used to test for evidence of immunoediting (antigen depletion) in colorectal cancers. The full data description is provided in the original manuscript https://pmc.ncbi.nlm.nih.gov/articles/PMC10888923/. The 11 colorectal cancers had been previously multiomic profiled with data described in the parts of this disposition.

  Study EGAS50000001154

• Validation_of_Exome_sequencing_of_S7RE_iPSC_lines

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000423

• Deep_sequencing_of_S7EPC_genome

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000437

• Egypt_Genome_Project___low_coverage_whole_genome_sequencing

  All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples.

  Study EGAS00001000480

• Tenk10k Phase 1: Whole Genome Sequencing

  TenK10K Phase 1 is a dataset of matched human whole-genome sequencing (WGS) from 1,925 individuals, and single-cell RNA sequencing (scRNA-seq) from over 5 million peripheral blood mononuclear cells across 28 immune cell types. Single-cell ATAC sequencing was additionally performed on a subset of 922 individuals. This EGA study consists of the WGS data from 1,925 individuals while a separate EGA study comprises the scRNA-seq and scATAC-seq data.

  Study EGAS50000001654

• The genomic landscape of recurrent ovarian high grade serous carcinoma: the BriTROC-1 study

  The BriTROC-1 study, spanning 15 centres across the United Kingdom, is a prospective observational project investigating putative causes of relapse in high-grade serous carcinoma (HGSC). Potential genomic changes associated with disease recurrence are examined by studying paired tumour samples collected from patients at diagnosis and after relapse after receiving platinum based chemotherapy. Shallow whole genome sequencing and targeted amplicon sequencing are used to identify copy number aberrations and short variants respectively.

  Study EGAS00001007292

• Recent genetic history of Denmark

  The "Where Are You From?" project explores the extent to which recent and more distant historical events left their mark on the genetic structure of the current Danish population. The project's ultimate goal is to gain insights into the historical complexity of Denmark from the genetic perspective. To this goal, a data set consisting of approximately 800 high school students from across Denmark was used to run an extensive genetic analysis.

  Study EGAS00001001868

• UROMOL 2020 - RNA-seq data

  The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we performed a large integrative multi-omics analysis of patients diagnosed with NMIBC (n=834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Both transcriptome-based subtyping and the level of chromosomal instability provide independent prognostic value beyond established prognostic clinicopathological parameters.

  Study EGAS00001004693

• Validation_of_SNVs_found_by_Exome_seq_in_S2_SF1___SF5_and__SF9_hiPSCs

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000464

• miRNA_expression_in_response_to_LPS_stimulus_in_macrophages

  Our lab is currently using macrophages as a model system for understanding how geneticvariation modulates the response to external environmental stimulus. We want to extend thisbeyond regular polyadenylated RNA to small RNAs such as miRNAs. This project wouldcover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed aspart of a rotation project in the lab. We will require a small number of miRNA libraries and asingle lane of MiSeq

  Study EGAS00001000691

• The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

  Here we aimed to contribute to the description of the genetic architecture of Congenital heart defect (CHD) in Down syndrome (DS), and report the results of a genome-wide association study using samples from DS individuals with and without CHD. CHD is a common developmental defect of DS occurring in 40% of cases. This case-control GWAS includes 187 DS with CHD as cases, and 151 DS without CHD as controls.

  Study EGAS00000000129

• Genetic Landscape of Esophageal Squamous Cell Carcinoma Defined by Exome Sequencing on Chinese Patient Cohort and Cell Lines

  Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. To define the genetic landscape of ESCC, whole exome sequencing was performed on 113 pairs of tumor and normal DNA samples collected from Chinese individuals with treatment-naive primary ESCC, along with 8 cell lines, including 7 from KYSE series ESCC cell lines and one immortalized esophageal squamous epithelial cell line Het-1A.

  Study EGAS00001000932

• Bulk and RIP-seq transcriptome datasets from skin fibroblasts in PTBP1- and PTBP2-related disorders

  PTBP1- and PTBP2-related disorders are rare human conditions that cause variable neurodevelopmental phenotypes, including intellectual disability and behavioral problems such as autism spectrum disorder, anxiety, aggressiveness, and attention disorders, with or without hyperactivity. PTBP1-related disorder is also associated with skeletal dysplasia. In this study, we generated bulk RNA sequencing and RNA immunoprecipitation sequencing (RIP-seq) data from skin fibroblasts obtained from patients and healthy controls.

  Study EGAS50000001210

• Rare Germline Variants in CDKN2A-Negative Children and Adolescents with Cutaneous Melanoma

  Cutaneous melanoma is a complex disease influenced by both environmental and genetic factors. Inherited susceptibility plays a significant role, involving a combination of high-, intermediate-, and low-penetrance genes. Melanoma in children and adolescents has been speculated to have a stronger genetic component due to the early onset. This study investigates germline variants in early-onset melanoma through exome sequencing of 154 patients in Australia diagnosed with cutaneous melanoma before the age of 20.

  Study EGAS50000001311

• Subclonal_analysis_in_S7RE2_and_S7RE14_iPS_cells

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000441

• Whole_genome_sequencing_of_a_Grem1_mutant_human_tumour

  The BMP antagonist Grem1 has been shown to be associated with a rare human polyposissyndrome (HMPS). We have shown that there is a 40KB duplication on chrom 15 found insome patients with HMPS. Traditional serrated adenomas (rare sporadic polyps) share somemorphological features with HMPS polyps and it has long been hypothesised that they are thesporadic version of HMPS polyps. We have obtained of one of theselesions and in this project we aim to characterise this tumour.

  Study EGAS00001000562

• Congenital Heart Disease in UK Families

  This project aims to identify highly penetrant coding variants increasing the risk of Congenital Heart Disease (CHD) performing whole exome sequencing on DNA samples from 23 affected individuals, selected from 10 families with presumed Autosomal Recessive Inheritance. This is a collaboration with Prof. Eamonn Maher and Dr. Chirag Patel from the Department of Medical and Molecular Genetics, University of Birmingham plans to sequence 23 indexed Agilent whole exome pulldown libraries on 75Bp PE HiSeq (Illumina).

  Study EGAS00001000066

• Detection of clinically relevant genetic and transcriptomic landscape in DLBCL uniformly treated by R-CHOP

  Recent studies using next-generation sequencing strategies have described the landscape of genetic alterations in diffuse large B-cell lymphoma (DLBCL). However, little is known about the clinical relevance of recurrent mutations and copy number alterations and their transcriptional footprints. This study examines the frequency, interaction and clinical impact of recurrent genetic aberrations in DLBCL using high-resolution technologies in a large population-based cohort.

  Study EGAS00001002657

• RNA-seq data from the EUROBATS Project in four tissues: Fat, LCL, Skin and whole Blood.

  EUROBATS consists of RNA-seq data for female twins in lisphoblastoide cell lines (LCL), abdominal adipose tissue (Fat), abdominal skin tissue (Skin) and whole blood (Blood). The samples are a combination of MZ twins, DZ twins and singletons. The goal of the project is to find biomarkers related with the ageing process and cellular senescence.

  Study EGAS00001000805

• Himalayan_population_genetic_study

  We genotyped 770 individuals belonging to 49 populations from Nepal, Bhutan, North India or Tibet at over 500,000 SNPs genomewide to investigate the demographic history of the region and the genetic adaptations to the harsh environment. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002731

• Arcagen – thoracic malignancies

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

  Study EGAS50000000123

• Exome sequencing of advanced hepatocellular carcinoma

  The aim of our project is to decipher the genomic of advanced hepatocellular carcinoma using whole exome sequencing. To this purpose, we aim to compare genetic landscape of advanced hepatocellular carcinoma with early tumor in order to understand the mechanisms of tumor progression. This work will also help to identify new therapeutic targets potentially useful to treat patients at advanced stage. This study contain whole exome sequencing aligned reads for 41 tumor with matched normal samples

  Study EGAS00001003130

• scRNAseq of acute myeloid leukemia

  This study analyzes T-cell transcriptional state in acute myeloid leukemia (AML) and healthy donors. The goal of the study is to correlate T-cell transcriptional states abundances with response to chemotherapy. 12 samples (5 baseline and post-treatment, 2 baseline-only) from AML patients and 3 samples from healthy donors were collected and sequenced on Illumina platforms. The files were created using the GRCh38 reference through CellRanger count (10xGenomics).

  Study EGAS50000000357

• Prognostic whole-genome and transcriptome signatures in colorectal cancers

  Colorectal cancer (CRC) is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. To understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary CRCs in a population-based cohort with long-term follow-up. This study constitutes the largest integrated genome and transcriptome analysis of CRC to date, and links mutations, gene expressions and patient outcomes.

  Study EGAS50000000124