3613 results for "*geneti*"

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• Identifying and Understanding Drivers of Chemoresistance in Small Cell Lung Cancer

  Using patient derived models of small cell lung cancer (SCLC), either the KEAP1 gene or the USP22 gene was deleted using lentiviral expression of a vector expressing CAS9 and single guide RNA (sgRNA) targeting KEAP1 or USP22. Control vector expressing models were also generated. RNA-Seq analysis was performed to compare gene expression in tumors growing in vivo, comparing KEAP1 deleted or USP22 deleted to control tumors under saline-treated and cisplatin/etoposide-treated conditions. Similar experiments were performed overexpressing USP22 or a control vector in a USP22-deleted patient derived xenograft model of SCLC. For USP22-deleted models, we also performed CUT&TAG analyses to examine the impact of USP22 loss on histone modifications.

  Study phs004087

• ChiLDReN/BA: Genetic Studies of Biliary Atresia in the Childhood Liver Disease Research Network

  Biliary atresia (BA) is a progressive necroinflammatory process initially involving the extra-hepatic biliary tree. Little is known about the factors that cause BA or the factors that influence disease progression. A variety of genetic, autoimmune, and environmental influences have been hypothesized to be important. Most studies to date have focused on the neonate and young child with BA, yet the older surviving child with BA can provide important information about genetics as well as natural history.The Childhood Liver Disease Research Network (ChiLDReN) conducts two longitudinal and observational studies that include BA patients: Biliary Atresia Study in Infants and Children (BASIC) and A Prospective Database of Infants with Cholestasis (PROBE). Using samples from participants in these two protocols, we have formed the largest known data set of biliary atresia patients in the world. ChiLDReN is performing a series of genomic analyses, with subsequent analyses being released as subsequent versions of this registration, phs003356. Version 1 concerns PKD1L1.About the PKD1L1 Analysis (phs003356.v1): While multiple factors have been implicated in the perinatal biliary injuries that characterize BA, a definitive etiology has not yet been established. This study is part of a larger project to characterize the largest cohort of pediatric BA patients through whole-exome sequencing (WES). In this analysis, we examine the WES of those with various laterality defects to determine whether genetic factors could be identified to explicate the etiopathogenesis of BA in biliary atresia splenic malformation (BASM) syndrome. We specifically explored variations in the PKD1L1 gene, which recently has been identified in mouse models as playing a role in laterality.

  Study phs003356

• Retrovirus Epidemiology Donor Study-II (REDS II) Donor Iron Status Evaluation Study (RISE) (REDS_II_RISE -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 The Retrovirus Epidemiology Donor Study-II (REDS-II) Donor Iron Status Evaluation Study (RISE) was designed to evaluate the effects of blood donation intensity on iron and hemoglobin (Hb) status, assess factors that could modify that relationship, and provide data to help formulate optimal whole blood donation frequency. Background Previous studies have shown that regular blood donors are at risk of iron deficiency. Also, a polymorphism in transferrin, which increases the likelihood that menstruating women will be iron deficient, and several genes for hemochromatosis were described in other previous studies. Findings from these studies lead to the possibility that genetic markers might define “at-risk” and “protected” donor groups with respect to iron depletion in blood donors. In addition, none of the previous donor studies had assessed the influence of racial/ethnic or socioeconomic factors, nor behavioral variables and dietary intake. Also, the availability of new tests of body iron status provided further opportunities to detect or prevent this problem. For these reasons, the National Heart, Lung, and Blood Institute's (NHLBI) Retrovirus Epidemiology Donor Study – II (REDS-II) program conducted the REDS-II Donor Iron Status Evaluation (RISE) whereby blood donors were followed prospectively for 15-24 months to provide an in-depth and contemporary evaluation of iron status in a US blood donor population.ParticipantsThe RISE study was a longitudinal multi-center study conducted between 2007 and 2009. All six REDS-II blood centers participated in the study: American Red Cross New England Region, Dedham, MA; the American Red Cross Southern Region, Atlanta, Georgia; the Blood Center of Wisconsin, Milwaukee, Wisconsin; the Hoxworth Blood Center/University of Cincinnati Medical Center, Cincinnati, Ohio; the Institute for Transfusion Medicine, Pittsburgh, Pennsylvania; and the Blood Centers of the Pacific, San Francisco, California. Two cohorts (2,425 whole blood or double red blood cell donors total) were established; one consisted of 888 first-time (FT) or reactivated (RA) donors and the other consisted of 1,537 frequent donors. The FT/ RA cohort consisted of men and women who had either never given blood before (FT) or had not given a donation in the two years before enrollment (RA). The frequent donor cohort consisted of men who had given the equivalent of ≥ 3 and women who had given ≥ 2 red blood cell units in the last year (or equivalent double-red blood cell donations). Male and females donors were recruited equally for each cohort. Most sites where donors were recruited were fixed rather than mobile sites. Only individuals who successfully donated whole blood or double-RBC units, were not deferred at their enrollment visit, and had agreed to donate frequently in the following 24 months were included in the study.DesignData on previous blood donation history; smoking history; diet; use of vitamins, supplements, and aspirin; and reproductive history (female donors) were collected through a self-administered enrollment questionnaire. Also, blood donation activity before and after enrollment, height, weight, country of birth, race and/or ethnicity, and highest educational level were compiled from blood center records and the donor information form that donors completed at the time of donation at the REDS-II centers. At enrollment, ferritin, soluble transferrin receptor (sTfR), and fingerstick and venous hemoglobin were determined. Models to predict two measures of iron deficiency, absent iron stores (AIS) and iron-deficient erythropoiesis (IDE), and hemoglobin deferral were developed. Absent iron stores (AIS) were indicated by a ferritin level of less than 12 ng/mL and iron-deficient erythropoiesis (IDE) by a log(sTfR/ferritin) value of 2.07 or greater, corresponding to the 97.5 percentile of the distribution of the log (sTfR/ferritin) in FT/RA males at enrollment. For hemoglobin deferral, a donor was deferred by current standards if their hemoglobin was ConclusionsA large proportion of both female and male frequent blood donors have iron depletion. Strong associations between higher prior donation intensity and a shorter time since last donation and iron depletion were observed. Iron depletion also developed in a high proportion of returning FT/RA donors (51% of females and 20% of male had IDE on follow up). Other than donation intensity and time since last donation, gender, weight, age, and the use of self-administered iron supplements were found to be important independent predictors of AIS and/or IDE. Time since last red cell donation was a highly significant factor for hemoglobin deferral as were black race, female gender and younger age in women. Reducing the frequency of blood donation is likely to reduce the prevalence of iron deficiency among blood donors, as might implementing routine iron supplementation.

  Study phs004507

• Tumor detection by analysis of both symmetric- and hemi-methylation of plasma cell-free DNA

  Aberrant DNA methylation plays a critical role in tumorigenesis. While DNA methylation has been used for cancer detection and classification, DNA hemi-methylation, a novel epigenetic mark has not been analyzed extensively in cancer epigenomes. Here we report a strand-specific (ss) sequencing method (MeDIP-Seq) for plasma cell free (cf) DNA (sscf-MeDIP-Seq), which can analyze both symmetrically methylated DNA regions (DMRs) as well as hemi-methylated regions (DHMRs). Using the sscf-MeDIP-Seq method, we analyzed plasma cfDNA methylomes of 271 samples from subjects with liver cancer and brain cancer and from individuals without cancer (controls). Among them, 215 samples were chosen as the discovery cohort for the identification of DMRs and DHMRs specific in each subject group and for the training of machine learning models of multi-cancer detection (MCD) using DMRs, DHMRs and DMRs+DHMRs as inputs. These models were then used to predict the 56 samples in the validation cohort. We found that models trained with DMRs+DHMRs as inputs in general outperformed models trained with DMRs or DHMRs alone, with AUROC being 0.971, 0.981, and 0.99 in predicting control, liver and brain cancer samples in the validation cohort, respectively, by the DMR+DHMR-trained models.

  Study phs003462

• A Depression and Opioid Pragmatic Trial in Pharmacogenetics (ADOPT PGx): Acute Pain Trial

  This study description pertains to the ADOPT PGx Acute Pain Trial.The overall ADOPT PGx study was comprised of three separate pharmacogenetic trials grouped into a single protocol due to similarities in the intervention, the hypotheses, and the trial design. The three trials are the Acute Pain Trial (this study), the Chronic Pain Trial, and the Depression Trial. Participants could enroll in only one of the three trials. Trial-specific outcomes will be compared between participants in the intervention arm and control arms who have an actionable phenotype. Acute Pain Trial: A prospective, multicenter, two arm randomized pragmatic trial. Participants meeting eligibility criteria were randomly assigned to either immediate pharmacogenetic testing and genotype-guided post-surgical opioid therapy (Intervention arm) or standard care and pharmacogenetic testing after 6 months (Control arm). Actionable phenotypes are defined as CYP2D6 intermediate metabolizers (IMs) and poor metabolizers (PMs) (i.e. CYP2D6 activity score ≤ 0.75) for the acute pain trial. This study includes approximately 1,610 participants with planned/elective surgery who are anticipated to start a pain control medication with existing CPIC guidelines after their surgery.

  Study phs004058

• NHLBI TOPMed: The Genetic Causes of Unexplained Cardiomyopathies (UNID_CM)

  This study is part of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Program. TOPMed is part of a broader Precision Medicine Initiative, which aims to provide disease treatments that are tailored to an individual's unique genes and environment. TOPMed will contribute to this initiative through the integration of whole-genome sequencing (WGS) and other -omics (e.g., metabolic profiles, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data. In doing so, this program aims to uncover factors that increase or decrease the risk of disease, to identify subtypes of disease, and to develop more targeted and personalized treatments. NHLBI TOPMed: The Genetic Causes of Unexplained Cardiomyopathies (UNID_CM) study performed whole genome sequencing (WGS) at usual and high read depths and transcriptome analyses (RNAseq) of blood (30x read depth) and cardiac tissues (90x read depth) from patients with Cardiomyopathies (Hypertrophic and Dilated). Samples were collected from patients with and without pathogenic mutations in cardiomyopathy genes. The goals of analyses were to advance the understanding of the molecular causes of heart diseases and to provide a robust collection of candidate molecules and mechanisms that cause or contribute to mutation-negative cardiomyopathy. We assessed the burden of these variants by comparison to variants described in publicly available mutation databases (e.g. CLINVAR for coding variants) and genomic sequence from unaffected (e.g. congenital heart disease subjects) and individuals with mutation-positive cardiomyopathies. We expect these analyses will define causes for mutation-negative cardiomyopathy. In addition, we predict that these “omic” datasets will substantially increase knowledge of the molecules, pathways, and mechanism that incite cardiac remodeling not only in cardiomyopathies but also in prevalent cardiovascular disorders.

  Study phs002382

• Genetics and Pathobiology of Disorders of Keratinization

  The goal of this study was to identify potential drivers of disorders of keratinization in human. Individuals diagnosed with disorders of keratinization were recruited with no exclusion criteria. Saliva or blood samples were taken from consented patients or family members and DNA harvested immediately. Whole exome sequencing was performed (150-bp paired end reads) to 80X coverage via an Illumina NovaSeq 6000 sequencer. Identification of germline mutations was performed using GATK.

  Study phs004172

• Sequencing of 3D Organoids Derived From Colorectal Cancer Patients

  This study focuses on the whole-exome sequencing (WES) of patient-derived organoids (PDOs) established from colorectal cancer (CRC) tumors collected at Columbia University. CRC remains a major cause of cancer-related mortality due to its metastatic progression and resistance to therapy. To model CRC at the patient level, we generated 3D organoid cultures from primary and metastatic tumors, preserving their genetic and phenotypic characteristics. The study cohort consists of 9 CRC patients with microsatellite-stable adenocarcinomas from the ascending, transverse, and descending colon, as well as the rectum, with differentiation statuses ranging from well to moderate and moderate-poor. Notably, for one patient, we generated organoids from both the primary tumor and matched liver metastases, allowing for a comparative analysis of tumor evolution. PDOs were derived from these tumors and subjected to WES at early passage to profile somatic mutations, copy number variations, and other genomic alterations to identify mutational signatures. Mutations identified in the PDOs were cross-referenced and confirmed with mutational data from the Columbia Solid Tumor Panel, which was conducted on all tumor tissues prior to organoid establishment. Molecular technologies employed include next-generation sequencing (NGS) for WES, enabling high-resolution characterization of the genomic landscape of CRC PDOs. WES of PDOs allowed us to classify tumor samples based on oncogenic mutations and mutation types, with a specific focus on PIK3CA. Notably, the efficacy of PI3Kα-specific pharmacologic inhibitors in suppressing organoid growth was dependent on the mutational status of KRAS and PIK3CA, underscoring the importance of genomic context in therapeutic response. The dataset available through dbGaP includes raw WES data from CRC PDOs.

  Study phs003965

• Genetic and Hormonal Contributions to Gene Expression in Immune Cells

  The origins of sex differences in human disease are elusive, in part because of difficulties in separating the effects of sex hormones and sex chromosomes. To isolate the effects of testosterone, estradiol, and sex chromosome complement (XX or XY) in humans, we implemented a four-state, cross-sectional study design of trans- and cisgender individuals, the former receiving exogenous testosterone or estradiol for at least a year as part of their gender-affirming medical care. This study design allowed us to compare four combinations of sex hormones and sex chromosomes in humans: XX individuals treated with exogenous testosterone (n=21), XY individuals treated with exogenous estradiol (n=13), untreated XX individuals (n=20), and untreated XY individuals (n=15). We chose to focus on the human immune system because it displays an impressively broad range of sex-differential biology. We collected blood samples from each individual and isolated PBMCs the same day. We performed 10X Genomics 3' single-cell RNA-sequencing (scRNA-seq) on PBMCs from the 69 individuals. We generated 150-bp paired end reads from a total of 358,426 cells (with an average of 48,007 reads/cell) and identified 18 distinct immune cell types. We found that testosterone, estradiol, and sex chromosome complement have unique, non-overlapping effects on PBMC cell abundances and gene expression.

  Study phs003860

• Processes Influencing Adult Health: Genotype and Epigenetic (DNA Methylation) for a Sample of Individuals who Experienced Poverty in Childhood

  This study evaluates the long-term consequences of childhood adversity on adult health. Individuals were aged 21-44 years and approximately half were women. During school-age years, these adults participated in research at Mt. Hope Family Center, including comprehensive assessments of psychological and interpersonal functioning and well as assessment of childhood adversity exposures. This follow-up study includes DNA methylation array data and SNP genotypes.

  Study phs004092