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• Strelka somatic snv vcfs for EGAS00001004572

  Bulk Strelka somatic snv vcfs from tumour-normal analysis in EGAS00001004572

  Dataset EGAD00001006907

• Reference epigenome ADMSC04_smRNA-Seq data generated from KEP study

  A ADMSC04_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003870

• Reference epigenome CKD23_C_Mesan_WGBS data generated from KEP study

  A CKD23_C_Mesan_WGBS paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003468

• Reference epigenome CKD27_C_Mesan_WGBS data generated from KEP study

  A CKD27_C_Mesan_WGBS paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003471

• Patient 16CH

  One file of patient 16 with WGS done on Illumina HiSeq X-Ten. For research purpose and authorised user only.

  Dataset EGAD00001003440

• Reference epigenome KNIH008 WGBS data generated from KEP study

  A KNIH008 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for adipocytes

  Dataset EGAD00001002756

• RNA-seq

  The RNA was extracted using the AS1390 PROMEGA kit according to the manufacturer’s instructions. The samples underwent sequencing using a Novaseq 6000 machine, equipped with an SP 200 cycles v1.5 cartridge. The sequencing process varied slightly across batches based on the input RNA and the library preparation kits used.

  Dataset EGAD50000002023

• ESGI___Whole_Genome_Sequencing_of_samples_from_the_Cilentogen_isolates

  Deep whole genome sequencing of sampels from the Cilento isolates. The samples are sequenced using the Illumina HiSeq X Ten system.

  Study EGAS00001001116

• The Mexican-American Coronary Artery Disease Study (MACAD)

  The MACAD Study, funded by NHLBI, was designed to explore genetic contributions to coronary artery disease and glucose homeostasis traits among Hispanics using a family-based design. The baseline examination of the cohort included the euglycemic hyperinsulinemic clamp test from which the two key phenotypes were obtained: insulin sensitivity (M) and metabolic clearance rate of insulin (MCRI). Genome-wide genotyping was obtained under separate funding by NIDDK as a part of the GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

  Study phs001397

• The Hypertension-Insulin Resistance Family Study (HTN-IR)

  The HTN-IR Study, funded by NHLBI, was designed to explore genetic contributions to hypertension and glucose homeostasis traits among Hispanics using a family-based design. The baseline examination of the cohort included the euglycemic hyperinsulinemic clamp test from which the two key phenotypes were obtained: insulin sensitivity (M) and metabolic clearance rate of insulin (MCRI). Genome-wide genotyping was obtained under separate funding by NIDDK as a part of the GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

  Study phs001394

• The genetic analysis of circulating tumor DNA in blood of the digestive cancer patients to investigate the prognostic factors of metastasis and reccurence.

  A Darwinian evolutionary shift occurred early in the neutral evolution of advanced colorectal carcinoma (CRC) and copy number aberrations (CNA) were essential in the transition from adenoma to carcinoma. Subsequent to the primary evolution, we now focus on the evolutionary principle of the genome to foster postoperative recurrence of CRC. SO, We compared CNA, single nucleotide variance (SNV), RNA sequences between 8 primary and 11 metastatic sites from 10 CRCR cases.

  Study JGAS000221

• DGCR8 and the six hit, three-step model of schwannomatosis

  In our manuscript, we report the second case of a patient with peripheral schwannomatosis and thyroid alterations cause by the germline pathogenic variant E518K in DGCR8 and analyzed a total of 13 schwannomas from patients in the two kindreds identified up to date. Our analyses revealed how path to tumorigenesis prompted by DGCR8 requires the loss of the wild type allele of Chrm22q and in more than two thirds of the tumors a complete inactivation of NF2.

  Study EGAS00001005665

• Whole Exome Sequencing analysis of three tumor biopsies from a LUAD patient

  Whole Exome Sequencing (WES) analysis was performed on three distinct tumor biopsies collected at different time points, along with their matched germline non-tumor sample, from the same LUAD patient. DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions and quantified using the Qubit Fluorometer assay (Life Technologies, Carlsbad, CA). To minimize FFPE-related sequencing artifacts (e.g., C:G > T:A transitions), the extracted DNA was treated with the DNA repair enzyme Uracil-DNA-Glycosylase (UDG) following the manufacturer’s protocol (New England Biolabs, Ipswich, MA). Whole-exome capture was performed with the Twist Human Core Exome + RefSeq + Mito-Panel kit (Twist Bioscience), in accordance with the manufacturer’s guidelines. Sequencing generated paired-end 100-bp reads on the Illumina NovaSeq 6000 platform. The resulting reads were aligned to the reference human genome (GRCh38) using the Burrows-Wheeler Aligner (BWA, v0.7.12).

  Dataset EGAD50000001198

• 16S-based fecal microbiota composition

  The dataset reports the 16S rRNA gene sequencing of the fecal microbiota of donors from the Milieu Intérieur Cohort. The Milieu Intérieur cohort includes a total of 1,000 healthy individuals of western European ancestry, recruited in France as part of the Milieu Intérieur project. To assess their fecal microbiota composition, 16S rRNA profiles were generated from stool samples of 863 of the 1,000 donors. Human stool samples were produced at home no more than 24 hours before the scheduled medical visit and collected in a double-lined sealable bag maintaining strict anaerobic conditions. Upon reception at the clinical site, the fresh stool samples were aliquoted and stored immediately at -80°C. DNA was extracted from stool and barcoding PCR was carried out using indexed primers targeting the V3-V5 region of the 16S rRNA gene. Equal volumes of normalized PCR reaction were pooled and thoroughly mixed. The amplicon libraries were sequenced on Illumina MiSeq.

  Dataset EGAD00001004979

• Myelodysplastic_Syndrome_Follow_Up_Series

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from MDS and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to discover the prevalence of our findings using bespoke pulldown methods and sequencing the products from a larger set of patient DNA.

  Study EGAS00001000224

• GINS3 fibroblast RNAseq

  The eukaryotic CDC45/MCM2-7/GINS (CMG) DNA helicase unwinds the DNA double helix during DNA replication. We report the identification of individuals presenting with a Meier-Gorlin syndrome (MGS) like phenotype, secondary to hypomorphic variants in the GINS3 gene.  To verify whether the GINS3 variant affected the transcriptome, RNA-seq was performed from 3 fibroblast cultures derived from a patient with compound heterozygous GINS3 variants, and 1 replicate of fibroblasts derived from each of the two parents.

  Study EGAS00001006038

• Multiomic Sequencing of Paired Primary and Metastatic Small Bowel Carcinoids

  Small bowel carcinoids are insidious tumors that often have metastatic spread at the time of diagnosis. Limited studies on the mutational landscape of carcinoids indicate that the tumors have a relatively low mutational burden. Loss of chromosome 18q and loss of CDKN1B have been reported in a minority of tumors. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors.

  Study EGAS00001006988

• The evolution of adult T-cell acute lymphoblastic leukemia

  We profile the whole-genome of 19 primary T-ALLs from adult patients and the corresponding relapse malignancies. Concretely, samples were taken at the time of diagnosis (primary), at time of remission (used as control) and at recurrence of the malignancy after treatment (relapse). The libraries were sequenced on HiSeq 4000 or NovaSeq 6000 (Illumina) with a paired-end read length of 2x151bp.

  Study EGAS00001004750

• The biology of cell-free DNA fragmentation and the roles ofDNASE1, DNASE1L3 and DFFB

  The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3 and DFFB

  Study EGAS00001003514

• Exome sequencing and disease analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis

  The study involves a single consanguineous Palestinian family with Hereditary Spastic Paraparesis (HSP). The affected individuals suffer from spasticity of the lower limbs and abnormal gait. Using exome sequencing and homozygosity mapping, our analysis implicated the causative mutation in the motor domain of KIF1A, a gene that functions in anterograde axonal transportation.

  Study phs000359

• Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype

  Due to the limited number of modifiable risk factors, secondary prevention strategies based on early diagnosis represent the preferred route to improve the prognosis of pancreatic ductal adenocarcinoma (PDAC). Here, we provide a comparative morphogenetic analysis of PDAC precursors aiming at dissecting the process of carcinogenesis and tackling the heterogeneity of preinvasive lesions.

  Study EGAS00001006793

• Biomarker Data from KATHERINE: A Phase III Study of Adjuvant Trastuzumab Emtansine versus Trastuzumab in Patients with Residual Invasive Disease after Neoadjuvant Therapy for HER2-Positive Breast Cancer

  Study EGAS00001006229

• Time course acetalax bisacodyl treatment

  RNA-Seq raw data of PDX treated with acetalaxor bisacodyl for 4h00 to 24h00.

  Dataset EGAD50000000875

• BelCovid_2_genotype

  Cohort: Raw genotype files for BelCovid2 cohort. Genotype Chip: Illumina Global Screening Array-24 v3.0 + Multi-Disease beadchip genomic build: b37

  Dataset EGAD00010002179

• GEN_COVID_genotype

  Cohort: Raw genotype files for GEN_COVID cohort. Genotype Chip: Illumina Global Screening Array-24 v3.0 + Multi-Disease beadchip genomic build: b37

  Dataset EGAD00010002177