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• Long-read whole-genome sequencing-based concurrent haplotype phasing and aneuploidy profiling of single cells

  This dataset contains long-read whole-genome sequencing (lrWGS) data from 14 samples. Five lrWGS data are from single-cell (sc, sc_2, sc_3), multi-cell (mc, 10 cells), and bulk samples of HG002. The remaining nine lrWGS data are from two preimplantation genetic testing (PGT) families, including four from blood bulk DNA of the parental pairs and five from trophectoderm biopsies of two embryos from one family and three embryos from another family. The data are provided in raw FASTQ format and were generated using the PromethION device from Oxford Nanopore Technologies.

  Dataset EGAD50000000787

• 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

• FASTQ files for Recommendations to mitigate FFPE-associated problems in NGS

  42 NGS libraries of a 13y/o FFPE sample, a tissue-and-patient-matched FF sample, and a GIAB sample (NA12878). In technical replicates (untreated DNA, treated DNA, two different library types, at least library duplicates for each case). Illumina NextSeq, HiSeq and NovaSeq paired-end sequencing.

  Dataset EGAD00001008399

• Whole exome sequencing of small cell neuroendocrine cancer of the cervix

  In order to improve treatment selection for high grade neuroendocrine carcinomas of the cervix (NECC), we performed a comparative genomic analysis between this rare tumor type and other cervical cancer types, as well as extra-cervical neuroendocrine small cell carcinomas of the lung and bladder. We performed whole exome sequencing on fresh-frozen tissue from 15 NECCs and matched normal tissue. We then identified mutations and copy number variants using standard analysis pipelines. Published mutation tables from cervical cancers and extra-cervical small cell carcinomas were used for comparative analysis. Descriptive statistical methods were used and a two-sided threshold of P < .05 was used for significance. In the NECC cohort, we detected a median of 1.7 somatic mutations per megabase (range 1.0-20.9). PIK3CA p.E545K mutations were the most frequency observed oncogenic mutation (4/15 tumors, 27%). Activating MAPK pathway mutations in KRAS (p.G12D) and GNAS (p.R201C) co-occurred in two tumors (13%). In total we identified PI3-kinase or MAPK pathway activating mutations in 67% of NECC. When compared to NECC, lung and bladder small cell carcinomas exhibited a statistically significant higher rate of coding mutations (P < .001 for lung; P = .001 for bladder). Mutation of TP53 was uncommon in NECC (13%) and was more frequent in both lung (103 of 110 tumors [94%], P < .001) and bladder (18 of 19 tumors [95%], P < .001) small cell carcinoma. These comparative genomics data suggest that NECC may be genetically more similar to common cervical cancer subtypes than to extra-cervical small cell neuroendocrine carcinomas of the lung and bladder. These results may have implications for the selection of cytotoxic and targeted therapy regimens for this rare disease.

  Study EGAS00001003142

• ABIS_1_MeDIP-seq

  We investigated changes in whole genome DNA-methylation in a group of 48 healthy five-year-old children differentiated by their hair cortisol levels. By combining this novel biomarker for chronic stress with methylated DNA immunoprecipitation sequencing (MeDIP-seq), we found that high cortisol were associated with a genome-wide decrease in DNA-methylation targeted to specific zinc finger transcription factor binding sites, repetitive elements and genes important for neurodevelopment and calcium transport. Large scale hypomethylation of repetitive regions, as well as a deficient calcium transport, have been reported in many stress related diseases, as well as in many cancers and biological aging. Thus our findings may aid in our understanding of how susceptibility to these diseases develops.

  Study EGAS00001001099

• Genomic profiling of IBC

  We collected matched pretreatment blood and tumor samples from 19 patients with primary TN-IBC enrolled in a phase II clinical trial (NCT02876107). Patients were treated with neoadjuvant chemotherapy (NAC) or the anti-EGFR antibody panitumumab (PmAb) plus NAC (PmAb/NAC). We conducted whole-exome sequencing, RNA sequencing, and CIBERSORT analyses for these TN-IBC samples and compare the genetic and molecular profiles with similarly analyzed stage III TN-non-IBC patient samples. We also compared the genetic and molecular characteristics of TN-IBC in patients who had a pathologic complete response (pCR) to NAC or PmAb/NAC treatment, a suitable surrogate endpoint for IBC, with those who did not have pCR (non-pCR).

  Study EGAS00001007520

• ESGI - Molecular diagnosis for mitochondrial disorders (2017-08-29)

  The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients. This dataset contains all the data available for this study on 2017-08-29.

  Dataset EGAD00001003596

• ERDERA WES reanalysis - DPF1 Batch 6

  This dataset comprises processed genomic data from 682 samples, corresponding to 682 whole-exome sequencing experiments. Data files include CRAM, gVCF (containing short variants, copy number variants, and structural variants), RoH (BED), B-allele frequencies (BW), and variant IGV visualizations (XML). Associated phenotypic and pedigree information for all samples is also included.

  Dataset EGAD50000002464

• ERDERA WES reanalysis - DPF1 Batch 5

  This dataset comprises processed genomic data from 1016 samples, corresponding to 1016 whole-exome sequencing experiments from ERDERA Data Processing Freeze1. Data files include CRAM, gVCF (containing short variants, copy number variants, and structural variants), RoH (BED), B-allele frequencies (BW), and variant IGV visualizations (XML). Associated phenotypic and pedigree information for all samples is also included.

  Dataset EGAD50000002516

• SAPCS 20 Blood RNA-seq from Prostate cancer patients.

  Raw RNA-seq reads (FASTQ format) and Mapped sequencing reads (BAM format) of 20 Prostate cancer patients in Southern African Prostate Cancer Study (SAPCS). Each patient exhibit different pathogenic variations. The Illumina RNA-sequencing is performed from Blood extraction (from QIAamp RNA Blood Mini Kit). rRNA was removed prior using SortMeRNA. STAR aligner program was used for mapping to human genome GRCh38.p14, resulting in an average genome coverage of 9x.

  Dataset EGAD50000000982