To contribute the order-made medicine for cancer treatments, we have originally searched several biomarkers in the last decade. Some have been used as immunohistochemically novel biomarkers for the cancer diagnosis, and the others have applied to molecular target for the cancer therapy. RB1-inducible coiled-coil 1 (RB1CC1; also known as FIP200) plays important roles in biological pathways such as cell cycle arrest and autophagy, and the nuclear expression has been established as a prognostic predictor in breast and salivary cancer patients. RECQL1 and WRN protein are RecQ DNA helicases that participate in suppression of DNA hyper-recombination and repair. We have found that both proteins are highly expressed and that siRNA-mediated silencing of either gene suppressed head and neck squamous cell carcinomas in vitro and in vivo. The data offer a preclinical proof-of-concept for RecQ proteins as novel therapeutic targets to treat aggressive head and neck squamous cell carcinomas. In testicular germ cell tumors, the fetal-specific methyltransferase-like protein DNMT3L is expressed, and has been used as a novel marker of human embryonal carcinoma. Further elucidation of the roles of DNMT3L in vivo warrants a possible significance as a therapeutic target of embryonal carcinoma. These novel biomarkers such as RB1CC1, RecQ, and DNMT3L provide new insight into cancer diagnosis and therapy; and will help to realize the order-made medicine.