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• DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism

  Plasma samples derived from a study population of control participants (DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism) were used to profile miRNA circulating in plasma. RNA was isolated from plasma samples using the Qiagen miRNeasy kit. Libraries were prepared using Illumina TruSeq Small RNA Library Prep Kit. Libraries were sequenced on a HiSeq. Data from this sequencing project will be available through dbGaP.

  Study phs003223

• Modelling Multi-Dimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research

  The Center for Cancer Research (CCR), of the intramural NCI undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers who were enrolled on other therapeutic trials to determine the feasibility of a genome guided precision therapy protocol in these patients.Note: NCIPM001blood - This sample was previously submitted with study phs002207, with sample ID NCIPM001blood_E and SRR ID SRR18544311.

  Study phs001052

• Genetic Evaluation of Autoinflammatory Diseases

  Many pediatric patients with early-onset autoinflammatory disease (AID) phenotypes are mutation-negative for genetically known AIDs. Recent data suggest a role for Type-I interferon (IFN) dysregulation in causing AID phenotypes with clinical features that are distinct from those found in patients with IL-1 mediated AIDs. We screened patients for the presence of an IFN-response gene signature (IRS) to characterize their clinical phenotypes, IFN-related biomarkers, and genetic causes.

  Study phs001946

• CIDR: Molecular Pathological Epidemiology of Colorectal Cancer

  Colorectal cancer, the second most commonly diagnosed cancer is a biologically heterogeneous disease. To characterize the molecular attributes of colorectal tumors, we conducted targeted sequencing at the Center for Inherited Disease Research (CIDR) on 4,518 tumor and matched normal DNA samples from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colon Cancer Family Registry (CCFR). These consortia are based on cohort and population-based case-control studies.

  Study phs001905

• Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways

  Hematopoietic stem cell (HSC) aging involves heterochromatin reorganization. These repressive marks together with DNA methylation are essential for suppressing transposable elements (TEs). In this study we analyze heterochromatin and transcriptomic changes occurring at genes and TEs in HSCs from chronic myelomonocytic leukemia, a severe myeloid malignancy affecting the elderly, compared to age-matched cells, and in the presence or absence of a combination of epidrugs.

  Study EGAS50000000688

• Understanding Determinants of Racial Disparities in Lung Cancer Incidence

  This is a nested case-control study designed to evaluate the association between common genetic variants and the risk of lung cancer. The study included 1258 cases and 1252 controls selected from the Southern Community Cohort Study (SCCS), a large, prospective observational cohort. Cases were identified from cancer registries across the catchment area of the SCCS. Cases and controls were frequency matched on age, sex, race, and enrollment site (community health center vs general population).

  Study phs003789

• Genomics Analysis Reveals Molecular Patterns of Tumorigenesis in HPV-Associated and HPV-Independent Sinonasal Squamous Cell Carcinoma

  The goal of this study was to identify molecular mechanisms of tumorigenesis in HPV-associated and HPV-independent sinonasal carcinoma using high-throughput sequencing approaches. Whole genome sequencing was performed for HPV-associated samples and whole exome sequencing for HPV-independent samples. Ultimately, we identified distinct molecular patterns of tumorigenesis between HPV-associated and HPV-independent disease. Data from patients for which informed consent allowed public sharing are included here.

  Study phs003591

• EASI-Genomics GM21886 Cell Line High Molecular Weight DNA Sequencing

  An interlaboratory study was performed with GM21886 cells to evaluate methods for high molecular weight (HMW) genomic DNA extraction and compare sample and sequencing QC metrics, and pipelines for structural variant (SV) calling. Four laboratories prepared HMW genomic DNA using four alternative extraction methods FireMonkey (Revolugen), Genomic Tip (QIAGEN), Nanobind (Circulomics), and Puregene (QIAGEN), followed by Short Read Elimination (Circulomics) and long-read sequencing with MinION and PromethION flowcells (Oxford Nanopore Technologies).

  Study phs003958

• Skin Microbiome of Monogenic Skin Disorder

  Ichthyosis introduces multiple sources of disturbance to the skin, including the direct biochemical consequences of the genotype, the phenotypic changes in skin physiology, and an altered skin microbiome. The association between changes in the skin microbiome and the disease's genotypic and phenotypic effects are historically obscured. Here we characterize the skin microbiome of healthy participants and ichthyosis patients, before assessing the association between these microbiome features and the ichthyosis genotype and phenotype while adjusting for contextual host covariables.

  Study phs003799

• Characteristics and Inflammatory Markers in Children with Eosinophilic Esophagitis (EoE)

  The overall protocol for the samples used in this study collects medical information, blood, and biopsy samples from children with eosinophilic esophagitis (EoE) over time to understand clinical characteristics and disease pathogenesis. Our patient population has confirmed EoE and symptoms of esophageal dysfunction characteristic endoscopic findings of EoE. Fibroblasts isolated from esophageal tissue samples from 2 subjects with active EoE and 2 control subjects were evaluated using single cell RNA-sequencing (scRNA-seq).

  Study phs003869

• Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration

  The human papillomavirus (HPV) genome is integrated into host DNA in most HPV-positive cancers, but the consequences for chromosomal integrity are unknown. We used continuous long-read sequencing of oropharyngeal cancers and cervical cancer cell lines to resolve structural variation induced by HPV. We discovered a previously undescribed form of structural variation, "heterocateny," characterized by diverse, interrelated, and repetitive patterns of concatemerized virus and host DNA segments within a cancer.

  Study phs003396

• An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases

  At 5' ends of RNAs, there is a unique "cap signature" derived from a 7-methylguanosine cap. By leveraging this signature, we developed ReapTEC (read-level pre-filtering and transcribed enhancer call), a method for simultaneously profiling gene expression and enhancer activities using 5'-end single-cell RNA sequencing (5' scRNA-seq). We applied ReapTEC and single-nucleus ATAC-seq to a total of ~1 million single human CD4+ T cells.

  Study JGAS000689

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• Research for genetic causes and mechanisms of Hirschsprung's or Hirschsprung's related diseases

  Hirschsprung's disease (HD) is an abdomen disorder which is caused by absence of enteric neurons. HD is a complex genetic disorder and several causing gene mutations have been identified including the receptor tyrosine kinase gene. However, the whole mechanism of HD remains unknown and additional genetic causalities are implicated. To further investigate the genetic causalities of HD, we conducted whole-exome sequencing of patients with HD and unaffected patient's families.

  Study JGAS000007

• Whole-exome sequencing of Helicobacter pylori-uninfected normal gastric gland

  Recent studies showed that somatic mutations accumulate in normal tissues with age; however, mutation accumulation in the Helicobacter pylori-uninfected normal gastric mucosa has not been reported. A total of 18 biopsied gastric mucosa were obtained from nine subjects without Helicobacter pylori-infection or gastric cancer. Gastric epithelia were manually dissociated from the lamina propria. Subsequently, single glands were picked up under a stereomicroscope. Genomic DNA isolated from each gland was subjected to whole-exome sequencing.

  Study JGAS000313

• Research for drug discovery and elucidation of pathophysiology using disease-specific iPS cells

  We investigated roles of KRAS on stemness maintenance and differentiation propensity in the context of induced pluripotent stem cells (iPSCs) using isogenic KRAS mutant (G13C/WT) and wild-type (WT/WT) iPSCs from the same RAS-associated autoimmune lymphoproliferative syndrome-like disease (RALD) patients. Exome-seq analysis was conducted to compare gene profiles of WT/WT and G13C/WT iPS cells. We have not found any differences of gene mutation in the two genotypes.

  Study JGAS000136

• Identification of responsible genes and development of standardized medicine for familial breast cancer by genetic analysis with NGS technology

  Aims: To clarify risk of germline variants of known causal genes for Hereditary Breast Ovarian Cancer Syndrome in Japan by combinatorial analysis of somatic and germline variants in the breast cancer tissue. Methods: Target caputure analysis by using Illumina HiSeq 2000; the panel genes are 119 genes including 30 HBOC known causal genes. Participants/Materials: 108 whole blood and 124 primary tumor samples from familial breast cancer patients.

  Study JGAS000224

• Influence of pre-analytical processing on blood protein profiles (AMED-Metabolites)

  The purpose of the present study was to assess the differences between the human serum and plasma proteomes, and the stability of human plasma proteins under different storage conditions following blood collection, by means of SWATH-MS analysis. We compared plasma samples prepared by centrifugation after storage of blood at room temperature for 0, 15 or 30 minutes, or under refrigeration at 0-5?C for 1, 4 or 8 hours.

  Study JGAS000223

• An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections

  We investigated the effects of different incubation temperatures and duration, and formalin scavenger (Tris) concentrations on the recovery of DNA from FFPE tissue sections. We optimized the conditions for preserving the integrity and maximizing the yield of DNA from FFPE tissue sections. Furthermore, DNA obtained using the optimized procedure was compared with that obtained using a commonly used extraction procedure with regard to their performance in whole-genome and targeted gene panel sequencing.

  Study JGAS000520

• Multi-omics characterization of KMT2A-rearranged infant acute lymphoblastic leukemia

  KMT2A gene rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is the most refractory subgroup of childhood leukemia, whose molecular heterogeneity remains largely unknown. To better understand the molecular pathogenesis of KMT2A-r infant ALL, we comprehensively analyzed the RNA sequencing, methylation array, whole exome sequencing, single-cell RNA sequencing data of diagnostic samples of KMT2A-r infant ALL. We also performed ChIP sequencing of infant ALL-derived cell lines.

  Study JGAS000385

• Deciphering the aggressive nature of morphoeic basal cell carcinoma

  Morphoeic basal cell carcinoma (mBCC) has a high risk of local recurrence compared to the more indolent nodular subtype reflected by a different set of driver mutations including FLNB and HECTD4. Surrounding mBCC stroma is abnormal, containing mutations such as EPHA3. Hedgehog pathway over-expression is seen in both the tumour and stroma of morphoeic tissue with the latter potentially being partly responsible for its aggressive nature and risk of recurrence.

  Study EGAS00001001915

• RNaseq of mantle cell lymphoma patient samples

  This study presents bulk RNA sequencing data from 78 clinical mantle cell lymphoma (MCL) samples. Following rigorous quality control and batch effect correction to account for sample type and redundancy, 62 samples from 59 patients were included in the final analysis. The transcriptomic profiles capture the molecular diversity across both solid and liquid tumor contexts and support investigations into the phenotypic plasticity and metabolic states of drug-tolerant persister (DTP) cells.

  Study EGAS50000001086

• Whole exome sequencing of Zimbabwean patients with suspected Mendelian disorders

  This study presents whole exome sequencing data from Zimbabwean individuals with suspected Mendelian disorders, including sickle cell disease, Fanconi anemia, haemophilia, and muscular dystrophy. The dataset includes both affected individuals and family members to support inheritance-based analyses. Variant calling was performed using the Illumina DRAGEN pipeline, with downstream variant prioritisation and interpretation conducted using the Zi-Mendelian bioinformatics pipeline. This study supports rare disease genomics and precision medicine efforts in African populations.

  Study EGAS50000001708

• Whole genome sequencing data of pediatric TCF3::PBX1 acute lymphoblastic leukemia

  TCF3::PBX1 leukemia is a rare subtype of B-cell acute lymphoblastic leukemia (B-ALL), occurring in approximately 3–5% of pediatric cases. It results from a chromosomal translocation t(1;19)(q23;p13), generating the TCF3::PBX1 fusion gene, which disrupts normal transcriptional regulation and contributes to leukemogenesis. Although historically associated with poor prognosis, contemporary risk stratification and intensified therapy have significantly improved outcomes, and both 5-years DFS and OS are nowadays ≥ 0.96.

  Study EGAS50000001257

• Single nuclei RNA sequencing on Primary and Maladaptive FSGS patient samples

  We used single-nucleus RNA-sequencing to identify differentially expressed transcriptional signatures in kidney biopsies of well-phenotyped primary vs. maladaptive FSGS patients. We included cryopreserved kidney biopsy cores from adult patients with newly diagnosed primary FSGS (n = 9, all nephrotic), maladaptive FSGS (n = 9, not nephrotic), proteinuric controls (PLA2R-positive membranous nephropathy, n = 3), and healthy controls (n = 4). We identified 120,751 high-quality nuclei, including 2,471 podocytes and 1,574 parietal epithelial cells (PECs).

  Study EGAS50000001070