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Germ cell neoplasia in situ (GCNIS) is the origin of TGCTs, namely, seminomas (SE) and a heterogeneous group of nonseminomas (NS) comprising embryonal carcinoma, teratoma, yolk sac tumor, and choriocarcinoma. Response to the treatment and prognosis, especially of NS, depend on precise diagnosis with a necessity for discovery of new biomarkers. We aimed to perform comprehensive in silico analysis at the DNA, RNA, and protein levels of six prospective (HOXA9, MGMT, CFC1, PRSS21, RASSF1A, and MAGEC2) and six known TGCT biomarkers (OCT4, SOX17, SOX2, SALL4, NANOG, and KIT) and assess its congruence with histopathological analysis in all forms of TGCTs. Cancer Hallmarks Analytics Tool, the Search Tool for the Retrieval of Interacting Genes\/Proteins database, and UALCAN, an interactive web resource for analyzing cancer OMICS data, were used. In 108 TGCT and 48 tumor-free testicular samples, the immunoreactivity score (IRS) was calculated. SE showed higher frequency in DNA alteration, while DNA methylation was significantly higher for all prospective biomarkers in NS. In GCNIS, we assessed the clinical positivity of RASSF1 and PRSS21 in 52% and 62% of samples, respectively, in contrast to low or nil positivity in healthy seminiferous tubules, TGTCs as a group, SE, NS, or all NS components. Although present in approximately 80% of healthy seminiferous tubules (HT) and GCNIS, HOXA9 was diagnostically positive in 64% of TGCTs, while it was positive in 82% of NS versus 29% of SE. Results at the DNA, mRNA, and protein levels on putative and already known biomarkers were included in the suggested panels that may prove to be important for better diagnostics of various forms of TGCTs.<\/jats:p>","DOI":"10.1155\/2020\/8841880","type":"journal-article","created":{"date-parts":[[2020,11,7]],"date-time":"2020-11-07T03:05:08Z","timestamp":1604718308000},"page":"1-18","source":"Crossref","is-referenced-by-count":13,"title":["In Search of TGCT Biomarkers: A Comprehensive In Silico and Histopathological Analysis"],"prefix":"10.1155","volume":"2020","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7507-0394","authenticated-orcid":true,"given":"Dora","family":"Raos","sequence":"first","affiliation":[{"name":"Department of Medical Biology, University of Zagreb School of Medicine, \u0160alata 3, 10000 Zagreb, Croatia"},{"name":"Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, \u0160alata 3, 10000 Zagreb, 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