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• Angiopredict Whole genome Shallow Sequencing

  Shallow sequencing of metastatic colorectal cancer samples for the Angiopredict and Nobev cohorts described in: van Dijk et al., JCO, in revision

  Dataset EGAD00001003990

• SCNA-Seq of tumor DNA samples

  Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping of corresponding tumor material

  Dataset EGAD00001002150

• Molecular Signatures of DCIS to Invasive Progression for Basal-Like Breast Cancers: An Integrated Mouse Model and Human Tumor Study

  We studied the genomic signatures of progression in breast ductal carcinoma in situ (DCIS) as it progresses towards triple negative invasive breast cancer (TNBC). Single cell RNA sequencing (scRNAseq) was performed on the C3Tag genetically engineered mouse model that forms human breast-like DCIS and TNBC. Bulk RNA sequencing was performed on RNA harvested from archival formalin-fixed, paraffin embedded (FFPE) pairs comprising of estrogen receptor (ER) positive (ER+) and negative (ER-) subsets of DCIS. 

  Study phs002443

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  SARS-CoV2 mRNA vaccination-induced CD4+ Th cells were isolated based on activation marker expression from human bone marrow (n=3), lung (n=5), liver (n=4) and paired blood samples (to liver donors, n=4) of virus-naive vaccinees after Spike peptide mix stimulation in vitro. The 10X platform was used for single cell transcriptome analysis, along with T cell receptor clonotype analysis in a total of 1985 cells. Samples were sequenced on a NovaSeq 6000 (Illumina).

  Study EGAS50000000045

• Patient tumour data (RNAseq, WGBS, ChIPseq, WGS)

  Content: 60 GB patient tumours and 4 normal brain samples combined in pairs by region (x2=8 total input samples). RNAseq: 1 lane per sample, total strand-specific rRNA-depleted (normal samples were combined = 2 lanes/samples per brain region). WGBS: 2 lanes per sample (normal samples were combined = 2 lanes/samples per brain region). ChIPseq (histone mark): a subset of 20 GB samples were profiled. For the same modification were multiplexed and sequenced on 4 lanes each (H3K27ac, H3K4me1) or a single lane (all others). WGS: used as matching input control for the 20 ChIPseq samples. Data type and technology: RNA-seq: PE 100bp sequenced on HiSeq2000. WGBS: PE 100bp sequenced on HiSeq2000/4000. ChIPseq: SE 50bp sequenced on HiSeq2000/4000. WGS: PE 150bp sequenced on HiSeq X.

  Dataset EGAD00001005492

• RNA-sequencing of ex vivo exhausted human antigen-specific T cells

  Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. To explore new pathways for reinvigoration of anti-tumor immune functions, we developed a human ex vivo exhaustion model by repetitive antigenic stimulation of primary CD8 T cells. This results in T cells that resemble patient-derived T cells in tumors on a phenotypic and transcriptional level. Four human healhy donor CD8+ T cells were isolated, transduced with an NY-ESO-1 TCR lentivirus construct, stimulated in four different conditions (Trested, Ttumor, Tex, Teff) with T2 tumor cells and specific peptides over 12 days. Cells were then sorted for TCR Vbeta 13.1+ (NY-ESO-1 TCR) CD8+ CD3+ CD56- CD4- DAPI- cells. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode (2x51bp) on 2 lanes of an Illumina NovaSeq 6000 flow-cell. FASTQ sequence files were generated with the Illumina RTA version 3.4.4 and Base-calling Version bcl2fastq-2.20.0.422.

  Dataset EGAD00001009754

• Papua New Guinean Lowlanders dataset

  The Papua New Guinean Lowlanders dataset includes 41 whole genome sequences for Papua New Guinean individuals sampled in Daru. DNA was extracted from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD50000000050

• ISA Nutrition 2015

  Comprehensive data on lifestyle-related modifiable factors, sociodemographic, anthropometric, economic, biochemical, and genetic markers related to the occurrence of cardiometabolic diseases as part of the observational cross-sectional survey (2015 Health Survey of Sao Paulo with Focus on Nutrition (2015 ISA-Nutrition), a population-based study. Data of 805218 SNPs for 841 individuals was genotyped using the Axioma 2.0 Precision Medicine Research Array in the Thermo Fisher Scientific laboratory (Affymetrix Inc, Santa Clara, CA).

  Dataset EGAD00010002678

• Anaplastic Thyroid Cancer germline variants

  Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller, to generate germline variant calls across the SureSelect All Exon V5+UTR target region. Variant calls are in VCF format. In total there are samples from 173 donors. 101 donors have calls generated from both normal and tumour samples tumour samples, 94 of which have a matched normal. Details for the call can be found in the vcf headers.

  Dataset EGAD00001004127

• OxyTarget mtDNA seq

  We studied 44 rectal cancer patients enrolled onto a prospective population-based biomarker study, who were planned for curative-intent radiation therapy before definitive surgery, yet at high risk of metastatic progression beyond the pelvic cavity. The patients had full-length mtDNA sequencing of whole blood (WB) and peripheral blood mononuclear cells (PBMC), sampled at the time of diagnosis. Metastatic events were recorded up to 60 months of follow-up after completion of the multimodal treatment.

  Dataset EGAD00001007992