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• Small molecule inhibitors of LOXL synergize with 5-AZA to restore erythropoiesis in myeloid neoplasms

  Objectives: Bone marrow (BM) stroma and microenvironmental factors in the BM milieu of myeloid neoplasms are increasingly being recognized as novel perspective therapeutic targets. Lysyl oxidases (LOX/LOXL) are crucial enzymes that cross-link collagen and contribute to the deposition of aberrant stiff extracellular matrix (ECM) in the BM of patients with myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN). Here, we studied whether inhibition of LOX/LOXL enzymes produced by BM-derived MSCs favors the differentiation of MDS/MPN hematopoietic stem cell and progenitor cells (HPSCs) and enhances the effects of 5-azacytidine (5-AZA). Methods: Primary co-cultures of MSCs and HPSCs were established from n=31 MDS/MPN patients and treated with the pan-LOX/LOXL inhibitor PXS-5505, 5-AZA or the combination of both for 4 days. At the end of co-culture, HSPC differentiation was assessed by CFU assays and flow cytometry. In some of the experiments, MSCs monolayers were pre-treated or not with PXS-5505 for 6 days and decellularized using 20 mM ammonia. Subsequently, autologous HSPCs were cultured on ECM matrices in the presence of 5-AZA or PXS-5505 + 5-AZA combination with or without inhibitors of integrin signaling such as blebbistatin, Y-27632 and αvβ3-integrin blocking antibodies. Patient-derived xenografts (PDX) were established in NSG mice based on intrafemoral co-injection of HSPCs and autologous MSCs. PDX were treated with 3 cycles of 5-AZA (75 mg/m2), PXS-5505 (30 mg/kg on alternate days for the duration of 5-AZA treatment) or combination of both. Results: MSCs of MDS and MPN patients displayed significant overexpression of LOX/LOXL transcripts as compared to healthy age-matched controls. Remarkably, LOX/LOXL inhibition in MSCs/HSPCs co-cultures increased erythroid differentiation of patient HSPCs that had suboptimal or no response to 5-AZA alone. From a total of n=31 advanced stage MDS/MPN patients, n=11 (35.5%) responded to the combination treatment, which was evidenced by a significant increase of CD235a+CD45- erythroid cell production compared to 5-AZA/PXS/untreated arms (p<0.05). Of note, combination treatment with 5-AZA + PXS-5505 facilitated differentiation of CD235+ erythroid progenitors from HSPCs sub-clones with low mutational VAFs. The presence of MSCs was necessary for the effects of the combination treatment and required direct cell contacts between MSCs and HSPCs. Moreover, PXS-5505-mediated alterations of the ECM composition alone were sufficient to induce erythroid differentiation. Inhibition of integrin-mediated signaling using blebbistatin, Y-27632 and αvβ3-integrin antibodies completely abrogated the effects of PXS-5505 induced erythroid differentiation. In vivo, the combination of PXS-5505 + 5-AZA favored erythroid differentiation of HSPCs and confirmed the in-vitro results. The combination treatment of 5-AZA + PXS-5505 induced the greatest reduction of disease burden as assessed by decrease of spleen indexes, total engraftment rates, BM fibrosis and mutational VAF profiles. Conclusions: The combination of 5-AZA + LOX/LOXL inhibitor PXS-5505 in MDS and MPN synergistically restores erythropoietic differentiation of primary HSPCs. The effect is dependent of contact interaction between HSPCs and niche components, such as MSCs and MSCs-derived ECM. Our data propose a strong rationale for a BM niche targeted combination treatment with 5-AZA + PXS-5505 in transfusion dependent MDS and MPN, which will be assessed in forthcoming clinical trials.

  Study EGAS00001006174

• PAS Pedigrees: Identification of novel genetic variants contributing to cardiovascular disease in pedigrees with premature atherosclerosis.

  PAS Pedigrees: Identification of novel genetic variants contributing to cardiovascular disease in pedigrees with premature atherosclerosis.

  Dataset EGAD00001000017

• Recurrent Somatic Mutations in CLL

  Recurrent Somatic Mutations in CLL

  Dataset EGAD00001000023

• Recurrent Somatic Mutations in CLL

  Recurrent Somatic Mutations in CLL

  Dataset EGAD00001000044

• CMMRD tumors sequencing data

  Whole exome sequencing data from the tumors of individuals with constitutional mismatch repair deficiency. These are 16 tumors from the bigger study of 41 tumors in total (from 17 individuals in total).

  Dataset EGAD50000000113

• UNC Tumor Donation Program Set 2021

  The goal of this study is to study gene expression patterns in primary, metastatic tumors, and normal tissues.

  Study phs002429

• Genomic characterization of 9p- syndrome

  We characterized the precise genomic breakpoints of the complex structural variant associated with 9p- syndrome in one individual.

  Study phs002054

• Targeted sequencing of genomics regions of interest in depression and obesity

  Data corresponding to the fastq of the 654 individuals included in the study.

  Dataset EGAD50000000476

• RNASeq of Calcoco2 in beta and fat cell lines

  Investigation of the function of Calcoco2 by knocking it down in beta and fat cell lines.

  Dataset EGAD00001008654

• piRNA analysis in human testis

  The dataset comprises RNAseq data of human testiculr tisue of fertile men with full spermatogenesis nd infertile men with biallelic variants in genes of the piRNA pathway.

  Dataset EGAD50000000585

• WTCCC2 Schizophrenia study

  A WTCCC2 project genome-wide case-control association study for schizophrenia (SP) in individuals from Ireland.

  Study EGAS00000000118

• WTCCC2 Ischaemic Stroke study

  Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke

  Study EGAS00000000103

• H3K27ac CUT&Tag in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives

  H3K27ac CUT&Tag performed in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives

  Dataset EGAD50000000711

• N2M2 methylation array data

  Methylation profiling of 228 samples, using the approach described in "Molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation (N2M2/NOA-20 phase I/IIa umbrella trial)"

  Dataset EGAD00010002747

• WES in Angolan and Cape Verdean triple-negative breast cancer samples

  WES (using the SureSelect Human All Exon V5 + UTRs target enrichment kit) in 23 Angolan and 7 Cape Verdean triple-negative breast cancer samples

  Dataset EGAD50000001482

• Targeted Capture DNA Sequencing

  We performed targeted capture DNA sequencing for 29 genes in extranodal NK/T-cell lymphoma, nasal type (n=67).

  Study JGAS000548

• DAC for lymphoma IFZ Essen

  This DAC is set in place to handle acess to data on lymphomas and immune cells submitted by scientists from the Institute of Cell Biology (Cancer Research) at the University of Duisburg-Essen in Essen, Germany.

  Dac EGAC50000000521

• Myeloproliferative_Neoplasms__MPN__Exome_Validation_Study

  Experiments using targeted pulldown methods will be sequenced to validate findings in the exomes of patients with Myeloproliferative Neoplasms (MPN).

  Study EGAS00001000404

• CMF_RNA_sequencing

  RNA sequencing will be undertaken to reconstruct rearrangements at level of transcription to determine pathogenomic genomic events in chondromyxoid fibroma

  Study EGAS00001000470

• Exome sequencing of hyperplastic polyposis patients

  In this project we are sequencing the exomes of patients with hyperplastic polyposis, and tumours from these patients.

  Study EGAS00001000040

• Functional dissection of inherited non-coding variation influencing multiple myeloma risk

  The project aimed at identification of genotype dependent chromatin accessibility in MM patients.

  Study EGAS00001005394

• Analyses of IACS-010759 treatment resistance on breast cancer bone metastases

  Identification of biological mecanisms involved in resistance of breast cancer bone metastases to IACS treatment.

  Study EGAS00001006429

• Bam files for the whole exome sequencing from the study on Spatial homogeneity in pediatric brain tumors.

  Bam files for the whole exome sequencing from the study on Spatial homogeneity in pediatric brain tumors.

  Dataset EGAD00001001055

• Case Report of a Leukemic Patient with Invasive Mucormycosis

  Whole exome sequencing of germline DNA was performed and subsequent polymorphisms in genes known and putatively involved in the innate immune response to fungi were identified

  Dataset EGAD00001001692

• Whole genome low pass sequencing data used in HF-GBM-Tumor-Neurosphere-Xenograft

  This data set consists of 82 whole genome low pass sequencing bams used in HF-GBM-Tumor-Neurosphere-Xenograft

  Dataset EGAD00001002245

• Rare coding variants in lupus risk genes

  Set of 133 bam files from patients affected with Lupus. BAM alignments for exonic variants present in 76 Lupus-related genes. VCF file describing the variants.

  Dataset EGAD00001004859

• Somatic evolution in the non-neoplastic IBD affected colon

  Whole genome and whole exome sequencing data supporting the manuscript 'Somatic evolution in the non-neoplastic IBD affected colon' by Sigurgeir Olafsson et al.

  Dataset EGAD00001006061

• Initial WGS of plasma cell neoplasms in fire fighters exposed to the WTC attack

  Initial WGS of plasma cell neoplasms in fire fighters exposed to the WTC attack

  Dataset EGAD00001006896

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  Dataset EGAD00001015386

• Assessing mitochondrial bioenergetics in coronary artery disease: A translational left ventricular tissue study in humans (The AMBITION study).

  Single nuclei transcriptomic data from the AMBITION study.

  Dataset EGAD00001011078

• Center for Common Disease Genomics [CCDG] - Inflammatory Bowel Disease (IBD) - Global Microbiome Conservancy Host Exomes

  The human body is a complex ecosystem, hosting tens of billions of bacteria, primarily in the gut. This community, known as the 'gut microbiome', is vital to human health, affecting functions ranging from metabolism, immunity, and development, to behavior. Conversely, reduced microbiome diversity and other imbalances of the gut community (dysbiosis) are associated with many diseases of the industrialized world, such as metabolic syndrome, asthma, and inflammatory bowel diseases among others. Microbiome-based interventions thus hold the potential to revolutionize our understanding of, and therapeutic approaches to, many aspects of human health and disease. Despite many advances, current understanding of the human microbiome is largely limited to majority ethnic groups in industrialized nations, and does not reflect the full diversity of human commensal microbiota. In addition to the scientific ramifications of minority underrepresentation, there are significant translational and ethical implications as well: First, failing to capture the full diversity of healthy human microbiota may limit our ability to understand and generate effective therapeutics for many microbiome-associated diseases. Second, underrepresented groups are less likely to benefit from microbiome-based medical advances tailored to well-studied populations, propagating healthcare inequities. The window of opportunity to characterize human microbiome diversity is closing rapidly. Human gut microbial diversity is diminishing around the globe, due to the spread of Westernized diets and lifestyles, which are associated with reduced microbiome biodiversity. The Global Microbiome Conservancy (GMbC) is a non-profit collaboration between scientists and communities around the world that aims to 1) preserve the full biodiversity of the human gut microbiome, 2) characterize its evolution across populations and host lifestyles and 3) investigate its interactions with the human host. We are collecting gut microbiome and human DNA samples from diverse populations around the world, from isolated groups to urbanized populations, to culture and study this essential biodiversity and to preserve it in a living "seed bank" as a long-term safeguard against future extinctions. The National Human Genome Research Institute (NHGRI) has funded a collaborative large-scale genome sequencing effort to comprehensively identify rare risk and protective variants contributing to multiple common disease phenotypes. Called the Centers for Common Disease Genomics (CCDG), this initiative will explore a range of diseases with the ultimate goal of: Undertaking variant discovery for enough different examples of disease architectures and study designs to better understand the general principles of the genomic architecture underlying common, complex inherited diseases. Understanding how best to design rare variant studies for common disease. Developing resources, informatics tools, and innovative approaches and technologies for multiple disease research communities and the wider biomedical research community. The initial focus of the CCDGs will be in cardiovascular disease (early-onset coronary artery disease, atrial fibrillation, hemorrhagic stroke), neuropsychiatric disease (epilepsy, autism), and autoimmune/inflammatory disease (type 1 diabetes, inflammatory bowel disease). The Broad Institute is one of four selected CCDG project centers. Both exome and genotyping information of GMbC participants will help understanding how recruited human populations are structured and genetically related. This human genetic structure will be analyzed in light of gut microbiome compositional and genomic differences to illuminate associations between specific microbiome traits and human groups and the evolutionary processes involved in the co-evolution of human hosts and their gut microbiome. It will also provide variant information for critical genes shaping the composition of microbiomes, such as genes involved in innate and adaptive immunity (e.g. antimicrobial peptides) or in the regulation of the immune response (e.g. Nod2). Association studies between specific variants in these genes and microbiome features will be performed, which will then be validated with in vitro and in vivo experiments. Human data from GMbC cohorts will also increase the genetic diversity of human populations, providing additional variant information for many susceptible loci that were found to be associated with Crohn's disease and ulcerative colitis. The whole genome sequencing data generated is comprised of samples from diverse and indigenous populations. Raw sequencing data, metadata, vcf and phenotype data at the individual level for a subset of the cohort's samples are available at https://anvilproject.org/data. For questions about availability, contact help@lists.anvilproject.org. Microbiome data for the samples sequenced in this study can be found in phs002235 Global Microbiome Conservancy Sequence Data.

  Study phs002205

• Sickle Cell Disease Implementation Consortium Registry (SCDIC Registry-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To understand the barriers to care and other factors related to reduced healthcare utilization after the transition from pediatric to adult SCD care which may contribute to increased morbidity and mortality.Background: Fifty years ago, it was rare for individuals with SCD to live beyond childhood. Advances in care delivery and treatment have more than doubled the life expectancy of individuals with sickle cell disease (SCD) since 1972. Beginning in the 1970s, measures such as newborn screening, prophylactic administration of penicillin, and immunization against bacterial infections decreased complications and morbidity, increasing the length and quality of life of children with SCD. Blood transfusions are currently the only proven way to prevent some of the major complications of SCD, especially recurrent stroke. They are also used frequently to help manage some of the acute complications of SCD. More recently, the use of hydroxyurea (HU) as a therapeutic agent to increase fetal hemoglobin has been shown to further reduce the debilitating symptoms of and improve survival in SCD. L-glutamine and crizanlizumab are additional treatments to reduce pain crises and voxelotor is approved to lower the risk of anemia and improve blood flow. In the absence of a widely accessible cure, treatment for SCD is usually aimed at avoiding crises, relieving symptoms, and preventing complications. Many of the advances in treatment have not translated into an increase in longevity or quality of life for adolescents and adults because of disparities in access to routine primary health care.Individuals with SCD experience a markedly increased mortality beginning in the second decade of life. The third and later decades of life are frequently associated with severe chronic pain progressive organ damage and frequent hospitalizations. The provision of evidence-based and expert opinion-based care in SCD is complicated by the difficulties that many patients experience in obtaining access to the health care system and in receiving long-term care from knowledgeable providers. A registry of 2,400 people with SCD was established to provide a rich resource to study the natural history of SCD and to understand barriers to care during the transition from pediatric to adult care. Participants: 2,438 participants with a confirmed diagnosis of SCD were enrolled into the registry over an 18-month period. At the time of enrollment, all participants were 15-45 years of age, English speaking, and without a bone marrow transplant.Design: The SCDIC Registry is a longitudinal observational cohort study. At enrollment, data collection included a medical record abstraction of clinical history, the most recent lab results, and a participant survey which included several patient reported outcomes from PROMIS, ASCQ-Me and NeuroQoL. Similar surveys were administered at annual follow-up. Four to five years after enrollment, a second record abstraction was completed with all clinical events that occurred since enrollment and another set of recent labs. There were many research questions proposed to be answered with the study data thus there was no primary outcome.Conclusions: As noted previously, there were no primary outcomes determined at the start of the study. Research questions included examination of co-morbidities, healthcare utilization, and patient reported outcomes. Key findings from the Registry include:Executive dysfunction, learning difficulties, and poor comprehension significantly associated with poor activities of daily living skills. Executive dysfunction also associated with HU non-adherence. Continuing HU after conception increased odds of miscarriage or stillbirth compared to women who were not using HU. Continuing HU after conception increased odds of low birth weight in infants. Compared to adolescents, young adults had significantly more severe pain, organ dysfunction, mental health disorders, sleep problems, and barriers to medical care. Young adults were significantly less likely to see a sickle cell specialist in the past 2 years. Females had higher pain frequency and severity, more pain episodes, anxiety, depression, hospitalizations, and higher fetal hemoglobin levels. Males had more respiratory, musculoskeletal, genitourinary, and cardiovascular complications, more skin ulcers, and more use of HU. Among 128 subjects that died during the study period, iron overload, pulmonary hypertension, and depression, were significant predictors of the risk of death in multivariate analyses.

  Study phs004203

• Cellular Origins and Genetic Landscape of Cutaneous GD T Cell Lymphoma

  Cutaneous gamma-delta T cell lymphomas are a rare and aggressive subtype of cutaneous lymphoma. In the present study, we analyzed these cancers by DNA and RNA sequencing in order to illuminate the genetic landscape for this rare disease. We obtained tumor samples from multiple institutions, including Northwestern University (Chicago, IL), University of Chicago (Chicago, IL), University of Virginia (Charlottesville, VA), and Massachusetts General Hospital (Boston, MA).

  Study phs001969

• Compilation of Aggregate Genomic Data for General Research Use

  This study contains all authorized aggregate genomic data from datasets currently in dbGaP that are approved for general research use (GRU) and have no further limitations beyond those outlined in model Data Use Certification Agreement. Access to this study will be granted for one year and any additional authorized aggregate GRU datasets that become available during this one-year period. This study does not include individual-level data.

  Study phs000501

• Dana-Farber Cancer Institute (DFCI) Brown Lab CLL Sequencing Study

  Chronic Lymphocytic Leukemia (CLL) is a hematological malignancy characterized by accumulation of CD5+CD19+ B cells in peripheral lymphoid organs, bone marrow and blood. In this study we analyze matched whole genome sequencing and RNA-seq data from CLL patients to characterize the mutational processes operative throughout tumor evolution. Source of tumor and normal DNA used is patient PBMC or B cells and saliva respectively.

  Study phs000879

• Single-Cell DNA Methylation Profiling with sciMETv2

  In this study we developed a high-throughput single-cell DNA methylation analysis technology, sciMETv2. This technique is rapid, cost-effective, and robust, enabling large-scale single-cell methylome dataset generation. We demonstrate this technology on human middle frontal gyrus, where we identified major cell types. We additionally performed target enrichment using sciMET-cap to enable a reduction in sequencing costs per cell while achieving comparable cell type identification.

  Study phs003091

• ScRNA sequencing and snp-array genotyping of peripheral immune cells in Type 1 diabetes mellitus (T1DM)

  Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes and has the potential to guide non-invasive test development and patient stratification.

  Dataset EGAD50000000345

• Whole Exome Sequencing

  The objective of this study was to better understand the molecular changes occurring in tumors during development of ICB (immune checkpoint blockade) resistance. Here, we performed Whole Exome Sequencing (WES) on biopsies from a cohort of melanoma patients after progression on anti-CTLA4 or anti-PD1 monotherapy and matched normal samples. Genetic alterations of antigen presentation and interferon gamma signaling pathways were observed in approximately 25% of ICB resistant cases.

  Study EGAS50000000259

• Clonal Evolution and Blastic Plasmacytoid Dendritic Cell Neoplasm - Two Cases

  Here we present two case studies of sequential whole exome sequencing (WES) in patients, who both developed BPDCN throughout their medical history but primarily presented with lymphoid cancers (clonally related ALK-negative anaplastic large-cell lymphoma (ALCL) and T-lymphoblastic lymphoma (T-LBL)) and whose bone marrow at remission exhibited a CMML phenotype, from which in both cases BPDCN clones arose that subsequently became treatment refractory.

  Study EGAS50000000214

• Mate-pair sequencing of 12q-amplified osteosarcomas

  Mate-pair sequencing of 12q-amplified osteosarcomas for the detection of structural variants. This was carried out in order to study the structure of the chromosome 12q-amplicons and whether material from other chromosomes is also intertwined and amplified in a bid to further characterise these tumours beyond CDK4 and MDM2 amplification. Mate-pair data was also used to verify gene fusions detected with RNA-seq.

  Study EGAS50000000493

• RNA sequencing data from 10 patient derived colorectal cancer organoids

  This dataset comprises RNA-sequencing data from ten colorectal cancer (CRC) organoids, derived from histologically verified primary tumor tissues of patients undergoing surgical resection. Paired-end sequencing produced 20 FASTQ.gz files. The organoids were cultured in Geltrex-based droplets using PDO culture medium and harvested for RNA extraction. Total RNA was isolated and subjected to full-length mRNA sequencing, producing high-quality RNA-seq data. The dataset includes transcriptomic profiles of seven microsatellite stable (MSS) and three microsatellite instable (MSI) tumors, providing a valuable resource for the analysis of non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline. This dataset aids in uncovering potential immunotherapy targets in CRC, particularly in hard-to-treat low-TMB MSS cases.

  Dataset EGAD50000000962

• Rearrangements of Viral and Human Genomes at Human Papillomavirus Integration Events and Their Allele-Specific Impacts on Cancer Genome Regulation

  We discovered genomic and epigenomic dysregulation originating at sites of human papillomavirus (HPV) integration following the Oxford Nanopore long-read analysis of 72 cervical cancer genomes. The integration events had allele-specific effects on the genome, methylome, and transcriptome, which sometimes resulted in the activation of cancer genes. We also examined the 72 samples using Illumina short-read analysis in phs000528.

  Study phs003780

• Germline WES of serrated polyposis syndrome

  The serrated polyposis syndrome (SPS) is a disease with a mainly unknown inherited genetic basis characterized by the presence of multiple and/or large serrated polyps in the colon and a higher associated risk for colorectal cancer (CRC). The objective of the present study was to identify new SPS/CRC germline predisposition genes by using whole-exome sequencing in two affected SPS patients from the same family.

  Study EGAS50000000765

• Whole-genome sequencing data of human hematopoietic stem and progenitor cells in post-transplant clonal hematopoiesis

  This dataset contains BAM files of whole-genome sequencing data of single human HSPCs after colony expansion, for three individuals who harbor a DNMT3A mutant clonal hematopoiesis clone in their blood system after hematopoietic cell transplantation. 29 samples are present in this dataset; 10 samples for LTHIT005, 10 samples for LTHIT131, and 9 samples for LTHIT069. In the sample name, samples are annotated for being DNMT3A wildtype (wt) or mutant (mut), except for LTHIT069 (wt samples: F13, H4, K2, L16, N12, mut samples: C8, E10, L9, N5). Whole-genome sequencing was performed after standard Illumina WGS library preparation and sequenced on a Novaseq 6000 using 150 bp paired-end sequencing. The sequencing depth is 15x genome coverage, or 50Gbases per sample.

  Dataset EGAD50000001347

• Identification of genetic polymorphism on aggressive periodontitis

  Periodontitis is an inflammatory disease with loss of gingival tissue and alveolar bone. Aggressive periodontitis is rapidly progressive form of periodontitis in young people. It has been demonstrated that the susceptibility to AgP is influenced by genetic risk factors. However few were established as a risk factor for aggressive periodontitis. To identify genetic risk factors for aggressive periodontitis in Japanese population, we conducted the exome sequence of unrelated patients.

  Study JGAS000040

• Identification of genetic polymorphism on aggressive periodontitis

  Periodontitis is an inflammatory disease with loss of gingival tissue and alveolar bone. Aggressive periodontitis is rapidly progressive form of periodontitis in young people. It has been demonstrated that the susceptibility to AgP is influenced by genetic risk factors. However few were established as a risk factor for aggressive periodontitis. To identify genetic risk factors for aggressive periodontitis in Japanese population, we conducted the exome sequence of unrelated patients.

  Study JGAS000024

• CLDN14 mutation identifed from Japanese sensorineural hearing loss patient.

  The CLDN14 gene, encoding claudin 14, is reported to be one of the rare causes of non-syndromic autosomal dominant sensorineural hearing loss. The detailed clinical characteristics of CLDN14 associated hearing loss is still remain unclear. In the present study, we performed CLDN14 mutation analysis using massively parallel DNA sequencing (MPS) to reveal the clinical characteristics of CLDN14-related hearing loss in a large hearing loss population.

  Study JGAS000191

• Viral evasion Strategy for Generating Hypoimmunogenic hiPSC Lines

  Mismatches in HLA haplotypes between donors and recipients significantly increase the risk of graft failure due to immune rejection. To address these limitations, we introduced a cytomegalovirus-derived US2 encoding sequence into the AAVS1 safe-harbor locus of a human induced pluripotent stem cell (hiPSC) line. US2 expression in iPSC abolished HLA-A2 alloreactive T-cell activation without increasing NK cell degranulation, indicating preserved inhibitory signaling.

  Study EGAS50000001618

• Transcriptomic profiling of myeloid cells from secondary lymphoid organs (lymph nodes and tonsils) from lymphoma patients and controls.

  Despite their recognized impact on the pathogenesis and prognosis of B-cell lymphoma, tumor-associated macrophages (TAM) have not been extensively explored in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). We investigated mononuclear phagocyte (MNP) heterogeneity using single cell RNA sequencing (scRNAseq) in B-cell lymphoma lymph nodes compared to reactive secondary lymphoid organs (lymph nodes and tonsils).

  Study EGAS50000001135

• RNAseq_of_ribosomal_footprints

  Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens.NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit

  Study EGAS00001001591