## 6 Biomarker Detection
### Next-Generation-Sequencing-Based Biomarkers  
Squamous cell carcinoma progresses because of changes at the genomic level. Next-generation sequencing (NGS) technology is a good way to find the mutations and copy number changes that cause these changes [15]. [PERSON] et al. performed whole-exome investigations on head and neck SCC from 74 patients and observed matched DNA pairs between tumors and peripheral whole blood [59]. This team had identified 130 coding mutations per tumor. Given that 14 percent of all cancers were HPV-positive, results from sequencing research show how these would have a genetic variation that was half that of HPV-negative tumors. This supports the idea that there are molecular differences among the two types of SCC. With the help of NGS which possess high sensitivity, the molecular characterization among the two SCCs may go even further, subdividing HPV-negative tumors not only by their precise location, but also by the frequency of specific nucleotide alterations. Aside from these findings, the presence of mutant NOTCH1 in 11% of all tumors examined was noteworthy, since it would be the first study linking genetic alterations in this gene to the genesis and progression of SCC. This research helps us better understand how this kind of cancer grows. It shows that the changes that happen at different stages of squamous differentiation have a big impact on the many genetic processes that drive SCC development [15; 60]. Another interesting finding is that a mutation at TP53 had a key influence in the development of this disease for the younger patients who are preferably non-smokers [61]. [PERSON] and his colleagues did a very detailed genomic study of OSCC in order to find out what causes the disease to become malignant and what biomarkers can be used to classify, predict, and treat it [62]. [PERSON] and his team used fresh-frozen malignant cells and nonmalignant cells from 38 patients with OSCC to study genome-wide copy number changes. They found strong correlations between gene expression and comparative copy numbers for 1721 genes. The NOTCH1 gene had many missense and truncating mutations in around one-tenth of the tumor samples, and this was confirmed by using a panel of HNSCC cell lines. With the previously described study group, they found comparable results. The absence of protein expression, along with other tests, such as in vivo experiments using mouse models, supports the hypothesis that the Notch signaling system had a major role in tumor-suppressive mechanisms in SCC [16]. This new but widely used method can help us understand not only the main molecular devices that play a role in SCC emer \begin{table}
\begin{tabular}{c c c} \hline \hline
**Sl. No.** & **Biomarker** & **Sample Type** & **Technique Used** \\ \hline \multicolumn{4}{c}{**Metabolomics-based biomarkers**} \\ \hline
151 & Glutamic acid & \\ \hline
152 & Threonine & \\ \hline
153 & Carnitine & \\ \hline
154 & Pipercolic acid & \\ \hline
155 & Lactic acid & \\ \hline
156 & Phenylalanine & \\ \hline
157 & Valine & \\ \hline
158 & Hypoxanthine & \\ \hline
159 & Guanine & \\ \hline
160 & Guanosine & Capillary \\ \hline
161 & Trimethylamine N-oxide & Saliva & electrophoresis–time-of-flight \\ \hline
162 & Spermidine & \\ \hline
163 & Pipecolate & \\ \hline
164 & Methionine & \\ \hline \hline \end{tabular}
\end{table} 
Table 2: _Cont._gence and development, but also other possible participants that play a role in the tumor transformation process. [PERSON] and his study team sought to investigate how bacteria might play a role in tumorigenesis, especially with SCC [63]. They collected saliva samples from three people who had OSCC and two people who were healthy (control). Then the bacterial gDNA was extracted, processed, and pyro-sequenced. After analyzing the data, the researchers discovered several bacterial species related to eight distinct taxonomic phyla, with the Firmicutes phylum being the best defined in samples compared to controls.