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• Endoresist panel sequencing

  Patients with endocrine-resistant breast cancer in Stockholm Sweden. DNA obtained from patients primary and relapse tumors, and tumor-free lymph nodes used as germline control. DNA was extracted from formalin-fixed paraffin-embedded tissue and sequenced by 370-gene panel-based sequencing with Kapa HyperPlus library preparation and Twist Bioscience hybrid capture. Custom bait sets (panels) from Twist Bioscience. Paired end 2x150 bp using NovaSeq X. The data is presented as fastq-files.

  Dataset EGAD50000000350

• RNAseq of paired FL and tFL samples

  This dataset contains RNA profiling of paired FL and tFL samples (n=11 pairs) sequenced by Illumina NextSeq500 instrument. Libraries used in this mRNA-seq dataset were prepared with QuantSeq FWD library preparation kit (Lexogen, Catalog Number: 015) with the addition of UMI module. RNAs used for library preparation were isolated from FFPE tissues using ALLPREP RNA/DNA FFPE kit (QIAGEN,Catalog number: 80234). Data are uploaded as FASTQ format.

  Dataset EGAD50000001384

• Targeted Sequencing Data for RESOLVE Clinical Trial

  This is a Phase II clinical trial. This research study is studying a combination of targeted therapies as a possible treatment for estrogen-receptor positive (ER+) endometrial cancer and low-grade serous ovarian cancer. The drugs involved in this study are: - Abemaciclib (also known as Verzenio™) - Letrozole (also known as Femara®) - Metformin (also known as Glucophage®) - Zotatifin (also known as eFT226) - Gedatolisib (also known as PF-05212384)

  Dataset EGAD50000001711

• WGS data of pediatric T-ALL acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one T-ALL patient (ALLT-317). Relapsed (BM ALLT-317L and Tonsil ALLT-3107L) sample files are in dataset set2 of this submission. Sequencing library was made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1 (PE150). Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000002013

• RNAseq

  Libraries for sixty-eight cases (23 EATL and 45 MEITL) were prepared starting from 1 µg of total RNA using the TruSeq Stranded total RNA Gold kit from Illumina (San Diego, California, USA) and were sequenced in three batches on a HiSeq 4000 machine from Illumina with an average output of 63 million reads per sample (range 49-126).

  Dataset EGAD50000001619

• This dataset includes FASTQ for single-nucleus RNA-seq of normal controls, and multiple system atrophy (MSA) or Parkinson's disease (PD) patients.

  The dataset includes more than 130k nuclei isolated using 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1. In total, 30 samples are included from 10 controls, 8 MSA (including one sample that was omitted during QC), or 12 PD patients. Samples were sequenced on Illumina Novaseq 6000 or NextSeq 550 instruments.

  Dataset EGAD50000002041

• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy fibroblasts

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of fibroblasts derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and a patient carrying a pathogenic variant in EHMT2 (P2). Ribosomal RNA was removed using an RNase H–based depletion method, and strand-specific libraries were prepared for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002343

• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy iPSCs

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of induced pluripotent stem cells (iPSCs) derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and two patients carrying pathogenic variants in EHMT2 (P1 and P2). Poly(A)-selected RNA was used for library preparation, and strand-specific libraries were generated for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002344

• Case Report: Pre-Clinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma

  We report a rare case of a young patient (VENUS 167) initially diagnosed with grade 1 endometrioid endometrial cancer, which, following endocrine treatment, presented with mixed aggressive carcinoma with three distinct histologic patterns: grade 1 endometrioid, large cell neuroendocrine, and undifferentiated carcinoma. The NGS fastq data are WES, RNAseq and ATAC

  Dataset EGAD50000002397

• Data for the study "Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer"

  Sequencing data from patients with bladder cancer. BAM files from targeted DNA sequencing of bladder cancer driver genes in 344 circulating tumor DNA and tumor tissue samples. BAM files from whole exome sequencing of 49 circulating tumor DNA and tumor tissue samples. Paired FASTQ files from RNA sequencing of 86 tumor tissue samples.

  Dataset EGAD00001006362

• Targeted Deep Sequencing of Shwachman-Diamond syndrome bone marrow samples

  This dataset includes amplicon based sequencing of myeloid malignancy associated genes as well as EIF6 in 99 patients with Shwachman-Diamond syndrome and 11 patients who are "SDS-like". SDS-like patients are those that have clinical features of the disease but do not have a confirmed disease-causing mutation. There are 421 samples from serial timepoints, denoted alphabetically or numerically. For each timepoint, there is a single BAM file.

  Dataset EGAD00001006800

• Transcriptome profiling (RNA-seq) of human acute leukemias

  Total RNA-seq of blasts derived from 131 adult T-ALL cases, 7 AML cases and 1 mixed myeloid/lymphoid leukemia with CpG Island Methylator Phenotype (CIMP). The other RNA-seq data used in this study has been previously published and is available at EGAD00001007581 (AML) and EGAD00001007646 (CD34+ cells).

  Dataset EGAD00001011054

• WGBS of CD14 monocytes dataset of covid19 patients from Quebec, Canada

  this dataset contains the raw data generated for CD14 monocytes WGBSof 7 covid19 hospitalized patients sampled at various time points (Admission, Day 5 and Day 15) in total 15 biospecimen are available. WGBS libraries have been sequenced on Illumina NovaSeq 6000.

  Dataset EGAD00001008718

• The University of Hong Kong Colon Cancer Ganciclovir Study WGS Data

  Human clonal intestinal organoids were treated with 1µM MMF (Roche), 20 μM GCV (Hainan Poly Pharm Co Ltd), or in combinations (1 µM MMF + 20 μM GCV or 1 µM MMF + 40 μM GCV) continuously for 4-6 weeks. DNA was extracted after drug treatment. WGS was performed with 150 bp PE sequencing at 30X using an Illumina Novaseq sequencer.

  Dataset EGAD00001009667

• Whole exome and RNA sequencing data from the OXIRI phase 1b clinical trial in Asian pancreatic ductal adenocarcinoma (PDAC) patients

  This dataset contains 8 samples, each of which has paired-end WXS fastq files for Tumour and Normal samples, as well as RNA-Seq fastq file.

  Dataset EGAD00001008632

• Smartseq2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This dataset is part of Smartseq2 data

  Dataset EGAD00001005960

• AT-AML samples dataset

  Serial samples from one AT-AML patient as described in publication Goldgraben et al Pediatric Blood & Cancer 2020. Whole exome sequencing of a AT-'germline' blood sample, one bone marrow sample (at AML diagnosis) and 3 AML blood samples. Library preped using the Illumina Nextera Rapid Capture Exome Enrichment Kit, and sequenced as PE150 on HiSeq4000. Provided: 5 BAM files (GRCh37); 2 VCF analyses (germline and somatic)

  Dataset EGAD00001006090

• 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

• Pre_clinical_evolution_of_haematological_malignancies

  Deep targeted sequencing of 291 peripheral blood samples taken 1-20 years prior diagnosis of a haematological malignancy alongside age- and sex-matched controls. Key objective is to distinguish indolent age-related clonal haematopoiesis from pre-cancer and to derive predictive models for early risk-stratification.

  Study EGAS00001002964

• Garvan/St Vincent’s Prostate Cancer Tissue and Data

  The cohort (n=53) consists of prostate cancer patients from Australia. For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B” as suffix and tumour BAMs are named with “-T” as suffix.

  Dataset EGAD00001009066

• This DAC is to control access to data contained within dataset EGAS00001001147, for Myeloma XI clinical trial patients.

  Dac EGAC00001000307

• Liberate Cohorts

  This DAC will govern access to WES data associated with publications belonging to Liberate Cohorts

  Dac EGAC50000000455

• 2017_ AML WGS analysis result

  This data is belong to 2017 AML genome data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003599

• 2017_ AML prospective data analysis result

  This data is belong to 2017 AML prospective data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003598

• 2014 AML WES analysis result

  This data is belong to 2014 AML patients' exome data which is aligned to human reference(human_g1k_v37.fasta). There are 51 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003932