Omics · study · 2026
Identification and validation of liquid biopsy-based methylation biomarkers for germ cell tumor subtypes [7]
Listed in NCBI GEO
Human germ cell tumors (GCTs) occur in infants, children, and adults, and present as germinomatous and/or non-germinomatous (embryonal carcinoma, teratoma, yolk sac tumor (YST), and choriocarcinoma) histologies at gonadal or extragonadal locations.
Description
Accurate subtyping is crucial for prognosis and treatment, but current clinical biomarkers lack sensitivity and specificity (serum proteins) or require a tissue biopsy (immunohistochemistry).
Hence, less-invasive and improved subtype-specific biomarkers have potential for clinical utility. We conducted a meta-analysis of DNA methylation data (450K/EPIC array) from 15 (three original and 12 published) datasets including 713 GCTs, 109 healthy testis, and 221 healthy peripheral blood samples, revealing that GCT histology is the primary driver of methylation profiles, regardless of tumor location and patient’s age or sex.
Read the rest (2 more)
Per subtype, we identified differentially methylated regions as potential biomarkers. As proof of concept, we identified and validated two YST-specific biomarkers, i.e., APC and DPP7 promotor methylation, using methylation-sensitive restriction enzyme-based qPCR, of which DPP7 was also detectable in GCT serum-derived cell-free DNA. In conclusion, we present a novel method for in silico identification and in vitro and in vivo validation of YST subtype-specific liquid biopsy-based biomarkers.
Our bioinformatic pipeline is also easily transferrable encouraging additional applications in pan(pediatric)-cancer studies beyond GCTs.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE303nnn/GSE303826 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE303826 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1297736 ncbi.nlm.nih.gov/bioproject/PRJNA1297736 ↗
project · from NCBI GEO
- PubMed 41998312 pubmed.ncbi.nlm.nih.gov/41998312 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Homo sapiens · Methylation profiling by array
- From keywords
- Life Sciences
- Inferred from text
- Cancer 65% · Germ cell tumor 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE303826 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[disease].local:disease:germ-cell-tumor | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:methylation-profiling-by-array | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |