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• Single-cell expression of Hodgkin and Reed-Sternberg (HRS) cell

  Hybrid capture sequencing was performed to 3 purified Hodgkin and Reed-Sternberg (HRS) cell samples. In brief, Probes for 177 genes were designed and synthesized by Twist Bioscience. Hybridization capture of DNA libraries was performed using Twist Hybridization and Wash Kit (Twist Bioscience). The captured library was measured using Agilent Bioanalyzer High Sensitivity chip and Qubit dsDNA HS Assay Kit and run on Illumina Nextseq550. The BAM files were generated from the raw sequencing data using Cell Ranger (v6.0.2) mkfastq and count commands

  Dataset EGAD00001010892

• TARGET-seq+ single-cell transcriptome sequencing

  Single-cell whole transcriptome sequencing data for bone marrow samples from 9 cases with clonal hematopoiesis and 4 control samples. The TARGET-seq+ protocol was used to generate plate-based 3' transcriptome data. For details on cell sorting and the TARGET-seq+ protocol see the methods section of the manuscript. One FASTQ file is provided per cell. Cells are named with their plate and well IDs and the subject ID. Empty wells (no-cell controls) are named "blank". Corresponding genotyping files use the same naming without the "_transcriptome" suffix.

  Dataset EGAD00001011175

• Single-Cell DNA Methylation Profiling via scTAMseq

  This dataset comprises single-cell DNA methylation and nuclear genotyping profiles of 7 total bone marrow aspirates (donors A.1-A.7) and 5 CD34+-enriched bone marrow samples (donors B.1-B.5) generated using the scTAMseq protocol. Sequencing was performed on the Mission Bio Tapestri platform, targeting a panel of 448 CpGs to assess epigenetic patterns and We also included 147 genomic regions commonly mutated in clonal hematopoiesis and 20 regions targeting chromosome Y. Samples B.1 & B.5, B.2 & B.4 and A.2 & A.5 were, in pairs, multiplexed into single tapestri lanes.

  Dataset EGAD00001015498

• scWGS dataset of Characterization of UV DNA damage in B-cell precursor acute lymphoblastic leukemia

  Extensive characterization of mutational signature SBS7a in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) samples. We aimed to describe the presentation of SBS7a in BCP-ALL, identify other pediatric cancers presenting with SBS7a, look into the link of SBS7a and UV-light in the context of BCP-ALL and cancers with provable UV exposure, and pinpoint when SBS7a was acquired.

  Dataset EGAD00001015601

• Comprehensive Genomic Profiling of a National Cohort of Pediatric Papillary Thyroid Carcinoma in Hungary

  Pediatric papillary thyroid carcinoma (PTC) is a rare childhood malignancy with increasing incidence and distinct clinicopathological features, including high rate of locoregional metastases and different molecular background compared to adult cases. Traditional treatments (surgery, radioactive iodine) are effective but pose long-term risks, prompting the exploration of targeted therapies. We performed comprehensive genomic profiling on 21 pediatric PTC patients applying Illumina TruSight Oncology 500 platform and detected mutations, gene fusions, copy number variations and revealed tumor mutational burden.

  Dataset EGAD50000002659

• Genomic Analysis of Low Grade B-Cell Lymphoma

  We included tumors from 64 newly diagnosed or untreated Low Grade B-Cell Lymphoma (LGBCL) patients, consisting of SMZL (n = 48), NMZL (n = 6), EMZL (n = 2), LPL (n = 5), and B-NOS (n = 3) in this study. Samples were selected from cases consented to the Molecular Epidemiology Resource (MER) of the University of Iowa and Mayo Clinic Lymphoma Specialized Program of Research Excellence (SPORE). RNA or DNA were extracted from 64 frozen LGBCLs tumors (with available matched germline DNA for N=61. For RNA sequencing, library preparation was done using the Illumina TruSeq RNA Exome Kit and sequenced with 100 nucleotide paired-end reads using the HiSeq 4000. For WES, library preparation was done using the Agilent SureSelect XT kit and sequenced with 100 nucleotide paired-end reads using the Illumina HiSeq 4000.

  Study phs002552

• National Cancer Institute Genome-Wide Association Study of Renal Cell Carcinoma

  The National Cancer Institute (NCI) genome-wide association study (GWAS) of renal cell carcinoma (RCC) was conducted to investigate common genetic variants associated with RCC risk. The GWAS includes 1,453 RCC cases and 3,531 controls of European background from 4 studies (3 cohort, 1 case-control), scanned using the Illumina InfiniumHumanHap 550, 610 and 660W chips. This project was supported by the Intramural Research Program of the National Institutes of Health and NCI. Data from this GWAS were pooled with those from another GWAS of RCC (2,639 cases and 5,392 controls) conducted in Europe by the International Agency for Research on Cancer and the Centre National de Gènotypage. Findings from this collaboration are described in an upcoming report (Purdue et al. Nature Genetics 2011;43(1):60-65; PMID: 21131975). Only data from the NCI scan are included in this dbGaP submission.

  Study phs000351

• Deciphering Maternal-Fetal Crosstalk in the Human Placenta During Parturition Using Single-Cell RNA-Sequencing

  Labor is a complex physiological process requiring a well-orchestrated dialogue between the mother and fetus. However, the cellular contributions and communications that facilitate maternal-fetal crosstalk in labor have not been fully elucidated. In this latest version (#5), scRNA-seq was applied to decipher maternal-fetal signaling in the human placenta and chorioamniotic membranes during term labor. Samples were obtained from women who underwent spontaneous labor (n = 24) or who were delivered in the absence of spontaneous labor (n = 18) at term. Samples from previous versions (#1-3) of this study include the placental villous tree, basal plate, and chorioamniotic membranes of women across a range of pregnancy physiologic and pathologic conditions, including the processes of labor (term labor and preterm labor), and COVID-19 (version #3). Version #4 includes samples from the human myometrium during spontaneous term labor.

  Study phs001886

• NHLBI TOPMed - NHGRI CCDG: Early-onset Atrial Fibrillation in the CATHeterization GENetics (CATHGEN) Cohort

  The CATHeterization GENetics (CATHGEN) biorepository collected biospecimens and clinical data on individuals age ≥18 undergoing cardiac catheterization for concern of ischemic heart disease at a single center (Duke University Medical Center) from 2000-2010; a total of N=9334 individuals were collected. Samples were matched at the individual level to clinical data collected at the time of catheterization and stored in the Duke Databank for Cardiovascular Diseases (DDCD). Clinical data included subject demographics, cardiometabolic risk factors, cardiac history including symptoms, age-of-onset of cardiovascular diseases, coronary anatomy and cardiac function at catheterization, laboratory data, and yearly follow-up for hospitalizations, vital status, medication use and lifestyle factors. AF cases were defined as individuals who had ever had AF based on any ECG available at Duke University or ICD-9 code for AF used for inpatient or outpatient billing.

  Study phs001600

• Dynamics of Genomic and Immune Responses During Primary Immunotherapy Resistance in Mismatch Repair Deficient Tumors

  We study a patient with dMMR lung cancer refractory to immunotherapy. Post-treatment tumor demonstrated compound heterozygous frameshift deletions located upstream of the kinase domain in the gene encoding JAK1 protein, downregulation of JAK1 and mediators of its signal transduction, and total loss of JAK1 phosphorylation. Importantly, one of the JAK1 mutations, despite not being detected in the pre-treatment tumor, was found at low variant allele frequency in the pre-treatment circulating tumor DNA, suggesting clonal selection of the mutation. This report provides the most detailed look yet of defective JAK1 signaling in the context of dMMR and immunotherapy-resistance. Together with observations of JAK1 frameshift indels being enriched in dMMR compared with MMR-proficient tumors, our findings demonstrate the critical function of JAK1 in immunological surveillance of dMMR cancer.

  Study phs002089