Development of cancer biomarker assays from dna in various bodily fluids
Springer, Simeon U
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Abstract DNA from cancer cells can enter surrounding fluid after apoptosis or necrosis. This DNA can be identified by sampling and sequencing the fluid looking for the mutations that gave rise to the cancer, referred to as a liquid biopsy. We have developed several liquid biopsies for the purpose of diagnosis and treatment selection through the use of targeted PCR and high throughput sequencing. We used the SafeSeqS methodology, a molecular barcoding technology previously developed in this lab, to further reduce sequencing errors to aid us in finding these rare mutations. We developed assays that identified genetic mutations from saliva, blood plasma, and pancreatic cysts. We investigating head and neck squamous cell carcinoma (HNSCC) from the oral cavity, oropharynx, hypopharynx, and larynx in 93 patients using a combination of saliva and plasma. We first identified either the E7 gene of HPV 16 or a primary mutation in the tumor and then tried to detect their presence in saliva and plasma. We collected saliva from every patient, while we only had plasma samples from 43 patients. We found that saliva performed best in oral cavity cancers detecting 100% of those patients, while plasma performed similarly across all sites detecting 87% of HNSCC patients. We detected mutations in 96% of patients when both saliva and plasma were available. Pancreatic cyst fluid was used to aid clinicians in the classification of pancreatic cysts. We created an 8 gene panel to look for mutations as well as additional tests for loss of heterozygosity and aneuploidy. We used DNA from fluid captured through endoscopic aspiration as well as from surgically resected cysts. When combined with the typical clinical features we were able to accurately predict which cysts needed surgery with a sensitivity and specificity of 89% and 69% respectively. Each of these projects began as an attempt to aid clinicians in dealing with these various diseases. Our results illustrate that liquid biopsies can be developed into an effective tool for the fight against cancer.