13376 results for ""60+mice"+"6+weeks"+diet+study+2014+2017+DOI"

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• Human non-malignant plasma cfRNA study - raw data

  mRNA capture sequencing on plasma sample from 88 patients with a non-malignant disease and from 37 healthy donors.

  Study EGAS50000001264

• Dataset-linking-WGS-and-WES-files-from-EGAS00001004276-via-README-for-new-study-EGAS00001005327

  This dataset contains 538 Tumor and Control WGS and WES files for samples already submitted and published in study EGAS00001004276

  Dataset EGAD00001007817

• SNP array data in Massim study

  The compressed file contains plink format file for the Illumina MEGA SNP array data of 255 individuals generated and analyzed in Liu et al study of genom-wide variation of the Massim region.

  Dataset EGAD00001008545

• WGS-TOF study

  Whole genome sequencing data (bam) of tetralogy of Fallot study, including data derived from iPSCs of two control and four patients with tetralogy of Fallot (two with DiGeorge syndrome (DG), two without DiGeorge syndrome (ND).

  Dataset EGAD00001008569

• There are 80 Brain cancer cases in this study and belong to GBM-CN project.

  There are 80 Brain cancer cases （160 samples）in this study and belong to GBM-CN project.

  Dataset EGAD00001003218

• Infant Spindle Tumour Study (2019-04-11)

  We aim to describe the transcriptomic landscape of infant spindle cell tumours. . This dataset contains all the data available for this study on 2019-04-11.

  Dataset EGAD00001004954

• Single-cell RNA-seq data from metastatic ovarian cancer for quality control study

  This study includes treatment-naïve fresh tissue sample from 4 HGSOC patients.

  Dataset EGAD00001006984

• Genomic gain of EBV's LMP-1 in NKTCL

  The study found a high recurrence of genomic gain of LMP1 locus within EBV-associated NKTCL. The pilot data set and extended dataset of 77 WGS NKTCLs found 18/77 tumoral genomes to harbour genomic gain of LMP-1 locus within the EBV viral genomes within NKTCL tumoral sequencing data. The study also found 1/10 NKTCL cell lines to be positive for LMP-1 locus gain within EBV genomes too. This dataset includes solely the confirmatory WGS data of LMP-1 gain from NKYS cell lines using Oxford Nanopore long-read sequencing technology.

  Study EGAS50000000260

• GSCAN GWAS Meta-analysis of Tobacco and Alcohol use (GSCAN-GWAS)

  This study was a meta-analysis of genome-wide association study (GWAS) of substance use across 1.2 million total participants with European ancestry (some phenotypes are based on fewer participants). The phenotypes were chosen to represent different stages and kinds of substance use from initiation (age of smoking initiation) to regular use (cigarettes per day and drinks per week) to cessation (smoking cessation). For each of those phenotypes, collaborators shared their GWAS summary statistics, which were then meta-analyzed using a method that incorporates into the meta-analytic weighting the sample size, allele frequency and imputation quality score.

  Study phs001809

• Biology and Molecular Analysis of Human Hematopoiesis Genetics

  In this study we have performed exome sequencing using the hybrid capture method that has previously been described (Gnirke et al., Nature Biotechnology, 2009) on genomic DNA samples from patients with the congenital bone marrow failure syndrome that affects the erythroid lineage, specifically, Diamond-Blackfan anemia. This disease is characterized by a hypoplastic anemia and approximately 50% of cases are attributable to mutations in ribosomal protein gene subunits. The other 50% of cases do not have a known genetic etiology and the purpose of this study is to attempt to delineate such causes.

  Study phs000474

• Pooled Genome-Wide Analysis of Kidney Cancer Risk (KIDRISK)

  Incidence rates of renal cell carcinoma (RCC) are rising and the latest estimates show that it accounts for over 300,000 cases and 120,000 deaths worldwide each year. Mechanisms underlying RCC occurrence are not fully understood and a large part of the disease heritability remains unexplained. The study aimed at augmenting the size of available RCC genome-wide association studies to increase the statistical power to detect genetic variants associated with the disease. The study includes genome-wide genotyping data from RCC cases (n=2,781) and controls (n=2,526) recruited in Western Europe, Central and Eastern Europe, and Australia.

  Study phs001271

• Biesecker Lab (NHGRI) Whole Genome Medical Sequencing for Gene Discovery

  We aim to use whole-genome medical sequencing (WGMS) to discover causative molecular lesions for a set of rare, severe phenotypes hypothesized to be caused by either somatic mutations, germline de nova heterozygous mutations, germline inherited recessive, or germline inherited dominant mutations in currently unknown or uncharacterized genes. The goal of this research is threefold: to identify causative sequence variants for disorders whose molecular etiology was previously unknown, to apply this insight to both the rare disorders under study and more common phenotypes, and to enhance the study of mutation on a genome-wide level.

  Study phs001348

• A Model of Human Asthma Exacerbation Identifies Mechanisms That Drive Allergic Asthma

  In this study, we will enroll allergic adults to undergo bronchoscopic segmental allergen challenge, in order to identify differences in the airway immune response to allergen in those with asthma compared to those without asthma. After a discussion about the study and potential risks, subjects giving written informed consent will undergo two bronchoscopies. During the first procedure, samples will be collected from the left lung and allergen will be administered to a small segment of the right lung. The second procedure will be performed 24 hours later, with collection of samples from the allergen-challenged lung segment.

  Study phs003101

• TCR Repertoire Sequencing to Evaluate the Diversity of Follicular Helper T Cells in HIV Infected Lymph Nodes

  The TCR repertoire of CD4+ T cells in human lymph nodes is a case-based analysis of the TCR repertoire of CD4+ T cells in human lymph nodes. The study aims to determine how HIV infection alters the repertoire complexity of follicular helper T cells (TFH) in relationship to other T cell subsets in the lymphoid compartment. This study performs TCR repertoire sequencing using Molecular Identifier Clustering-based Immune Repertoire Sequencing (MIDCIRS). We found TFH cells become clonally expanded and convergently selected in LNs from patients with chronic HIV infection.

  Study phs001548

• Functional Analysis of Genetic Variants in African Americans with Breast Cancer

  The goal of this study is to identify and characterize novel genetic variants associated with a predisposition to breast cancer (BCa) in African Americans (AAs) using a family case-family control study design. Variants of unknown clinical significance (VUS) were characterized using bioinformatics tools. Future studies will further characterize select VUSs using in vitro genomic editing methods and functional assays to determine the functional consequences. The targeted sequencing data is made available for 85 actionable cancer genes. These genes have been previously classified with deleterious mutation(s) and whose phenotype results in a specific, defined medical recommendation(s).

  Study phs002977

• Population Genetics Analysis Program: Immunity to Vaccines/Infections - Smallpox Vaccination (NIAID/NIH)

  The study examines the role of candidate human immune response gene polymorphisms (and their receptors, expression and function) and variations in immune response, among 1,000 active duty members of the military who were recently vaccinated with ACAM2000 or Dryvax Smallpox vaccine. In addition to the phenotype and genotype data available through dbGaP, extensive clinical data are available through NIAID's ImmPort data portal; information to map the the data available in dbGaP to the data available in ImmPort is provided in the dataset pht005302.v1.p1 of the current study, dbGaP phs001057.v1.p1.

  Study phs001057

• Analysis of the Genetic Basis of Height in Large Jewish Nuclear Families

  This is a family based study of the genetic basis of height, which focused on very large nuclear families (10 siblings or more, average of 12), all from a founder (Jewish) population. All participants have completed their growth. This study design increases the frequency of some genetic variants that are rare in a cosmopolitan population but segregate in our cohort. Participants were genotyped with a ~630,000 SNP array (Affymetrix Axiom Biobank), and their standing height, sitting height and arm span were measured with high accuracy (±0.1 cm, with 4 technical repeats). All genomic coordinates refer to genome build hg19.

  Study phs001852

• RNA-Seq of Whole Blood from Pediatric Sickle Cell Anemia (SCA) Patients

  The aim of this study is to define the immune cell transcriptome by next generation RNA sequencing in blood from individuals with SCA, in comparison to healthy African American controls. This study has a cross-sectional case-control design. We will compare the transcriptome profiles of blood mononuclear cells from healthy age-matched African American children without cardiovascular disease or risk factors (“Controls”) to those of children with SCA, age 5 -21 years, who are not receiving chronic red blood cell transfusions or hydroxyurea therapy to identify genes that are differentially expressed in SCA. 

  Study phs002687

• Correction of the cytosine deamination artifacts in FFPE-based sequencing experiments

  Formalin-fixed paraffin-embedded (FFPE) samples are widely used in research and diagnostics, but cytosine deamination during fixation introduces sequencing artifacts, particularly C>T substitutions, which complicate reliable mutation detection. In this study, we systematically evaluated five computational methods and an enzymatic repair approach for FFPE artifact removal, as well as their combined application, using a custom dataset based on whole exome sequencing. Our results demonstrate that while computational strategies improve data quality, the enzymatic approach provides the most effective artifact correction. The study provides guidelines for both computational and enzymatic artifact correction strategies for reliable downstream analyses.

  Study EGAS50000001354

• Aberrant expression of SLAMF6 constitutes a targetable immune escape mechanism in acute myeloid leukemia

  In this study, we demonstrate that aberrant expression of SLAMF6 on acute myeloid leukemia (AML) cells serves as a novel immune escape mechanism that can be inhibited by antibodies against the SLAMF6 dimerization site. This constitutes a novel mechanism of checkpoint inhibition, which paves the way for immunotherapy in AML and other SLAMF6-expressing cancers. This study utilizes single cell sequencing data from the AML cell line HNT-34 co-cultured with normal T cells, with and without antibody targeting SLAMF6, as well as single cell data of 38 primary AML samples.

  Study EGAS50000001085

• Whole exome sequencing and RNA sequencing of cervical cancer

  We designed this study to identify molecular markers involved in the development and prognosis of cervical adenocarcinoma. In this study, we would like to elucidate the molecular biological characteristics of cervical adenocarcinoma in relation to the carcinogenesis of other cervical cancers (squamous cell carcinoma), vaginal and vulvar cancers. In addition, some squamous cell carcinomas of the cervix develop at a young age and have a poor prognosis. Furthermore, small cell carcinoma of the cervix also progresses rapidly and has a poor prognosis, making the establishment of diagnostic and therapeutic methods an urgent task.

  Study JGAS000586

• Whole exome sequencing and RNA sequencing of cervical cancer

  We designed this study to identify molecular markers involved in the development and prognosis of cervical adenocarcinoma. In this study, we would like to elucidate the molecular biological characteristics of cervical adenocarcinoma in relation to the carcinogenesis of other cervical cancers (squamous cell carcinoma), vaginal and vulvar cancers. In addition, some squamous cell carcinomas of the cervix develop at a young age and have a poor prognosis. Furthermore, small cell carcinoma of the cervix also progresses rapidly and has a poor prognosis, making the establishment of diagnostic and therapeutic methods an urgent task.

  Study JGAS000582

• Lethal malformation syndrome

  Identification of the genetic basis of rare monogenic diseases can provide insights into disease mechanisms, biological pathways and potential therapeutic targets. Exome sequencing has proven to be a powerful, efficient strategy for the identification of the genes underlying rare Mendelian disorders. The genetic defect behind the lethal malformation syndrome under study is known in some cases and has proven useful in revealing the primary underlying defect. We have six typical unrelated families with no known mutation. The aim of this study is to identify the locus associated with this lethal malformation syndrome in these families using exome sequencing.

  Study EGAS00001000061

• DNA from colon cancer samples and matched normal samples was hybridized on Human 660W-Quad SNP arrays and sequenced in Illumina HiScanSQ.

  DNA from colon cancer samples and matched normal samples was hybridized on Human 660W-Quad SNP arrays and sequenced in Illumina HiScanSQ. The objective of the study was to introduce methodology for the detection of genomic copy number alterations (CNAs) using high-throughput sequencing data. The samples in this study allow the comparison of the results from the seqCNA R package with those from other methods that detect copy number alterations (CNAs) in tumoural samples, either using SNP-array data or high-throughput sequencing data.

  Study EGAS00001000558

• SNP genotyping data in genes related to trace element homeostasis

  In this study we provide data regarding sample charactheristics and genotypes in 150 human samples of European origin for SNPs located around genes related to metal homeostasis. SNPs were genotyped with the Illumina VeraCode technology (192-plex format). The genotyped SNPs were used to identify quantitative trait loci in the same samples. Data referring to the quantification of 18 micronutrients, the expression levels of 90 genes and the protein abundances of 40 proteins related to metal homeostasis in the same samples are directly available as supplementary material in the publication of this study.

  Study EGAS00001001292