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• scRNA-seq and snRNA-seq of trophoblast stem cells (TSCs) differentiation into extravillous trophoblast organoids (EVTs)

  This dataset is part of a study that aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. This specific dataset includes scRNA-seq and snRNA-seq data from trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) together with EVT differentiation media. This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells. Data for primary trophoblast organoids is available under E-MTAB-12650.

  Dataset EGAD00001010017

• Colorectal cancer organoid-stroma biobank cohort

  In colorectal cancers (CRC) the tumor microenvironment plays a key role for prognosis and therapy efficacy. Patient-derived tumor organoids (PDTOs) show enormous potential for preclinical testing, however, purely epithelial cultures features including the ‘consensus molecular subtypes’ (CMS) are largely eradicated. To better reflect the cell type heterogeneity, we established the CRC organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAFs) from 30 patients. Whole exome sequencing and transcriptome analysis in various in vitro and in vivo contexts was performed to study the influence of the TME on the CRC phenotype.

  Dataset EGAD00001011173

• UCSF-CASCADE analysis of metastatic prostate cancer

  Targeted cancer therapy inevitably selects for tumor cells that harbor some form of therapy resistance. This phenomenon is a principle reason why advanced prostate cancer, which can be treated with agents targeting androgen signaling dependency and DNA repair failure, is a lethal condition. The influence of a patient's clinical history and disease evolution on how their disseminated tumors develop resistance has been difficulty to study, because few autopsy studies have been performed in heavily treated patients with DNA-repair deficient metastatic castration-resistant prostate cancer (mCRPC). Here, we assessed how resistance to targeted cancer therapies evolved in an autopsy cohort of 54 mCRPC tumors from six men. This dataset includes targeted sequencing, exome sequencing, and RNA-seq conducted on these biopsies.

  Dataset EGAD00001010275

• NLG-LBC-05 ctDNA project sequencing data

  Low-pass whole-genome sequencing of pretherapy lymphoma cfDNA and targeted sequencing of cfDNA, tumor tissue and whole-blood samples of NLG-LBC-05 patient samples and cfDNA of nine subjects with no known cancer. Hybrid capture target enrichment; panel target and sequencing information provided in PMID:34932792. FASTQ files provided for targeted sequencing, separate sequencing runs per sample noted with prefix "run" if applicable. Sequences from DTX1 and KLHL6 targets are advised to be excluded from analyses due to PCR/plasmid contaminants of in-house origin.

  Dataset EGAD00001009337

• Single-cell RNA sequencing of human kidney transplant nephrectomies with chronic rejection or non-alloimmune graft injury

  This dataset contains raw single-cell RNA sequencing (scRNA-seq) data for five new kidney allograft nephrectomy samples used to construct the described in the following study: https://www.biorxiv.org/content/10.1101/2022.10.28.514222v2.full. The full description of processing is described in the manuscript. Briefly, samples were digested into a single cell suspension and run according to the 10X Genomics Chromium 5’ single cell kit (v2). Sequencing was performed using an Illumina Novaseq instrument. Samples were designated as TXN2 (EGAN00002519570, mycotic pseudoaneurysm, control dataset), TXN3 (EGAN00002235628, renal vein thrombus, control dataset), TXN5 (EGAN00002519573, chronic transplant rejection), TXN6 (EGAN00002519572, chronic pyelonephritis and renal artery stenosis, non-alloimmune graft injury dataset), TXN7 (EGAN00002519576, recurrent focal segmental glomerulosclerosis, non-alloimmune graft injury dataset).

  Dataset EGAD00001015631

• Acral Melanoma PDXs from the admixed Brazilian Population - filtered PDX sample BAM files - RNAseq

  BAM files containing the whole exome data for the Patient Derived Xenograft samples mapped to build GRCh38. All files have been processed with XenofilteR to remove mouse reads. Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like in Latin America, it can account for a significant proportion of cutaneous melanoma cases. Here, we performed comprehensive genomic and functional profiling of AM from a uniquely diverse Brazilian cohort. Whole-exome and transcriptome sequencing was performed on both tumours and patient-derived xenograft (PDX) samples. The PDX were obtained from a comprehensive collection of patient-derived xenograft (AM-PDX) models that we established which faithfully retained the histopathological and genomic features of the original tumours.

  Dataset EGAD00001015746

• Whole exome sequencing data of tumor/normal pairs for the study "TGF-β attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells"

  Tumor DNA was extracted from formalin-fixed and paraffin embedded tumors of a large cohort of bladder cancer patients before treatment with anti-PD-L1. Normal DNA was extracted from matched PBMCs. Whole exome sequencing was performed. This is a subset of patients for which RNA sequencing is also provided (with more detailed phenotypic information).

  Dataset EGAD00001004218

• Targeted sequencing of 72 prostate cancer driver in 712 plasma cell free DNA samples

  Dataset contains targeted sequencing data of 712 plasma cell free DNA samples and 428 white blood cell samples collected from 428 men with metastatic prostate cancer. Target capture was performed using a hydridization-based custom Roche SeqCap EZ Choice kit, designed to capture all exons of 72 prostate cancer driver genes. Cell free DNA was extracted from 10 mL blood samples. Libraries were sequenced using Illumina HiSeq 2500 or Illumina MiSeq instruments to a median coverage of 750x. 62% of samples had ctDNA fraction above 2% of total cfDNA. Note that "Dataset type" is erroneously listed as "Amplicon sequencing", because "Captured-based targeted sequencing" or "Hybridization-based targeted sequencing" were not available options in EGA at the time of submission.

  Dataset EGAD00001004208

• Genomic alterations in MM - BAM

  Tumor DNA was extracted from 100 bone marrow aspirate samples where CD138+ selection had been performed to enrich plasma cells from patients with multiple myeloma. Patient matched control DNA from either peripheral blood leukocytes or CD34+ stem cell harvests was also isolated. Both tumor and control DNA underwent library preparation using the Hyperplus kit (KAPA Biosystems) and were hybridized to baits for a targeted SeqCap myeloma panel (Nimblegen) encompassing 129 genes, regions for SNPs for copy number determination, and the IGH, IGK, IGL loci, as well as approximately 5 Mb surrounding the MYC locus. Samples were sequenced on a HiSeq2500 using 100 bp paired end reads. Resulting BAM files were returned along with annotations for somatic events including single nucleotide mutations, indels and structural rearrangements.

  Dataset EGAD00001004117

• The National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics Resource Center: DNA and Cell Line Repository (the NINDS Repository): Motor Neuron/Amyotrophic Lateral Sclerosis (ALS) Study

  The National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics Resource Center: DNA and Cell Line Repository (the NINDS Repository), banks phenotypic data and biological samples, including from individuals with motor neuron disease, in order to facilitate gene discovery in neurological disorders. Those samples are used in a number of studies, and genotyping data from studies using this resource are encouraged to be shared via dbGaP. Many studies have already shared data in this fashion, which in turn, can be linked back to the biologicals banked at the NINDS Repository. Motor Neuron Disease is characterized by selective degeneration of the motor neurons of the spinal cord, brainstem, or motor cortex. Clinical subtypes are distinguished by the major site of degeneration. In Amyotrophic Lateral Sclerosis (ALS), there is involvement of upper, lower, and brainstem motor neurons. In progressive muscular atrophy and related syndromes, the motor neurons in the spinal cord are primarily affected. With progressive bulbar palsy, the initial degeneration occurs in the brainstem. In primary lateral sclerosis, the cortical neurons are affected in isolation (Adams et al, Principles of Neurology, 6th ed, p 1089). The Motor Neuron Disease Collection of DNA and cell lines in the NINDS Repository is largely Amyotrophic Lateral Sclerosis cases (others include progressive muscular atrophy, primary lateral sclerosis, progressive bulbar palsy, Kennedy's disease). Amyotrophic lateral sclerosis (ALS) is the most common form of motor neuron disease (MND). Although ALS is the most common MND, it is still a relatively rare disease with an incidence of around 1.6 per 100,000 in the United States. It is currently incurable and treatment is largely limited to supportive care. Family history is associated with an increased risk of ALS, and many Mendelian causes have been discovered (including SOD1). However, most forms of the disease are not obviously familial. It is suspected that the sporadic forms of neurodegenerative disorders are caused by multiple genetic variants that individually make relatively weak contributions to risk. There is also an associated Control collection (see dbGaP and Coriell). Studies in motor Neuron Disease may use cases from the NINDS repository, controls from the NINDS repository, as well as cases, and controls, from other sources. A subset of subjects from The National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics Resource Center: DNA and Cell Line Repository (the NINDS Repository): Motor Neuron/Amyotrophic Lateral Sclerosis (ALS) Study was utilized in the Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data study. Note: The publication Chio et al., 2009 states that "Raw sample-level genotype data from the initial GWAS study ... are available for download through the dbGAP portal (phs000006.v1.p1)". Instead, please follow this link: phs000101.v1.p1.

  Study phs000006