Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas

Abstract

To explore the potential of tumor-specific DNA as a biomarker for head and neck squamous cell carcinomas (HNSCC), we queried DNA from saliva or plasma of 93 HNSCC patients. We searched for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n = 10) and 95% (n = 37), respectively. When segregated by site, tumor DNA was detected in 100% (n = 15), 91% (n = 22), 100% (n = 7), and 100% (n = 3) of patients with tumors of the oral cavity, oropharynx, larynx, and hypopharynx, respectively. In saliva, tumor DNA was found in 100% of patients with oral cavity cancers and in 47 to 70% of patients with cancers of the other sites. In plasma, tumor DNA was found in 80% of patients with oral cavity cancers, and in 86 to 100% of patients with cancers of the other sites. Thus, saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in saliva was found postsurgically in three patients before clinical diagnosis of recurrence, but in none of the five patients without recurrence. Tumor DNA in the saliva and plasma appears to be a potentially valuable biomarker for detection of HNSCC.

Noninvasive Molecular Screening for Oral Precancer in Fanconi Anemia Patients

“…The somewhat unexpected source of leukocyte DNA indicates that we have to develop more sensitive assays, especially for transplanted patients. New genetic assays, using next generation sequencing approaches, might improve the applicability of this noninvasive screening tool and might have a higher sensitivity (47). However, it is important to realize that these approaches are still expensive, usually require larger amounts of input DNA and will also be influenced by the presence of leukocyte DNA.…”

Tumor Evolution as a Therapeutic Target

“…Similarly, cfDNA collected from thoracic effusions and malignant ascites might be highly informative: Krimmel and colleagues successfully identified TP53 mutations in cfDNA from peritoneal fluid from patients with high-grade serous ovarian tumors (31), and bronchoalveolar lavage and pleural fluids were successfully used to detect EGFR mutations in advanced NSCLC (32). ctDNA has also been isolated from saliva and urine (33,34). Therefore, analysis from multiple sources could be useful in dissecting interlesion heterogeneity.…”

Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues

“…Conventional nextgeneration sequencing (NGS) technologies have a high false positive error rate, which precludes reliable detection of mutations at frequencies <1/100 (1). "Molecular tagging" of single-stranded DNA decreases the rate of false mutations to less than 1 per 10,000 sequenced nucleotides and has been successfully applied to the detection of mutant cancer DNA in a variety of clinical samples (2)(3)(4)(5)(6). However, this false positive error rate limits the specificity of this method in challenging situations in which ultra-deep sequencing is needed to detect extremely low frequency mutant molecules (e.g., <1/10,000), as is the case of ovarian cancer DNA in Pap smears (5).…”