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Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes Using a TaqMan Low-Density Array [Human Clariom D array]

ABSTRACT: Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes Using a TaqMan Low-Density Array [Human Clariom D array]

PROVIDER: PRJNA543103 | ENA |

REPOSITORIES: ENA

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Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes Using a TaqMan Low-Density Array [Taqman Low Density Array]

Project description:Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes Using a TaqMan Low-Density Array [Taqman Low Density Array]

| PRJNA543777 | ENA

Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes Using a TaqMan Low-Density Array [Human Clariom D array]

Project description:Diagnosis of glioma into the hierarchy of human brain development would greatly facilitate mechanistic studies and clinical services in combating glioma. By analysing the multi-dimension big data of glioma genome and clinical manifestations, we have recently developed an EM/PM classification scheme anchored in the brain development and glioma pathogenesis (Sun et al., PNAS 111:3538-3543, 2014). To translate the EM/PM classification into a clinical diagnostic tool, we here designed and validated a TaqMan low-density RT-PCR array (TLDA) and a support vector machine (SVM) based prediction model that enables individual diagnosis of gliomas into the EM/PM subtype with high accuracy and precision. Results of 153 individually diagnosed adult diffuse gliomas of WHO grades II-IV derived from Chinese or Swedish patients confirmed our previous data base investigations: EM and PM gliomas show distinct prognosis, occur at different ages, and harbor mutually exclusive patterns of genomic alterations detected by Sanger sequencing and shallow-coverage whole genome sequencing (WGS). Further, we show that shallow-coverage WGS enabled a systematic identification of clonal and subclonal copy number variations (CNV) in glioma genomes, and the extent and the pattern of CNV can serve as an objective marker of tumor progression in the PM gliomas harboring IDH mutations.

2019-05-16 | GSE131273 | GEO

Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes Using a TaqMan Low-Density Array [Taqman Low Density Array]

2019-05-21 | GSE131464 | GEO

Clariom D gene array of HBMEC cells

Project description:Clariom D gene array of HBMEC cells

| PRJNA991457 | ENA

Clariom D gene array of Bone Marrow derived macrophages

Project description:Clariom D gene array of Bone Marrow derived macrophages

| PRJNA1113971 | ENA

Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes

Project description:Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes

| PRJNA543775 | ENA

Individual Assignment of Adult Diffuse Gliomas into the EM/PM Molecular Subtypes

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-05-21 | GSE131465 | GEO

Human Clariom S Array in OVCAR8 cells after silencing HSD17B14

Project description:Human Clariom S Array in OVCAR8 cells after silencing HSD17B14

| PRJNA724979 | ENA

TaqMan mouse miRNA array profile of LY6CHigh and LY6Clow monocyte

Project description:TaqMan mouse miRNA array profile of LY6CHigh and LY6Clow monocyte

| PRJNA566405 | ENA

Analysis of DCIS using Clariom D transcriptomics array

Project description:Experiment description to give context to the data set: Ductal carcinoma in situ (DCIS), the most common type of pre-invasive lesion of breast, is being detected with increasing frequency with the advent of mammographic screening. Surgery is the mainstay for the treatment of DCIS. Based on the clinic-pathological features of DCIS, this may be followed by radiotherapy and/or endocrine therapy. The qualitative assessment of histological grade, expression of single protein biomarkers and more recently, mRNA analysis (DCIS Score) have been used to make these decisions. However, these factors do not fully predict the likelihood of development of invasive breast cancer treated with breast-conserving surgery. A majority of women with ductal carcinoma in situ (DCIS) receive breast-conserving surgery (BCS) but then face a risk of development of invasive breast cancer. Using Human Clariom D Pico Assay, we aim to compare the transcriptome profiles of DCIS in relation to development of invasive breast cancer (INV-BC) versus Non-INV-BC cases. Experimental Methods Clariom D Pico Human Transcriptome Array were performed according to Applied Biosystems/Thermo Fisher Scientific’s instructions. Experimental protocols are summarized in detail in Supplementary Methods (Supplementary Data). Sample annotation We compared the relative gene expression in development of invasive breast cancer (INV-BC) versus Non-INV-BC cases in Singapore cohort-59 cases (discovery cohort) and Italian cohort-50 cases (validation cohort). Microplate Plate and Well IDs are also provided as Clariom D ID list per cohort. Author information Dr. Sunil Badve is the Principal Investigator. Raw Data Probe Cell Intensity (CELL) and .ARR files which contain the design information for this study are provided (Human Clariom D Pico Assay).

2022-06-02 | E-MTAB-9856 | biostudies-arrayexpress

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