Project description:Array CGH of gDNA extracted from leukemic cells at diagnosis of ALL. Goal was to determine CNV polymorphisms linked with phenotype of ALL and Leri-Weill syndrome.
Project description:whole-genome aCGH analysis also showed us that the patient carried a 12.01-1M Mb deletion region at chromosome bands 9q31.1-q32 (105,190,105-117,195,154). The deleted region encompasses 22 genes including SMC2 Two-condition Samples, Cornelia de Lange Syndrome vs. Normal cells.
Project description:We aimed to identify genes with considerable expression changes between male and female patients with idiopathic carpal tunnel syndrome (ICTS). For this purpose, we collected subsynovial connective tissues from 6 male and 6 female patients diagnosed with idiopathic carpal tunnel syndrome during surgery. We extracted the total RNA from the collected specimens and performed a comprehensive gene expression analysis using RNA sequencing by comparing between male and female patients. We analyzed the changes in gene expression in male patients relative to that in female patients, and as a result, 26 genes were extracted. In the RNAseq analysis, the expression of these genes (IGF1, COL1A1, and COL3A1) was upregulated in the male patient group.
Project description:whole-genome aCGH analysis also showed us that the patient carried a 12.01-1M Mb deletion region at chromosome bands 9q31.1-q32 (105,190,105-117,195,154). The deleted region encompasses 22 genes including SMC2
Project description:Turner syndrome is a relatively rare condition that is usually associated with the loss of all or part of an X chromosome. Amniotic fluid is a complicated biological material, could contribute to the understanding of turner syndrome pathogenesis. In this study, ATAC-seq analysis of Turner syndrome (45X) and Female (46XX) amniotic fluid cells was applied to illustrate that genome wide chromatin accessible landscapes. Our results show that Turner Syndrome has higher chromatin accessibility than Female on autosomes and has lower chromosome accessibility on the X chromosome. We identified candidate genomic regions and transcript factors that may play an important role in Turner syndrome pathogenesis. Our analysis suggests that the phenotype of Turner Syndrome should be the result of abnormal regulation of gene expression in the whole genome, not just the result of insufficient doses of X chromosome haploids.
Project description:Comparison of human iPSC lines, ESC and fibroblasts to determine their expression patterns. All early passage female lines profiled expressed XIST RNA which is an indicator of an inactive X chromosome. Genes on the X-chromosome were also analyzed for overall levels of gene expression compared to human fibroblasts.
Project description:X chromosome dosage compensation is one of the most important epigenetic events in female mammalian development. Although the mouse has served as the primary model to study how genetic equality is established between male and female mammals, it is now appreciated that these mechanisms are not fully conserved in humans. Using human primordial germ cells (hPGCs) as a model together with single cell RNA-sequencing, in vitro differentiation of hPGC like cells and human embryo attachment culture, we show that X-linked gene expression in female hPGCs is compensated to levels found in female somatic cells though a mechanism related to X chromosome dampening rather than X chromosome inactivation. Loss of dampening and decompensation of both X chromosomes occurs when female hPGCs enter meiosis and is coincident with loss of the long non-coding RNAs XIST and XACT. In contrast, differentiation of male hPGCs results in no change in compensation despite loss of XACT. Taken together, future studies of X-linked gene regulation and function in human germ cell development and fertility must take into account the unique and sexually dimorphic dosage compensation occurring during in the prenatal human germline prior to birth.
Project description:Acute febrile neutrophilic dermatosis (Sweet syndrome) is a potentially fatal multiorgan inflammatory disease characterized by fever, leukocytosis, and rash with a neutrophilic infiltrate. Disease pathophysiology remains elusive. Corticosteroids and steroid sparing agents remain mainstays of treatment, but refractory cases pose a clinical challenge. Transcriptomic profiling of a refractory Sweet syndrome patient will improve our understanding of pathophysiology of the disease and, ultimately wiil help us to find a guided therapy. We used microarray to perform molecular characterization of a particular refractory Sweet Syndrome patient and to identify altered pathways that may be targeted via currently available small molecular inhibitors.