12305 results for ""statistically+reactive"+taxa+in+microbial+community"

in 81.58 milliseconds.

• Human Cancer-Targeted Immunity via Transgenic Hematopoietic Stem Cell Progeny

  Analysis of a patient biopsy from the clinical trial (NCT03240861), a first-in-human study of transgenic NY-ESO-1 TCR- T cells and NY-ESO-1 TCR+ sr39tk autologous hematopoietic stem cells tandem therapy for solid tumors after myeloablative conditioning chemotherapy with busulfan and fludarabine. Single-cell RNAseq and single-cell ATACseq analysis from peripheral blood mononuclear cells obtained from subject NYSCT-03.

  Study phs003898

• Whole exome sequencing and RNA sequencing of lineage-switched acute myeloid leukemia with KMT2A-AFF1 rearrangement

  We performed whole exome sequencing and RNA sequencing of lineage-switched acute myeloid leukemia (LS AML) with KMT2A-AFF1 rearrangement to elucidate the feature and potential treatment targets. Notably, LS AML possessed gene expression signatures of monocytic myeloid derived suppressor cells (M-MDSCs). Several known genes related to MDSCs were highly expressed in LS AML, which could be novel treatment targets.

  Study JGAS000631

• Mutational signatures in normal tissues of patients treated with clinical stage G-quadruplex binder CX5461

  Drug induced photoreactions following exposure to UVA have been documented for several therapeutic compound classes, including psoralens and fluoroquinolones. We used deep (~80X) whole genome sequencing to examine the mutagenic spectrum of CX5461, quinolone-derived small molecule, in normal tissues of cancer patients undergoing treatment. We compared the distribution of somatic base substitutions and short indels from skin biopsies taken from non-sun exposed areas pre and post CX5461 exposure of patients. To further characterize the mutational pattern of CX5461 photoreactivity, we compared mutational profiles of human retinal pigment epithelial cells exposed to UVA, CX5461, or a combination of both UV and CX5461.

  Dataset EGAD50000001640

• T cell and Antibody Responses in Rituximab-Treated Lymphoma Patients After SARS-CoV-2 Vaccination

  This dataset contains T cell receptor (TCR) sequencing data from 51 RNA samples, each processed into three independent libraries (tot 153 FASTQ files). Sequencing was performed on an Illumina NextSeq 500 platform using the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles), generating paired-end FASTQ files with dual 10 bp barcodes and 5% PhiX as internal control. Libraries were quantified with the Qubit HS dsDNA kit and assessed for fragment size distribution using the Agilent Tapestation D1000 system before isochoric pooling to 4 nM and sequencing in two independent runs. The resulting dataset enables analysis of TCR β-chain CDR3 sequences for clonal expansion and diversity studies.

  Dataset EGAD50000001714

• Single-nucleus RNA-sequencing data of kidney biopsies from patients with primary FSGS, maladaptive FSGS, proteinuric controls and healthy controls

  This dataset includes FASTQ files of single-nucleus RNA sequencing of cryopreserved kidney biopsy cores from adult patients with diagnosed primary FSGS (n = 9, all nephrotic), maladaptive FSGS (n = 9, not nephrotic), proteinuric controls (PLA2R-positive membranous nephropathy, n = 3), and healthy controls (n = 4). A total of 120,751 high-quality nuclei were identified, including 2,471 podocytes and 1,574 parietal epithelial cells (PECs). In addition to the raw FASTQ files, the dataset includes processed data files from all 25 samples, generated using Seurat in R: barcode files, features, count matrices, and associated metadata. Details regarding the bioinformatics pipeline can be found at https://github.com/lambrechtslab/FSGS_Deleersnijder_et_al

  Dataset EGAD50000001557

• scRNAseq - Notch Signaling Maintains a Progenitor-Like Subclass of Hepatocellular Carcinoma

  To clarify the cellular composition and the mechanism of efficacy following JAG1/NOTCH2 inhibition, we performed single-cell sequencing of LIV78 tumors isolated from control animals or following inhibition of JAG1 or NOTCH2. The results suggest that sensitive tumors consist of heterogeneous populations of cells in distinct transcriptional states and that Notch signals emerge from ligand-receptor co-expressing cells.

  Study EGAS50000000517

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000001043

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000000407

• Data access to Small RNA-Seq of MicroRNA's in Tear EV's of Ushers Syndrome patients

  Via this DAC you can get access to Small RNA-Seq dataset of MicroRNA's in Tear EV's of Ushers Syndrome patients. The study involved genetically confirmed USH1B patients and their healthy relatives, with additional fibroblast samples from Spanish collaborators, to ensure a robust comparison of small non-coding RNAs (sncRNAs). Tear and blood samples were collected using non-invasive methods, and extracellular vesicles (EVs) were isolated from both tears and hiPSC-derived retinal pigment epithelium (RPE) cells. RNA was extracted from these EVs and assessed for quality before preparing libraries using the TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating data for comparative analysis of sncRNA profiles between patients and controls.

  Dac EGAC50000000711

• Canadian prostate cancer samples (CPC-GENE) for PanProstate study

  CPC-GENE has sequenced the genomes of 350 intermediate risk prostate cancers to identify genetic signatures that differ in cancers that responded well to treatment compared with those that did not. CPC-GENE also has sequenced multiple regions of prostate cancer from the same gland to determine if and how the genetic make-up of prostate cancer varies within an individual man’s prostate

  Study EGAS00001003037

• scCRISPRi/a-seq Control and IFN treated iPS derived human GPC/OPCs

  Datasets consists of 2 batches of human glial progenitors (iPS), cells were sequenced as controls and IFN treated. Using the 10Genomics platform from the samples 2 libraries were built forgene expression libraries (scRNA-seq) and captured guides sequencing library (gRNA) on a set of Multiple Sclerosis associated SNPs. Batch one includes KRAB and P300 perturbed cells in 2 rounds sequenced RNA libraries for Ctrl and IFN and 1 round of capture guides for Ctrl and IFN. Batch 2 includes 1 round of both RNA expresison library and captures guides for KRAB and P300 perturbations in Ctrl and IFN treated cells.

  Dataset EGAD50000002053

• Comprehensive molecular profiling for breast cancer patients and high-risk individuals.

  Although germ-line mutations in BRCA1 and BRCA2 gene are responsible for familial breast and ovarian cancer, the detailed mechanism of tumorigenesis is yet unknown. Here, we performed next-generation sequencing to determine the genomic profiles of familial breast cancer tumorigenesis. Target-capture sequencing of fresh-frozen or formalin-fixed-paraffin-embedded (FFPE) samples of breast cancer or normal breast tissue were performed.

  Study JGAS000368

• Molecular investigation of BCC HHI-ICI combination therapy

  We collected skin biopsies and PBMCs of patients with advanced BCC who underwent HHI-ICI combination therapy. We analyzed the skin biopsies with STx and the PBMCs with scRNA-seq to characterize the response of the immune cells, tumor cells and the tumor microenvironment to this therapy. We were interested in immune activation upon HHI and how that synergises with subsequent ICI.

  Study EGAS50000001481

• RNA-seq of STIC lesions and adjacent normal samples

  In this study, we characterize premalignant lesions of the fallopian tube (serous tubal intraepithelial carcinomas) to explore the earliest events of tumorigenesis following mutation of the TP53 tumor suppressor gene. We conduct laser capture microdissection to isolate premalignant cells from adjacent normal cells, and subject isolated tissues to RNA-seq. Our findings reveal the earliest transcriptional changes established during premalignancy within the fallopian tube.

  Study EGAS50000000200

• Whole-exome sequencing performed on a patient with chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia

  We studied the rare case of a patient who underwent transformation of myelodysplastic syndrome to chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia. We used fluorescence-activated cell sorting and whole-exome sequencing to identify driver mutations in the various clones. This allowed us to propose a model of branching clonal evolution with a possible germline predisposition to cancer.

  Study EGAS00001005117

• Familial_Thrombocytosis_germline_exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 3 relatives from a family with multiple affected familial thrombocytosis (FT) patients. Germline DNA from 2-4 patients affected with FT will be used to prepare libraries and sequenced in one lane of HiSeq sequencing, mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000088

• Genetic_screening__of_GPI_anchor_protein_synthesis__

  This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. 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/

  Study EGAS00001001256

• Whole genome landscape of 25 metastatic cutaneous squamous cell carcinoma cSCC patients

  whole genome sequencing on lymph node metastases and blood DNA from 25 cSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic cSCC. This study contains the majority of 15 samples which are previously submitted in EGAC00001001100.

  Study EGAS00001006378

• Myelodysplastic_Syndrome_Exome_Sequnecing

  Cancer is driven by mutation. Illumina GA massively parallel sequencing technology will be applied to Agilent exome hybridisation capture libraries and total genomic paired-end libraries. Bespoke algorithms are being developed to identify the somatically acquired structural variants, point mutations, insertions and deletions in these samples. This project will give unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with Myelodysplastic Syndrome development.

  Study EGAS00001000089

• Congenital_anosmia_2

  Congenital anosmias can be complete (the lack of a sense of smell) or specific (the inability to detect specific smells). Here we obtained genomic DNA from families with multiple individuals with anosmia, suggesting they are congenital. These include those inherited in a manner consistent with dominant and recessive alleles. We have sequenced the exomes of both affected and unaffected family members on the Illumina platform.

  Study EGAS00001001429

• Transcriptomes_of_human_lymphocytes

  In this study we will compare the single cell transcriptomes of immune cells from asthmatics responding to steroids, those refractory to steroids, and a control population.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/

  Study EGAS00001001755

• APCDR AGV Project: WGS of South African Zulu

  The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. As part of the AGVP we sequenced the genome of 100 unrelated Zulu from Durban area to about 4x depth.

  Study EGAS00001000286

• ET_Exome

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Essential Thrombocythemia Myeloproliferative Disease samples and matched normal DNA from the same patients. Samples will be multiplexed in one lane of Illumina HiSeq. Sequencing to a coverage of at least 30x will be performed and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000102

• De_novo_mutations_in_cell_free_foetal_DNA__cffDNA_

  This project is to develop and validate a method to detect de novo mutations in a foetal genome through deep sequencing of cell-free DNA from the plasma of pregnant women.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/

  Study EGAS00001000322

• APCDR AGV Project: WGS of an Ugandan population

  The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. As part of the AGVP we sequenced the genome of 100 unrelated Baganda from rural Uganda to about 4x depth.

  Study EGAS00001000363

• Whole-exome sequencing of extranodal NK/T cell lymphoma

  Extranodal NK/T cell lymphoma (ENKTCL) is an aggressive Epstein-Barr virus-associated T/NK neoplasm that predominantly affects Asians. To explore the causative somatic events, we conducted a comprehensive genetic analysis of 19 ENKTCL patients including whole-exome sequencing (N = 16). Commonly deregulated gene pathways in ENKTCL included epigenetic modifiers followed by human leukocyte antigen (HLA) and related genes and JAK-STAT pathway.

  Study EGAS00001004357

• Analysis of transcriptomic profiles from affected and recovered muscle biopsies from children with reversible infantile respiratory chain deficiency.

  All patients carry mitochondrial mutation m.14674T>C but not must also carry mutations in related genes such as TRMU and EARS2. Analysis compares muslce biopsies of affected patients to controls, a patient after recovery to themselves during the the disease phase, and compared patients with additional EARS2 mutations to patients without pathogenic EARS2 mutations.

  Study EGAS00001004647

• Whole transcriptome and exome sequencing of childhood ALL

  Gene fusion is a major class of genomic abnormalities in childhood acute lymphoblastic leukemia (ALL) and sentinel chromosomal rearrangements involving EP300 and CREBBP may cause global epigenetic deregulation during leukemogenesis with potentials for therapeutic targeting. This dataset includes whole transcriptome sequencing of 231 children with acute lymphoblastic leukemia from a Singapore-Malaysia frontline clinical treatment protocol.

  Study EGAS00001001858

• Cylindromas_sun_protected_and_exposed

  The project aims to look at mutational signatures in a rare inherited skin tumour syndrome called CYLD cutaneous syndrome. These patients develop multiple skin tumours that are seen at sun exposed and sun protected sites. We plan to carry out WGS on carefully curated tumours from such patients. We then plan to analyse this data for mutational signatures, comparing this between sun exposed and sun protected sites.

  Study EGAS00001002521

• Misoprostol-induced high fever GWAS study

  Genome-wide association (GWAS) meta-analysis study of misoprostol-induced fever was conducted on two South American cohorts (Argentina and Ecuador). DNA was collected from blood of women who were screened for postpartum haemorrhage (PPH) and administered misoprostol were included in the study. Genotypes were acquired from the Global Screening Array (Illumina). Meta-analysis of these cohorts was completed using METAL software.

  Study EGAS00001005455

• Exome sequencing of paired primary tumor and metastatic breast cancer

  Prognosis evaluation of advanced breast cancer and therapeutic strategy are mostly based on clinical features of advanced disease and molecular profiling of the primary tumor. Very few studies have evaluated the impact of a prospective documentation of metastatic subtyping. The genomic landscape of metastatic breast cancer has mostly been described in very advanced, pretreated disease, limiting its transferability to clinical use.

  Study EGAS00001004578

• NIHR BioResource Common Disease Patients 2016

  NIHR BioResource Common Disease Patients 2016. The dataset includes 13489 samples from blood donors, they were not screened for any particular disease, and therefore they are representative of the general population. Genomic data includes 845487 snps collected using the UK BioBank V1 Affymetrix array. Phenotypic data includes gender, age, ethnicity and disease. According to our internal quality check there are 81 duplicates in this dataset.

  Study EGAS00001004870

• SDH_deficient_renal_tumours___WGS_

  Succinate dehydrogenase (SDH) deficient renal cancers are a rare and understudied subtype of renal cancer. As such they represent an unmet need in kidney cancer research. Here, we seek to describe the genomics and transcriptomics of SDH deficient renal cancers by sequencing five such tumours. We document their mutational burden, define driver mutations, demonstrate typical patterns of structural variants, and estimate the cell of origin and cellular composition.

  Study EGAS00001004102

• Benchmarking dataset for ProSolo, a probabilistic single nucleotide caller for single cell DNA sequencing data

  This is the dataset used in the benchmarking of ProSolo, a new probabilistic single nucleotide variant caller for single cell DNA sequencing data that provides control over the false discovery rate of different single cell events at genomic sites (e.g. alternative allele presence or allele dropout). It provides the whole exome sequencing data used in assessing ProSolo's performance that is not available elsewhere, namely bulk whole exome sequencing data of a patient with a constitutional mismatch repair defect (MSH6-) and their parents and siblings, a bulk whole exome sample of granulocytes from that patient and 5 single granulocytes whole exome sequenced after whole genome amplification.

  Dataset EGAD00001005929

• Gene expression profiles of single disseminated breast cancer cells

  A set of 56 EpCAM-positive cells derived from bone marrow aspirates of breast cancer patients or patients without a cancererous disease (30 cells from 21 M0-stage and 11 cells from five M1-stage breast cancer patients, 15 cells from seven non-cancer patients serving as controls). EpCAM-positive cells from breast cancer patients were considered disseminated tumor cells as they harbored copy number alterations and showed high expression of the epithelial marker EpCAM and the mammary luminal progenitor marker KIT in comparison to EpCAM-positive bone marrow cells from non-cancer patients. Paired-end RNA-Sequencing of the samples was performed on Illumina NovaSeq6000, raw data are provided in the Fastq format.

  Dataset EGAD00001006359

• T-VEC CBCL scRNA

  We are presenting raw and processed data of our study where we analyze fine-needle aspirate (FNA) samples of primary cutaneous B-cell lymphoma patients undergoing oncolytic virotherapy (https://clinicaltrials.gov/ct2/show/NCT03458117). We are uploading single cell RNA-sequencing and immune repertoire profiling data of 29 FNA samples from four pCBCL patients. The four patients have three different subtypes of primary cutaneous B-cell lymphoma: pCDLBCL-LT, pCFCL and pCMZL. The samples are taken at different time points following T-VEC injection (from baseline up to 91 days after injection). We are uploading the sequences in BAM format and the outputs of the cellranger pipeline (count matrices and filtered VDJ contigs) in CSV format.

  Dataset EGAD00001006829

• sWGS on cfDNA and matching tumor DNA in pediatric cancer

  This dataset contains shallow whole genome sequencing data from paired cfDNA - tumor DNA samples of various pediatric cancer entities (total 215 samples). Files are provided in fastq format. Samples were sequenced on an Ion Proton sequencer (Thermo Fisher Scientific) or a Hiseq3000 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Dataset EGAD00001007508

• Genomic characterisation of SDH deficient renal cell carcinoma - RNA

  SDH deficient renal cell carcinomas are a rare and recently defined subtype of kidney cancer, often associated with an inherited mutation in one of the SDH gene subunits. This dataset sought to understand the genomic events that underpin tumour formation, from putative cell of origin, characterisation of the tumour microenvironment, to the genomic evolution of these rare tumours. We performed whole genome and RNA sequencing of 4 patients with SDH deficient renal cell carcinomas, including one patient who had an additional paraganglioma. An addition patient in this cohort had the initial diagnosis revised to a clear cell renal cell carcinoma.

  Dataset EGAD00001008470

• Unravelling the contribution of HIF pathway and its therapeutic potential in human AML leukemia-initiating cells

  We performed single cell RNA sequencing (scRNA-seq) from bone marrow on 11 pediatric (0-14 years-old) and adolescent and young adult (AYA) (15-39 years-old) de novo AML samples (Dx) (4 inv(16), 3 t(8;21) and 4 rMLL). In addition, for some patients also relapse sample was sequenced (2 inv(16), 2 t(8;21) and 3 rMLL). Cells were sorted into CD34+/CD38- and CD34-/CD38+ and sequenced separately.

  Dataset EGAD00001008514

• Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild type primary glioblastoma

  We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

  Dataset EGAD00001010156

• Longitudinal RNA-seq datasets from patients after abdominal surgery

  This dataset consists of RNA-seq data of 126 whole-blood samples derived from patients after abdominal surgery. Total-RNA collected preoperatively and at 3-time points postoperatively (2-6, 24 and 48hrs) were analysed using RNA-sequencing. RNA was collected in PAXGene (Qiagen) tubes and extracted using the PAXGene RNA extraction kit, with a DNase step to remove contaminating DNA. Globin and ribosomal RNA were removed via a Ribo-zero kit (Illumina) and library preparation was carried out using the TruSeq Stranded Total RNA Library Prep Kit (Illumina). Next generation sequencing was performed on the NovaSeq sequencing platform (Illumina) at the Wellcome Centre for Human Genetics (WCHG) in Oxford.

  Dataset EGAD00001011102

• Reconstruction of complex rearrangement patterns causing the initiation of clear cell renal cell carcinoma.

  The genomic hallmark of clear cell renal cell carcinoma is the loss of the short arm of chromosome three. This appears to be the earliest genomic event in the formation of these cancers. Often chromosome 3 is lost at the same time as part of chromosome 5 is duplicated via an unbalanced translocation, often with features consistent with focal chromothripsis. In this study, we sought to reconstruct the chromothriptic event that underlies the initiation of kidney cancer. We used long read sequencing (promethION, Oxford Nanopore Technologies) of patient tumour-derived DNA to elucidate how a single cell division error can generate cancer genome complexity.

  Dataset EGAD00001005495

• A standardised framework for robust fragmentomic feature extraction from cell-free DNA sequencing data

  Fragmentomic features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. However, a lack of systematic evaluation of biases in feature quantification has hindered the adoption of such applications. We compared features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes, and validated them in 1,182 plasma samples from published studies. Our results clarify the variations resulting from library preparation and feature quantification methods. We designed the Trim Align Pipeline and the cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualisation, aiming to standardise multimodal feature engineering and integration for machine learning.

  Dataset EGAD00001015535

• Whole Genome, RNA, and ChIP Sequencing of matched brain tumor-normal pairs (ICGC)

  Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009);duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA.Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa.This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads):GBM103 macroH2A1: 17x H3K36me3: 20xMB59 macroH2A1: 11x H3K36me3: 11x

  Dataset EGAD00001000664

• European Prospective Investigation into Cancer and Nutrition BAMs

  516 DNA samples were collected from individuals upon enrollment into the European Prospective Investigation into Cancer and Nutrition study between 1993 and 1998 across 17 different centers. 126bp pair-end reads sequencing data from the Illumina platform were converted to fastq format, the 2bp molecular barcode information at each read of the pair was trimmed and was written in the reads name. The Thymine nucleotide required for ligation was removed from the sequences. Burroughs-Wheeler Aligner (BWA-mem) was used for alignment of the processed fastq files to the reference hg19 genome, following indel-re-alignment using GATK. An in-house algorithm was written to collapse read families that share the same molecular barcode sequence

  Dataset EGAD00001003583

• DNA repair in BLM deficient hiPSCs

  We are aiming to investigate repair of a double strand break (DSB) within the genome in the presence and absence of the BLOOM protein. Zinc Finger Nucleases introduce DSBs at specified loci within the genome. Using sequencing we will assess the size of the deletion following repair. Protocol 1. Transfect normal and BLOOM deficient human iPS cells with ZFNs, using AMXA 2. Harvest cells after 5 days 3. Perform column extraction of DNA 4. PCR-amplify the ZFN region 5. Sequence and analyse repair of the DSB 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 EGAD00001000819

• GoT2D: Genetics of Type 2 Diabetes, a study of the the genetic architecture of type 2 diabetes

  The GoT2D study includes ~2800 samples, half T2D cases and half T2D controls, of Northern European ancestry sequenced over 3 three technologies: deep whole exome sequencing, low-pass (4x) whole genome sequencing, and OMNI 2.5M genotyping. Samples were ascertained to be phenotypically "extreme" (e.g. leaner, younger cases and older, more obese controls). Genotypes (SNVs, INDELs, and SVs) were called separately for each technology and then integrated via genotype refinement into a single phased reference panel; samples and variants were then excluded based on QC procedures described in Fuchsberger et al. Please note that 2 of the samples in the GoT2D vcf do not have phenotype data.

  Dataset EGAD00001002247

• Tumor-derived cell lines as pharmacogenomic models to predict therapeutic vulnerabilities in hepatocellular carcinoma

  Hepatocellular carcinoma (HCC) is a heterogeneous aggressive malignancy with low efficacy of current therapies at advanced stages. We integrated molecular and pharmacological profiling of a large panel of liver cancer cell lines (LCCL) to assess their clinical relevance as HCC preclinical models and identify new effective therapies and biomarkers of response. Here, we performed multi-omic analysis including whole-exome, RNA and microRNA sequencing in a series 34 LCCL. Molecular profiles of LCCL and primary HCC were compared and we searched for molecular features associated with drug response. Our panel of LCCL faithfully recapitulated the most aggressive molecular “proliferation class” of HCC.

  Dataset EGAD00001004938

• Exome sequencing of a Novel Primary T Cell Immunodeficiency Kindred (2019-08-19)

  Primary T cell immunodeficiency disorders have a heterogeneous genetic basis. This study will focus on one case characterised by severe T cell lymphopenia in the index case. We aim to sequence the complete exomes of this individual, her three unaffected siblings and parents in an effort to identify the causative genetic mutation responsible for this disorder. We will perform exome capture using Agilent SureSelect system, followed by sequencing on the HiSeq platform. Our study has the potential to uncover genes important for T cell development and novel therapeutic strategies to treat T cell immunodeficiencies. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005263

• Genomic Evolution of Breast Cancer Metastasis and Relapse

  Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling.

  Dataset EGAD00001002698