13393 results for ""pdc"+"heritage+language"+census+study"

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• Targeted Germline Sequencing of the Leeds Melanoma Cohort

  In this project we performed targeted sequencing of known and suspected melanoma susceptibility genes in a cohort of melanoma patients and matched controls. Our aim was to identify variants that predispose to melanoma development. The melanoma cases used in this study were population ascertained.

  Dataset EGAD00001007520

• CITEseq data

  CITEseq data of CLL patients receiving VEN treatment for resistance study

  Dataset EGAD00001008366

• WGS of tissues from members of family with germline POLD1 L474P variant

  The study includes WGS data for DNA extracted from blood, fibroblasts or buccal swabs from sixteen family members, who represent four sub-families, each including two parents and one to three children, comprising a total of eight offspring. In two sub-families POLD1 L474P was carried by the father; in one sub-family, by the mother; and in the other sub-family, both parents had wild-type POLD1.

  Dataset EGAD00001009282

• Whole Genome Sequences of 18th century African descended individuals from Charleston, South Carolina.

  This study presents Whole Genome Sequencing results from the Anson Street African Burial Ground Project, which is a community-based initiative aimed at understanding the histories of 37 Ancestors in Charleston, South Carolina. Here we report fastq files for all 37 Ancestors. DNA was extracted at the University of Tennessee-Knoxville following Dabney et al. 2013, and dual index libraries prepared using a modified NEBNext Ultra II kit with partial USER enzyme digestion. Libraries were then enriched for human genomic DNA (MyBaits) and sequenced on Illumina Platforms.

  Dataset EGAD00001009643

• IntEnd study

  Formalin-fixed, paraffin-embedded samples from 643 colorectal adenomas collected in different hospitals in Norway, from which DNA was extracted, were analysed for DNA copy number alterations. Some adenomas had more than one block (n=42), thus 643 individuals, 685 blocks. Low-coverage whole genome sequencing was run in all samples. For 529 individuals all the clinical information was available. A subset was matched for follow-up time, age and sex in a nested case-control approach (n=366; cases - individuals who developed later on CRC; controls - individuals who did not develop CRC within the same follow-up time).

  Dataset EGAD00001010119

• Single cell RNA-sequencing of tissues from NSCLC patients treated with chemoimmunotherapy

  The goal of this study is to characterize immune cell populations by single cell RNA-sequencing (scRNA-seq) in tumor and uninvolved normal tissues from non-small cell lung cancer (NSCLC) patients with resectable non-small cell lung cancer and who received neoadjuvant chemoimmunotherapy. scRNA-seq was performed on seven pairs of tumor and normal tissues as well as one lymph node (LN) sample. Data set includes pair-end fastq files for single cell RNA sequencing of 7 neo-immuno patients. (Total 15 samples and 50 runs).

  Dataset EGAD00001009778

• Dataset for Sarcoma-WGS linked from study EGAS00001004813

  Sequencing data of 77 sarcoma tumor and control runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

  Dataset EGAD00001010257

• Organoid Derivation Project - GRCh38 - RNAseq (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011092

• Genome and transcriptome sequence data from a rosette-forming glioneuronal tumor (RGNT) tumor patient

  Genome and transcriptome sequence data from a rosette-forming glioneuronal tumor (RGNT) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015320

• Genome and transcriptome sequence data from a metastatic malignant peripheral nerve sheath tumor tumor patient

  Genome and transcriptome sequence data from a metastatic malignant peripheral nerve sheath tumor patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015322

• Genome and transcriptome sequence data from a diffuse midline glioma, H3K27 mutant tumor patient

  Genome and transcriptome sequence data from a diffuse midline glioma, H3K27 mutant patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015326

• Genome and transcriptome sequence data from a CNS non-germinoma germ cell tumour tumor patient

  Genome and transcriptome sequence data from a CNS non-germinoma germ cell tumour patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015327

• Genome and transcriptome sequence data from a GBM (H3 K27M mutant) tumor patient

  Genome and transcriptome sequence data from a GBM (H3 K27M mutant) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015328

• Genome and transcriptome sequence data from a high-grade glioma, glioblastoma tumor patient

  Genome and transcriptome sequence data from a high-grade glioma, glioblastoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015336

• Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

  The dataset for the study Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer includes 207 bam files from hybrid capture targeted error-correction next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 30 individuals with non-small cell lung cancer, alongside 46 bam files from whole exome sequencing of tumor and matched normal DNA for 21 individuals with non-small cell lung cancer who received immunotherapy-containing regimens.

  Dataset EGAD00001011991

• TCR β-chain repertoire characterization of regulatory and conventional T cells in peripheral blood from breast cancer patients and healthy individuals.

  Identification of tumor-specific effects on peripheral TCRβ repertoire formation in humans, investigation of the clonal origin of regulatory T cells in breast cancer patients and impact analysis of the tumor-specific conversion of conventional T cells into induced regulatory T cells on the peripheral Treg repertoire in humans.

  Study EGAS00001002699

• TCR β-chain repertoire characterization of regulatory and conventional T cells in breast tumors from breast cancer patients.

  Identification of tumor-specific effects on peripheral TCRβ repertoire formation in humans, investigation of the clonal origin of regulatory T cells in breast cancer patients and impact analysis of the tumor-specific conversion of conventional T cells into induced regulatory T cells on the peripheral Treg repertoire in humans.

  Study EGAS00001004671

• CTSP: Clinical Trial Sequencing Project

  For the Clinical Trials Sequencing Project (CTSP), National Cancer Institute (NCI) will utilize whole genome sequencing and/or whole exome sequencing in conjunction with transcriptome sequencing to try to identify recurrent genetic alterations (mutations, deletions, amplifications, rearrangements) and/or gene expression signatures that would be important to the hypothesis(es) submitted by the investigators. The samples will be processed and submitted for genomic characterization using pipelines and procedures established within The Cancer Genome Analysis (TCGA) project. Data analysis will be performed as a collaboration between the National Clinical Trials Network (NCTN) Group and its investigators submitting the proposal. The investigators at the NCI-sponsored Genomic Data Analysis Center (GDAC) will characterize the samples. The NCTN Group will be responsible for providing the clinical data needed for the proposal to the open clinical system maintained by NCI CCG's Biospecimen Core Resource (BCR) at Nationwide Children's Hospital in Columbus, Ohio. The project team (Network Group/investigators and GDAC) will analyze the data together. Additionally, clinical and genomic data related to the analyses will also need to be registered by NCI and will be made available to qualified researchers via a controlled-access database (e.g., dbGaP) upon publication of the primary analysis described in the study proposal. A substudy description and its molecular data information are provided under its own page: phs001184 CTSP Diffuse Large B-Cell Lymphoma (DLBCL) CALGB 50303

  Study phs001175

• Genome and Transcriptome Assembly Reveals SVA-Mediated Aberrant Splicing in X-Linked Dystonia Parkinsonism

  X-linked Dystonia-Parkinsonism (XDP, DYT3) is a long-standing quandary in human disease genetics. XDP is predominantly observed on Panay island in the Philippines. This study is one of the first of its kind to interrogate an unsolved Mendelian disorder by integrating genome and transcriptome assembly methods using Illumina, 10X Genomics, Pacific Biosciences, and Agilent genome targeting technologies. These data provide strong evidence for a pathogenic link between a noncoding SVA retrotransposon and XDP. We demonstrate that this Mendelian disorder is associated with a sine-VNTR-Alu (SVA) retrotransposon that inserted into the TAF1 gene and is shared by all XDP probands, yet never observed in controls from worldwide populations. Transcriptome assembly in iPSC-derived neural stem cells (NSCs) and neurons revealed that this SVA caused aberrant splicing and significant intron retention, which was negatively correlated with TAF1 expression. Remarkably, CRISPR/Cas9 excision of the SVA rescued the aberrant transcriptional signature and normalized expression of TAF1 in patient-derived NSCs. We have also interrogated iPSC-derived microglia to investigate the contribution of glial components to the cellular and molecular deficit, effect of TNF treatment on XDP transcriptional signatures. To further understand what XDP may have in common with other hereditary dystonias (such as DYT6), we are further comparing these signatures to ones associated with dystonia-specific variants in proteins that, like TAF1, are also involved in regulating transcription, i.e. THAP1. 

  Study phs001525

• MAITS in HCC

  Hepatocellular Carcinoma (HCC) is a leading cause of cancer-related death and can be considered a prototype of inflammation-derived cancer arising from chronic liver injury. The cell composition of the HCC tumor immune microenvironment (TiME) has a major impact on cancer biology as the TiME can have divergent capacities on tumor initiation, progress, and response to therapy. Recent development of multi-omics and single-cell technologies help us to comprehensively quantify the cellular heterogeneity and spatial organization of the TiME and to further our understanding of antitumor immunity. We investigated the cellular composition of liver cancer patient samples (n=8) using single-cell RNA-seq. For this purpose, mononuclear cells were isolated from human liver cancer samples. Three locations within the tumor-bearing liver were used: adjacent liver, rim and tumor core. Then, cells were FACS sorted (either CD45+ cells or MAIT cells) and subjected to 10X Chromium-based scRNA-seq. We investigated immune cell changes and the cellular heterogeneity of the HCC TiME with a focus on MAIT cells. Annotated H5 files are provided. Clinical metadata including TMN stage, sex, gender, ethnicity, pretreatment, and histopathological reports are available for all patient samples. Further details on the study can be obtained in our paper once it’s published.A complementary dataset derived from ultrahighplex CO-Detection by indEXing (CODEX) from paired patient samples can be accessed through The Cancer Imaging Archives (TCIA) under DOI: https://doi.org/10.7937/bh0r-y074.

  Study phs003279

• Cellular Indexing of Transcriptomes and Epitopes Sequencing (CITE-Seq) Analysis to Investigate the Impact of Granulocyte-Colony Stimulating Factor on CRISPR/Cas9 Gene Edited Human Hematopoietic Stem Cell Function

  Our research using in-vivo preclinical xenograft mouse models demonstrated that G-CSF impedes engraftment of CRISPR-Cas9 gene edited human hematopoietic stem cells (HSCs). In this CITE-seq study, we sought to investigate the mechanisms by which G-CSF negatively impacts long-term repopulating functions of CRISPR-Cas9 gene edited human HSCs. Accordingly, human CD34+ cells were obtained from a healthy volunteer and edited with Cas9 alone (Cas9 group), Cas9+AAVS1-targeting gRNA (RNP group), or Cas9+AAVS1-targeting gRNA+GSE56 (RNP/GSE56 group). Then, these edited cells were transplanted into busulfan-conditioned NSG mice, and these mice subsequently received 3 days of phosphate buffered saline (PBS) or G-CSF. Each mouse was subsequently euthanized and harvested for bone marrow cells and human CD34+cells were isolated using immunomagnetic beads. Isolated CD34+ cells from a total of 6 mice were individually stained with Total seq B CITE-seq antibodies (CD38, CD45RA, CD90, CD49f) + hashtag oligo antibodies 1, 2, 3, 4, 5 and 6. Fluorescence activated cell sorting (FACS) was used to purify ~2,500 cells from each group that were subsequently pooled for CITE-seq library preparation and sequencing. Seurat was used to demultiplex data into 6 individual groups and differential gene expression analysis was performed to evaluate the impact of G-CSF within Cas9, RNP and RNP/GSE56 groups.

  Study phs003277

• Biomarkers in Transplant Recipients

  Biliary atresia causes jaundice and liver failure in newborn children. In this study, single nucleotide polymorphisms were characterized in children with biliary atresia and identified ARF6 as a susceptibility gene for this disease. Knockdown of this gene in zebrafish embryos impaired formation of bile ducts and excretion of bile from the zebrafish liver. Subject enrollment: Children with biliary atresia were enrolled at Children's Hospital of Pittsburgh (CHP) after obtaining written consent from parents for the University of Pittsburgh IRB approved protocol number 0405628. At the Center for Applied Genomics (CAG), all subjects were enrolled after obtaining written consent from parents per Children's Hospital of Philadelphia IRB approval number 06-004886 Genotyping array: Genotyping of DNA obtained from blood was performed with the Infinium HumanHap550K BeadChip (Illumina, San Diego, CA). Statistical methods and software: SNP genotype frequencies were compared between cases and controls with a chi-square test statistic applied in Plink [Purcell et al, 2007] for SNPs with at least 90% call rate and 1% minor allele frequency (MAF). Cases and controls: All DNA samples had excellent data quality with call rates > 98%. A total of 63 Caucasian BA cases and 1907 controls were compared at > 550000 SNPs, and demonstrated a very low genomic inflation factor of 1.00627. Description of Cases: Biliary atresia patients had received a Kasai procedure and demonstrated histopathological features of biliary obstruction, and were recruited at evaluation for transplantation or after liver transplantation.

  Study phs000960

• Deletion of FUNDC2 and CMC4 on chromosome Xq28 is sufficient to cause hypergonadotropic hypogonadism in men

  Hypergonadotropic hypogonadism (HH) is characterized by low sex steroid levels and secondarily elevated gonadotropin levels with either congenital or acquired etiology. Genetic factors leading to HH have yet to be fully elucidated. We submit genome and transcriptome data analyses from a male patient with HH and history of growth delay who has an inherited deletion of chromosome Xq28. Expression analyses were done for this patient and his unaffected family members, and compared to normal controls to identify dysregulated genes due to this deletion. Our patient's Xq28 deletion is 44,806 bp and contains only two genes, FUNDC2 and CMC4. Expressions of both FUNDC2 and CMC4 are completely abolished in the patient. Gene ontology analyses of differentially expressed genes in the patient in comparison to controls show that significantly up-regulated genes in the patient are enriched in Sertoli cell barrier regulation, apoptosis, inflammatory response and gonadotropin-releasing regulation. Indeed, our patient has an elevated FSH level, which regulates Sertoli cell proliferation and spermatogenesis. In his mother and sister, who are heterozygous for this deletion, X-chromosome inactivation is skewed towards the deleted X, suggesting a mechanism to avoid FSH dysregulation. Compared to the previously reported men with variable sized Xq28 deletions, our study suggests that the loss of function of FUNDC2 and/or CMC4 results in dysregulation of apoptosis, inflammation and FSH, and is sufficient to cause Xq28-associated HH.

  Study phs002234

• The preterm infant microbiome: biological, behavioral and health outcomes at 2 and 4 years of age

  This project follows a cohort of 78 Very Low Birth Weight (VLBW) previously enrolled infants in a R21 grant plus additional 25 infants through their Neonatal Intensive Care Unit (NICU) stay until they reach the age of 4 years. The data, gathered over 6 weeks of the NICU stay, includes multiple factors, such as prenatal and postnatal events and illnesses, received human milk amount, weekly means of cytokines, chemokines, growth factors, and secretory Immunoglobulin A in the milk, and weekly levels of fecal calprotectin. These factors could potentially alter the gut microbiome. Microbiome species and diversities will be measured in the laboratory of Dr. Jack Gilbert at Argonne National Laboratory using state of the science deep sequencing and amplification of microbial sRNA genes. The microbiome will again be measured in stool samples from those children at the ages of 2 and 4 years. Relationship between the prenatal and postnatal factors, human milk volume and immunobiology, fecal calprotectin levels, and the very early microbiome will be analyzed. The predictive power of the VLBW infant gut microbiome for determining later childhood microbiomes will be analyzed prospectively. The relationships between microbiomes across time and later growth, development and health will be determined. VLBW infants are at risk for both early and later health effects, and the role of the microbiome in these effects will be measured in this prospective study.

  Study phs001578

• Spit for Science

  Spit for Science™ is a university-wide research opportunity with the scientific goal of understanding how genetic and environmental factors come together to influence substance use and emotional health across the college years and beyond. To address this goal, we have comprehensively and longitudinally studied eligible incoming freshmen (18 years or older) from a diverse urban university, assessing a wide range of risk and protective factors, including both biological susceptibility and environmental risk, and a variety of outcome measures, particularly alcohol use and other substances, and difficulties with emotional health. Our goal is to assess how risk and protective factors dynamically interact to contribute to behavior health outcomes over time and plan to use findings from the project to inform prevention and intervention efforts and aid in university policy and programming in ways that can support and promote student success. Methods: In the fall of their freshman year, first-time college students over the age of 18 are invited to complete an online survey containing broad questions about personality and behavior, as well as family, friends, and experiences growing up. Students can also provide a saliva sample and participate in the DNA component of the project (participation in the DNA component is not a requirement for participation in the survey). Each subsequent spring students are asked to complete a follow-up survey, enabling researchers to study patterns of substance use and emotional health across the college years.

  Study phs001754