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• Cell-free DNA TAPS for early cancer detection

  Multimodal, genome-wide characterization of epigenetic and genetic information in circulating cell-free DNA (cfDNA) could enable more sensitive early cancer detection. However, due to technological challenges associated with DNA methylation sequencing in low input cfDNA samples, most studies have been limited by DNA damage caused by bisulfite sequencing, or the qualitative nature of enrichment-based sequencing. Recently, we developed TET-assisted Pyridine Borane Sequencing (TAPS), which is a mild, bisulfite-free method for base-resolution direct DNA methylation sequencing. Here we optimized TAPS for cfDNA (cfTAPS) to provide high-quality and high-depth whole-genome cell-free methylomes. We applied cfTAPS to 85 cfDNA samples from patients with hepatocellular carcinoma (HCC) or pancreatic ductal adenocarcinoma (PDAC) and non-cancer controls. From just 10 ng cfDNA (1-3 mL of plasma), we generated the most comprehensive cfDNA methylome to date. We demonstrated that cfTAPS provides multimodal information about cfDNA characteristics, including DNA methylation, tissue of origin, and DNA fragmentation. Integrated analysis of these epigenetic and genetic features enables accurate identification of early HCC and PDAC.

  Study EGAS00001004962

• alopecia areata

  exome sequencing files from 25 alopecia areata samples from spain.

  Dataset EGAD00001006370

• CancerLocator: Non-Invasive Cancer Diagnosis and Tissue-of-Origin Prediction Using Methylation Profiles of Cell-Free DNA

  Background: The detection and characterization of cell-free DNA in plasma is one of the most promising new areas in cancer diagnosis. Liquid biopsy, unlike traditional tissue biopsy, has the potential to diagnose a variety of different malignancies. Results: Here we propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. We comprehensively evaluate CancerLocator with simulations and real data, and compare its performance with that of two established multi-class classification methods. We show that the predicted tumor burdens are highly consistent with the true values. In addition, when the proportion of tumor-derived DNAs in the cell-free DNAs is low, the two popular machine learning methods completely fail for cancer diagnosis, while CancerLocator successfully overcomes the challenge. CancerLocator also achieves promising results on patient plasma samples, despite the fact that the DNA methylation data from these samples has very low sequencing coverage. Conclusions: CfDNA methylation may be developed as an important approach for non-invasive early cancer diagnosis.

  Study EGAS00001002211

• DAC for "Copy number variations and fragmentation features in cell-free DNA predict response in advanced non-small cell lung cancer patients under anti-PD-(L)1 therapy"

  DAC for "Copy number variations and fragmentation features in cell-free DNA predict response in advanced non-small cell lung cancer patients under anti-PD-(L)1 therapy" with Florian Janke (f.janke@dkfz-heidelberg.de) and Holger Sültmann (h.sueltmann@dkfz-heidelberg.de)

  Dac EGAC50000000308

• The dataset for Detection of brain cancer using genome-wide cell-free DNA fragmentomes

  The dataset for “Detection of brain cancer using genome-wide cell-free DNA fragmentomes” includes 310 bam files from whole genome next-generation sequencing on the Illumina Novaseq 6000. The dataset analyzed include plasma cfDNA samples from patients with cancer, patients with neurological conditions, and healthy individuals.

  Dataset EGAD50000001445

• Paired Biopsy Project: West Coast Dream Team

  This project contains the 16 WGS tumor samples and the corresponding 15 WGS normal tissue samples (germline control) not yet deposited in the public domain (e.g., EGA, dbGaP) at the time of submission of the manuscript (Zhu et al.)

  Dataset EGAD50000000473

• PETAL Network: Outcomes Related to COVID-19 Treated With Hydroxychloroquine Among Inpatients With Symptomatic Disease (ORCHID) Trial

  ORCHID was a multicenter, blinded, placebo-controlled randomized trial conducted at 34 hospitals in the US between April 2 and June 19, 2020. Adults hospitalized with respiratory symptoms from severe acute respiratory syndrome coronavirus 2 infection were enrolled, with the last outcome assessment on July 17, 2020. The planned sample size was 510 patients with five interim analyses; however, the trial was stopped at the fourth interim analysis for futility with a sample size of 479 patients.The distribution of the day 14 clinical status score (measured using a 7-category ordinal scale) was not significantly different for patients randomized to receive hydroxychloroquine compared with placebo.Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

  Study phs002299

• RNAseq SCLC Cell lines MYC

  RNAseq data set (Mollaoglu et al., MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition) RNA isolation from primary tumors and healthy lungs was performed using RNeasy Mini Kit (Qiagen) with the standard protocol. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (cat# RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001). Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).

  Dataset EGAD00001003099

• Epigenetic analyses of methylation and nucleosome occupancy in cell-free DNA (cfNOMe)

  Cell-free DNA (cfDNA) has become essential in cancer diagnostics and prenatal testing. We investigate enzymatic cytosine conversion for epigenetic analyses of cfDNA and find that it reliably measures cytosine methylation and nucleosome occupancy. Whereas previously, separate experiments had to be performed to study either epigenetic marking, this approach delivers reliable results for both, enabling more comprehensive and inexpensive epigenetic profiling of cfDNA.

  Study EGAS00001004370

• Longitudinal Study of Vaginal Flora

  This prospective observational study aims to advance our knowledge of the natural history and abnormal alteration in vaginal microbial flora, and to identify risk factors that are associated with these changes. A total of 5500 healthy, non-pregnant women of reproductive age will be enrolled and followed up in Birmingham, Alabama, for one year (baseline visit plus once every three months afterwards, totaling 5 visits). Detailed information on sociodemographic status, medical history, hygiene practice, sexual behavior and psychosocial stress will be collected through in-person interviews. Routine gynecological and dental examinations will be carried out during the study visits. Samples of vaginal secretion and blood will be collected. Laboratory tests to quantify vaginal microbial flora and to identify infection of bacterial vaginosis as well as common sexually transmitted diseases will be conducted. Future submissions may contain metadata or molecular data from additional subjects.

  Study phs002367

• Stress and Treatment Response in Puerto Rican and African American Children with Asthma (STAR)

  The Stress and Treatment Response in Puerto Rican and African American Children with Asthma Study (STAR) was a 6-week study of response to inhaled corticosteroids (ICS) in youth aged 8-20 years recruited at the University of Puerto Rico Medical Center and UPMC Children's Hospital of Pittsburgh from June 5, 2018 to May 16, 2022. At a baseline visit, participants completed questionnaires and underwent collection of nasal specimens. After nasal sampling, participants were treated with daily medium-dose inhaled Mometasone for 6 weeks, with adherence measured using a dose-counter. Spirometry and fractional exhaled nitric oxide (FeNO) measurements were conducted at baseline and after 6 weeks of ICS. STAR was approved by the institutional review boards (IRBs) of the University of Puerto Rico and the University of Pittsburgh. Written parental consent and assent were obtained from participants

  Study phs004052

• The dataset for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

  The dataset for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer includes 57 BAM files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from individuals with and without cancer.

  Dataset EGAD00001010891

• T cell receptor repertoire in cell-free DNA as a proxy for tumor infiltrates in patients treated with pembrolizumab

  Bulk TCR sequences from tumor, peripheral blood mononuclear cell (PBMC), and cell-free DNA (cfDNA) samples from 81 patients with solid tumors treated with pembrolizumab.

  Dataset EGAD50000001857

• DAC for cell free DNA TAPS study

  Dac EGAC00001001903

• A dataset compiled as a resource a for orthogonal assessment of exon CNV calling in NGS data

  The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM and PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs the most difficult exon CNV to detect. The full dataset includes FASTQ files, target BED file, and MLPA results.

  Study EGAS00001002428

• Nucleosome footprinting in plasma cell-free DNA for diagnosis of ovarian cancer

  Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals.

  Study EGAS00001005361

• Targeted sequencing of cell-free DNA and white blood cells from 24 men with metastatic prostate cancer

  This dataset consists of aligned DNA sequencing data in BAM file format from cell-free DNA and white blood cells from 24 men with metastatic prostate cancer. One cell-free DNA sample and one white blood cell sample is available for each patient, resulting in 48 total BAM files in this dataset. The sequencing was performed using a hybrid capture-based targeted panel of 73 prostate cancer driver genes.

  Dataset EGAD00001004486

• Prostate cancer datasets WGS

  Low pass WGS: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (Next Seq )

  Dataset EGAD00001004466

• Single cell RNA sequencing data of advanced melanoma patients treated with checkpoint inhibitor immunotherapy

  Single cell RNA libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3’ v2 reagents. The samples were barcoded and each library were pooled with two samples at equimolar concentrations. The pooled libraries (n=4) were sequenced on the NextSeq 500 machine (Illumina) with paired-end sequencing and dual indexing as recommended in the manufacturer’s protocol; 26 and 98 cycles for the respective Read 1 and 2, and 8 cycles for i7 index.

  Dataset EGAD50000000493

• The dataset for Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers

  The dataset for “Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers” includes 409 cram files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD50000000695

• The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer

  The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer includes 538 bam files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD00001005339

• Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

  Patients with metastatic urothelial cancer (n=29) were treated with atezolizumab (anti-PD-L1). All 29 patients had T-cell receptor sequencing (TCR-seq) of the pre-treatment blood; 24 also had TCR-seq on at least one post-treatment blood sample. 24 patients had TCR-seq of their pre-treatment tumors. TCR-seq data can be found at http://doi.org/10.5281/zenodo.546110. 26 patients also had RNAseq of their tumors and whole exome sequencing (WES) of their tumors and matched normal blood. WES results for one sample were excluded from our analysis after failing to meet coverage requirements.

  Study phs001743

• Evolution of Structural Rearrangements in Prostate Cancer Intracranial Metastases

  Intracranial metastases in prostate cancer are uncommon but clinically aggressive. We sought to characterize prostate cancer intracranial metastases in order to improve our understanding of their pathogenesis and to promote the search for new treatment strategies. We evaluated the clinical and molecular characteristics of 36 patients with metastatic prostate cancer to either the dura or brain parenchyma. We performed whole genome sequencing (WGS) on samples from 21 patients. The WGS samples include 10 intracranial prostate cancer metastases, as well as WGS of primary prostate tumors from men who later developed metastatic disease (n=6) and non-brain prostate cancer metastases (n=26).

  Study phs003357

• Exome-sequencing of human B cell lymphoma cell lines

  26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x.

  Study EGAS00001001463

• GEDI: A Developmental Model of Gene-Environment Interplay in SUDs: Combined Genotype Dataset from the "Great Smoky Mountains Study" and the "Caring for Children in the Community Study".

  1. Great Smoky Mountains Study (GSMS; Costello et al. 1996, 1997) Three cohorts of boys and girls, aged 9, 11, and 13 years at intake in 1993, were selected from a rural population of some 20,000 children using a household equal probability design. A two-phase procedure was used for White and African-American youth to increase power by oversampling children at risk for psychiatric and SUDs. Parents (usually mothers) of the first stage random population sample completed a questionnaire about their child's behavioral problems. Of 4,195 subjects selected, 95% (N=3,896) of parents completed the screen. All children scoring above a predetermined threshold (the top 25% of the total scores), plus a 10% random sample of the remaining 75%, were recruited for detailed interviews. Results can be back-weighted to population levels for analyses. Half of the sample consists of females, and 6% are African Americans, reflecting the population of the study area. The interviewed sample of white and African-American subjects was 1,070 (80% of those recruited). American Indian youth were oversampled (100%) because they are an understudied group known to be at high risk for stressful events, substance disorders, and mood disorders. Of 431 age-eligible children, 350 (81% boys, 49% girls) participated. Thus, the size of total GSMS sample is 1,070 + 350 = 1,420. Data collection is complete for ages 9-26, and age 30 interviews are in progress. By age 26 a total of 9,858 interviews had been completed; the average number of interviews per subject was seven, and by age 26, 97.3% completed two or more interviews. 2. The Caring for Children in the Community Study (CCC; Angold et al., 2002) This representative study of psychiatric illness and service use in African-American and White youth took place in four rural counties in the southeastern USA. The two-stage sampling design and methods are similar to those used in the GSMS. Of 4,500 youth randomly selected from the 17,117 9- to 17-year-olds in the public school's database, 3,613 (80.0%) were successfully contacted and agreed to complete the behavioral screen. Of the 1,302 selected to participate in the study, 920 (70.7%) interviews were completed. Because CCC was also the only study in GEDI to contain more than a very few African-American participants, these were omitted from the multi-site analyses. Reprinted with permission from Cambridge University Press from Costello et al., 2013: PMID: 23461817 References: Costello et al., 1996: PMID: 8956679 Costello et al., 1997: PMID: 9184514 Angold et al., 2002: PMID: 12365876

  Study phs000852