12501 results for ""non-traditional+communal+storytelling+approach"+novel+segment+noted+in+critical+commentary"

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• Phase I Clinical Trial Describing the Pharmacogenomics of Aspirin

  The study protocol for both cohorts has been previously described (Journal of Thrombosis and Thrombolysis 2012:1-12). HV1 cohort: Briefly 50 healthy volunteers were exposed to two weeks of 325mg/day aspirin after which whole blood RNA was collected in PAXgene tubes and profiled by microarray before and after aspirin exposure. The pre-aspirin samples were profiled on the U133A 2.0 array and the post-aspirin samples were profiled on the U1333plus 2.0 array. HV2 cohort: Briefly 53 healthy volunteers were exposed to four weeks of 325mg/day aspirin after which whole blood RNA was collected in PAXgene tubes and profiled by U133plus 2.0 array before and after aspirin exposure.

  Study phs000548

• Germline

  This study is part of the 'First 1,000 Days of Life and Beyond' study at the Inova Translational Medicine Institute. Whole-genome sequencing data from 1,291 parent-offspring trios was used to study the properties of clustered de novo mutations. The maternal clusters were found to be enriched in regions with accelerated maternal mutation rate and show distinct mutational signatures. For additional details, please refer to: "Germline de novo mutation clusters arise during oocyte aging in genomic regions with increased double-strand break incidence". Jakob M. Goldmann, Vladimir B. Seplyarskiy, Wendy S.W. Wong, Thierry Vilboux, Pieter B. Neerincx, Dale L. Bodian, Benjamin D. Solomon, Joris A. Veltman, John F. Deeken, Christian Gilissen, John E. Niederhuber. Nature Genetics.

  Study phs001522

• Ameloblastoma Cell Line Resource

  Ameloblastoma (AB) is an odontogenic tumor that is locally destructive to the jaw bone. Treatment entails surgical resection, but AB often recurs locally. Recent driver mutations have been identified in the MAPK and Hedgehog pathways. However, translation to molecularly-targeted therapies has been hampered by the lack of AB cell line models. The goal of our study has been to create a new AB cell line resource that reflects the spectrum of AB driver mutations. We created 6 new AB cell lines, and by targeted exome sequencing, defined their driver mutations. We showed the utility of these cell lines in preclinical studies of oncogene dependence and drug sensitivity (which includes whole transcriptome assays).

  Study phs002753

• Longitudinal Study of the Porphyrias

  This is an observational, longitudinal study of approximately 800 individuals with various types of porphyria. Those participants will be evaluated annually for 5 years, or longer if they agree. Participation in this project will include: Participating in annual visits or contacts. Providing samples, including blood, buccal cells (cells from inside of the mouth), saliva, and urine. The type of samples and amounts may vary from person to person, depending on the type of porphyria. Giving permission for samples to be stored and used for porphyrias research. Granting permission to obtain your medical records. Providing information about your medical history and family history. Completing a questionnaire about your porphyria symptoms and quality of life.

  Study phs001278

• Sweden-Schizophrenia Population-Based Case-Control Exome Sequencing

  Current findings of the genetic risk of schizophrenia and bipolar disorder emerging from genome wide association studies (GWAS) support a highly polygenic model displaying the full spectrum of causal alleles that includes the extremes of rare, penetrant alleles as well as common alleles of small effect. Lower frequency polymorphism, rare variants and private mutations have eluded measurement by GWAS studies and thus association with disease. In order to create a comprehensive catalogue of low frequency or rare coding variation in individuals with psychiatric disease and to build a foundation for future genetic studies of schizophrenia and bipolar disorder, we have obtained whole exome DNA sequence from a population-based schizophrenia and bipolar disorder Swedish case-control cohort.

  Study phs000473

• Multiethnic Cohort Adiposity Phenotype Study (MEC-APS)

  A total of 1,861 healthy men and postmenopausal women aged 60-77 years with body mass indexes (BMIs) of 17.1-46.2 kg/m2 were enrolled into the study. Stratified sampling was conducted based on sex, race/ethnicity, and six BMI categories (18.5-21.9, 22-24.9, 25-26.9, 27-29.9, 30-34.9, and 35-40 kg/m2) to balance the sample size across the wide range of BMI and optimize adjustment for total adiposity in populations with different BMI distributions. Study participants underwent body composition assessment, in person interview, blood collection, and completed a self-administered questionnaire. A genome-wide association study of obesity phenotypes was conducted among five racial/ethnic groups of the Multiethnic Cohort Study.

  Study phs001689

• National Institute of Mental Health (NIMH) Amish Mennonite Bipolar Genetics Study (AmBiGen)

  Bipolar affective disorder is a severe, heritable condition affecting about one percent of the population. The mode of inheritance is poorly understood and probably involves multiple loci of small to moderate effect. In this project, we use genetic mapping and sequencing methods to identify genetic markers and variations that contribute to the risk of bipolar disorder. Individuals diagnosed with bipolar disorder are studied, along with their relatives. Phenotypic information obtained from clinical interviews and family history is correlated with genotypic information obtained from genetic marker and sequencing methods. The goal is to identify genes involved in bipolar disorder and related conditions so that better methods of diagnosis, treatment, and prevention can be developed.

  Study phs000899

• Mega-GWAS ALS I

  Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder clinically characterized by rapidly progressive paralysis and death due to respiratory failure, typically within two to three years of symptom onset. The number of ALS cases across the globe will increase to nearly 400,000 in 2040, predominantly due to aging of the population. Unraveling the genetics underlying ALS provides insights into the cellular mechanism leading to motor neuron death and provides targets for therapeutic intervention. We performed a genome-wide association study involving a meta-analysis of 20,806 ALS cases and 59,804 controls. The current study release makes available genotype data of the 15,480 subjects assayed in the Laboratory of Neurogenetics for this effort.

  Study phs000101

• NHLBI TOPMed - NHGRI CCDG: UCSF Atrial Fibrillation Study

  The University of California San Francisco (UCSF) Cardiovascular Research Institute (CVRI) Resource in Arteriosclerosis and Metabolic Disease is an ongoing multi-ethnic study of adults ≥ 18 years of age which was started in 1989 and now includes 28,000 participants recruited from the UCSF medical system. Within the Resource lies data and biospecimens from nearly 1,000 patients presenting to the electrophysiology laboratory for electrophysiology procedures that were densely phenotyped for electrophysiologic characteristics with biospecimens collected from various intra and extra-cardiac chambers. Phenotyping of all participants was achieved via interview and review of medical records. A subset of 113 participants with early-onset atrial fibrillation underwent WGS as a part of the TOPMed Program.

  Study phs001933

• Single-cell RNA sequencing of pediatric Hodgkin Lymphoma to study the inhibition of T cell subtypes

  Here, we applied single-cell RNA-sequencing (scRNA-seq) on isolated HRS cells and the immune cells from the same cHL tumors. This allowed us to identify genes of cell surface proteins that are consistently overexpressed in HRS cells and can potentially be used as targets for antibody-drug conjugates or CAR T cells. Finally, we identify potential interactions by which HRS cells inhibit T cells, among which the Galectin-1/CD69 and HLA-DRA/LAG3 interactions. However, high levels of inter-patient heterogeneity of the interaction strength were observed. In conclusion, this study identifies new potential therapeutic targets for cHL and highlights the importance of studying heterogeneity when identifying therapy targets.

  Study EGAS50000000432

• Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients

  Our previous studies in mechanically ventilated Intensive Care Unit (ICU) patients with extrapulmonary sepsis revealed that pulmonary dysbiosis within 8 h from sepsis diagnosis was associated with ICU mortality. These observations offer promising options that could be technologically adapted to rapidly identify those patients at higher risk of death. However, they relied on 16S rRNA sequencing experiments which impedes deep characterization of the bacterial communities that could help to further substantiate the association. To further discern this association, here we assessed the pulmonary bacterial communities in these patients by leveraging metagenomics and evaluated if the presence of antibiotic resistance genes could explain the higher mortality of the patients.

  Study EGAS50000000384

• A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy

  The accurate identification and prioritization of antigenic peptides is crucial for the development of personalized cancer immunotherapies. Publicly available pipelines to predict clinical neoantigens do not allow direct integration of mass spectrometry immunopeptidomics data, which can uncover antigenic peptides derived from various canonical and non-canonical sources. To address this, we present an end-to-end clinical proteogenomic pipeline, called NeoDisc, that combines state-of-the-art publicly available and in-house software for immunopeptidomics, genomics and transcriptomics with in-silico tools for the identification, prediction, and prioritization of tumor-specific and immunogenic antigens from multiple sources, including neoantigens, viral antigens and high-confidence tumor-specific antigens.

  Study EGAS50000000228

• Emirati T2T Assembly

  This study generates a telomere-to-telomere (T2T) trio-based genome assembly for a female Emirati individual, creating a high-quality reference representative of an understudied population. We produced multi-platform sequencing for a single family trio: PacBio HiFi (>60× per parent, >120× offspring), ONT ultra-long reads (>110× offspring), and Illumina short-read WGS (>100× for all three). The offspring genome was assembled in a trio framework to leverage parental information for accurate phasing and error resolution. Scaffolding and finishing utilized NTLink for initial scaffolding, RagTag for reference-guided refinement, and Quartett for gap filling, resulting in a contiguous, population-relevant assembly suitable for downstream variant discovery and pangenome integration.

  Study EGAS50000001235

• Whole blood RNAseq from a large ALS case-control study at Univ of Michigan

  Patients with amyotrophic lateral sclerosis (ALS), a rare fatal neurodegenerative disease, face a lengthy diagnostic process, and, although most survive only 2 to 4 years from diagnosis, lack information regarding their specific anticipated disease course due to a lack of prognostic tools. Although ALS is a heterogeneous disease of varied etiology, peripheral immune system dysfunction is ubiquitous, reflected in altered whole blood transcriptome. Herein, we profiled whole blood gene expression by RNA sequencing in a large cohort of ALS cases versus controls. Several machine learning classifiers trained on our gene expression dataset predicted case-control status and survival, and integration analysis with external cohorts led to the identification of drug candidates.

  Study EGAS50000001019

• CAGE analysis for non-small cell lung carcinoma

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. The most effective regimen in lung cancers is different between squamous cell carcinoma (SCC) and adenocarcinoma (AD). Therefore a precise diagnosis is crucial, but this has been difficult, particularly for poorly differentiated SCC (PDSCC) and AD without a lepidic growth component (non-lepidic AD). Biomarkers enabling a precise diagnosis are therefore urgently needed. To achieve this goal, we performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 97 frozen tissues from surgically resected lung cancers (22 SCC and 75 AD). The result was followed up by by immunohistochemical analysis (IHC) in an independent group.

  Study JGAS000070

• Long-read whole genome sequencing of gastric cancer

  Gastric cancer (GC) remains a significant health challenge globally, with a particularly high incidence in Asia, including Singapore. Understanding the genomic landscape of normal gastric and the different GC subtypes along with its precursor lesions such as intestinal metaplasia (IM) as well as GC metastatic sites is crucial for advancing diagnostics, prognostics, and therapeutics. Long-read sequencing technologies offer an opportunity to delve deeper into the genomic and epigenetic alterations underlying these conditions and to complement existing short-read omics data. By integrating these data with previously generated in-house multi-omics data (such as RNA sequencing and whole exome sequencing), we hope to better elucidate the molecular mechanism underlying GC initiation and progression.

  Study EGAS50000001607

• Identification_of_genes_involved_in_congenital_disorders_of_glycosylation_and_3_methylglutaconic_aciduria

  Identification of genes involved in congenital disorders of glycosylation and 3-methylglutaconic aciduria. There are more than 100 genes known for congenital disorders of glycosylation and new disorders are discovered each year. WE included patients with a so far unsolved glycosylation disease. The diagnostic group 3-methyglutaconic aciduria is a heterogenous group of disorders mostly caused by abnormal phospholipid synthesis or in association with mitochondrial dysfunction. We included patients with a so far unsolved disease and 3-methylglutaconic aciduria. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002064

• Illumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001002598

• ProjectMinE :llumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001003383

• Genomic Analysis of Primary Plasma Cell Leukemia reveals Complex Structural Alterations and High Risk Mutational Patterns

  Primary plasma cell leukemia (pPCL) is a rare and aggressive form of multiple myeloma (MM) that is characterized by circulating plasma cells. Overall survival remains poor despite advances of anti-MM therapy. In an attempt to identify key biological mechanisms that result in the aggressive pPCL phenotype we performed whole exome sequencing of 23 patients with pPCL. For matched non-tumor control for each patient to exclude germline variants we used CD34+ cells from stem cell harvest (n=20) or cells obtained from buccal swabs (n=3). Tumor samples were from bone marrow derived CD138+ cells. Tumor samples were compared to the germline control to identify somatic abnormalities.

  Study EGAS00001003834

• Genomic profiling of IBC

  We collected matched pretreatment blood and tumor samples from 19 patients with primary TN-IBC enrolled in a phase II clinical trial (NCT02876107). Patients were treated with neoadjuvant chemotherapy (NAC) or the anti-EGFR antibody panitumumab (PmAb) plus NAC (PmAb/NAC). We conducted whole-exome sequencing, RNA sequencing, and CIBERSORT analyses for these TN-IBC samples and compare the genetic and molecular profiles with similarly analyzed stage III TN-non-IBC patient samples. We also compared the genetic and molecular characteristics of TN-IBC in patients who had a pathologic complete response (pCR) to NAC or PmAb/NAC treatment, a suitable surrogate endpoint for IBC, with those who did not have pCR (non-pCR).

  Study EGAS00001007520

• Genome-to-genome analysis highlights the impact of the human innate and adaptive immune systems on the hepatitis C virus

  Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. We use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals chronically infected with HCV, predominately genotype 3. We show that both HLA alleles and interferon lambda innate immune system genes drive viral genome polymorphism, and that IFNL4 genotypes determine HCV viral load through a mechanism that is dependent on a specific polymorphism in the HCV polyprotein. We highlight the interplay between innate immune responses and the viral genome in HCV control.

  Study EGAS00001002324

• Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers

  To characterize the effects of neoadjuvant chemotherapy (NAC) on the genome, transcriptome and tumor infiltrating leukocytes (TILs), we have conducted whole exome and whole transcriptome sequencing of a comprehensive, longitudinal breast cancer cohort consisting of 146 cases and 281 paired tumor samples. In total, 52 (38%) patients achieved pathologic complete response (pCR) while 85 patients (62%) had residual disease with standard chemotherapy regimen. Tumor biopsies were collected for each patient at three time points – pre-treatment, three weeks after the first cycle of anthracycline and cyclophosphamide (AC) and at the time of surgery after 3 more cycles of AC followed by 4 cycles of taxane or taxane plus Herceptin in case of HER2+ subtype.

  Study EGAS00001003354

• Autoimmunity_and_immunodeficiency_COVID19

  Cell Atlas of COVID-19 patients with Pre-existing Autoimmunity and Immunodeficiency conditions COVID-19 disease is characterized by hyperinflammation of the lungs and poor immune response against the virus, leading to acute respiratory distress syndrome. Patients with pre-existing medical conditions strongly correlated with poorer clinical outcomes upon SARS-CoV-2 infection. This study aims to characterize the cellular response to SARS-CoV-2 infection in controls and in patients with primary immunodeficiency and autoimmune disease. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001004489

• Alveolar Rhabdomyosarcoma case report

  Rhabdomyosarcoma (RMS) is a mesenchymal malignancy phenocopying muscle and is among the leading causes of death from childhood cancer. Metastatic alveolar rhabdomyosarcoma is the most aggressive subtype with an 8% five-year disease-free survival rate when a chromosomal fusion is present, and 40% five-year disease-free survival rate when negative for a fusion event. The underlying biology of PAX-fusion negative alveolar rhabdomyosarcoma remains largely unexplored and is exceedingly rare in Li-Fraumeni syndrome patients. Here, we present the case of an 11-year old male with fusion-negative alveolar rhabdomyosarcoma studied at end of life with a comprehensive functional genomics characterization, resulting in identification of potential therapeutic targets for broader investigation.

  Study EGAS00001004828