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• HipSci_RNASEQ_Usher syndrome and congenital eye defects

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Usher syndrome and congenital eye defects.

  Study EGAS00001001997

• Whole genome and whole exome sequencing of epilaptic patients

  In this project, we aim to identify genetic changes that predispose to epilepsy and those that predict the response to various anti-epileptic drugs. We sequenced whole genomes and whole exomes of epileptic individuals with different range of response to anti-epileptic drugs, and their relatives.

  Study EGAS00001002825

• The Role of GPD1L in the Pathogenesis of Brugada Syndrome

  This study performed exome sequencing on a proband with Brugada Syndrome, as well as high-density SNP array data from the proband, affected family members, and unaffected family members. The principal findings of this study were the identification of GPD1L-A280V as the only plausible variant present in a linkage region on chromosome 3, which co-segregated with the Brugada Syndrome phenotype in this family. Exome sequencing data of the proband, as well as SNP array data from the family, are available.

  Study phs003468

• Gut microbiota analysis after 3months probiotic-like bacteria or placebo treatment in subjects with metabolic syndrome

  Background: Probiotic-like bacteria treatment has been described to be associated with gut microbiota modifications. Goal: To decipher if the effects of the tested probiotic-like bacteria are due to the bacteria itself or due to the effects of the bacteria on the gut microbiota. Methodology: In this study, gut microbiota has been analyzed from feces samples of subjects with metabolic syndrome and treated with one of the 2 tested probiotic-like bacteria or with the placebo during 3months.

  Study EGAS00001003585

• HipSci HumanHT 12v4 Expression BeadChip analysis-Rare_BBS

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome.

  Study EGAS00001001276

• HipSci HumanHT 12v4 Expression BeadChip analysis - monogenic diabetes

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with monogenic diabetes.

  Study EGAS00001001277

• HipSci HumanHT 12 Expression BeadChip analysis - Hereditary Spastic Paraplegia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Spastic Paraplegia.

  Study EGAS00001002021

• Mutational profiling of LUAD in young never-smokers

  NSCLC has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients with lung adenocarcinomas (LUADs). Our study provides a detailed mutational portrait of LUADs occurring in young never-smokers and gives insights into the molecular pathogenesis of this NSCLC subgroup

  Study EGAS00001002773

• HipSci HumanHT 12 Expression BeadChip analysis - Hereditary Cerebellar Ataxias

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Cerebellar Ataxias.

  Study EGAS00001002020

• HipSci HumanHT 12 Expression BeadChip analysis - Primary immune deficiency

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Primary immune deficiency.

  Study EGAS00001002027

• 46 patients primary malignant glioma cohort in Chinese population

  We recruited 46 Chinese patients with primary malignant glioma. All the patients were analyzed with whole-exome sequencing (WES) and 27 of them were analyzed with RNA-seq. We compared the molecular features between patients in different WHO grades. We used six-month progression-free survival (PFS6) status to group glioblastoma (GBM) patients to a good and a poor survival compared two groups genomic profiles.

  Study EGAS00001005583

• Genomic and immune signatures predict clinical outcome in newly diagnosed multiple myeloma treated with immunotherapy regimens

  In this study we performed whole genome sequencing on matched tumor-normal CD138+ bone marrow mononuclear cells from 60 patients with newly diagnosed multiple myeloma treated with daratumumab, carfilzomib, lenalidomide, and dexamethasone (NCT03290950-MANHATTAN trial). In addition, we performed 5’-single-cell RNA-sequencing (10X Genomics) coupled with V(D)J sequencing and capture of the surface protein markers (TotalSeq-C, Biolegend) of the CD138- bone marrow mononuclear cells to interrogate the composition of the immune microenvironment at baseline and after eight cycles of induction therapy in 22 patients with newly diagnosed multiple myeloma. Samples were multiplexed using hashtag oligo.

  Dataset EGAD00001011132

• Single cell and whole tissue transcriptomes investigating Barrett's oesophagus

  Data consists of 4,640 RNA-sequencing sample libraries. These libraries were sequenced from four sites of the upper gastro-intestinal tract (Barrett’s oesophagus, proximal normal oesophagus, proximal normal stomach, and duodenum) in two experiments. 4,587 libraries were produced in the first experiment in which whole transcriptomes were isolated single cells dissociated from endoscopic biopsy tissue obtained from the four previously mentioned tissues. The other 53 libraries were produced in the second experiment in which whole transcriptomes were isolated from whole tissue from endoscopic biopsies of the four previously mentioned tissues. The data found here are stored in the raw fastq file format from paired end sequencing.

  Dataset EGAD00001004344

• Whole exome sequencing, RNA sequencing and single-cell RNA sequencing of 4 melanoma patients

  We perfomed whole exome sequencing and RNA sequencing of 4 melanoma patients to assess the detailed biological mechanisms of resistance to immune checkpoint inhibitors.

  Study JGAS000285

• Whole Exome Sequencing of Bipolar cases and matched a cohort from Edinburgh, Scotland, UK

  Whole Exome Sequencing of 1260 Bipolar cases and matched controls performed at the Broad Institute on a cohort from Edinburgh, Scotland, UK. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000623

• The evolutionary landscape of colorectal tumorigenesis

  The genetic events that cause colorectal adenomas to progress to carcinomas remain largely undetermined. Using multi-region genome/exome sequencing of 24 benign and malignant colorectal tumours, we probe the evolutionary fitness landscape occupied by these neoplasms. Unlike carcinomas, advanced adenomas frequently harbour sub-clonal driver mutations, hence lack selective sweeps, and have relatively high genetic heterogeneity. Carcinomas are distinguished from adenomas not by nucleotide-level mutations (drivers or burden), but by widespread aneusomies that are usually clonal and often accrue in a “punctuated” fashion. Adenomas evolve across an undulating fitness landscape, whereas carcinomas occupy a sharper fitness peak, probably owing to stabilising selection.

  Study EGAS00001003066

• Comprehensive genetic analysis of Epstein-Barr virus-associated hematological malignancy

  Comprehensive genetic analyses including whole-exome sequencing, targeted sequencing, and whole-genome sequencing of the human genome and the Epstein-Barr virus (EBV) genome were performed to reveal the molecular pathogenesis of EBV-associated hematological malignancy.

  Dataset EGAD00001004286

• Single nucleus and in situ RNA sequencing reveals cell topographies in the human pancreas

  To investigate the cellular composition of the human pancreas, we performed single-nucleus sequencing from snap frozen biopsies of pancreata from adult, neonatal and diseased (chronic pancreatitis) human donors.

  Dataset EGAD00001006396

• Single-cell profiling reveals mechanisms of response to anti-PD-L1 versus anti-PD-L1 combined with anti-CTLA4 in head and neck squamous cell carcinoma

  Cancer patients often receive a combination of PD-(L)1 and CTLA4 inhibitors, but the mechanisms underlying their concerted actions remain unclear. We conducted a neoadjuvant study in head and neck squamous cell carcinoma (HNSCC) involving anti-PD-L1 monotherapy versus anti-PD-L1/anti-CTLA4 combination. Single-cell profiling of on- versus pre-treatment biopsies confirmed T-cell expansion as response biomarker. We identified a type 1 immune response accompanying T-cell expansion on-treatment across treatment arms, and herein characterized co-localized IgG plasma cell expansion as important contributor. In pre-treatment biopsies, similar features correlated with expansion upon anti-PD-L1, but not anti-PD-L1/anti-CTLA4. By profiling tumor-draining lymph nodes, we found the addition of anti-CTLA4 to trigger activation and subsequent trafficking of CD4+ T-cells via the blood, to become T-helper 1 cells in the tumor. anti-PD-L1/anti-CTLA4 indeed facilitated co-localized expansion of CD4+ and CD8+ T-cells in tumors versus mostly CD8+ T-cells with anti-PD-L1 alone. Hence, we identify complimentary mechanisms underlying anti-PD-L1/anti-CTLA4 therapy in HNSCC.

  Study EGAS50000000037

• Partially methylated domains across multiple cell types

  Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them.

  Study EGAS00001003157

• Dissecting Autoimmune Cellular and Molecular Networks in Vitiligo

  This study consists of suction blister biopsies of primary human skin samples, collected from healthy patients, or patients with vitiligo. Healthy patients had healthy skin sampled. Vitiligo patients had both unaffected (non-lesional) and affected (lesional) skin sampled. The generated data consists of scRNA-seq samples generated following the inDrops method (Klein et al., 2015; PMID: 26000487).

  Study phs002455

• Aligned reads from specific genomic locations derived from Illumina HiSeqX and HiSeq2000 whole genome sequence data

  This dataset includes bam files from 3,001 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion. Additionally, these bam files also contain reads that are aligned to any of 29 pre-determined off target locations where the aligners are known to mis-align reads associated with this repeat expansion. These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner.

  Dataset EGAD00001003513

• GCAT| WGS Imputation Panel V1

  This dataset includes the .hap, .legend and .sample files from the GCAT|Panel (Iberian reference panel), built from 785 samples, after QC, from the 808 WGS GCAT cohort, including 30.3M SNVs, 5M Indels and 89K SVs. This resource has been generated using Shapeit4 and WhatsHap software. Technology used HiSeq 4000, read length 150 bp, inner mate disatance 300 bp.

  Dataset EGAD00010002153

• Exome sequencing of samples taken at multipl time points to monitor therapy response in AML

  As part of our individualized systems medicine program, personalized treatment options are identified and administered to chemorefractory AML patients based on exome sequencing and ex-vivo drug sensitivity and resistance testing data. In this study, we developed this approach further to take into account clonal heterogeneity and analyzed responses of 13 AML patients to chemotherapy and six patients to targeted treatments by using exome and ultra-deep amplicon resequencing. The data submitted includes fastq files from exome sequencing of multiple time-point samples collected from the 13 patients. In this study we identified rare subclonal variants present at diagnosis or later relapse samples and developed a correlation-based method to compare subclonal responses in serial samples across multiple time-points. Significant subclone-specific responses were observed subsequent to chemotherapy and specifically to targeted therapy in five patients.

  Study EGAS00001001948

• single cell RNA-seq of small cell lung cancer circulating tumor cells

  This study investigated the transcriptomic profile of circulating tumor cells from three small cell lung cancer patients. CTCs were enriched from the blood of three SCLC patients using the CTC-iChip followed by magnetic depletion of RBCs. The enriched samples were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system.

  Study EGAS50000001401