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• Unmatched WGS from bone marrow samples of 5 chr21 amplified blast phase myeloproliferative neoplasm patients

  We describe recurrent chromothripsis of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ~25% of patients (‘chr21amp’). Chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. Here we provide high-depth whole genome sequencing (WGS) in five chr21amp BP-MPN cases, to a median coverage of 81x [range 77-86] and purity 79% [range 58-88%].

  Dataset EGAD00001011280

• Cambridge_INTERVAL_SomaLogic_pQTLs

  This dataset contains four data files relating to the Cambridge Interval SomaLogic pQTL study to go with the corresponding genetic data: (1) Genome-wide pQTL summary associations for each analyte. (2) Mapping table for the genetic variants analysed - containing rsID, position and allele information. (3) Normalised quantitative readouts for each analyte, along with covariates used for the pQTL analysis. (4) Table of SOMAmer analytes mapped to their protein targets. Please see the readme file in the dataset for more information.

  Dataset EGAD00001004080

• Metaplastic breast cancer in a patient with neurofibromatosis type 1 and somatic loss of heterozygosity

  Targeted genetic sequencing was performed on a 41-year-old female with metaplastic breast cancer (MBC) and neurofibromatosis type I (NF1). A custom panel capturing 279 cancer related genes was used to identify a germline pathogenic SNV in NF1, as well several other somatic alterations.

  Study phs001566

• Impact of allogeneic umbilical-cord derived mesenchymal stromal cells on B-cell scRNAseq in patients with systemic lupus erythematosus

  The impact of MSC(UC) on peripheral B cells from Systemic Lupus Erythematosus (SLE) patients was studied by 10X scRNAseq. This scRNAseq study encompassed 3 SLE patients at 3 time points: before or after (1 month, and 3 months) MSC injection in order to analyze B cell subsets and their DEG. The aim of this study was to observe the potential changes of B cell subsets after MSC(UC) injection in SLE patients.

  Dataset EGAD50000000471

• RNA-seq

  Our cohort represents infants with ALL in whom KMT2Ar was not detected by FISH or by standard cytogenetics. Whole-transcriptome sequencing (WTS) libraries were prepared using the NEBNext Ultra II RNA Directional library kit for samples with at least 100ng RNA (n=19), the Clontech double stranded cDNA conversion kit plus the Nextera XT library protocol for samples with less than 100ng RNA (n=4), or ribodepletion using NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) for Total RNA (n=1). Libraries were paired-end sequenced using the Illumina HiSeq 2500.

  Dataset EGAD50000000595

• RNA-Seq Brest Patient-derived Tumor Organoids

  This dataset includes 14 RNASeq samples from 8 patients. For some patients, organoids at different passages have been profiled. They can be identified by their alias, composed of the following structure: <subjectId>_O<organoid_number>_<passage>_RNA. For example, ICSBCS002_O1_1_RNA indicates the earlier passage of organoid 1 for subject ICSBCS002, and ICSBCS002_O1_2_RNA indicates the later passage. Additionally, WCM2137_O1_RNA and WCM2137_O2_RNA indicate two organoids (O1 and O2) derived from different tissues. More information about the passages and tissues can be found in the sample information table.

  Dataset EGAD50000000960

• Illumina GSA-MD v3 genotyping arrays for 183 samples

  Genotyping arrays for 183 samples from patients with a neuroendocrine tumor of the small intestine. All samples have been hybridized on Illumina GSA-MD v3 arrays with standard automated protocols. Reading of the chips was performed on Illumina iScan+ scanners and this file is the result of primary analysis done using Illumina GenomeStudio software. It contains data for 147 tumors, 2 adenomas, 1 lymph node, 19 mesenteric nodules, 6 liver metastasis and 8 normal ileum samples.

  Dataset EGAD50000000905

• Transcriptome sequencing of neuroendocrine tumors of the small intestine

  This dataset contains 206 RNASeq samples from a cohort of patients with neuroendocrine tumors of the small intestine. Libraries were prepared using a Illumina TruSeq Stranded mRNA kit following the manufacturer’s recommendations. Sequencing was performed on Illumina Novaseq6000 machine with a 2x75bp paired-end fashion. This dataset contains data for 169 tumors, 22 mesenteric nodules, 8 liver metastases, 2 adenomas, 1 lymph node and 4 normal ileum samples.

  Dataset EGAD50000000906

• AWI-Gen Phase 1 GWAS Genotype data

  The samples were genotyped on the H3Africa array (~2.3M SNPs) using the Illumina FastTrack Sequencing Service2. The default Illumina pipeline was used for the genotype calling (build GRCh37/hg19). The data was converted to PLINK using the h3abionet/h3agwas/call2plink pipeline and QC done using the h3abionet/h3agwas/qc pipeline

  Dataset EGAD00010001996

• Somatic L1 retrotransposition mapping in high-grade serous ovarian carcinoma using LDI-PCR/Nanopore-sequencing (part 2)

  Somatic L1 retrotransposition was mapped in high-grade serous carcinoma (HGSC) tumors using LDI-PCR/Nanopore-seq method. This method identifies somatic L1 insertions originating from two active L1 loci at chr22q12.1 and chrXp22.2. Multiple tumors from the same patient were utilised to understand L1-mediated intrapatient heterogeneity. Long-read data generated by LDI-Nanopore sequencing was aligned to the reference genome (GRCh38). This dataset contains the remaining file of this study.

  Dataset EGAD50000001757