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• Genome and transcriptome sequence data from a locally advanced breast cancer patient

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

  Dataset EGAD00001004897

• Whole exome sequencing and target gene sequencing of ESCC cases and healthy controls from Henan high-risk region

  In total, 186 FH+ ESCC cases were sequenced using whole-exome sequencing, then 1935 ESCC cases and 1186 geographically-matched healthy controls were sequenced using 7 Mb custom designed Roche SeqCap kit which targeted about 600 genes. The libraries were constructed and then sequenced in Illumina platform.

  Dataset EGAD00001004556

• Transcriptomic sequences of small intestinal Plasma cells from Celiac disease patients

  Transcriptomic sequences of small intestinal Plasma cell (PCs)s from Celiac disease patients. RNAseq data produced using Illumina paired-end (75bp) reads. Includes only raw data of sequences (fastq format). Samples from seven Celiac disease patients and four healthy controls. Samples from Celiac disease patients contain sub-groups of PCs that are either specific or not specific to autoantigen of the disease (TG2).

  Dataset EGAD00001004481

• WES analysis in identifying additive genetic factors that may contribute to the occurrence of moyamoya in neurofibromatosis type 1

  Five subjects from pedigree with co-occurrence of neurofibromatosis type 1 and moyamoya were sequenced in duplicate (0 and1). Kinship and phenotype: NF025, NF026 and NF027 were sibling all affected by neurofibromatosis type 1. NF026 also presented moyamoya. NF0262 and NF0263 were sibling both affected by neurofibromatosis type 1. NF0262 also presented moyamoya. NF026 and NF0262 were first cousins.

  Dataset EGAD00001004157

• The spatio-temporal evolution of lymph node spread in early breast cancer

  Set of multi-region sequenced breast cancer primary samples, lymph nodes and ctDNA. We collected samples from 11 breast cancer patients with lymph node involvement but no sign of distant metastasis. We performed a mix of whole-exome sequencing, targeted capture sequencing, and whole-genome sequencing of primary tumour samples and lymph nodes, as well as targeted capture sequencing of circulating tumour DNA.

  Dataset EGAD00001004122

• Bulk RNASeq on CD8+CD69+CD103+ and CD8+CD69+CD103- T cells form breast cancer.

  CD8+CD69+CD103+ and CD8+CD69+CD103- T cells were flow sorted from 1 primary triple negative breast cancer, 1 primary HER2 amplified breast cancer, and 1 triple negative liver metastasis. Prior to flow sorting, fresh tumor samples were digested to produce single cell homogenates on the day of surgery. Following RNA extraction, RNASeq was performed using polyA selection.

  Dataset EGAD00001003964

• Tumor-reactive heterotypic CD8 T cell clusters from clinical samples

  Emerging evidence suggests a correlation between CD8+ T cell-tumor cell proximity and anti-tumor immune response. However, it remains unknown whether these cells exist as functional clusters that can be isolated from clinical samples. By conventional and imaging flow cytometry, we show here that from 21/21 human melanoma metastases, we could isolate heterotypic clusters, comprising CD8+ T cells interacting with one or more tumor cells and/or antigen-presenting cells (APCs). Single-cell RNA-sequencing revealed that T cells from clusters were enriched for gene signatures associated with tumor reactivity and exhaustion. Clustered T cells exhibited increased TCR clonality indicative of expansion, while TCR-matched T cells showed more exhaustion and co-modulation when conjugated to APCs than to tumor cells. T cells that were expanded from clusters ex vivo exerted on average 9-fold increased killing activity towards autologous melanomas, which was accompanied by enhanced cytokine production. Upon adoptive cell transfer into mice, T cells from clusters showed improved patient-derived melanoma control, which was associated with increased T cell infiltration and activation. Together, these results demonstrate that tumor-reactive CD8+ T cells are enriched in functional clusters with tumor cells and/or APCs and that they can be isolated and expanded from clinical samples. Typically excluded by single cell gating in flow cytometry, these distinct heterotypic T cell clusters serve as a valuable source to decipher functional tumor-immune cell interactions, while they may also be therapeutically explored.

  Study EGAS50000000785

• LBC1936 fastq files

  1075 members of the LBC1936 were sequenced using the Illumina HiSeq X platform. This dataset contains the paired fastq files.

  Dataset EGAD00001008774

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of eight hyperdiploid ALL patients (ALLT-364, ALLT-367, ALLT-368, ALLT-371, ALLT-377, ALLK-111, ALLT-382, ALLT-395). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002427

• Oxford Nanopore Adaptive Sampling WGS

  Eight samples were analyzed on an Oxford Nanopore MinION flow-cell, and to evaluate multiplexing, four samples were run together on one flow-cell on the P2 Solo device. Using adaptive sampling, we targeted 10 regions of different structural variant types, including deletions, translocations and complex rearrangements. MinION sequencing resulted in between 14.1-18.3 Gb of data per flow cell, with mean autosomal on-target coverage of 28.4x and off-target read depth coverage of 5.3x.

  Dataset EGAD50000001821