14519 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Evolutionary analysis of pancreatic neoplastic cysts through whole-exome and targeted sequencing

  Intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs) are non-invasive neoplasms that are often observed in association with invasive pancreatic cancers, but their origins and evolutionary relationships are poorly understood. In this study, we analyzed 148 samples from IPMNs, MCNs, and small associated invasive carcinomas from 18 patients using whole exome or targeted sequencing.

  Study EGAS00001004473

• Genomic and transcriptomic analysis of baseline PDAC patients' tumors from the OXIRI phase 1b clinical trial

  This study was aimed at investigating the genomic and transcriptomic features associated with response to the OXIRI regimen (oxaliplatin, irinotecan, capecitabine) in pancreatic ductal adenocarcinoma (PDAC) tumors. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) on baseline tumor samples obtained from 8 patients recruited in the OXIRI phase 1b clinical trial (NCT02368860).

  Study EGAS00001006073

• mutational landscape of normal human breast

  The accumulation of somatic mutations in the healthy breast throughout life and pregnancy is poorly understood. Here we describe whole genome sequencing analysis of epithelial and stromal compartments from the normal breast. We aimed to study how pregnancy and age affect both the mutational burden and the clonality of the healthy breast, and the subsequent implications on breast cancer risk.

  Study EGAS00001004672

• Separation, characterization, and identification of individuals from multi-person blood mixtures with single cell transcriptome sequencing and a novel bioinformatics pipeline

  We report a deconvolution and identification strategy of scRNA-seq datasets using mixed PMBCs data. After sequencing the data were processed with the de-goulash pipeline and analyzed with aim to identify and aquire biogeogrpahical ancestry of the involved individuals. The study includes samples of biological mixtures and in silico mixtures.

  Study EGAS00001006202

• Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

  In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

  Study EGAS00001004925

• COVID-19 GWAS in Japanese

  The Japan COVID-19 Task Force (JCTF) was established in early 2020 as a nation-wide multicenter consortium to overcome the COVID-19 pandemic in Japan. We conducted a genome-wide association study (GWAS) involving 2,393 Japanese COVID-19 cases collected in initial pandemic waves with 3,289 controls. GWAS genotyping was performed using Infinium Asian Screening Array (Illumina, USA).

  Study EGAS00001006284

• ALLoreactive T-Cell receptOr RePertoire in kidnEy tranSplantation

  A prospective study for investigating the T-cell receptor (TCR) repertoire in T-cell mediated rejection (TCMR) after kidney transplantation. The pre-formed donor-reactive TCR repertoire was tracked in blood and tissue of patients after kidney transplantation and characteristics of TCR repertoires from patients experiencing a rejection were compared to patients with no histopathological signs of rejection.

  Study EGAS00001005299

• cis-eQTL mapping of TB-T2D comorbidity in a five-way admixed SA cohort

  The aim of the study was to identify ancestry-specific genetic variants associated with differentially expressed genes in TB-T2D comorbid patients compared to T2D patients, as well as between TB patients and healthy controls. Both global and local ancestry was incorporated in regression models to account for the genetic heterogeneity in our complex multi-way admixed population.

  Study EGAS00001007059

• Whole-Exome Sequences from Imazighen and non-Imazghen from Algeria

  Study of high-coverage whole-exome sequences from Amazigh (Tamazight-speakers) and non-Amazigh individuals (Arab-speakers) from Algeria to analyze the impact of demography in functional genomic variation in the complex demographic context of North Africa. Amazigh individuals were sampled in Oum El Bouaghi, Batna, Khenchela, and Ghardaïa, and non-Amazigh individuals were sampled in Algiers.

  Study EGAS00001007236

• Chinese Alternating Hemiplegia of Childhood (AHC) Disease Study

  AHC is a rare and severe neurological disorder, and characterized by episodic hemiplegia or quadriplegia attacks, accompanied by other paroxysmal symptoms of oculomotor abnormalities, dystonia, seizures and autonomic disturbances; the age of onset usually occurrs before 18 months of life. Sodium-potassium ATPase alpha3 subunit (ATP1A3) has recently been identified as a causal gene for sporadic AHC by three groups. However, there has not been any large genetic study on a Chinese cohort. In the submitted data, whole-exome sequencing of three trios and three sporadic cases in a Chinese cohort produced an average of 18.8 gigabases of raw sequence. Through our analysis pipeline including BWA mapping, GATK recalibration, variant calling and filtering, all six patients contained missense mutations in ATP1A3 which were further confirmed as de novo mutations. Along with validation in additional patients, this study confirmed ATP1A3 as a causal gene in Chinese AHC patients, and reported six novel mutations.

  Study phs000660