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• Gastric cancer RNA-seq data

  strand-specific RNA-seq data from 19 gastric tumors and their adjacent normal tissues, plus 16 gastric cancer cell lines, one normal gastric cell line, and 3 normal stomach RNAs

  Dataset EGAD00001003448

• Whole-genome array data for 42 Roma and 52 non-Roma from Czech Republic

  This dataset contains one VCF file with 94 individuals genotyped with the Human Origins Array.

  Dataset EGAD50000001103

• RNA Sequencing of mCRC xenografts under cetuximab treatment.

  RNA sequencing on cetuximab treated, untreated and release samples of one metastatic colorectal xenograft. 3 cetuximab treated samples, 3 placebo and 3 release - paired fastq.

  Dataset EGAD00001005185

• JIA family

  Exome sequencing data for two sibs with juvenile idiopathic arthitis and one unaffected sib

  Dataset EGAD00001004806

• Genomic Characterization CS-MATCH-0007 Arm Z1D

  The CS-MATCH-0007 protocol is a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing, RNA sequencing and if possible, whole-genome, methylation and miRNA sequencing using pre-and posttreatment tumor biopsy specimens from all patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to their corresponding genomic alterations. Arm Z1D is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with MMR deficiency are treated with nivolumab. This subprotocol is one of the treatment arms in the EAY-131 trial included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood and RNA from tumor tissue. A fuller genomic landscape of tumors from these patients will enable discovery of potential molecular features correlated to clinical outcomes or lay the foundation for future studies leading to new and more effective treatments.

  Study phs001859

• Genomic Characterization CS-MATCH-0007 Arm Y

  The CS-MATCH-0007 protocol is a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing, RNA sequencing and if possible, whole-genome, methylation and miRNA sequencing using pre-and post-treatment tumor biopsy specimens from all patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to their corresponding genomic alterations. Arm Y is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with AKT mutations are treated with AZD5363. This subprotocol is one of the treatment arms in the EAY-131 trial included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood and RNA from tumor tissue. A fuller genomic landscape of tumors from these patients will enable discovery of potential molecular features correlated to clinical outcomes or lay the foundation for future studies leading to new and more effective treatments.

  Study phs001904

• Mechanisms of Restoring T Cell Immunity after Cure of Chronic Viral Infection

  We analyzed hepatitis C virus (HCV)-specific T cells and non-specific memory T cell populations from 6 patients with chronic HCV infection receiving 12 weeks of direct-acting antiviral (DAA) therapy with aritaprevir/ritonavir/ombitasvir + dasabuvir + ribavirin. All patients were treated successfully. Peripheral blood mononuclear cells were obtained from blood draws right before treatment initiation (Pre-DAA) and 12 months after the end of treatment (Post-DAA). In each patient, HCV-specific cells were sorted using two different HCV multimers: One representing an epitope present in the circulating HCV genome and one epitope where the virus had escaped the T cell response and thus the corresponding T cells did not receive a TCR signal in vivo. Sorted specific T-cell populations and memory T cell subpopulations were analyzed by extracting RNA and performing RNA sequencing using the Smart-Seq2 protocol. A group of 8 patients with acute self-limited HCV infection (resolvers) were included as control representing natural control of infection. These patients were studied 24 weeks after their last detectable HCV viremia. Finally, we confirmed the data from chronically treated patients in a confirmatory cohort, consisting of 9 patients after successful antiviral treatment.

  Study phs002510

• Genomic Characterization CS-MATCH-0007 Arm H

  The CS-MATCH-0007 protocol is a collaboration between the Center for Cancer Genomics (CCG) and the Division of Cancer Treatment and Diagnosis (DCTD) to perform whole-exome sequencing and RNA sequencing using pre-and post-treatment tumor biopsy specimens from all patients enrolled on a treatment arm of the NCI-MATCH Clinical Trial (EAY131). The goal of this study is to identify the molecular basis for response and resistance to targeted therapies that are matched to their corresponding genomic alterations. Arm H is one of the treatment sub-protocols within the NCI-MATCH Clinical Trial (EAY131) where patients with BRAF V600K/V600E mutations are treated with Dabrafenib and Trametinib. This subprotocol is one of the treatment arms in the EAY-131 trial included in the CS-MATCH-0007 protocol and will provide specimens for the program including DNA from tumor tissue and whole blood and RNA from tumor tissue. A fuller genomic landscape of tumors from these patients will enable discovery of potential molecular features correlated to clinical outcomes or lay the foundation for future studies leading to new and more effective treatments.

  Study phs001888

• Genomic Analysis of Prostate Tumor Heterogeneity in Metastasis

  To investigate the molecular changes, mutations, and signaling pathways that characterize the initial steps of prostate cancer metastasis to the lymph nodes, we analyzed 19 discrete lymph node (LN) metastases, 97 primary tumor foci, 39 benign lymph nodes, and 10 normal adjacent prostate tissue samples from 43 patients enrolled in a clinical trial (NCT01808222) of extended lymphadenectomy and metastasis excision guided by [18F]-fluciclovine PET imaging for high risk, newly diagnosed prostate cancer conducted at Emory University. These patients fell within high or very high-risk groups (T3a, Gleason score 8-10, or PSA greater than 20 ng/ml). Of these patients, 16 had LN metastases at least 4 mm in diameter, and 20 patients had no metastases. For metastatic patients, we performed RNA and Whole Exome Sequencing (WES) on three primary tumor foci, one benign LN, and all LN metastases greater than 4mm in diameter. For non-metastatic patients, we sequenced two primary tumor foci and one benign LN. In total, RNAseq was performed on 165 tissue samples from 43 patients, and WES was performed on 137 samples from 35 patients.

  Study phs003404

• Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

  Summary: Single-cell transcriptome analysis of skin and blood samples from individuals with Kaposi's sarcoma Aims: Elucidate the cellular composition and gene expression profiles of Kaposi sarcoma herpesvirus (KSHV) infected cells and non-infected tumor infiltrating cells, and peripheral blood samples from the same individuals, with or without specific therapies, such as antiretroviral therapy for HIV, immunotherapies (such as immune checkpoint inhibitors and immune modulator drugs like pomalidomide), or angiogenesis inhibitory agents. Population: Age 18 and older, both genders, including individuals from North America and other areas of the world (including Africa). Individuals with or without HIV are included. Molecular Technologies: Single-cell RNAseq using 10x Genomics Principal Findings: Two distinct populations of endothelial cells were found infected with KSHV, one CD34+ and one CD34-Both clusters include lytic and latent KSHV gene expressionThe KSHV infected cell clusters differ in expression of housekeeping genes, proliferative markers, ribosomal and secretory vesicle genesBiomarkers of KSHV infected cells were identified, including sodium channel SCN9A Changes in cell composition with therapy are noted Clonal amplification of TCR+ T-cells were noted in the skin and blood Data Available through dbGaP: scRNA-seq data

  Study phs003800

• Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys

  Human in vitro oogenesis provides a framework for clarifying the mechanism of human oogenesis. To create its benchmark, it is vital to promote in vitro oogenesis using a model physiologically close to humans. Here, we establish a foundation for in vitro oogenesis in cynomolgus (cy) monkeys: cy female embryonic stem cells harboring one active and one inactive X chromosome (Xa and Xi, respectively) differentiate robustly into primordial germ cell-like cells, which in xenogeneic reconstituted ovaries develop efficiently into oogonia and, remarkably, further into meiotic oocytes at the zygotene stage. This differentiation entails a comprehensive epigenetic reprogramming, including Xi reprogramming, yet, as partly observed in vivo, Xa and Xi remain epigenetically asymmetric with incomplete Xi reactivation. In humans and monkeys, the Xi epigenome in pluripotent stem cells functions as an Xi-reprogramming determinant. We further show that developmental-pathway over-activations with suboptimal up-regulation of relevant meiotic genes impede in vitro meiotic progression. Cy in vitro oogenesis exhibits critical homology with the human system, including with respect to bottlenecks, providing a salient model for advancing human in vitro oogenesis.

  Study JGAS000573

• A Single-Cell and Spatial Atlas of Early Human Olfactory Development

  The human nasal region is a complex anatomical structure comprising neural crest- and placode-derived lineages, yet its developmental dynamics in humans remain poorly understood due to limited access to fetal tissue and challenges in resolving its spatial and cellular complexity. We built a single-cell and spatial transcriptomic atlas of the human fetal nasal region from 10 fetuses spanning post-conceptional weeks 7 to 12. Using snRNA-seq, we identify 34 cell types in the fetal nasal region and reconstruct lineage trajectories in the olfactory epithelium (OE). Spatial analyses uncover regionalized OE organization, dorsoventral gradients of olfactory receptors (ORs) and high-resolution OR expression. Combining snRNAseq and MERFISH, we reveal early onset of OR gene expression, with most olfactory sensory neurons (OSNs) following the one neuron-one receptor rule already during the first trimester. This work provides the first integrated molecular and spatial framework of early human nasal region and it provides an unprecedented molecular blueprint of the human olfactory system development. In addition, this study offers a foundational resource for embryologists and developmental biologists investigating sensory neurogenesis, epithelial patterning, and congenital diseases.

  Study EGAS50000001203

• Rapid brain tumor classification from sparse epigenomic data

  Although the intraoperative, molecular differential diagnosis of the approximately one hundred different brain tumor entities described to date has been a goal of neuropathology in the last decade, this has not yet been achieved in a clinically relevant time frame of less than one hour after biopsy collection. Recent advances in third-generation sequencing technologies have brought this once-elusive goal within reach. However, established machine learning techniques rely on concepts and methods, impractical for live diagnostic workflows in clinical applications. Here, we present MethyLYZR, a Naïve Bayesian framework enabling fully tractable live classification of cancer epigenomes. MethyLYZR can be run in parallel with an ongoing Nanopore experiment with negligible computational cost and provides clinically relevant and accurate cancer classification results within 15 minutes of sequencing. Therefore, only the time required for DNA extraction and the Nanopore sequencer's maximum parallel throughput remain limiting factors for even faster time-to-results. We demonstrate the potential utility of the MethyLYZR framework not only for the neurosurgical intraoperative use case but also for other oncologic indications and cell-free DNA from liquid biopsies.

  Study EGAS50000000559

• Circulating tumor cells Exome sequencing from breast cancer

  Single cell technologies allow interrogating the extent of tumor heterogeneity, providing novel insights into tumor evolution and treatment resistance mechanisms. Here, we investigated the level of genetic heterogeneity among circulating tumor cells (CTCs) at the single nucleotide variation and copy number aberration (CNA) levels and compared it to synchronous matched primary tumor/metastatic lesion from 3 metastatic breast cancer patients with triple-negative (TNBC), HER2-positive (HER2+) and estrogen-receptor-positive (ER+) tumors. Whole exome sequencing was performed on 3 synchronous bulk tumor tissue and 21 single/pooled CTC samples. When comparing bulk tissue with CTCs from the same patient, we found similar CNA profiles and the same patient-specific driver mutations for the HER2+ and TNBC tumors. Different CNA profiles and driver mutations were found for the ER+ tumor, with two distinct clones being identified in the CTCs, one harboring an activating ESR1 mutation, the other one bearing a TP53 mutation. These data suggest that tumor tissue and CTCs provide in a subset of patients complementary clinically relevant information to map tumor heterogeneity and monitor tumor evolution. Further validation is needed.

  Study EGAS00001005228

• Embryonal Rhabdomyosarcoma sequencing data

  This dataset contains samples from 9 patients with embryonal rhabdomyosarcoma. 9 samples have whole exome tumor data (one has multiple). 7 samples have tumor RNAseq data. 1 sample has matched normal dna sequence data

  Dataset EGAD00001007939

• Lowpass whole genome sequencing of single circulating tumor cells (CTCs) in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

  Lowpass whole genome sequencing of 43 single CTCs and one tumor biopsy

  Dataset EGAD00001007700

• Reliable detection of somatic mutations in single DNA molecules from sperm

  Nanoseq data from sperm from 2 individuals, including technical replicates from one individual (10 total sequences). 8 additional samples and 2 matched normals to call mutations in NanoSeq data (dataset EGAD00001006459).

  Dataset EGAD00001007028

• Single cell sequencing data from Shwachman-Diamond syndrome bone marrow samples

  This dataset includes single cell amplicon based sequencing from 10 samples from SDS patient bone marrow samples, including one patient with serial samples. There are two fastq files per sample.

  Dataset EGAD00001006799

• Whole genome sequencing generated from metastatic gliosarcoma patient samples

  This dataset contains whole genome sequencing data aligned to the b37 reference genome for 4 spatially and temporally distinct tumors from one patient with a matched normal blood sample.

  Dataset EGAD00001005745

• High-Risk Breast Cancer GWAS

  The GWAS includes High Risk Women from the following epidemiological studies of breast cancer, comprising a total of 3,719 cases and 3,642 controls (cases/controls: MEC, 0/200; ABCFR, 326/418; FCCC, 56/3; BCFR-UT, 66/32; CNIO-BC, 87/92; GESBC, 65/0; LIFE, 164/0; MARIE, 41/105; MAYO, 208/210; MNYR, 293/409; MSKCC, 310/0; NC-BCFR, 234/233; OFBCR, 553/560; POSH, 377/0; HBOC, 47/47; BBCS, 612/1333; UPENN, 280/0 This study was funded by a grant CA165038 to Christopher Haiman (University of Southern California) and John Hopper (University of Melbourne) from the National Cancer Institute, National Institute of Health. The contributing studies: Multiethnic Cohort (MEC). This study was supported by grant UM1 CA164973 from the National Cancer Institute, National Institute of Health. Ontario Familial Breast Cancer Registry, the Ontario site of the Breast Cancer Family Registry Cohort (OFBCR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Utah Breast Cancer Family Registry (BCFR-UT). This study was supported by grant UM1 CA164920 from the National Cancer Institute. New York site of the Breast Cancer Family Registry (MNYR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Northern California site of the Breast Cancer Family Registry (NC-BCFR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Australian Breast Cancer Family Registry (ABCFR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Breast Cancer Study (CNIO-BC). This study has been partially funded by The Spanish Network on Rare Diseases (CIBERER) and the Spanish National Genotyping Center (CEGEN). Genetic Epidemiologic Study of Breast Cancer (GESBC). The GESBC was supported by the Deutsche Krebshilfe e. V. [70492] and German Cancer Research Center (DKFZ). Mammary Carcinoma Risk Factor Study (MARIE). This study was supported by the Deutsche Krebshilfe e.V. [70-2892-BR I, 106332, 108253, 108419], the Hamburg Cancer Society, the German Cancer Research Center (DKFZ) and the Federal Ministry of Education and Research (BMBF) Germany [01KH0402]. Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH). Funding for the POSH study was provided by Cancer Research UK (grant refs A7572, A11699, C22524), the Breast Cancer Campaign (grant number: 2013MayPR044) and from 2003-2006 by a grant from The Wessex Cancer Trust. Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH). Funding for the POSH study was provided by Cancer Research UK (grant refs A7572, A11699, C22524), the Breast Cancer Campaign (grant number: 2013MayPR044) and from 2003-2006 by a grant from The Wessex Cancer Trust. Hereditary Breast and ovarian Cancer: Genetic and Molecular Studies (HBOC). This study was supported by National Cancer Institute grant CA58860 and The Lon V Smith Foundation: LVSF-44528. Mayo Clinic inherited breast and ovarian cancer study (MAYO). This study was supported by the Breast Cancer Research Foundation, NIH grants CA192393, CA176785, and an NIH CA116201 Specialized Program of Research Excellence (SPORE) in Breast Cancer. British Breast Cancer Study (BBCS); Mammographic oestrogens and growth factor study (MOG). The BBCS and the MOG study are funded by Cancer Research UK and Breakthrough Breast Cancer and acknowledge NHS funding to the NIHR Biomedical Research Centre, and the National Cancer Research Network (NCRN). Genotyping of non-BRCA1/2 mutation carriers (UPENN). The study is supported by the Basser Research Center at the University of Pennsylvania, Rooney Family Foundation, NIH grants CA176785 and CA192393, the Breast Cancer Research Foundation, the Susan G. Komen Foundation for the Cure and Macdonald Family Foundation. Clinical Significance of Germline BRCA Mutations (MSKCC). The study is supported by the Robert and Kate Niehaus Clinical Cancer Genetics Research Initiative, The Breast Cancer Research Foundation, and the Cancer Center Support Grant from the National Institute of Health, National Cancer Institute 5P30 CA08748-40. Women's Learning the Influence of Family and Environment (LIFE). This study was supported by grants CA17054 and CA74847 from the National Cancer Institute, National Institutes of Health, No. 4PB-0092 from the California Breast Cancer Research Program of the University of California. Philadelphia site of the Breast Cancer Family Registry at Fox Chase Cancer Center (FCCC). This study is supported by NIH grant CA164920.

  Study phs000929

• PacBio data: Rapid brain tumor classification from sparse epigenomic data

  This dataset contains 16 samples sequenced in pools on SMRT Cells 25M on a PacBio Revio instrument. One unaligned BAM file per sample is provided.

  Dataset EGAD50000000798

• MATCH-molecular driver

  Patients were biopsied at progression on molecular targeted agents and WES and/or WTS were performed to identify resistance mechanisms. 271 underwent one or sequential tissue biopsies.

  Dataset EGAD50000000697

• Single-cell somatic copy number variants in brain using different amplification methods and reference genomes

  This dataset contains 224 paired fastq files (112 single cells) from the following samples: brains from two Multiple System Atrophy patients and one control, and non-brain controls (fibroblasts, NA12878)

  Dataset EGAD50000000030

• Illumina genome sequencing data for HICF2 craniosynostosis families (Genome Medicine)

  BAM files for two families recruited to the HICF2 genome sequencing project due to craniosynostosis. One family is a singleton and the other is an affected mother-daughter duo.

  Dataset EGAD00001011373

• Clinical data

  Clinical data for IMpower150 (one patient per line): anonymized_patient_id, train_test_split, ctDNA_status, ARM1, OS_months, OS_event, PFS_months, PFS_event, TTEOS_rebaseline_BL, TTEPFS_rebaseline_BL, TTEOS_rebaseline_C2D1, TTEPFS_rebaseline_C2D1, TTEOS_rebaseline_C3D1, TTEPFS_rebaseline_C3D1, TTEOS_rebaseline_C4D1, TTEPFS_rebaseline_C4D1, TTEOS_rebaseline_C8D1, TTEPFS_rebaseline_C8D1, pdl1_high, number_metastatic_sites, baseline_ECOG, age, sex_female, history_of_tobacco_use, sld_baseline, sld_wk6, sld_percent_change_bl_to_wk6, sld_difference_bl_to_wk6, AGEGRP, tumor_assessment_week_6, tumor_assessment_week_12, tumor_assessment_week_18, tumor_assessment_week_24, PFS_days, days_between_randomization_c3

  Dataset EGAD00001009726