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Sarcoma Classification by DNA-methylation profiling

UID: 10782

Author(s): Schrimpf, Daniel

Description
Summary and Overall design from the GEO: "DNA methylation classification reference set (1077) and validation set (428) of 1505 sarcoma samples using Illumina HumanMethylation450 BeadChips or Illumina Infinium HumanMethylation850 BeadChips"

This data set is used to support the classification of soft tissue and bone tumors using a machine learning classifier algorithm based on array-generated DNA methylation data. The tool created is available at: www.molecularsarcomapathology.org.

Abstract from the study:
"Sarcomas are malignant soft tissue and bone tumours affecting adults, adolescents and children. They represent a morphologically heterogeneous class of tumours and some entities lack defining histopathological features. Therefore, the diagnosis of sarcomas is burdened with a high inter-observer variability and misclassification rate. Here, we demonstrate classification of soft tissue and bone tumours using a machine learning classifier algorithm based on array-generated DNA methylation data. This sarcoma classifier is trained using a dataset of 1077 methylation profiles from comprehensively pre-characterized cases comprising 62 tumour methylation classes constituting a broad range of soft tissue and bone sarcoma subtypes across the entire age spectrum. The performance is validated in a cohort of 428 sarcomatous tumours, of which 322 cases were classified by the sarcoma classifier. Our results demonstrate the potential of the DNA methylation-based sarcoma classification for research and future diagnostic applications."
Subject of Study
Homo sapiens
Subject(s)
Bone Neoplasms
Neoplasms, Connective and Soft Tissue
Sarcoma
Access via GEO

Plain Text and IDAT files of methylation profiling by array
Accession #: GSE140686

Access via BioProject

Additional information about the overall initiative.
Accession #: PRJNA590525

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus and BioProject databases provide open access to these files.
Associated Publications
Koelsche C, Schrimpf D, Stichel D, et al. Sarcoma classification by DNA methylation profiling. Nature Communications. 2021; 12:498.
Data Type
Genomic
Equipment Used
Illumina HumanMethylation450 BeadChip
Illumina Infinium MethylationEPIC

Methylation profiling microarray with coverage of CpG islands, genes, and enhancers. Use for epigenome-wide association studies.

Dataset Format(s)
Plain Text, IDAT
Data Tool(s)
Methylation (CpG)
Dataset Size
33.4 GB
Data Catalog Record Updated
2021-11-04