Methods: A total 56 archival formalin fixed paraffin embedded (FFPE) samples inclusive of 5 patients with POPML (total of 15 samples), 9 patients with NPOPML (total of 34 samples) and 7 normal oral epithelium were included in this study. Subsequent to genomic DNA isolation, exomic DNA libraries were constructed according to the SureSelectXT target enrichment system for SOLiD 5500 multiplexed sequencing, with slight modifications. Enriched libraries were sequenced on SOLiD 5500XL platform and ColorSpace fastq sequences were extracted from each of the sequence XSQ sequence libraries using proprietary methods and formatted sequence reads were mapped to the human genome. The mean depth-of-coverage across the sequence collection was 250X coverage and from the complete Exome target size of 50,621,019 bp, at least 85 % was covered to a minimal level of at least 50X. Genetic variants in sequenced exomes were identified relative to the reference human genome using a pipeline based on the GATK software.
Result: Trends and functional pathways of exomic variations will be discussed
Conclusion: Observed differences in nature and number of mutations amongst POPML and NPOPML samples could be of potential benefit in formulating treatment plans as part of personalized patient care in oral oncology.
Funding: Queensland Government Smart Futures Co-Investment Fund, Cancer Australia, Agilent Technologies, Life Technologies.