RNA sequencing profiles for thyroid tumor tissue specimens
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE138042 | GEO | 2019/12/01
REPOSITORIES: GEO
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Project description:The inherent diagnostic limitations of thyroid fine needle aspiration (FNA), especially in the “indeterminate” category, can be partially overcome by molecular analyses. We aimed at the identification of miRNAs that could be used to improve the discrimination of indeterminate FNAs. miRNA expression profiling was performed for 17 follicular carcinomas (FTCs) and 8 follicular adenomas (FAs). The microarray results underwent cross-comparison using three additional microarray data sets. Candidate miRNAs were validated by qPCR in an independent set of 32 FTCs and 46 FAs. Sixty-eight differentially expressed miRNAs were identified. Thirteen miRNAs could be confirmed by cross comparison. A two-miRNA-classifier was established improving the diagnostic applicability and resulted in a sensitivity of 82% and a specificity of 49%. We present a classifier that has the potential to be successfully evaluated in cytology material for its capability to discriminate (mutation negative) indeterminate cytologies and thereby improving the pre-surgical diagnostics of thyroid nodules.
2014-10-07 | GSE62054 | GEO
Project description:The inherent diagnostic limitations of thyroid fine needle aspiration (FNA), especially in the “indeterminate” category, can be partially overcome by molecular analyses. We aimed at the identification of miRNAs that could be used to improve the discrimination of indeterminate FNAs. miRNA expression profiling was performed for 17 follicular carcinomas (FTCs) and 8 follicular adenomas (FAs). The microarray results underwent cross-comparison using three additional microarray data sets. Candidate miRNAs were validated by qPCR in an independent set of 32 FTCs and 46 FAs. Sixty-eight differentially expressed miRNAs were identified. Thirteen miRNAs could be confirmed by cross comparison. A two-miRNA-classifier was established improving the diagnostic applicability and resulted in a sensitivity of 82% and a specificity of 49%. We present a classifier that has the potential to be successfully evaluated in cytology material for its capability to discriminate (mutation negative) indeterminate cytologies and thereby improving the pre-surgical diagnostics of thyroid nodules. miRNA expression profiling was performed for 17 follicular carcinomas (FTCs) and 8 follicular adenomas (FAs). All samples are independent, coming from different patients.
2014-10-07 | E-GEOD-62054 | biostudies-arrayexpress
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Associated BioSamples accessions: <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397999">SAMEA2397999</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398167">SAMEA2398167</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398916">SAMEA2398916</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397948"> SAMEA2397948 </a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399112">SAMEA2399112</a>,<a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399257">SAMEA2399257</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398553">SAMEA2398553</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398821">SAMEA2398821</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398316">SAMEA2398316</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2469778">SAMEA2469778</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399037">SAMEA2399037</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398656">SAMEA2398656</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398428">SAMEA2398428</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2469777">SAMEA2469777</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397959">SAMEA2397959</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398442">SAMEA2398442</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398024">SAMEA2398024</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398450">SAMEA2398450</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA3402864">SAMEA3402864</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA3110364">SAMEA3110364</a>
2016-06-06 | PXD003903 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE23384: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples) GSE23385: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples) Refer to individual Series
2011-06-22 | E-GEOD-23386 | biostudies-arrayexpress
Project description:PURPOSE: Thyroid cancer is frequently difficult to diagnose due to an overlap of cytological features between malignant and benign nodules. This overlap leads to unnecessary removal of the thyroid in patients without cancer. While providing some improvement over cytopathologic diagnostics, molecular methods frequently fail to provide a correct diagnosis for thyroid nodules. These approaches are based on the difference between malignant nodules and normal adjacent thyroid tissue and assume that normal thyroid tissues are the same as benign nodules. However, in contrast to normal thyroid tissues, benign thyroid nodules can contain genetic alterations that can be found in cancerous nodules. PATIENTS AND METHODS: For the development of a new molecular diagnostic test for thyroid cancer, we evaluated DNA methylation in 109 thyroid tissues by using genome wide single base resolution DNA methylation analysis (Reduced Representation Bisulfite Sequencing). The test was validated in the retrospective cohort containing 64 thyroid nodules. RESULTS: By conducting Reduced Representation Bisulfite Sequencing in 109 thyroid specimens, we found significant differences between normal tissue, benign nodules, and cancer. Based on tissue-specific epigenetic signatures for benign and malignant nodules, we developed a new epigenetic approach for thyroid diagnostics. According to the validation cohort, our test has an estimated specificity of 97% (95% CI, 80 to 100), sensitivity of 100% (95% CI, 86 to 100), PPV of 97% (95% CI, 82-100), NPV of 100% (95%, 85 to 100). CONCLUSION: These data show that epigenetic testing can provide outstanding diagnostic accuracy for thyroid nodules by evaluating tissue specific DNA methylation.
2018-11-30 | GSE107738 | GEO
Project description:While thyroid nodules per se are frequent (4%–50%), thyroid cancer is rare (∼5% of all thyroid nodules). The minimally invasive Fine Needle Aspiration Cytology (FNAC) is the current gold standard for the diagnosis thyroid nodule malignancy. However, proper discrimination of follicular neoplasias often require more invasive diagnostic techniques. To develop a novel molecular classification system for thyroid cancer malignancy, we performed a genome-wide epigenetic profiling of 54 fresh frozen Follicular like thyroid samples using the Illumina Human DNA Methylation EPIC platform.
2022-09-01 | E-MTAB-10906 | biostudies-arrayexpress
Project description:Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer among women worldwide. It is confirmed mainly by fine-needle aspiration biopsy (FNAB), an invasive diagnostic method. The key proteins responsible for thyroid hormone biosynthesis are glycosylated. Changes in site-specific glycosylation are associated with thyroid cancer. Integrated quantitative proteomic and glycoproteomic analyses of body fluids from patients with PTC may identify potential noninvasive biomarkers, improve diagnostic accuracy, and elucidate the basic mechanisms of tumor development. In the present study, we demonstrated a novel integrated method of body fluid proteome and glycoproteome analysis. We showed that it is highly reproducible and fast. It may also quantitatively profile protein glycosylation. Intact N-glycopeptides from the urine and plasma of healthy controls (HC), PTC, and PTC with Hashimoto’s thyroiditis (PHT) were enriched by hydrophilic interaction liquid chromatography. Sialic acid was removed from the N-glycopeptides with trifluoroacetic acid and heat. The desialo-N-glycopeptides were analyzed by HCD-MS/MS using stepped collision energies and several search engines for quantitative profiling. Ninety-two altered proteins and 134 intact N-glycopeptides were isolated from the plasma and urine samples of the three groups (90 samples from 15 subjects). To the best of our knowledge, this study is the first to compare the plasma and urinary proteomes and glycoproteomes of HC, PTC, and PHT. Moreover, we revealed a novel indicator (ratio of fucosylated to non-fucosylated N-glycopeptide or F/NF) through desialo-N-glycopeptide analysis. These differently expressed glycoproteins and F/NF may serve as biomarkers contributing to clinical cancer diagnostics and could be used to improve diagnostic accuracy noninvasively.
2019-12-09 | PXD015360 | Pride
Project description:Cavitating ultrasonic aspirator devices are frequently used in pediatric neurosurgery for efficient microsurgical resection of brain tumours while minimizing tissue damage to surrounding healthy brain. Within this study molecular diagnostics using methylation-based classification of ultrasonic aspirated samples was performed and performance against routine microarray diagnostics was assessed.
2024-02-08 | GSE255044 | GEO
Project description:Multiple myeloma (MM) is a hematological cancer which arises from abnormal antibody producing white blood plasma cells. MM affected approximately 500 000 people and results in ~100 000 deaths annually, being currently considered treatable but uncurable. There are several MM chemotherapy treatment regimens, among which ten include bortezomib, a proteasome-targeted drug. Patients with MM respond differently on bortezomib, and new prognostic biomarkers are needed to personalize treatments. However, there is a shortage of clinically annotated molecular profiles of MM that could be used to establish novel molecular diagnostics. In this study we report new molecular profiles for 58 MM patients annotated with data on two chemotherapy regimens which include bortezomib, doxorubicin, and dexamethasone (PAD) or bortezomib, cyclophosphamide, and dexamethasone (VCD). MM biosamples were taken prior to first line chemotherapy treatments and subjected to RNA sequencing.
2021-10-01 | GSE159426 | GEO
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2016-07-24 | MSV000080004 | MassIVE