Differences in DNA methylation profiles by histologic subtype of paediatric germ cell tumours: a report from the Children’s Oncology Group

• Published in: British journal of cancer 2018-10, Vol.119 (7), p.864-872
• Main Authors: Williams, Lindsay A., Mills, Lauren, Hooten, Anthony J., Langer, Erica, Roesler, Michelle, Frazier, A. Lindsay, Krailo, Mark, Nelson, Heather H., Bestrashniy, Jessica, Amatruda, James F., Poynter, Jenny N.
• Format: Article
• Language: English
• Subjects: 631/67/1679; 631/80; Adolescent; Angiogenesis; Biomedical and Life Sciences; Biomedicine; Cancer Research; Child; Child, Preschool; Children; Deep Learning; DNA Methylation; DNA probes; Drug Resistance; Dysgerminoma - genetics; Endodermal Sinus Tumor - genetics; Epidemiology; Epigenesis, Genetic; Epigenomics - methods; Female; Germ cells; Germinoma - genetics; Histology; Humans; Infant; Infant, Newborn; Male; Molecular Medicine; Neoplasms, Germ Cell and Embryonal - genetics; Oncology; Ovarian Neoplasms - genetics; Pediatrics; Principal Component Analysis; Promoter Regions, Genetic; Seminoma; Seminoma - genetics; Testicular Neoplasms - genetics; Tumors; Yolk; Yolk sac
• ISSN: 0007-0920; 1532-1827; 1532-1827
• DOI: 10.1038/s41416-018-0277-5

Background Abnormal DNA methylation may be important in germ cell tumour (GCT) aetiology, as germ cells undergo complete epigenetic reprogramming during development. GCTs show differences in global and promoter methylation patterns by histologic subtype. We conducted an epigenome-wide study to identify methylation differences by GCT histology. Methods Using the Illumina HumanMethylation450K array we measured methylation in 154 paediatric GCTs (21 germinomas/seminomas/dysgerminoma, 70 yolk sac tumours [YST], 9 teratomas, and 54 mixed histology tumours). We identified differentially methylated regions (DMRs) between GCT histologies by comparing methylation beta values. Results We identified 8,481 DMRs (FWER