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• Extreme intratumor heterogeneity and driver evolution in mismatch repair deficient gastro-esophageal cancer

  The dataset includes multi-region exome sequencing (MSeq) of four resected treatment naïve mismatch repair deficient gastro-esophageal cancers. Paired-end sequencing was performed on the Illumina HiSeq 2500 or NovaSeq 6000 with a target depth of 200X. Seven primary tumor regions along with tumor-adjacent non malignant tissue were subjected to MSeq. An additional two lymph node metastases were also included from each of two cases.

  Dataset EGAD00001004594

• Whole-exome sequencing of BCP HD ALL on Illumina HiSeq 2000, 100 bp paired-end

  Genomic DNA from leukemic and remission bone marrow mononuclear cells was isolated with the QIAamp DNA Blood Extraction Kit (Qiagen, Venlo, The Netherlands). Libraries were prepared with the Illumina TruSeq DNA Sample Prep and TruSeq Exome Enrichment Kits (Illumina, San Diego, CA, USA) according to the manufacturer's recommendations. 100 bp paired-end sequencing was performed on a HiSeq 2000 (Illumina) to about 80x coverage.

  Dataset EGAD00001002653

• MiRNome_pituitary_adenoma

  Small RNA (<100 bases in length) were purified from total RNA using miRNeasy kit (Qiagen), then sequenced. Libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq small RNA protocol (Illumina), starting from 1 µg of high quality total RNA. Single read (1 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on miRBase v.2052, then counted with STAR (v.2.5.2a).

  Dataset EGAD00001004998

• RNAseq_pituitary_adenoma

  Total RNA was extracted using RNAble (Eurobio), cleaned-up with RNeasy columns (Qiagen) and sequenced. The libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq Stranded mRNA protocol (Illumina), starting from 1 µg of high quality total RNA. Paired end (2 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on hg19 (GRCh37) human reference genome with STAR (v.2.5.2a)

  Dataset EGAD00001004996

• BulkTCR-sequencing data from different human intestinal CD8 T cell subsets.

  5000 cells of each subset of CD8 T cells (CD103-KLRG1+, CD103-KLRG1- and CD103+ from LP and CD103+ IELs) were sorted into tubes. A modified SMART protocol was used in first-strand cDNA synthesis, and TCRalpha / TCRbeta genes were amplified in two rounds of semi-nested PCR reaction, following the method described in detail in Risnes et al., 2018.

  Dataset EGAD00001005049

• Whole genome sequencing of 40 rainforest hunter-gatherers and neighbouring farmers from Central Africa

  Exome sequencing of 20 rainforest hunter-gatherers (RHG) and 20 neighbouring farmers (AGR) from western central Africa was performed using 101-bp paired-end reads on Illumina HiSeq 2000. All individuals presented very low rates of missing values ranging from 0.5% to 4%, and a mean depth of coverage of 6.5× (ranging from 4× to 13×)(Lopez et al., Curr Biol 2019).

  Dataset EGAD00001005139

• AT-AML samples dataset

  Serial samples from one AT-AML patient as described in publication Goldgraben et al Pediatric Blood & Cancer 2020. Whole exome sequencing of a AT-'germline' blood sample, one bone marrow sample (at AML diagnosis) and 3 AML blood samples. Library preped using the Illumina Nextera Rapid Capture Exome Enrichment Kit, and sequenced as PE150 on HiSeq4000. Provided: 5 BAM files (GRCh37); 2 VCF analyses (germline and somatic)

  Dataset EGAD00001006090

• Single-cell RNA-seq data of bronchoalveolar lavage (BAL) fluid in late severe COVID-19

  We performed single-cell RNA-sequencing of cells in the bronchoalveolar lavage (BAL) fluid of late severe COVID-19. This study provides detailed insights into the alveolar macrophage response to SARS-CoV-2 infection and reveals a profibrotic macrophage response in severe COVID-19 patients.

  Dataset EGAD00001008161

• 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

• Genetic and immune landscape evolution defines subtypes of MMR deficient colorectal cancer

  Genomic data from a cohort of 19 MMR deficient colorectal cancers and 1 MMR proficient colorectal cancer. All cases were target gene DNA sequenced using multiple primary and where available metastatic tumour regions from surgical resection samples.

  Dataset EGAD00001008334

• Characterization of Leukemic Stem Cells in DNMT3Amut and NPM1mut AMLs

  Using a novel sorting strategy, we performed ultra low input RNAseq from FACS-sorted populations from diagnostic DNMT3Amut and NPM1mut AML patients. Primary samples were retrospectively collected based on their mutational profile. Samples were thawed, stained and FACS sorted using combination of lineage markers, CD34, GPR56 and NKG2DLigands. RNA was extracted and library prepared from 13 samples.

  Dataset EGAD00001009293

• Transcriptomic Profile of Colorectal Cancer Samples

  Samples encompass primary colorectal tumors or metastasis of 75 patients, collected by Medical Pathologists from surgically removed specimens. Tissues were embedded in optimal cutting temperature (OCT) medium, snapshot frozen in liquid nitrogen within 40 minutes of collection and preserved at -80ºC. Samples were collected between June 2010 and October 2017 as part of a prospective biobanking project.

  Dataset EGAD00001009506

• Prostate cancer m6A epitranscriptome

  Using meRIP-sequencing, we profiled N-6 methyladenosine (m6A) in a cohort of 148 primary prostate cancer samples as part of the Canadian Prostate Cancer Genome Network project (CPC-GENE). Paired-end sequencing of 150 bp reads were mapped to GRCh38.p13 using annotations from gencode.v34.chr_patch_hapl_scaff.annotation.gtf. Peaks were called using MeTPeak, joint peaks were identified and IP reads were quantitated, normalized and adjusted using Input reads to obtain estimates of m6A abundance.

  Dataset EGAD00001009869

• Single-cell RNA and TCR sequencing of 37 PBMC pools of advanced HCC patients.

  scRNAseq and scTCRseq of serial peripheral blood mononuclear cell (PBMC) samples (n=72) taken at various timepoints before and during treatment (Week 0 (W0), Week 3 (W3), Week 6 (W6)). PBMC samples were pooled together into 37 pools, loading 2 or three samples per lane in the 10X Genomics chip, in equal proportions, according to a pre-designed pooling matrix.

  Dataset EGAD00001011345

• Lobular Carcinomas In Situ Display Intra-Lesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Disease

  This study comprises prospectively accrued, microdissected fresh frozen samples of multifocal lobular carcinoma in situ (LCIS), ductal carcinoma in situ (DCIS), invasive lobular carcinoma and invasive ductal carcinoma from patients undergoing prophylactic or therapeutic mastectomies after a diagnosis on LCIS diagnosed and managed at Memorial Sloan Kettering Cancer Center (MSKCC). Microdissected samples were subjected to paired-end whole exome sequencing on an Illumina HiSeq 2000. The data generated were used to define the landscape of somatic genetic alterations of LCIS, DCIS, invasive lobular carcinoma and invasive ductal carcinoma, to define clonal relatedness of these lesions and to investigate the clonal shifts in the progression from in situ to invasive breast cancer.

  Study phs001006

• Whole Genomic Sequencing of Nine Primary Colorectal Adenocarcinoma Tumor/Germline Pairs

  This study was the first-known effort to complete the complete genome sequencing of primary colorectal adenocarcinomas and the matched germline genome. Nine colorectal adenocarcinomas selected on the basis of having chromosomal instability were subjected to 'shotgun' Illumina sequencing with 101-bp paired end reads to an approximate goal of 30x coverage of tumor and of normal. From these sequences, we used various computational techniques to identify somatic point mutations, insertion/deletions and structural rearrangements in these tumors. From these data, we identified new insights into the rates of background mutations in these cancers, new spectrums of structural alterations including the identification of a novel in-frame fusion gene.

  Study phs000374

• Human periportal liver assembloids recapitulate periportal liver tissue in vitro

  In vitro expansion of human hepatocytes from fresh patient tissues has not yet been achieved, limiting the possibility of modelling liver composite structures in vitro. Here, we developed human hepatocyte organoids from patient-donors that sustain the long-term expansion of hepatocytes in vitro. We profiled them using RNAseq to determine their gene expression pattern and compared this with the original native fresh isolated liver cell. Then, we used them to generate periportal liver assembloids by combining them with portal mesenchyme and cholangiocyte organoids. By increasing the number of mesenchymal cells we obtained structures with a fibrotic ratio of portal mesenchyme and we performed scRNAseq analysis to determine their gene expression and cell-cell interactions.

  Study EGAS50000000994

• hereditary BrEAst Case CONtrol study

  The BEACCON study aimed to address the lack of power of previous studies to identify novel BC predisposition genes by performing extensive sequencing in 12,000 women (11,511 analysed following exclusions) and further enhancing power by using an ‘extreme phenotype’ design with enrichment of familial non-BRCA1 and BRCA2 cases, compared with a control population of older women with ongoing confirmation of cancer-free status at June 2019. Three-quarters of the 1303 candidate genes screened were selected based on empiric evidence from local (69 multi-case BC families) or international whole exome sequencing studies, and the remainder were included to provide detailed coverage of functional pathways with established associations with BC

  Study EGAS00001005043

• The genetic footprint of the European Roma diaspora: Evidence from the Balkans to the Iberian Peninsula

  Our genomic approach focuses on: (i) the internal genetic structure of Roma and its correlation with geography; (ii) the relationships between Iberian Roma and other non-Roma populations to explore possible contacts during the period of population upheaval following the Roma’s arrival on the Iberian Peninsula; (iii) estimation of the admixture events in the Iberian Roma before and after their arrival to the Iberian Peninsula; and (iv) the assessment of endogamy patterns and assortative mating of the European Roma. Our study provides a detailed analysis of the intricate population history of the Iberian Roma, offering insights from both micro-geographical and large-scale perspectives on the population history of European Roma.

  Study EGAS50000000746

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___visium

  This study will reconstruct the single cellular phylogeny of tumour and immune cells in relation to both genomic, functional, and spatial location. 20 tumours in total will be studied, including non-progressing small renal masses, progressing small renal masses, relatively indolent larger tumours, and high risk tumour with metastatic sampling. We aim to: Generate a focused, comprehensive phylogenetic characterisation of tumour cells Understand the dependencies of the cancer genome, transcriptome, tissue architecture and the single cellular micro-environment Quantify the single cellular composition and functional intra- and inter- tumoural heterogeneity Determine the phylogeny of tumour associated lymphocytes and their relationship to neo-epitopes and the immune microenvironment Investigate the mechanisms by which the tumour-normal interface constrains tumoural growth.

  Study EGAS00001006045

• Genome and transcriptome sequence data from a non-small cell lung cancer patient

  Genome and transcriptome sequence data from a non-small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003639

• Genome and transcriptome sequence data from a metastatic prostate cancer patient

  Genome and transcriptome sequence data from a metastatic prostate cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003638

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003637

• Genome and transcriptome sequence data from a metastatic paraganglioma patient

  Genome and transcriptome sequence data from a metastatic paraganglioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003636

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003635