14666 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Temporal Dissection of Tumorigenesis in Primary Cancers

  The earliest genetic abnormalities in cancer represent a unique opportunity for timely clinical diagnosis. Classic deep sequencing of tumors identifies many aberrations acquired later in cancer progression. In this study, data regarding simple mutation and chromosomal aberration were integrated to trace the evolution of cutaneous squamous cell carcinomas and ovarian adenocarcinomas. Only after the second allele of TP53 was lost did the genome enter a window of extreme genomic vulnerability, in both cancer types, eventually acquiring more than 100,000 mutations in skin cancers. Inactivating Notch mutations were also identified as prevalent secondary changes. These results add context to the idea of TP53 mutation as dominant negative and occurring later in tumorigenesis.

  Study phs000418

• Epilepsy Genetics Initiative

  The Epilepsy Genetics Initiative (EGI) was created in 2014 with the goal of amassing a database of clinically-generated exome sequence data for patients with epilepsy who have had diagnostic whole exome sequencing. Most of the subjects enrolled in the study did not receive a secure genetic diagnosis from their initial sequencing. Following participant/family consent, EGI transfers raw data from the respective clinical lab to the Institute for Genomic Medicine at Columbia University Medical Center. The strategy of the initiative has been to carry out systematic reanalysis of data to identify new diagnoses that were not possible or missed at the time of initial sequencing and to aid in novel gene discovery in epilepsy.

  Study phs001551

• Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

  In this study, we analyzed a series of colorectal cancers using a new sequencing technology that sequences more than 200 microsatellite regions in parallel. With this technology, we evaluated mono-, di- , tri- and tetranucleotide repeats to provide a broad spectrum of microsatellite instability (MSI) events. This deep sequencing technology provides greater than 2000X coverage and eliminates the need for PCR amplification. Because every read corresponds to a single DNA molecule, we eliminated artifacts introduced by PCR that obscured true MSI events. Also included in our analysis is a new method for detection of somatic copy number changes in 83 cancer genes, with which we can infer chromosomal instability (CIN) status.

  Study phs001914

• Cutaneous Melanoma GWAS Combining Multiple Populations and Risk Phenotypes

  Most genetic susceptibility to cutaneous melanoma (CM) remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 melanoma cases (67% newly-genotyped) and 375,188 controls identified 54 significant loci with 68 independent SNPs. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with nevus count and hair colour GWAS, and transcriptome association approaches, uncovered 31 potential secondary loci, for a total of 85 CM susceptibility loci. These findings provide substantial insights into CM genetic architecture, reinforcing the importance of nevogenesis, pigmentation, and telomere maintenance together with identifying potential new pathways for CM pathogenesis.

  Study phs001868

• Whole Exome Sequencing Analysis of Carfilzomib-Related Cardiotoxicity in Multiple Myeloma Patients

  This study investigated the contribution of germline genetic variants in protein-coding genes in carfilzomib-related cardiovascular adverse events among patients with multiple myeloma using whole-exome sequencing (WES) analysis. We analyzed 247 patients with multiple myeloma who had been treated with carfilzomib at the Moffitt Cancer Center. We identified a missense mutation in the TMSB10/TRABD2A locus that appeared to be associated with a higher risk for cardiovascular adverse events in these patients. In this submission, we will provide all the genotype data along with the phenotype data of whether or not a patient developed cardiovascular adverse events after carfilzomib treatment and all the covariates used in this analysis.

  Study phs003308

• Malnutrition and Enteric Disease Network (Mal-ED) Birth Cohort in Brazil

  The Malnutrition and Enteric Disease Network (Mal-ED) Birth Cohort in Brazil enrolled 242 children between 2010 and 2014; an additional 101 infants recruited under the ICIDR (International Center for Infectious Disease Research) program and evaluated by the same procedures as Mal-ED were included in the cohort. The aim of the study was to evaluate the role of enteropathogens in causing intestinal inflammation and a failure of growth and development.This submission includes genetic and corresponding anthropometric data on a subset of 279 participants. More information on this project and its related projects can be found here: Studies of diarrheal susceptibility, growth, and development, in pediatric populations in Northeastern Brazil

  Study phs003172

• Diabetes Multi-Omic Investigation of Drug Response (DIAMOND)

  The Diabetes Multi-omic Investigation of Drug Response (DIAMOND) cohort is a population-based cohort of individuals with type-2 diabetes (T2D) who receive their care through a large health system serving southeast Michigan and metropolitan Detroit. The cohort represents the diversity of the population from which it was created. Because of their health plan membership, participants have a rich dataset of longitudinal clinical health information related to their care. The intent of the DIAMOND study is to use genomic profiling, drug exposure information, and electronic health record (EHR) derived outcome data to identify genetic predictors of treatment response. Genome-wide genotyping was performed using the AxiomTM Precision Medicine Research Array (ThermoFisher Scientific Inc.).

  Study phs003350

• Cryptic Splice Mutation in the Fumarate Hydratase Gene in Patients With Clinical Manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC)

  Four patients with hysterectomy were evaluated for biochemical and molecular evidence of autosomal dominant Fumarate Hydratase (FH) alterations causing Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC). HLRCC is an autosomal dominant condition characterized by the development of cutaneous and uterine leiomyomas, and risk for development of an aggressive form of papillary renal cell cancer. Enzyme assay, western blot analyses, direct nanopore RNA sequencing, and whole genome sequencing (WGS) were utilized. The study identified a cryptic splice mutation in intron 9 of the FH gene that results in retention of 57 base pairs of intronic sequence in the affected allele of the mature FH mRNA.

  Study phs003381

• Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

  Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. In version 1.0 of this study, we performed RNA-based next generation sequencing (mNGS) on 41 lower respiratory samples collected from 34 children. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Potential pathogens were detected in half of samples previously negative by clinical diagnostics. In version 2.0, we included an addition 278 samples from 229 pediatric stem cell transplant patients with pulmonary disease.

  Study phs001684

• Developing Biomarkers Incorporating High Throughput RNA, DNA, Small RNA Sequencing and Protein Expression in Inflammatory Bowel Disease Using Formalin-Fixed, Paraffin-Embedded (FFPE) Tissue Samples

  This study included pediatric patients with suspected inflammatory bowel disease (IBD) who underwent endoscopy between 2008 and 2012. This included 101 colonic tissue samples and 100 ileal tissue samples. Biopsies were obtained at the time of diagnosis, and patients were followed for a mean of 6 years to record clinical characteristics. These included baseline characteristics, such as age of diagnosis and initial Montreal classification, as well as outcomes, such as stricturing or fistulizing complications, disease remission, or progression to surgery.Genes with significant results in the non-IBD vs CD comparison in colonic tissue are listed in the "Links to Related Genes" section of this page.

  Study phs003156