Non-invasive swab biopsies accurately and reproducibly query oral cancer genomes

摘要: For patients with oral squamous cell carcinoma (SCC), neck (cervical) metastasis is the primary determinant for prognosis; however, currently there are no satisfactory clinical, pathologic or molecular markers that can be used to discriminate levels of metastatic risk for these cancers. Recurrent cancer genome DNA copy number aberrations offer potential as biomarkers and are currently in clinical use as aids in diagnosis, prognosis and surveillance. Two DNA copy number biomarkers have been proposed to discriminate oral cancer patients at risk for occult lymph node metastasis. Therefore, we developed a non-invasive swab biopsy procedure for acquisition of oral cancer DNA to allow pre-surgical assessment of the cancer genome for DNA copy number biomarkers of metastatic risk, including alterations involving chromosome 3q, 8p, 8q and 20 and amplification of chromosome 11q13. 3. We show that high quality DNA can be obtained from the swab biopsy with yields sufficient for DNA copy number measurement by next generation DNA sequencing. The biopsies yield reproducible information and there is a good correlation between DNA copy number profiles obtained with DNA isolated from the swab biopsies and the formalin fixed paraffin embedded archival excised cancer tissue. We conclude that the swab biopsy of oral cancer lesions is a promising tool for non-invasive presurgical assessment of the cancer genome.