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• single nuclei multiomics (ATAC-RNA) of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  We processed nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. Cells differentiated with a first iteration were RNA and ATAC-sequenced, to understand our protocol caveats to address for optimization. Cells differentiated with a second protocol and in vivo were RNA-sequenced to validate the identities of our cells.

  Study EGAS50000001418

• Comprehensive molecular and clinicopathological profiling of salivary duct carcinoma

  Molecular targets and predictive biomarkers for prognosis in salivary duct carcinoma (SDC) have not fully identified. We conducted comprehensive molecular profiling to discover novel biomarkers for SDC. A total of 67 SDC samples were examined with DNA sequencing of 464 genes and transcriptome analysis in combination with the clinicopathological characteristics of the individuals.

  Study JGAS000534

• Clonal structure and oncogenic potential of liver cirrhosis tissues.

  Hepatocellular carcinoma (HCC) recurrently develops in cirrhotic liver composed of numbers of regenerative nodules (RNs). The biologic or genetic basis of RNs for hepatocarcinogenesis remains unclear at present. Thus, to uncover the basis of cirrhotic liver for multicentric tumorigenesis, we investigated the oncogenic potential of RNs in LC tissues using multi-omics analysis.

  Study JGAS000134

• Comprehensive genomic analysis of patient derived orthotopic xenograft model in primary central nervous system lymphoma

  The purpose of this study is to investigate genetic background of orthotopic xenograft cells and aseess consistency with parent tumor cells. For exome sequencing, we used two distinct PCNSL cells (YML9 and YML11). We also performed RNA sequencing for 7 PCNSL patient tumor cells to compare NF-kB pathway activation.

  Study JGAS000178

• An Organoid Biobank of Rare Human Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping

  We performed whole genome sequencing and RNA-sequencing of neuroendocrine neoplasm. The aim of this study was to provide genetic landscape of neuroendocrine neoplasm, to construct available animal models, and to engineer neuroendocrine neoplasm from normal colon epithelium. The reference genomes used are GRCh37 for whole genome sequencing and GRCh38 for RNA-sequencing.

  Study JGAS000237

• Benchmark and validation of whole exome sequencing of a trio and singleton

  Whole exome paired-end sequencing data was obtained for a trio and a fourth unrelated individual sequenced to high depth (95x) using a paired-end library with the Illumina HiSeq platform and aligned by BWA 0.5.9. The bam files were analysed and experimentally vaidated for the novel insertion of mobile elements.

  Study EGAS00001000852

• Y_phylogeny_haplogroupDE

  High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002674

• Mutator phenotype and specific mutational signature explain an increased risk of hematological malignancies in patients with Xeroderma Pigmentosum

  In this study we report for the first time the unique collection of 6 leukemias and two sarcomas from XP-C. Comprehensive WGS-based mutational analysis provides genetic explanation for the increased incidence of leukemia in XP-C and describes an unique mutational process in internal tumors associated with NER deficiency.

  Study EGAS00001004511

• Mutation tracking in single cell RNA-Seq reveals consequences of subclonal evolution in acute myeloid leukemia

  Total bone marrow from AML patients was FACS index sorted with staining for Lineage markers (Lin), CD33, CD34, CD38, CD45RA, CD90, CD99, Tim3 and GPR56, and enrichment for Lin- and Lin-CD34+ cells. Single cells were subjected to a modified smart-seq2 protocol with targeting of mutant sites of interest ("MutaSeq”).

  Study EGAS00001003414

• Exome sequencing of patients with rare neurological disorders

  Exome sequencing of patients and their families with diverse rare neurological disorders. Some families have prior linkage data identifying a specific chromosomal interval or interest, other families do not have linkage data available. Many of these families come from special populations whose demography or preference for consanguineous marriages make them particularly tractable for genetic studies.

  Study EGAS00001000159

• A somatic reference standard for cancer genome sequencing.

  Paired PCR-free whole genome sequencing data of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. The data was generated with mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

  Dataset EGAD00001002142

• CCA WGS data (16 CCA with matched normal, 4 cell-line)

  Fastq files for WGS for 16 CCAs (with matched normal tissues), and 4 cell lines in an AA-treatment experiment (0, 10, 20, 40ug AA treatment after 180 days; 2 runs each for 10ug and 40ug experiments). Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen). Sequencing libraries were prepared from DNA extracted using the SureSelect XT2 Target Enrichment System for the Illumina Multiplexed Sequencing platform (Illumina) according to the manufacturer’s instructions. Whole genome sequencing was performed on Illumina HiSeq4000 sequencer with paired-end sequencing.

  Dataset EGAD00001012100

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): a Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study - for Samples Collected at Johns Hopkins

  UC-GENOME is a real-world cohort of patients with metastatic urothelial carcinoma (UC). The study consisted of two co-equal aims: 1) to provide targeted DNA sequencing for clinical decision making at no cost to patients; and 2) to create a resource for collaborative translational science including a clinically annotated biobank. The submitted data represents the foundational analysis of 218 patients accrued at 7 academic medical centers. The analysis includes 176 patients with both targeted DNA sequencing and RNA sequencing. The genomic data was combined with clinical variables to model response to chemotherapy and immune checkpoint inhibitors (ICI).The larger dataset for this study can be found in dbGaP study phs003066.

  Study phs003094

• BPH Tissues for Cell Culture and Analysis - A Patient-Derived Xenograft Model Using Benign Prostatic Tissues

  Our goal was to establish and characterize a patient-derived xenograft model for benign prostatic hyperplasia (BPH) using human benign prostatic tissues. Characterization of the model was done by histology, immunohistochemistry, proteomics, and transcriptome analysis (RNAseq). The RNAseq data will be deposited in dbGaP. Subjects were undergoing prostatectomy for prostate or bladder cancer, with concurrent BPH, and consented to the use of surplus tissue for research studies. The RNAseq studies included 6 patients. Phenotypic data include patient age, sex, prostate size, serum prostate-specific antigen (PSA) level, and international prostate symptom score (IPSS). Sequencing was done on an Illumina NovaSeq 6000, and data were analyzed using Kallisto. Data are submitted as raw sequencing (fastq) files.

  Study phs003692

• DNA Repair Capacity for Lung Disease Risk Assessment

  A focus of this work was to address the extent to which susceptibility for lung cancer varies by gene-environment-phenotype interactions involving DNA repair capacity and differences in risk from environmental stressors. GWAS from a subset of subjects from the Lovelace Smokers Cohort and New Mexico Lung Cancer cohort were used to derive polygenic risk scores for DNA repair pathways (nucleotide excision, base excision, single strand break, non-homologous, homologous recombination). Logistic regression analysis was used to examine the association between polygenic risk score and lung cancer status. Polygenic risk scores were grouped by quartiles. Only diminished base excision repair was associated with increased risk for lung cancer at the 25-50% quartile and approached significance at the 50-75% quartile.

  Study phs004063

• NIH Roadmap Epigenomics Program - Broad Institute

  For the NIH Roadmap Epigenomics project, we applied ChlP-Seq, HTBS and WGBS pipelines to generate comprehensive high-resolution maps of chromatin state and DNA methylation for 100 diverse cell types. Cell types were selected for their biological and medical importance, and for their potential to maximize the comprehensiveness of acquired epigenomic data. They include human ES cells, ES-derived cells, mesenchymal stem cells, reprogrammed stem cells and primary tissues. Comprehensive characterization of epigenetic marks ("the epigenome") is a critical step towards a global understanding of the human genome in health and disease. In this study we provide unprecedented views of the human epigenetic landscape and its variation across cell states, which offer fundamental insight into the functions and interrelationships of epigenetic marks, and provide a framework for future studies of normal and diseased epigenomes. The Roadmap Epigenomics Broad cohort is utilized in the following dbGaP sub-study. To view molecular data and derived variables collected in this sub-study, please click on the following sub-study below or in the "Sub-studies" box located on the right hand side of this top-level study page phs000700 the Roadmap Epigenomics Broad cohort. phs000610 RM_Epigenomics_Broad_Alz

  Study phs000700

• Cholesterol and Pharmacogenetics (CAP) Study

  The Cholesterol and Pharmacogenetics Study was a 6-week open label, non-randomized study of 40mg/day simvastatin treatment in 335 black and 609 white (944 total) men and women. Plasma lipids and lipoproteins were measured on two occasions prior to treatment and at 4 and 6 weeks of treatment. The study was designed to test for genetic associations with baseline measurements and changes in response to simvastatin treatment. Whole genome genotyping was performed on 592 white CAP study participants in two stages. In Stage 1, 304 were genotyped for 314,621 SNPs to tag for common genomic variation. In Stage 2, 290 participants were genotyped, including 280 who were genotyped for 620,901 SNPs. Two samples were excluded due to gender discrepancies. More recently, CAP self-reported black participants were genotyped on Illumina Omni2.5Exome chips. PolyA-selected strand-specific RNA-seq libraries were generated in several batches from lymphoblastoid cell lines (LCLs) derived from 268 white and 165 black CAP participants. The LCLs were exposed to sham buffer (control) or 2 uM activated simvastatin for 24 hours, producing a total of 866 100/101 bp paired end RNA-seq libraries sequenced on Illumina HiSeq 2000 machines.

  Study phs000481

• Pharmacogenomics of HIV Therapy - Atazanavir Bilirubin-related Side Effects

  This is an evaluation of genetic associations with atazanavir (ATV) discontinuation for bilirubin-related causes within 12 months of treatment. Patients were treated at an HIV primary care clinic in Nashville TN from 1998 to 2012. A previously known SNP in UGT1A1 (rs887829) was used to define metabolizer genotypes (extensive, intermediate, slow metabolizer). Over 500,000 SNPs from genome-wide genotyping were used to define MDS (Multidimensional Scaling) coordinates to account for population stratification. Patients were defined as cases if they discontinued ATV for bilirubin-related causes within 12 months of treatment, otherwise they were defined as controls if they did not stop treatment. Among 321 evaluable patients, 15 (4.6%) had bilirubin-related atazanavir discontinuation within 12 months. Homozygosity for rs887829 T/T was present in 28.1% of black, 21.4% of Hispanic, and 8.6% of white patients. Among all patients the hazard ratio (HR) for bilirubin-related discontinuation with T/T versus C/C genotype was 7.3 (95% C.I.: 1.7 to 31.5; p = 0.007). Among 152 white patients the HR was 14.4 (95% CI: 2.6 to 78.7; p = 0.002), but among 153 black patients the HR was 0.8 (95% C.I. 0.05 to 12.7; p = 0.87).

  Study phs001484

• Cohort-Based Genome-Wide Association Study of Glioma (GliomaScan)

  We conducted a new independent GWAS of adult glioma using 1,856 cases and 4,955 controls from 14 cohort studies belonging to the Cohort Consortium, 3 case-control studies, and 1 population-based case only study. Cases were newly diagnosed glioma [ICDO-3 codes 9380-9480 or equivalent], and controls were cancer-free at the time of glioma diagnosis. We found evidence of strong replication for three of the seven previously reported associations at 20q13.33 (RTEL), 5p15.33 (TERT), and 9p21.3 (CDKN2BAS), and consistent association signals for the remaining four at 7p11.2 (EGFR both loci), 8q24.21 (CCDC26) and 11q23.3 (PHLDB1). The direction and magnitude of the signal were consistent for samples from cohort and case-control studies, but the strength of the association was more pronounced for loci rs6010620 (20q,13.33; RTEL) and rs2736100 (5p15.33, TERT) in cohort studies despite the smaller number of cases in this group, likely due to higher grade tumors being captured in the cohort studies. Our findings suggest that larger studies focusing on novel approaches as well as specific tumor subtypes or subgroups will be required to identify additional common susceptibility loci for glioma risk.

  Study phs000652

• Pediatric Investigation of Genetic Factors Linked with Renal Progression (PediGFR): Chronic Kidney Disease in Children Cohort (CKiD)

  The Pediatric Investigation for Genetic Factors Associated with Renal Progression (PediGFR) (RO1-DK082394) is an international collaborative study among three large prospective cohort studies of children with chronic kidney disease. The participating parent cohort studies are the "Chronic Kidney Disease in Children (CKiD)", the "Effect of Strict Blood Pressure Control and ACE Inhibition on CRF Progression in Pediatric Patients (ESCAPE)", and the "Cardiovascular Comorbidity in Children with Chronic Kidney Disease (4C)" study. In these cohorts, pediatric subjects with CKD have been prospectively followed with standardized measurements for renal progression. The current version of the upload includes the genotype and baseline phenotype for the CKiD cohort. In brief the CKiD study is a prospective study of children with chronic kidney disease (CKD) between the ages of 1 year to 16 years of age and an estimated glomerular filtration rate (eGFR) by Schwartz equation between 30 and 75 ml/min per 1.73m2. Included in this upload are the phenotypic data for anemia traits utilized for the sub-study, "Role of Genetic Variation in the Anemia of Chronic Kidney Disease" (K24DK078737), with the RBC trait and anemia data pertaining to CKiD as well.

  Study phs000650

• The taxonomic composition of the human microbiome of CRC patients and healthy donors

  In this study, single homogenized human stool samples from five healthy donors and one CRC patient were analyzed by shotgun sequencing to generate a baseline for the establishment of humanized microbiome to be transferred into mice. Briefly, fecal DNA was isolated from these samples using the DNeasy PowerSoil DNA Isolation Kit (Qiagen), according to the kit manual, except that samples were homogenized using the TissueLyzerII for five minutes at 40Hz instead of intense vortexing. The extracted DNA was further purified and concentrated using the DNA Clean and Concentrator Kit (Zymo Research). This DNA was thawed and refrozen once at -80°C for 16s sequencing before being thawed again for WGS. 200 ng of DNA was used for metagenomic library preparation using the Next Generation Sequencing DNA Library Prep Kit (Westburg), according to the user manual using an average insert size of libraries of 450 base pairs. Following quantification and quality control (Qubit® dsDNA BR Assay Kit (Thermofisher Scientific); Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Technologies)), sequencing was performed on a NextSeq500 instrument using 2×150 base pair read lengths.

  Study EGAS50000000759

• 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

• Error-corrected flow-based sequencing at whole genome scale and its application to circulating cell-free DNA profiling

  Differentiating sequencing errors from true variants is a central genomics challenge calling for error suppression strategies that balance costs when sparse material or ultra-rare variants require high-accuracy methods. For example, circulating cell-free DNA (ccfDNA) sequencing for cancer monitoring is limited by sparsity of circulating tumor DNA (ctDNA), abundance of genomic material in samples, library preparation error rates and sequencing errors. Whole-genome sequencing (WGS) can overcome the low abundance of ccfDNA by integrating signal across the mutation landscape, but higher cost limits adoption compared with targeted panels, where ccfDNA abundance limits maximal coverage depths. Here we applied deep (~120x) lower-cost WGS (Ultima Genomics) with analytic error correction for tumor-informed ctDNA detection within the part-per-million range. We further developed high-coverage duplex error-corrected WGS of ccfDNA, achieving 7.7x10-8 error rates, to assess disease burden in melanoma and urothelial cancer patients without matched tumor sequencing. Together, we show that deeply sequenced error-corrected WGS accurately calls somatic variants, demonstrating the feasibility of WGS for tumor-informed and tumor-agnostic ctDNA detection.

  Study EGAS50000000844

• WTCCC2 Visceral Leishmaniasis (VL) samples

  A WTCCC2 project genome-wide association study for visceral leishmaniasis (VL) in individuals from India, Brazil and Sudan, genotyped on the custom Illumina 670k array. The WTCCC2 analysis of the Brazilian and Indian samples is described in Fakiola et al. [Nat Genet. 2013 Feb;45(2):208-13].It should be noted that due to expected family structure in the data, normal analyses of these data should include an estimation of the relatedness between the samples. For more details about sample collection for the project please refer to the Methods section of the paper above. The samples from India were all collected from Bihar state in northeastern India. The Brazilian samples were collected from a wide area of northern Brazil, and managed at two laboratories in Natal and Belem. For more details on the geographic distribution of the Brazil samples please see Jamieson et al. [Genes Immun. 2007 Jan;8(1):84-90]. We have not generated qc_passed or info files for the Sudanese data, a preliminary scan of the data indicated that there may be DNA quality issues with these samples.

  Study EGAS00001000773

• PCR-free shallow whole genome sequencing for chromosomal copy number detection from plasma of cancer patients is an efficient alternative to the conventional PCR-based approach

  Somatic copy number alterations (SCNAs) can be detected in tumor cell-free DNA (cfDNA) by shallow whole genome sequencing (sWGS). Polymerase chain reaction (PCR) is typically included in library preparations, but a PCR-free method could be an effective alternative for research and diagnostics. Peripheral blood samples (n=22) were collected in EDTA-containing tubes from non-small cell lung cancer patients (n=10) and healthy donors (n=12). PCR and PCR-free library preparations underwent sWGS and the following metrics were compared: mapping quality, proportion of duplicate reads, genome coverage, sequencing read length and copy number profiles. The PCR-free method was further evaluated on archived plasma samples (n=33) of varying pre-analytical quality collected in EDTA or lithium heparin tubes. Archived samples were from acute myeloid leukaemia (n=15) and B-cell lymphoma (n=18) patients. The percentage of unique reads was significantly higher for the 22 samples analysed by PCR-free (95.7%) compared to PCR (84%). PCR-free libraries from 33 archived samples produced data of a comparable quality, with 95.4% unique reads. All other evaluated metrics were highly comparable for PCR and PCR-free library preparations. We conclude that SCNA detection can be performed by PCR-free sWGS on cfDNA from cancer patients and is feasible for diagnostic and archival plasma collected in EDTA- or lithium heparin-containing tubes. Our results pave the way for an automated cfDNA workflow for cancer plasma samples.

  Study EGAS00001004692