16587 results for "sec+and+unspecified+malignant+neoplasm"

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• HiChIP data and analysis in OCI-AML3

  Data and analysis of HiChIP assay of shZNF143 and shControl in OCI-AML3. CTCF was the ChIP antibody. Data files are paired-end reads in FASTQ format from the Illumina NovaSeq 6000 sequencer. Analysis files are paired-end bed files produced by FitHiChIP.

  Dataset EGAD50000001376

• Single cell characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

  Leukemic bone marrow in primary ETV6-RUNX1 positive acute lymphoblastic leukemia samples (Six diagnostic and two 15 days after treatment) using Chromium 3' single cell RNA-seq. Samples sequenced on 1-3 lanes and raw fastq files provided for each sample.

  Dataset EGAD00001006074

• RNA-seq data from DMD patients and healthy controls

  This dataset comprises RNA-seq expression profiles from 57 subjects, of which 39 are DMD patients and 18 healthy controls. The data are described in the following article: Signorelli, Ebrahimpoor et al. (in review). Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients.

  Dataset EGAD00001006826

• Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-be Heart Health Study (nuMoM2b Heart Health Study)

  Participants from study sites that recruited during the original study funded by NICHD of pregnant people, called nuMoM2b, participated in this study. The nuMoM2b-HHS1 was a prospective observational follow-up study of the nuMoM2b cohort consisting of interval contacts via phone or web every 6 months to about a year, and an in-person visit 2 to 7 years after the end of the nuMoM2b pregnancy including: Demographics Self-administered questionnaires Clinical measurements Lab results An in-home sleep breathing assessment for the subset of participants with at least one valid sleep breathing assessment during nuMoM2b Abstraction of medical records for pregnancies subsequent to nuMoM2b involving self-reported adverse pregnancy outcomes or multiple births Abstraction of medical records of selected cardiovascular risk-related events or procedures reported by participants. The study capitalized on the rich and unique data prospectively collected during nuMoM2b (biomarkers, uterine artery Doppler studies, fetal growth, psychosocial determinants, sleep, and blood pressure) and rigorous definitions of adverse pregnancy outcomes. These data are stored in the NICHD repository DASH (https://dash.nichd.nih.gov/study/226675). A total of 8,838 nuMoM2b participants were targeted for contact during nuMoM2b-HHS and 7,872 participants were reached, of whom 7,003 completed one or more interval contacts. Of these, 5,206 agreed to the visit, and 4,508 attended an in-person visit.

  Study phs002808

• Memorial Sloan Kettering (MSKCC) Single Cell Mutational Profiling in Myeloid Malignancies

  Myeloid malignancies have previously been characterized by large scale bulk molecular profiling studies on patient samples. These studies, while clinically informative, are unable to delineate mutation order as well as clonal architecture and complexity. To investigate the clonal framework of myeloid malignancies, the Single Cell Mutational Profiling in Myeloid Malignancies study was designed. This study performed sequencing of 148 samples from 117 adult patients diagnosed with clonal hematopoiesis (n = 21), myeloproliferative neoplasms (MPN; n = 14), and acute myeloid leukemia (AML; n = 82) between 20 and 87 years of age. Sequencing of all samples was performed using the Tapestri single cell DNA sequencing platform from Mission Bio, Inc. The platform utilizes a custom amplicon panel covering 109 amplicons across 31 genes frequently mutated in myeloid malignancies (CH, MPN, AML). Using the single cell DNA sequencing data, we were capable of elucidating clonal architecture and clonal complexity in each sample. In a subset of samples, we also performed simultaneous single cell DNA sequencing and cell surface protein expression analysis using the Tapestri DNA + Protein platform. This study allowed us to determine the expression of 7 cell surface proteins (CD3, CD11b, CD19, CD34, CD38, CD45RA, and CD90) at single cell resolution. We performed DNA+ Protein sequencing on samples from CH patients (n = 7) as well as AML patients (n = 17).

  Study phs002049

• Osteosarcoma Genomics

  In this study we attempt to elucidate the genomic characteristics of osteosarcoma. Clinical characteristics 58 tumor / normal pairs from 58 patients were included in the study. Median age at diagnosis was 12 years. 49% of the patients were male and 47% had metastases at diagnosis. 5 year overall survival was 49% for the entire population, 33% for patients with metastatic disease and 64% for patients with localized disease. Patients with metastatic disease at diagnosis had a significantly worse overall survival. All cases except 2 were sporadic and no patients had stigmata of Rothmund-Thomson, Bloom's or Werner's syndromes or Paget's disease. Two familial cases were affected siblings from a family in which there were 2 unaffected parents and 2 unaffected siblings. None of the patients had known Li Fraumeni or hereditary retinoblastoma. Sample Selection and Clinical Data Samples were contributed by hospitals in Brazil, Spain, Mexico and the United States. All patients had histopathology confirmed to be osteosarcoma by a pathologist at the local institution. All but 5 tumor specimens sequenced were obtained pre-chemotherapy from the primary tumor at the time of diagnosis. 2 tumor specimens were obtained pre-chemotherapy from a metastatic tumor at the time of diagnosis. 3 tumor specimens were obtained post-chemotherapy from a metastatic tumor.

  Study phs000699

• Genomics of Hepatocellular Carcinoma

  Despite the growing incidence of hepatocellular carcinoma (HCC) due to increased hepatitis C virus infection and non-alcoholic steatohepatitis in Western populations, the genetic determinants of this cancer have yet to be established. A minority (15-20%) of HCC occurs in livers without cirrhosis or other chronic disease. Because the liver is functionally preserved in these patients and surgical resection of the tumor may be performed safely, and because of the scarcity of livers available for transplantation, non-cirrhotic patients undergo surgical resection for HCC treatment. These resected tumors present investigatory opportunities in two ways: First, they provide tumor specimen which have not been treated with chemotherapy and embolization. Second, the absence of cirrhosis may provide an unconfounded background from which to investigate the genetic tumorigenesis of HCC. In livers with cirrhosis, genetic instability is prevalent as assessed by assays for microsatellite instability, loss of heterozygosity and aberrant DNA methylation. In contrast, in livers without cirrhosis, the non-tumor tissue surrounding HCC have been found to have fewer genetic aberrations. It has been postulated that the pathologic process of cirrhosis may result in the accumulation of many "passenger"; as well as "driver" mutations, and that the examination of the HCC cancer genome may be facilitated in non-cirrhotic livers because of the absence of an accumulated background noise of mutations.

  Study phs001106

• Transformation of Dysplasia in Barrett's Esophagus

  Complex chromosomal alterations are a hallmark of advanced cancers but rarely seen in normal tissue. The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations that can drive their transformation through focal oncogenic amplifications. However, the etiology and evolution dynamics of these alterations are poorly understood. Here we study chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) by multi-regional whole-genome sequencing analysis of BE samples with dysplasia and microscopic EAC foci. Through haplotype-specific copy-number analysis of BE genome evolution, we identified distinct patterns of episodic copy-number evolution consistent with the outcomes of abnormal mitosis and dicentric chromosome breakage. While abnormal mitosis, including whole-genome duplication, accounts for most chromosome or arm-level copy-number changes, segmental copy-number alterations display signatures of multi-generational evolution of unstable dicentric chromosomes. Continuous evolution of dicentric chromosomes through breakage-fusion-bridge cycles and chromothripsis rapidly increases genomic complexity and diversity among BE cells, culminating in the generation of distinct focal amplifications. These mutational processes enable multiple subclones within small dysplastic areas to undergo parallel transformation to cancer following acquisition of distinct oncogenic amplifications. Our results demonstrate how chromosomal instability drives clonal diversification in precancer evolution and promotes tumorigenesis in primary human samples.

  Study phs002706

• Heterogeneity in Lysosomal Storage Disorders

  Gaucher disease (GD) is an inherited lysosomal storage disorder caused by biallelic pathogenic variants in GBA1, which encodes glucocerebrosidase. Additionally, GBA1 variants are a well-established genetic risk factor for Parkinson's disease (PD), leading some PD research centers to incorporate GBA1 screening to identify patients who may benefit from targeted therapeutics. However, detecting GBA1 variants remains challenging due to the gene's high sequence homology with its pseudogene, which can give rise to complex recombinant alleles. This study evaluates the performance of Gauchian, a recently developed software tool for identifying GBA1 variants from whole genome sequencing (WGS) data. The assessment was conducted in a cohort of 90 individuals with GD and five GBA1 heterozygotes, all previously characterized through Sanger sequencing. While Gauchian successfully identified the most common genotypes, it demonstrated limitations in detecting rare or de novo variants due to its restricted internal database and heavy reliance on intergenic structural variants. These limitations led to misclassified homozygosity, incomplete genotyping, and undetected recombination events, ultimately reducing the tool's utility for comprehensive variant screening and precluding its application in diagnostic settings. The study dataset includes WGS from the 90 individuals used in the Gauchian pipeline. This data will be available through dbGaP to facilitate further research on GBA1 variant detection, genotype-phenotype correlations in GD and PD, and the development of improved bioinformatics tools for complex variant identification.

  Study phs003459

• Re-Evaluation of Systemic Early Neuromuscular Blockade

  This study of the ROSE trial data explored two distinct molecular subtypes of ARDS (Acute Respiratory Distress Syndrome) to better understand the disease's complexity and potential for personalized treatment. Previous studies had identified different inflammatory profiles in ARDS patients, with this research addressing three key questions: Can these molecular subtypes be consistently identified in a more severe group of ARDS patients? Do these subtypes respond differently to neuromuscular blockade treatment? What specific biological processes differentiate these inflammatory profiles? Advanced transcriptomic and protein analyses examined blood samples from ARDS patients. Analysis of these data revealed two main molecular phenotypes: Hypoinflammatory phenotype (60.4% of patients) Hyperinflammatory phenotype (39.6% of patients) Key findings demonstrated that the hyperinflammatory subtype was associated with:Significantly higher mortality rates relative to hypoinflammatory (61.6% vs. 30.3%)Significantly higher mortality rates relative to hypoinflammatory (61.6% vs. 30.3%)Distinct gene expression patterns related to immune responseUnique changes in genes associated with tissue remodeling and cellular processes Notably, the neuromuscular blockade treatment showed no difference in effects across these subtypes. Complex relationships emerged between gene expression and protein levels, with some genes closely matching their protein counterparts and others displaying more variable connections. The study concludes that these molecular phenotypes possess distinct clinical, protein, and genetic characteristics, suggesting potential for more precise, personalized approaches to ARDS treatment in the future.

  Study phs003929