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• EGAS00001001730_REL-2016-04

  HipSci - Embryonic Stem Cells - Expression Array - April 2016

  Dataset EGAD00010000910

• chr6_allsamples_imputated

  Chromosome 6 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002539

• chr11_allsamples_imputated

  Chromosome 11 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002538

• chr14_allsamples_imputated

  Chromosome 14 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002527

• chr7_allsamples_imputated

  Chromosome 7 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002528

• chr13_allsamples_imputated

  Chromosome 13 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002531

• chr4_allsamples_imputated

  Chromosome 4 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002529

• chr5_allsamples_imputated

  Chromosome 5 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002536

• chr10_allsamples_imputated

  Chromosome 10 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002530

• chr21_allsamples_imputated

  Chromosome 21 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002532

• chr16_allsamples_imputated

  Chromosome 16 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002534

• chr20_allsamples_imputated

  Chromosome 20 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002537

• chr9_allsamples_imputated

  Chromosome 9 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002535

• chr12_allsamples_imputated

  Chromosome 12 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002517

• chr22_allsamples_imputated

  Chromosome 22 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002518

• chr8_allsamples_imputated

  Chromosome 8 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002519

• chr18_allsamples_imputated

  Chromosome 18 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002520

• chr3_allsamples_imputated

  Chromosome 3 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002521

• chr19_allsamples_imputated

  Chromosome 19 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002524

• chr1_allsamples_imputated

  Chromosome 1 imputed genotypes of samples genotyped on the Axiom Human Genotyping SARS-CoV-2 array (GRCh38)

  Dataset EGAD00010002525

• sc-RNA-Seq soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001009002

• HipSci - Embryonic Stem Cells - Exome Sequencing - April 2016

  HipSci - Embryonic Stem Cells - Exome Sequencing - April 2016

  Dataset EGAD00001001999

• Illumina_WXS_CONT

  Whole-exome sequencing on Illumina HiSeq2000/2500 of normal colon control tissue

  Dataset EGAD00001002094

• High response rate to anti PD-1 therapy in desmoplastic melanoma

  Desmoplastic melanoma (DM) is a rare subtype of melanoma characterized by dense fibrous stroma, resistance to chemotherapy and a lack of actionable driver mutations, but is highly associated with ultraviolet light DNA damage. We analysed 60 patients with advanced DM treated with programmed cell death 1 (PD-1) or PD-1 ligand (PD-L1) blocking antibody therapy. Objective tumor responses were observed in 42 of the 60 patients (70%, 95% confidence interval 57-81%), including 19 patients (32% overall) with a complete response. Whole-exome sequencing revealed a high mutational load and frequent NF-1 mutations (14 out of 17 cases). Immunohistochemistry (IHC) analysis from 19 DM and 13 non-DM revealed a higher percentage of PD-L1 positive cells in the tumor parenchyma in DM (p = 0.04), highly associated with increased CD8 density and PD-L1 expression in the tumor invasive margin. Therefore, patients with advanced DM derive significant clinical benefit from PD-1/PD-L1 immune checkpoint blockade therapy despite being a cancer defined by its dense desmoplastic fibrous stroma. The benefit is likely derived from the high mutational burden and a frequent pre-existing adaptive immune response limited by PD-L1 expression.

  Study phs001469

• Human Pilocytic Astrocytoma Single Cell RNA Sequencing

  Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma with a single driver BRAF rearrangement. Here, we perform scRNAseq in six PAs using methods that enabled detection of the rearrangement. When compared to higher-grade gliomas, a strikingly higher proportion of the PA cancer cells exhibit a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibit a progenitor-like phenotype with evidence of proliferation. These express a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Immune cells, especially microglia, comprise 40% of all cells in the PAs and account for differences in bulk expression profiles between tumor locations and subtypes. These data indicate that MAPK signaling is restricted to relatively undifferentiated cancer cells in PA, with implications for investigational therapies directed at this pathway. Note that 931 out of 1234 samples in the Sequence Read Archive (SRA) passed QC and have transcript count data available from the Broad Institute Single Cell Portal. The transcript count data can be found at https://singlecell.broadinstitute.org/single_cell/study/SCP271/pilocytic-astrocytoma-single-cell-rna-seq#study-download

  Study phs001854