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• 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

• 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

• 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

• 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

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_WGS_Managed_Access

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007437

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_Spatial_Managed_Access_

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007152

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_RNA_Managed_Access_

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007151