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Rapid DNA methylation-based classification of pediatric brain tumours from ultrasonic aspirate specimens

ABSTRACT: Rapid DNA methylation-based classification of pediatric brain tumours from ultrasonic aspirate specimens

PROVIDER: PRJNA1073412 | ENA |

REPOSITORIES: ENA

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Rapid DNA methylation-based classification of pediatric brain tumours from ultrasonic aspirate specimens

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

Ultrasonic surgical aspirate is a reliable source for adult neural progenitor cells (aNPCs)

Project description:Adult neural progenitor cells (aNPCs) are a potential source for cell based therapy for neurodegenerative diseases and traumatic brain injuries. We show that the ultrasonic aspirate samples that are typically considered as a waste after surgery are a great source for aHNPCs.

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Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens.

Project description:BackgroundAlthough cavitating ultrasonic aspirators are commonly used in neurosurgical procedures, the suitability of ultrasonic aspirator-derived tumor material for diagnostic procedures is still controversial. Here, we explore the feasibility of using ultrasonic aspirator-resected tumor tissue to classify otherwise discarded sample material by fast DNA methylation-based analysis using low pass nanopore whole genome sequencing.MethodsUltrasonic aspirator-derived specimens from pediatric patients undergoing brain tumor resection were subjected to low-pass nanopore whole genome sequencing. DNA methylation-based classification using a neural network classifier and copy number variation analysis were performed. Tumor purity was estimated from copy number profiles. Results were compared to microarray (EPIC)-based routine neuropathological histomorphological and molecular evaluation.Results19 samples with confirmed neuropathological diagnosis were evaluated. All samples were successfully sequenced and passed quality control for further analysis. DNA and sequencing characteristics from ultrasonic aspirator-derived specimens were comparable to routinely processed tumor tissue. Classification of both methods was concordant regarding methylation class in 17/19 (89%) cases. Application of a platform-specific threshold for nanopore-based classification ensured a specificity of 100%, whereas sensitivity was 79%. Copy number variation profiles were generated for all cases and matched EPIC results in 18/19 (95%) samples, even allowing the identification of diagnostically or therapeutically relevant genomic alterations.ConclusionMethylation-based classification of pediatric CNS tumors based on ultrasonic aspirator-reduced and otherwise discarded tissue is feasible using time- and cost-efficient nanopore sequencing.

| S-EPMC11269392 | biostudies-literature

Ultrasonic surgical aspirate is a reliable source for culturing glioblastoma stem cells

Project description:Glioblastoma stem cells (GSCs) are thought to be the source of tumor growth and therapy resistance. Core biosies that are used to generate GSC cultures are ususally taken from one part of the tumor and are thus unlikely to represent intra-tumoral heterogeneity. This study shows that the ultrasonic aspirates (UA), that are usually considered as a biological waste, can be used as a reliable source of GSCs. Furthermore the UA aspirates seem to be capturing the tumorigenic signature better than the traditional biopsies.

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Transcription profiling of 65 surgical specimens of human breast tumours from 42 different individuals

Project description:Set of 65 surgical specimens of human breast tumours from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. Gene expression variation patterns within this set provided a distinctive molecular portrait of each tumour. Twenty of the tumours were sampled twice, before and after a 16-week course of doxorubicin chemotherapy, and two tumours were paired with a lymph node metastasis from the same patient. Gene expression patterns in two tumour samples from the same individual were almost always more similar to each other than either was to any other sample.

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Evaluation of chromosomal abnormalities and copy number variations in fetuses with ultrasonic soft markers

Project description:This study aimed to evaluate the clinical value of copy number variations (CNVs) in fetuses with ultrasonic soft markers. Among 1131 fetuses, 729 had single ultrasonic soft marker, 322 had two ultrasonic soft markers, and 80 had three or more ultrasonic soft markers. All fetuses underwent single nucleotide polymorphism (SNP) array analysis. Among 1131 fetuses with ultrasonic soft markers, 46 had chromosomal abnormalities. In addition to the 46 fetuses with chromosomal abnormalities consistent with the results of the karyotyping analysis, the SNP array identified additional 6.1% (69/1131) abnormal CNVs. No significant difference was found in the rate of abnormal CNVs among the groups. The SNP array can fully complement conventional karyotyping in fetuses with ultrasonic soft markers, improve detection rate of chromosomal abnormalities, and affect pregnancy outcomes.

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Project description:Bladder tumours used to construct a tumour stage classifier Keywords = bladder cancer, disease stages, classification Keywords: other

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