13313 results for ""pdc"+"heritage+language"+census+study"

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• Large Scale Meta-analysis Characterizes Genetic Architecture for Common Psoriasis-associated Variants

  The genotypes obtained from the Affymetrix Biobank Plus array constituted one of eight Caucasian datasets used in a large genome-wide meta-analysis of the association of psoriasis cases versus unaffected controls. With a combined effective sample size of > 39,000 individuals, this study identified 16 new psoriasis loci achieving genome-wide significance, increasing the total number of identified psoriasis loci for European-ancestry populations to 63.

  Study phs001306

• Genomic Analysis of Nucleic Acid Sequences from Pancreatic Cancer

  Our study aims to perform multi-omics analysis of pancreatic ductal adenocarcinoma. We performed dual single-cell RNA sequencing and whole genome sequencing on fresh tumor specimens and dual bulk RNA-sequencing and 16S amplicon sequencing on frozen tumor specimens to identify human and non-human nucleic acid sequences. Additionally, we identified microbial sequences and found that bacterial taxonomic profiles from the same sample strongly correlated across technologies.

  Study phs003035

• Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma

  Lymphomas are a prevalent and heterogeneous family of cancers arising in cells of the immune system. Drivers of lymphomagenesis include genomic rearrangements that juxtapose active regulatory elements with specific oncogene targets, as well as mutations affecting specific transcription factors and chromatin regulatory proteins. This study seeks to combine genome-wide genetic and epigenetic datasets to better understand mechanisms of oncogene dysregulation across distinct lymphoma types.

  Study phs000939

• Non-Coding Mutations Cause Enhancer Targeting Resulting in Protein Synthesis Dysregulation During B-Cell Lymphoma Progression

  In this study, we performed whole-genome sequencing of longitudinal tumor pairs, representing transformation of follicular lymphoma (FL) to high grade B-cell lymphoma with MYC and BCL2 rearrangements (known as "double hit lymphoma" or DHL), a very aggressive class of non-Hodgkin B cell lymphoma (B-NHL). We identified coding and noncoding genomic alterations acquired during the course of lymphoma progression.

  Study phs003398

• Cellular Heterogeneity in Early Human Development at Stage CS16

  In this study, we applied 10x Genomics Multiome assays for single-nucleus profiling of gene expression and chromatin accessibility simultaneously to a Carnegie stage 16 (37-42 days) specimen. These data can be used to identify and characterize diverse human cell types and annotate them with respect to marker genes, expression, and regulatory modules. These data comprise a rich resource for the exploration of human biology.

  Study phs003532

• 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

• Single Cell Analysis of Healthy and Diseased Temporomandibular Joint Synovial Fluid

  Temporomandibular joint disorders (TMJDs) are a set of complex, poorly understood painful conditions that negatively affect many children and adults in the US. In this study, we establish a protocol to utilize irrigation fluid from TMJ arthrocentesis to perform single-cell RNA sequencing on cells contained in TMJ synovial fluid. Our results should help investigators better understand these conditions and identify novel therapeutic options.

  Study phs003645

• Evolving Cell States and Oncogenic Drivers during the Progression of IDH-Mutant Gliomas

  The study aims to understand the changes in cell states during the progression of IDH mutant gliomas. We generated scATAC-seq data from tumor samples of patients with IDH mutant gliomas, ranging from grade 2 to grade 4, including both IDH mutant oligodendroglioma and IDH mutant astrocytoma samples. Additionally, we have generated scRNA-seq data from patient-derived organoids that were treated with a DNMT1 inhibitor.

  Study phs003697

• Single-Cell RNA-Sequencing of Bone Marrow and Circulating Tumor Cells from Patients with Multiple Myeloma and its Precursor Conditions

  We performed single-cell RNA and V(D)J-sequencing of tumor cells from bone marrow and peripheral blood specimens and patients with Monoclonal Gammopathy of Undetermined Significance (MGUS), Smoldering Multiple Myeloma (SMM), and Multiple Myeloma (MM), as well as healthy donors. In this study we aimed to shed light on the mechanisms underlying tumor cell circulatory capacity and dissemination.

  Study phs003855

• Analysis of genes associated with autistic spectrum disorder, schizophrenia, and bipolar disorder.

  Autism spectrum disorders (ASD) represent a heterogeneous group of neurodevelopmental disorders with strong genetic predispositions. Although an increasing number of genetic variants have been implicated in the pathogenesis of ASD, little is known about the relationship between ASD-associated genetic variants and individual ASD traits. We performed case-control association study of 32 Japanese children with ASD (mainly with high-functioning autism) and 36 with typical development.

  Study JGAS000731

• Evaluation of clonal hematopoiesis regarding TP53 mutation status in 140,597 individuals

  The existence of clonal hematopoiesis, in which somatic mutations accumulate in the peripheral blood with age and expand clonally, is becoming clear, and various clinical implications are being suggested. This study analyzed clonal hematopoiesis regarding TP53 mutation status by targeted sequencing in 140,597 individuals, including those with breast cancer, gastric cancer, colorectal cancer, heart failure, stroke, etc. The clinical characteristics of clonal hematopoietic carriers were evaluated.

  Study JGAS000782

• Childhood Cancer Data Initiative (CCDI): Texas Pediatric Patient Derived Xenograft 

  The DNA/RNA samples of patients for which PDX models were developed were from a population of children, adolescents, and young adults from South Texas. Consent was obtained for collection of malignant and non-malignant tissue samples for genetic analysis and for the development of models to study new ways to treat cancer. For additional details, please refer to these publications: PMID: 37915590; PMID: 37990009.

  Study phs003215

• Shotgun metagenome sequencing of saliva samples using PromethION

  Using PromethION, we conduct shotgun metagenome sequencing of human saliva, where both bacteria and bacteriophages are densely living, to study both microbiome and virome. We aim to explore, for example, relative abundance of bacteira and bacteriophages, distribution of contig lengh. types of phages and prophages, frequency of novel phages revealed by the long-reads and their taxonomic classification, and characteristics of genes encoded by the phages.

  Study JGAS000186

• 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

• Target bisulfite sequencing of endometrial cancer

  This study aims to investigate epigenetic alterations in the HLA-A locus in endometrial cancer. Targeted bisulfite sequencing was performed to evaluate DNA methylation status of the HLA-A region in a cohort of endometrial cancer samples. The resulting data were used to assess the association between HLA-A methylation and tumor immune microenvironment. These findings contribute to understanding the role of epigenetic regulation of antigen presentation in endometrial cancer.

  Study JGAS000897

• 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

• Meta-analysis of Genome-Wide-Association Sudies for plasma Factor XI

  Coagulation factor XI (FXI) has become increasingly interesting for its role in pathogenesis of thrombosis. We performed a genome-wide association study (GWAS) for plasma FXI levels, using novel data imputed to the 1000 Genomes reference panel. Individual GWAS analyses, including a total of 16,169 European individuals from the ARIC, GHS, MARTHA and PROCARDIS studies, were meta-analyzed, and results are presented here.

  Study EGAS00001002123

• Identification Of Pathogenic Mutations And Application Of Polygenic Risk Scores In Early-Onset Diabetes Patients

  Maturity-onset Diabetes of the Young (MODY) presents a diagnostic challenge. In this study we investigate the genetic background of Latvian early-onset diabetes patients, using whole-genome sequencing data. Additionally, we investigate the utility of previously published and available type 1 diabetes (T1D) and type 2 diabetes (T2D) polygenic risk scores in differentiating monogenic diabetes (MODY) from T1D and T2D cases.

  Study EGAS50000000991

• Non_Hodgkin_lymphoma_project___mutational_burden_of_chemotherapy_in_normal_blood

  his study aims to further investigate the mutational burden induced by chemotherapy in the normal stem and progenitor cell of individuals treated for Non -hodgkins lymphoma. Single cell derived progenitor colonies have been grown and DNA extracted. 5-10 colonies from a number of individuals exposed to chemotherapeutic regimens for lymphoma will undergo whole genome sequencing to address the question of the extent of mutational impact of these different regimens.

  Study EGAS00001006733

• Transcriptomic changes in amniotic fluid associated with the fetal inflammatory response

  The fetal inflammatory response (FIR) increases the risk of perinatal brain injury, particularly in extremely low gestational age newborns (ELGANs, < 28 weeks of gestation). Most FIR cases are subclinical, i.e., usually FIR does not trigger observable symptoms in the mother beyond those associated with premature birth. The study of transcriptomic changes asssociated with FIR in amniotic fluid could help finding new clinical actionable FIR biomarkers.

  Study EGAS50000000866

• VariantMedium: Sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental confirmation data

  This study contains whole-exome sequencing (WES) and results of targeted deep-sequencing data of three matched tumor and normal cell lines, with two technical WES replicates each. The calls by Mutect2, Strelka2, and VariantMedium were confirmed using targeted deep sequencing on Illumina Miseq The targeted deep sequencing was performed in three runs and the results are summarized under VCF files.

  Study EGAS50000001661

• Reproducibility of variant calls in replicate next generation sequencing experiments

  In this study, we examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA. We performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. Seventeen breast cancer samples were sequenced in duplicate (n=14) or triplicate (n=3) to assess concordance of all calls and single nucleotide variant (SNV) calls.

  Study EGAS00001000826

• Exome_sequencing_of_Congenital_Heart_Disease_families_from_the_Competence_Network_Berlin

  This project aims to study exomes from families and trios withcongenital heart disease (CHD). The samples have been collected underthe Competence Network - Congenital Heart Defects in Berlin, Germany.The phenotypes are mainly left ventricular outflow obstruction (aorticstenosis, bicuspd aortic valve disease coarctation and hypoplasticleft heart), but will also include samples with hypoplastic rightheart and atrioventricular septal defects. We will perform whole exomesequencing using Agilent sequence capture and Illumina HiSeqsequencing.

  Study EGAS00001000368

• Whole_Genome_sequencing_of_individuals_from_Val_Borbera__Italy

  This study includes Phase 2 whole-genome sequencing data (at 4x depth)of 100 individuals from an Italian genetic isolate population (Val Borbera, abbreviated VBI) of the Italian Network of Genetic Isolates (INGI). The INGI-VBI_SEQ2 project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.

  Study EGAS00001000458

• Long-read sequencing for cell-free DNA analysis (human)

  In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Cell-free DNA from plasma samples of 31 pregnant women at different trimesters, 6 hepatitis B carriers, and 8 patients with hepatocellular carcinoma were sequenced with the two platforms.

  Study EGAS00001006328