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• (RNA-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  Raw and processed RNA-seq data from a patient-derived xenograft (yielding 18 samples) and the VOA1066 undifferentiated endometrial carcinoma cell-line (yielding 15 samples). PDX samples were treater with either compound-14, dBRD9, or were untreated. VOA1066 samples were treated with either compound-12, dBRD9, or were untreated. Samples were sequenced on an Illumina NextSeq 500 using 37-bp single-end sequencing. Raw fastq files and gene count tables are included for each sample.

  Dataset EGAD50000001471

• (ATAC-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  Raw and processed ATAC-seq data from the VOA1066 undifferentiated endometrial carcinoma cell-line (10 samples). Samples were treated with DMSO, dBRD9, or compound 12, without doxycycline; some samples instead received doxycycline-induced ARID1A treatment, or doxycycline alone. Samples were sequenced on Illumina NextSeq 500 using 37 bp paired-end sequencing parameters. Raw fastq fastq files, bigwig files giving normalized genomic coverage per region, and called broad peaks are included for each sample.

  Dataset EGAD50000001472

• MASQ targeted amplicon sequencing data of AML samples at presentation, remission, and relapse, and MASQ data demonstrating performance ranges of the method.

  MASQ targeted amplicon sequencing of AML blood or bone marrow at presentation, and relapse, when available, for 5 patients. Remission samples of both blood and bone marrow are included for 5 patients. Multiple batches (b1,b2) are used for 2 patients. There are 25 assays of AML data. MASQ data demonstrating sensitivity, input range, and batch size are also included, as 12 assays. All data is provided in paired FASTQ files.

  Dataset EGAD00001005121

• Sequencing data for oesophageal and related samples - ICGC DCC release 28 (WGS)

  WGS sequencing for 409 cases (832 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 28

  Dataset EGAD00001004137

• Candidate diagnostic variants reported into DECIPHER, Wright NEJM 2023

  Candidate diagnostic variants reported into DECIPHER by 4 April 2022, annotated with clinical and automated pathogenicity assertions (see DOI: 10.1056/NEJMoa2209046). Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland, Wright et al, NEJM 2023.

  Dataset EGAD00001010137

• RNAseq from PDAC samples

  BAM files from RNA-seq of PDAC samples used in the COMPASS hENT1 study

  Dataset EGAD00001009409

• FFPE_normals_v2_gbm_wtsi_panel

  Targeted pulldown of approx 60 ffpe normal samples to use as normal controls

  Study EGAS00001002124

• Engineered Human Primary T Cell transcriptome study

  Study of transcriptome responses to different human T cell engineering approaches.

  Study EGAS00001006125

• Nasal Polyp RNAsequencing, Skaraborg Sweden

  Whole-transcriptome sequencing (RNAseq) in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and controls. Differential expression patterns in genes involved in cilia, viral defense and NKT-cell specific pathways, suggesting a role of viral immunity in combination with cilia functionality in CRSwNP.

  Study EGAS00001007088

• Duplex sequencing

  An additional 320 buccal swab samples were subjected to error-corrected sequencing (duplex sequencing).

  Study EGAS50000000443

• Low_input_LC__WGS_

  R&D project to develop low input library construction methods.

  Study EGAS00001001855

• Transcriptomic profiling of RIRCD patient skeletal muscle, comparing muscle during affected phase to healthy control, and affected patient with and without additional EARS2 mutations.

  Illumina Nextseq total RNA sequencing profiles of skeletal muscle biopsies of 5 affected patients (F3/2M, F4/1F, F5/1M, F2/2F, F2/1M) compared to 6 control (Control040500, Control3509, Control3934, Control3949, Control4994, Control5106) and comparing 3 patients with additional EARS2 mutations (F2/2F, F2/1M, F5/1M) to 2 patients without (F3/2M, F4/1F). Illumina MiSeq total RNA sequencing profiles of skeletal muscle biopsies from patient F3/1M during affected disease phase (4 replicates: F3-1M_Affected_1, F3-1M_Affected_2, F3-1M_Affected_3, F3-1M_Affected_4) compared to recovered phase (F3-1M_Recovered_1, F3-1M_Recovered_2, F3-1M_Recovered_3, F3-1M_Recovered_4).

  Dataset EGAD00001006381

• Molecular profiling of an AML case following treatment with a BCL2 inhibitor

  Molecular profiling of a single AML case. Exome sequencing was performed at diagnosis and after treatment with conventional chemotherapy and BCL2i. Some samples required whole genome amplification. Data will be made available to researchers upon completion of a data transfer agreement; use is restricted to ethically approved research focused on haematological malignancy, and precludes germline analysis.

  Study EGAS00001004841

• Multiple_myeloma_precursor_genomics

  Whole genome sequencing of up to 45 multiple myeloma precursor samples and matched normals pairs.

  Study EGAS00001006312

• ICARUS-LUNG01 dataset

  A total of 46 frozen tumor biopsies underwent WES analysis, while 41 blood samples were used as germline controls.Tumor samples qualified for whole exome sequencing (WES) if they contained ≥10% tumor cells. For bulk RNA-seq, 20 paired baseline and on-treatment frozen tumor biopsies were analyzed. Tumor samples qualified if they contained ≥30% tumor cells. For GeoMx spatial transcriptomic study we used 7 patients from the ICARUS LUNG01 trial focusing on tumour and immune cell compartments. We selected 7 paired baseline and on-treatment patient samples for analysis. We selected up to 4 regions of interest (ROI) per sample tissue. We identified tumour and immune cell areas of illumination (AOI) using CK and CD45 antibodies respectively

  Dataset EGAD50000001014

• Exome and RNA sequencing of pancreatic cancer biopsies and PDX models

  Pancreatic cancer biopsies and matching normal controls from 10 patients were exome sequenced. The same biopsies and PDX models derived from these were also subject to RNA sequencing.

  Dataset EGAD00001008113

• Functional dissection of inherited non-coding variation influencing multiple myeloma risk

  This dataset contains ATAC sequencing of plasma cells from multiple myeloma (MM) patients. The data was used to investigate genotype-specific chromatin accessibility quantitative trait locus (caQTL) using caQTLseg (https://github.com/abhisheknrl/caQTLseg). This dataset contains 161 bam files.

  Dataset EGAD00001007814

• Dataset for Sarcoma-WES linked from study EGAS00001004813

  Sequencing data of 144 sarcoma tumor and control runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

  Dataset EGAD00001010258

• Reference single cell SNP array dataset from Coriell for training and validation of method for accurate single cell genotyping

  This dataset contains DNA from B-lymphocytes from 2 Coriell families and 4 individuals hybridized to HumanKaryomap BeadChip Array. Single cells from subjects GM12878 and GM7228 were amplified using multiple displacement amplification (SureMDA) according to Infium Karyomapping Assay Guide. Bulk DNA was processed and hybridized to an array for subject GM12878, GM07224 and GM07225.

  Dataset EGAD00001006376

• Duplex sequencing

  A total of 387 buccal swab samples were subjected to error-corrected sequencing (duplex sequencing).

  Study EGAS50000000054

• CRISPR screen M14, NCI-H3122

  Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung

  Dataset EGAD00001001389

• Japanese population-specific reference panels (BioBank Japan genotype data)

  Develop Japanese population-specific reference panels to improve imputation quality for GWAS

  Study JGAS000738

• Palbociclib resistance analyses on breast cancer bone metastasis PDX

  Identify mecanisms of metastatic breast cancer resistance to palbociclib by RNAseq analyses.

  Study EGAS00001006428

• ERBB2/HER2 transmembrane and juxtamembrane domain mutations in cancer

  In this study, we identified several recurrent activating HER2 somatic mutations in transmembrane and juxtamembrane domain in multiple cancers and demonstrate that patients carryingthese mutations are candidates for anti-HER2 therapy. We have also identified a germline mutation in HER2 transmembrane domain.

  Study EGAS00001003213

• Targeted myeloid panel DNA-Sequencing Mutations Matrix Validation Cohort

  Profiling of co-mutations was done by targeted resequencing using the TruSight Myeloid assay (Illumina, Chesterford, UK) covering 54 genes recurrently mutated in AML: BCOR, BCORL1, CDKN2A, CEBPA, CUX1, DNMT3A, ETV6, EZH2, IKZF1, KDM6A, PHF6, RAD21, RUNX1, STAG2, ZRSR2, ABL1, ASXL1, ATRX, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CSF3R, FBXW7, FLT3, GATA1, GATA2, GNAS, HRAS, IDH1, IDH2, JAK2, JAK3, KIT, KRAS, MLL, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PTEN, PTPN11, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, TET2, TP53, U2AF1 and WT1. For each reaction, 50 ng of genomic DNA was used. Library preparation was done as recommended by the manufacturer (TruSight Myeloid Sequencing Panel Reference Guide 15054779 v02, Illumina). Samples were sequenced paired-end (150 bp PE) on NextSeq- (Illumina) or (300 bp PE) MiSeq-NGS platforms, with a median coverage of 3076 reads (range 824–30565). Sequence data alignment of demultiplexed FastQ files, variant calling and filtering was done using the Sequence Pilot software package (JSI medical systems GmbH, Ettenheim, Germany) with default settings and a 5% variant allele frequency (VAF) mutation calling cut-off. Human genome build HG19 was used as reference genome for mapping algorithms.

  Dataset EGAD00001008506