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• Aligned reads in the 2kb region centered on the HTT repeat expansion from Illumina HiSeqX and HiSeq2000 whole genome sequence data

  This dataset includes bam files from 58 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the HTT repeat expansion. These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and aligned using bwa. Twelve of the samples used TruSeq Nano library preparation and 46 samples used TruSeq DNA PCR-free sample preparation.

  Dataset EGAD00001003512

• Variant Calling used in ABB project

  This dataset has two Variants Files in VCF format used in ABB project (https://github.com/Francesc-Muyas/ABB). One has the variants found in a Rare Variant Association Study performed in CLL patients. This has 1217 samples represented. The other variant file has 209 SNPs predicted in 10 samples by GATK HaplotypeCaller and selected for Sanger Sequencing Validation. Raw reads were aligned against the Human Reference genome (Hg19) with BWA mem and variants were obtained using GATK HaplotypeCaller.

  Dataset EGAD00001004132

• CD49f single-cell methylomes

  74 CD49f single-cell methylomes are from cord blood of donor1, and 84 from cord blood of donor2. Samples from donor1 have one sequencing lane, and samples from donor2 have five sequencing lanes. This dataset was generated using Post-Bisulfite Adapter Ligation (PBAL), a bisulfite based whole genome protocol. In total this dataset consists of 494 runs.

  Dataset EGAD00001003913

• Contribution of Retrotransposition to Developmental Disorders

  Variants and WGS data for Gardner et al. 2018 (biorxiv 471375). One VCF each for Alu, L1, and SVA. Flat text file and WGS for processed pseudogenes.

  Dataset EGAD00001004586

• Whole genome sequencing of a Grem1 mutant human tumour

  The BMP antagonist Grem1 has been shown to be associated with a rare human polyposis syndrome (HMPS). We have shown that there is a 40KB duplication on chrom 15 found in some patients with HMPS. Traditional serrated adenomas (rare sporadic polyps) share some morphological features with HMPS polyps and it has long been hypothesised that they are the sporadic version of HMPS polyps. We have obtained of one of these lesions and in this project we aim to characterise this tumour.

  Dataset EGAD00001002182

• Indonesian RNA-seq dataset

  This dataset contains 4 batches of Indonesian RNA-seq data from Mentawai, New Guinea and Sumba islands. One RNA-seq batch was prepared without Globin depletion, and three batches were Globin depleted using the Illumina Globin-Zero Gold Kit. There are 179 runs in total, including 119 unique samples. Dataset includes multiple batch control samples.

  Dataset EGAD00001005053

• Whole exome sequencing data for Molecular Characterization of ETMRs

  This dataset contains exome sequencing data from 21 samples. Sequencing of samples using whole-exome sequencing was per- formed by creating libraries using the IlluminaTruSeq exome enrich- ment kit following the manufacturer’s instructions after size selection. Size selection was performed by fractionation using a Covaris ultra- sonicator and subsequent selection was performed using a 1.5% gel Pippin Prep cassette (Sage Science). One lane per sample has been sequenced resulting in 42 Fastq files (paired end).

  Dataset EGAD00001006210

• Somatic mutations reveal embryonic genetic bottlenecks generating placental mosaicism

  The human placenta harbours chromosomal aberrations that are absent from the fetus in one to two percent of pregnancies. This confined mosaicism suggests that embryonic genetic bottlenecks exist, which phylogenetically segregate placental tissue. Here, we studied the somatic genetic landscape of human placentas by whole genome sequencing of 86 placental biopsies and of 106 microdissections.

  Dataset EGAD00001006337

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): A Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study

  UC-GENOME is a real-world cohort of patients with metastatic urothelial carcinoma (UC). The study consisted of two co-equal aims: 1) to provide targeted DNA sequencing for clinical decision making at no cost to patients; and 2) to create a resource for collaborative translational science including a clinically annotated biobank. The submitted data represents the foundational analysis of 218 patients accrued at 7 academic medical centers. The analysis includes 176 patients with both targeted DNA sequencing and RNA sequencing. The genomic data was combined with clinical variables to model response to chemotherapy and immune checkpoint inhibitors (ICI). Due to additional sharing restrictions, data from one site can be found in phs003094.

  Study phs003066

• Homozygous Duplication Identified by Whole Genome Sequencing Causes LRBA Deficiency

  In more than one third of primary immunodeficiency (PID) patients, extensive genetic analysis including whole exome sequencing (WES) fails to identify the genetic defect. Whole genome sequencing (WGS) is able to detect variants missed by other genomics platforms, enabling the molecular diagnosis of otherwise unresolved cases. Here, we report two siblings, offspring of consanguineous parents, who experienced similar severe events encompassing early onset of colitis, lymphoproliferation and hypogammaglobulinemia, typical of lipopolysaccharide (LPS)-responsive and beige-like anchor protein (LRBA) or cytotoxic T-lymphocyte-associated protein 4 (CTLA4) deficiencies. WGS of these patients detected a 12.3 kb homozygous tandem duplication that was absent in control cohorts and is predicted to disrupt the reading frame of the LRBA gene.

  Study phs002557