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• Whole exome sequencing study of cholesteatoma patients from affected families

  This study used whole exome sequencing on 21 patients with cholesteatoma from 10 families in order to identify variants that may attribute to cholesteatoma aetiology. Exomes were enriched for using hybridisation selection and subject to DNA-sequencing. This datasets is formed of two batches as they were sequencing at different times. Batch-1 exomes were selected for using Nimblegen capture (4-plex) and sequenced on Illumina Hiseq 4000 and batch-2 was exome selected using Agilent SureSelect Human All Exon v6 and sequenced on the Illumina NovaSeq 6000. All samples within the same family were processed within the same batch. This dataset is comprised on BAM files mapped using cgpMAP v3.2.0 (bwa-mem) using the GRCh38.

  Dataset EGAD00001008671

• RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mamals

  In mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess a single X chromosome, while females (XX) undergo X inactivation. To compensate for this reduction in dosage compared to two active copies of autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation. However, the existence and mechanism of X-to-autosome dosage compensation are still under debate. Here, we show that X-chromosomal transcripts are reduced in m6A modifications and more stable compared to their autosomal counterparts. Acute depletion of m6A selectively stabilises autosomal transcripts, resulting in perturbed dosage compensation in mouse embryonic stem cells. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation is partly regulated by epitranscriptomic RNA modifications.

  Dataset EGAD00001010194

• WGS of cell-free DNA derived from plasma of CRC patients and healthy controls, and WGS of matched tumor tissue and saliva

  This dataset contains: 1.) Whole-genome sequencing (WGS) data (~6x) of 259 cfDNA samples obtained from 50 colorectal cancer (CRC) patients and 61 healthy controls. Paired-end sequencing was performed with 2x101 bp reads on the NovaSeq 6000 system. Data is provided as mapped .bam files (aligned to GRCh38/hg38). 2.) WGS data (~1x) of 50 tumor biopsy and 45 saliva samples from CRC patients. Paired-end sequencing was performed with 2x101 bp reads on the NovaSeq 6000 system. Data is provided as mapped .bam files (aligned to GRCh38/hg38).

  Dataset EGAD00001009309

• Low coverage whole-genome sequencing of samples from the Cretan Greek isolate collection HELIC-MANOLIS

  Whole-genome sequencing at 1x of samples from the Cretan Greek isolate collection HELIC-MANOLIS. Genome-wide association studies of complex traits have been successful in identifying common variant associations, but a substantial heritability gap remains. The field of complex trait genetics is shifting towards the study of low frequency and rare variants, which are hypothesised to have larger effects. The study of these variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. This work focuses on an isolated population from Crete, Greece. Sequencing is very efficient in isolated populations, because variants found in a few samples will be shared by others in extended haplotype contexts, supporting accurate imputation.

  Dataset EGAD00001001637

• Identification of genes involved in congenital disorders of glycosylation and 3-methylglutaconic aciduria (2018-03-14)

  Identification of genes involved in congenital disorders of glycosylation and 3-methylglutaconic aciduria. There are more than 100 genes known for congenital disorders of glycosylation and new disorders are discovered each year. WE included patients with a so far unsolved glycosylation disease. The diagnostic group 3-methyglutaconic aciduria is a heterogenous group of disorders mostly caused by abnormal phospholipid synthesis or in association with mitochondrial dysfunction. We included patients with a so far unsolved disease and 3-methylglutaconic aciduria. 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/ . This dataset contains all the data available for this study on 2018-03-14.

  Dataset EGAD00001004038

• Whole exome sequencing for clarification of rare causes of axonal Charcot-Marie-Tooth disease (2017-08-16)

  The project is focused on the axonal forms of Charcot-Marie-Tooth (CMT) disease. We have selected 13 families (7 from Spain and 6 from Czech Republic) that have been indepth clinically assessed and previously tested for mutations in known CMT genes without causal variants characterised. In these patients we expect to discover several CMT2 genes. Thus, we requested for exome sequencing of 45 DNAs:27 exomes in families from Spain and 18 exomes in the families from Czech Republic. 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/ This dataset contains all the data available for this study on 2017-08-16.

  Dataset EGAD00001003565

• Genome Diversity in Africa Project - ancient samples - standard libraries

  Given the central importance of Africa to studies of human origins, genetic diversity and disease susceptibility, large-scale and representative characterisation of genetic diversity in Africa is needed. Analyses of ancient DNA from Africa would complement sequencing of modern African populations and provide unique opportunities to transform our understanding of the pre-history of the region. This approach would greatly refine our understanding of population structure and gene flow in Africa and globally, including genetic signatures of ancient admixture. This low coverage sequencing experiment will allow us to test and refine our pipeline for ancient DNA sequencing. 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/

  Dataset EGAD00001002211

• RNA-seq BAM files from newborn screening dried blood spot samples

  Paired-end RNA-seq BAM files from 21 newborn screening dried blood spot (DBS) samples. These DBS samples were obtained from extremely low gestional age newborns, where 10 of them were affected by a fetal inflammatory response (FIR) before birth, and 11 were unaffected. Total RNA was sequenced using an Illumina NextSeq-500 instrument. The sample preparation protocol included the depletion of rRNA and globin mRNA using the Globin Zero Gold rRNA Removal Kit from Illumina. Libraries were prepared using the NebNext Ultra TM II Directionl RNA LIbrary Prep Kit (New England Biolabs). There is one BAM file per sample and there is an additional BAM file, corresponding to sample BS13, which was downsampled to 1/4 of its original depth (see BS13_README file for details).

  Dataset EGAD00001005009

• Genomic Signatures of Intestinal Metaplasia in Six Countries with Varying Incidence of Stomach Cancer

  Intestinal metaplasia (IM) is a pre-cancerous condition associated with gastric cancer (GC), a deadly malignancy with varying geographic incidence. Performing a genomic analysis of over 1,500 IM samples from six countries, we identified 46 significantly mutated genes. We observed IM driver genes associated with high-risk populations and worse prognosis (ARID1A), members of the KRAS/MAPK signalling pathway (KRAS, BRAF, MAP2K1, MAP3K1, MAP2K4, NF1), and altered mucosal immunity (PIGR).

  Study EGAS50000001056

• Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 403 healthy individuals

  Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 403 healthy individuals. Additional associated phenotype information is available for all individuals included in this study directly from CIBMTR. Data are available under controlled access release upon reasonable request and execution of a data use agreement. Requests should be submitted to CIBMTR at info-request@mcw.edu and include the study reference IB17-04.

  Study EGAS00001006033

• Metabolic and molecular consequences of the TBC1D4 p.Arg684Ter variant in human skeletal muscle

  Skeletal muscle of Inuit homozygous carriers of the common Greenlandic TBC1D4 p.Arg684Ter variant is severely insulin resistant but have normal metabolic responses during exercise

  Dataset EGAD50000000059

• PacBio data: Rapid brain tumor classification from sparse epigenomic data

  This dataset contains 16 samples sequenced in pools on SMRT Cells 25M on a PacBio Revio instrument. One unaligned BAM file per sample is provided.

  Dataset EGAD50000000798

• South African breast cancer GWAS genotype data in VCF format

  South African breast cancer GWAS genotype data for 2823 female African breast cancer cases. The data was generated using the H3Africa Custom microarray and genotyped on the Illumina HiScan instrument. The dataset is in VCF format.

  Dataset EGAD00010002732

• Clinical and ctDNA data for IMpassion031

  Clinical and ctDNA data for IMpassion031, including survival, response, and ctDNA data from baseline through post-surgery time points. 222 samples run on Signatera assay. File type is csv.

  Dataset EGAD50000001420

• DynaTag for efficient profiling of transcription factors in small samples and single cells

  The dataset included Dynatag data for the occupancy of transcription factors and single nuclei RNA-seq data. Corresponding metadata is provided for both experiments.

  Dataset EGAD50000001562

• Meniere Disease Genomic Data Access Committee

  This Data Access Committee is responsible for reviewing and managing data access requests related to genomic variant files from whole exome sequencing of patients diagnosed with Meniere disease. This includes data from both familial and sporadic forms of the disease.

  Dac EGAC50000000708

• pediatric AML genomic sequences

  This dataset contains whole sequencing data from 30 patients with pediatric AML. For each patient, there is one dataset derived from tumor cells and one dataset derived from a matched non-malignant control.

  Dataset EGAD50000001572

• mFAST-SeqS

  mFAST‑SeqS, or modified Fast Aneuploidy Screening Test‑Sequencing System, is a streamlined and cost-effective approach to estimate the fraction of ctDNA in blood samples by detecting genome-wide aneuploidy in cfDNA

  Dataset EGAD50000001670

• RNA sequencing of AML with 3q26 rearrangements

  RNA sequencing of 44 AML cases with diverse 3q26 rearrangements. This dataset is complementary to EGAD00001000726 (which only contains t(3;3)/inv(3)) and to EGAD00001006123.

  Dataset EGAD00001015629

• Single-cell colony targeted DNAseq

  Targeted DNA sequencing was applied to colonies grown from single-cells of patient A.6. The protocol followed is described in https://doi.org/10.1038/s41467-021-21650-1 and the methods of the manuscript

  Dataset EGAD00001010193

• Strand-specific RNA Sequencing of initial and recurrent gliomas

  Four RNA-sequencing datasets from two patients with initial low-grade glioma and copy number alteration at IDH1 upon recurrence. Data is provided as bam files.

  Dataset EGAD00001003764

• Poikiloderma syndrome RNAseq

  We will sequence the RNA of lymphoblast samples, transformed with EBV, which have poikiloderma syndrome with mutations in c16orf57. The aim of the experiment is to characterise RNA structural effects in this disease.

  Dataset EGAD00001000324

• Shank2 Gene knockout/modified WGS data

  Whole genome sequncing data of original/SHANK2 modified/SHANK2 knockout. Note that the SHANK2 knockout sample is a different sample from 1_0441_003. Please refer to other paper for the data.

  Dataset EGAD00001004575

• TCELL PILOT ATAC-SEQ

  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/

  Dataset EGAD00001001317

• Chondromyxoid fibroma

  Chondromxoid fibroma is a benign tumour of bone with unknown underlying pathogenesis. To determine pathognomic genomic event in chondromyxoid fibroma whole genome sequencing will be undertaken to reconstruct rearrangements and find underlying mutations.

  Dataset EGAD00001001063