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• Bulk BCR NGS data from metastatic breast tumours from donors with therapy-resistant lethal metastatic breast cancer.

  Bulk B Cell Receptor high-throughput sequencing data across 27 metastatic breast tumours obtained from 8 donors with therapy-resistant lethal metastatic breast cancer at the time of a warm autopsy. The 35 samples were sequenced on an Illumina MiSeq instrument and their raw FastQ files deposited here.

  Dataset EGAD00001010023

• Single-cell ATAC-seq of matched pediatric AML tumors

  Single-cell ATAC-seq of pediatric AML tumours from patients enrolled in the clinical trial AAML1031. Obtained using the 10X Chromium NextGEM Single Cell ATAC Reagent Kit, v1.1. A total of 64 samples were obtained from biopsies at diagnosis, remission and relapse from 25 patients.

  Dataset EGAD00001011194

• Single-cell RNA-seq of matched pediatric AML tumors

  Single-cell RNA-seq of pediatric AML tumours from patients enrolled in the clinical trial AAML1031. Obtained using the 10X Chromium Single Cell 3’ Reagent Kit, v3.0. A total of 75 samples were obtained from biopsies at diagnosis, remission and relapse from 28 patients.

  Dataset EGAD00001011195

• Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort.

  Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort (n=18).

  Dataset EGAD00001011068

• DAC of the BriTROC-1 project

  Dac EGAC00001003291

• THE GENOMIC LANDSCAPE OF ACTINIC KERATOSIS

  Dac EGAC00001001926

• Head of the Sequencing Unit

  Dac EGAC00001002698

• The AGGA Data Access Committee

  Dac EGAC00001003019

• Longitudinal Immune Dynamics of Mild COVID-19 Define Signatures of Recovery and Persistence

  SARS-CoV-2 has infected over 160 million and caused more than 3 million deaths to date. Most individuals (>80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive activation, including an early cellular and proteomic signature that correlated with the amplitude of virus-specific humoral responses after day 30. We characterized signals associated with recovery and convalescence to define a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC).

  Study phs002576

• Genomic Copy-Number Variants Drive Apoptotic Resistance and Relapses on Immune Checkpoint Inhibitors

  We investigated the genomic mechanisms underlying acquired resistance (AR) to immune checkpoint inhibitors (ICIs) across tumor types, specifically by examining how copy number variant (CNV)-driven subclonal evolution contributes to clinical relapses in melanoma patients. We analyzed longitudinal clinical melanoma samples from patients who experienced relapses on ICI therapy, complemented by isogenic human melanoma cell line models (M486) and murine melanoma tumor systems. Single-cell whole-genome sequencing (scWGS) was employed to resolve subclonal CNV patterns in AR tumors. The scWGS data revealed that AR-dominant subclones systematically deleted pro-apoptotic genes while amplifying anti-apoptotic genes and innate resistance pathway components. Notably, shared and private AR subclonal CNVs preexisted selective pressure, with convergent evolution targeting apoptosis-regulatory pathways and resulting in downregulated apoptotic/mitochondrial priming that enables ICI resistance. scWGS datasets from isogenic human melanoma cell lines, patient-matched tumor samples, and murine melanoma models will be made available through dbGaP, enabling researchers to access high-resolution subclonal CNV profiles that define the genomic landscape of acquired ICI resistance evolution.

  Study phs004102