The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers

The Next Chapter in Cancer Diagnostics: Advances in HPV-Positive Head and Neck Cancer

Human papillomavirus (HPV)-associated head and neck squamous cell carcinoma (HNSCC), particularly oropharyngeal squamous cell carcinoma (OPSCC), is an increasingly prevalent pathology worldwide, especially in developed countries. For diagnosing HPV in HNSCC, the combination of p16 immunohistochemistry (IHC) and polymerase chain reaction (PCR) offers high sensitivity and specificity, with p16 IHC being a reliable initial screen and PCR confirming HPV presence. Advanced techniques like next-generation sequencing (NGS) and RNA-based assays provide detailed insights but are primarily used in research settings. Regardless of HPV status, standard oncological treatments currently include surgery, radiation, and/or chemotherapy. This conventional approach does not account for the typically better prognosis of HPV-positive HNSCC patients, leading to increased chemo/radiation-induced secondary morbidities and reduced quality of life. Therefore, it is crucial to identify and detect HPV positivity and other molecular characteristics of HNSCC to personalize treatment strategies. This comprehensive review aims to summarize current knowledge on various HPV detection techniques and evaluate their advantages and disadvantages, with a focus on developing methodologies to identify new biomarkers in HPV-positive HNSCC. The review discusses direct and indirect HPV examination in tumor tissue, DNA- and RNA-based detection techniques, protein-based markers, liquid biopsy potentials, immune-related markers, epigenetic markers, novel biomarkers, and emerging technologies, providing an overall insight into the current state of knowledge.

Identification of Stage-Specific microRNAs that Govern the Early Stages of Sequential Oral Oncogenesis by Strategically Bridging Human Genetics with Epigenetics and Utilizing an Animal Model

Oral squamous cell carcinoma (OSCC) is a highly prevalent and aggressive malignancy, with mortality rates reaching 60%, mainly due to its excessive diagnostic delay. MiRNAs, a class of crucial epigenetic gene-expression regulators, have emerged as potential diagnostic biomarkers, with >200 molecules exhibiting expressional dysregulation in OSCC. We had previously established an in silico methodology for the identification of the most disease-specific molecules by bridging genetics and epigenetics. Here, we identified the stage-specific miRNAs that govern the asymptomatic early stages of oral tumorigenesis by exploiting seed-matching and the reverse interplay between miRNA levels and their target genes' expression. Incorporating gene-expression data from our group's experimental hamster model of sequential oral oncogenesis, we bioinformatically detected the miRNAs that simultaneously target/regulate >75% of the genes that are characteristically upregulated or downregulated in the consecutive stages of hyperplasia, dysplasia, and early invasion, while exhibiting the opposite expressional dysregulation in OSCC-derived tissue and/or saliva specimens. We found that all stages share the downregulation of miR-34a-5p, miR124-3p, and miR-125b-5p, while miR-1-3p is under-expressed in dysplasia and early invasion. The malignant early-invasion stage is distinguished by the downregulation of miR-147a and the overexpression of miR-155-5p, miR-423-3p, and miR-34a-5p. The identification of stage-specific miRNAs may facilitate their utilization as biomarkers for presymptomatic OSCC diagnosis.

PDZ-binding kinase inhibitor OTS514 suppresses the proliferation of oral squamous carcinoma cells

OBJECTIVE

PDZ-binding kinase (PBK) has been reported as a poor prognostic factor and is a promising molecular target for anticancer therapeutics. Here, we aimed to investigate the effect of specific PBK inhibitor OTS514 on the survival of OSCC cells.

METHODS

Four OSCC cell lines (HSC-2, HSC-3, SAS, and OSC-19) were used to examine the effect of OTS514 on cell survival and apoptosis. DNA microarray analysis was conducted to investigate the effect of OTS514 on gene expression in OSCC cells. Gene set enrichment analysis was performed to identify molecular signatures related to the antiproliferative effect of OTS514.

RESULTS

OTS514 decreased the cell survival of OSCC cells dose-dependently, and administration of OTS514 readily suppressed the HSC-2-derived tumor growth in immunodeficient mice. Treatment with OTS514 significantly increased the number of apoptotic cells and caspase-3/7 activity. Importantly, OTS514 suppressed the expression of E2F target genes with a marked decrease in protein levels of E2F1, a transcriptional factor. Moreover, TP53 knockdown attenuated OTS514-induced apoptosis.

CONCLUSION

OTS514 suppressed the proliferation of OSCC cells by downregulating the expression of E2F target genes and induced apoptosis by mediating the p53 signaling pathway. These results highlight the clinical application of PBK inhibitors in the development of molecular-targeted therapeutics against OSCC.

Review of Disease-Specific microRNAs by Strategically Bridging Genetics and Epigenetics in Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most prevalent human malignancies and a global health concern with a poor prognosis despite some therapeutic advances, highlighting the need for a better understanding of its molecular etiology. The genomic landscape of OSCC is well-established and recent research has focused on miRNAs, which regulate gene expression and may be useful non-invasive biomarkers or therapeutic targets. A plethora of findings regarding miRNA expression have been generated, posing challenges for the interpretation and identification of disease-specific molecules. Hence, we opted to identify the most important regulatory miRNAs by bridging genetics and epigenetics, focusing on the key genes implicated in OSCC development. Based on published reports, we have developed custom panels of fifteen major oncogenes and five major tumor suppressor genes. Following a miRNA/target gene interaction analysis and a comprehensive study of the literature, we selected the miRNA molecules which target the majority of these panels that have been reported to be downregulated or upregulated in OSCC, respectively. As a result, miR-34a-5p, miR-155-5p, miR-124-3p, miR-1-3p, and miR-16-5p appeared to be the most OSCC-specific. Their expression patterns, verified targets, and the signaling pathways affected by their dysregulation in OSCC are thoroughly discussed.

Identification of Potential Molecular Mechanisms and Prognostic Markers for Oral Squamous Cell Carcinoma: A Bioinformatics Analysis

Aims and Objectives

The goal of this study was to uncover crucial biochemical pathways, prognostic indicators, and therapeutic targets in patients with oral cancer in order to enhance therapy strategies.

Materials and Methods

Five gene expression omnibus datasets were analyzed by using bioinformatics approaches to identify differentially expressed genes (DEGs). To determine biological alterations, gene ontology (GO) and KEGG pathway analyses were implied using the identified DEGs. Hub genes were determined using protein-protein interaction (PPI) network analysis and an interactome was constructed using NetworkAnalyst. Furthermore, five hub genes were evaluated for use as prognostic markers by using the human protein atlas (HPA) and the GEPIA2.0 database. In addition, the correlations between hub-gene expression and immune cell infiltration of oral squamous cell carcinoma (OSCC) tumors were analyzed using the tWumor immune estimation resource (TIMER) database.

Results

A total of 2071 upregulated genes and 1893 downregulated genes were identified. GO and pathway analysis showed DEGs were enriched in multiple immune response terms and interaction of inflammatory cytokines. From the PPI network, five hub genes were identified that have a crucial role in OSCC. These included interferon regulatory factor 4 (IRF4), chemokine receptor 7 (CCR7), TNF receptor superfamily member 17 (TNFRSF17), CD27, and sphingosine-1-phosphate receptor 4 (S1PR4), which were predicted to be favorable prognostic markers for OSCC using HPA. Overall survival analysis revealed that low expression of the five hub genes was significantly associated with worse overall survival. Our analysis of tumor-associated immune infiltration revealed that increased IRF4 expression was positively correlated with the gene expression profiles suggestive of infiltration of all immune cell types, whereas increased CCR7 expression was negatively correlated with neutrophil infiltration. Increased expression of CD27, S1PR4, and TNFRSF17 was found to be negatively correlated with dendritic cell, M0 macrophage, and neutrophil infiltration.

Conclusion

In summary, inflammation, and the immune response play an important role in OSCC. All five hub genes were good predictors of OSCC prognosis, suggesting that they could be used as potential therapeutic targets and tumor markers.

Role of Nanozymes in Oral Cancer the Road Ahead

Oral cancer is a result of diverse interactions in the tumor microenvironment (TME), genetic alterations along with associated risk factors such as lifestyle and microbial infections. Various modalities are employed in the diagnosis and therapeutics of oral cancer. Nanozymes which are artificial enzymes have a great potential in the diagnostic and therapeutic approach of tumors. They have enormous advantages compared to natural enzymes and possess inherent biological and physical properties. A web-based search was performed via the Google scholar, PubMed database, Web of Science with keywords nanozymes, nanoparticles in cancer and oral cancer. The other keywords used were diagnosis, therapy, TME, microbiome, molecular alterations, biosensor, targeted therapy, imaging and tissue regeneration. Original research studies, reviews, case reports published from 2012 to 2022 were included to appraise different subsections. An absolute lack of literature on nanozymes was observed in oral cancer. The present review is the first attempt to describe the role and application of nanozymes in oral cancer by correlating its outcome in tumor biology and biomedical research. Rapid development of nanotechnology has created a paradigm shift in cancer diagnosis and therapeutics. Nanozymes with novel designs can be anticipated in the future in oral cancer management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11244-022-01729-9.

Immunology of Oral Squamous Cell Carcinoma-A Comprehensive Insight with Recent Concepts

This review aims to understand the concept of oral cancer immunology through the notion of immune profiling, immunoediting and immunotherapy, and to gain knowledge regarding its application for the management of oral cancer patients. Oral cancer is an immunogenic tumor where the cells of the tumor microenvironment play an important role in tumorigenesis. Understanding the mechanism of these modulations can help design immunotherapeutic strategies in oral cancer patients. This article gives an overview of immunomodulation in the oral cancer tumor microenvironment, with concepts of immune profiling, immunoediting and immunotherapy. English literature searches via Google Scholar, Web of Science, EBSCO, Scopus, and PubMed database were performed with the key words immunology, tumor microenvironment, cells, cross talk, immune profiling, biomarkers, inflammation, gene expression, techniques, immunoediting, immunosurveillance, tumor escape, immunotherapy, immune checkpoint inhibitors, vaccines in cancer, oral cancer, and head and neck cancer. Original research articles, reviews, and case reports published from 2016-2021 (n = 81) were included to appraise different topics, and were discussed under the following subsections. Literature published on oral cancer immunology reveals that oral cancer immune profiling with appropriate markers and techniques and knowledge on immunoediting concepts can help design and play an effective role in immunotherapeutic management of oral cancer patients. An evaluation of oral cancer immunology helps to determine its role in tumorigenesis, and immunotherapy could be the emerging drift in the effective management of oral cancer.

PLCE1 as a diagnostic and prognostic biomarker by promoting the growth and progression of oral squamous cell carcinoma

OBJECTIVE

This study aimed to explore the role of phospholipase C epsilon1 (PLCE1) in the growth and progression of oral squamous cell carcinoma (OSCC) and determine its potential as a biomarker with respect to diagnosis, prognosis and treatment of OSCC.

METHODS

The expression level of PLCE1 in tissue specimens was detected by immunohistochemistry (182 OSCC cases and 76 controls) and its relationship to clinicopathological parameters was analyzed. Then, the diagnostic value of PLCE1 in OSCC was verified by constructing the receiver operating characteristic (ROC) curve. Kaplan-Meier and Cox analysis were performed to investigate the role of PLCE1 in predicting the prognosis of OSCC patients. Furthermore, the effects of PLCE1 on the occurrence and development of OSCC were revealed by knocking down the level of PLCE1.

RESULTS

PLCE1 was mainly located in the cytoplasm of OSCC cells, and its level in OSCC tissues was obviously higher than in adjacent normal tissues. While the expression of PLCE1 did not correlate with clinicopathological parameters of OSCC. The area under the ROC curve (AUC) of PLCE1 was 0.865 with a sensitivity of 75.8% and a specificity of 78.8%. Besides, high expression of PLCE1 suggested a worse prognosis in OSCC patients than those with low expression. The knockdown of PLCE1 obviously inhibited proliferation, migration, and invasion of OSCC cells, and induce G0 cell cycle phase arrest and apoptosis, thus preventing the progression of OSCC.

CONCLUSION

PLCE1 may cause carcinogenesis and development of OSCC, which provide a novel possibility in diagnosis, prognosis and treatment of OSCC. This article is protected by copyright. All rights reserved.

Liquid Biopsy and Circulating Biomarkers for the Diagnosis of Precancerous and Cancerous Oral Lesions

Oral cancer is one of the most common malignancies worldwide, accounting for 2% of all cases annually and 1.8% of all cancer deaths. To date, tissue biopsy and histopathological analyses are the gold standard methods for the diagnosis of oral cancers. However, oral cancer is generally diagnosed at advanced stages with a consequent poor 5-year survival (~50%) due to limited screening programs and inefficient physical examination strategies. To address these limitations, liquid biopsy is recently emerging as a novel minimally invasive tool for the early identification of tumors as well as for the evaluation of tumor heterogeneity and prognosis of patients. Several studies have demonstrated that liquid biopsy in oral cancer could be useful for the detection of circulating biomarkers including circulating tumor DNA (ctDNA), microRNAs (miRNAs), proteins, and exosomes, thus improving diagnostic strategies and paving the way to personalized medicine. However, the application of liquid biopsy in oral cancer is still limited and further studies are needed to better clarify its clinical impact. The present manuscript aims to provide an updated overview of the potential use of liquid biopsy as an additional tool for the management of oral lesions by describing the available methodologies and the most promising biomarkers.

Diversity of the Origin of Cancer Stem Cells in Oral Squamous Cell Carcinoma and Its Clinical Implications

Simple Summary

Oral squamous cell carcinoma (OSCC) histopathologically accounts for ≥90% of oral cancer. In this review article, we focus on the diversity of the origin of OSCC and also discuss cancer stem cells (CSCs). CSCs are a subset of cancer cells that occupy a very small portion of the cancer mass and have characteristics of stem cells. When gene abnormalities accumulate in somatic stem cells, those cells transform into CSCs. CSCs as the origin of cancer then autonomously grow and develop into cancer. The histopathological phenotype of cancer cells is determined by the original characteristics of the somatic stem cells and/or surrounding environment. OSCC may be divided into the following three categories with different malignancy based on the origin of CSCs: cancer from oral epithelial stem cell-derived CSCs, cancer from stem cells in salivary gland-derived CSCs, and cancer from bone marrow-derived stem cell-derived CSCs.

Abstract

Oral squamous cell carcinoma (OSCC) histopathologically accounts for ≥90% of oral cancer. Many clinicopathological risk factors for OSCC have also been proposed, and postoperative therapy is recommended in guidelines based on cancer stage and other risk factors. However, even if the standard treatment is provided according to the guidelines, a few cases rapidly recur or show cervical and distant metastasis. In this review article, we focus on the diversity of the origin of OSCC. We also discuss cancer stem cells (CSCs) as a key player to explain the malignancy of OSCC. CSCs are a subset of cancer cells that occupy a very small portion of the cancer mass and have characteristics of stem cells. When gene abnormalities accumulate in somatic stem cells, those cells transform into CSCs. CSCs as the origin of cancer then autonomously grow and develop into cancer. The histopathological phenotype of cancer cells is determined by the original characteristics of the somatic stem cells and/or surrounding environment. OSCC may be divided into the following three categories with different malignancy based on the origin of CSCs: cancer from oral epithelial stem cell-derived CSCs, cancer from stem cells in salivary gland-derived CSCs, and cancer from bone marrow-derived stem cell-derived CSCs.

A prognostic model for oral squamous cell carcinoma using 7 genes related to tumor mutational burden

Background

Oral squamous cell carcinoma (OSCC) is a rising problem in global public health. The traditional physical and imageological examinations are invasive and radioactive. There is a need for less harmful new biomarkers. Tumor mutational burden (TMB) is a novel prognostic biomarker for various cancers. We intended to explore the relationship between TMB-related genes and the prognosis of OSCC and to construct a prognostic model.

Methods

TMB-related differential expressed genes (DEGs) were screened by differential analysis and optimized via the univariate Cox and LASSO Cox analyses. Risk Score model was constructed by expression values of screened genes multiplying coefficient of LASSO Cox.

Results

Seven TMB-related DEGs (CTSG, COL6A5, GRIA3, CCL21, ZNF662, TDRD5 and GSDMB) were screened. Patients in high-risk group (Risk Score >  − 0.684511507) had worse prognosis compared to the low-risk group (Risk Score <  − 0.684511507). Survival rates of patients in the high-risk group were lower in the gender, age and degrees of differentiation subgroups compared to the low-risk group.

Conclusions

The Risk Score model constructed by 7 TMB-related genes may be a reliable biomarker for predicting the prognosis of OSCC patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-022-02193-3.

Next generation sequencing-based salivary biomarkers in oral squamous cell carcinoma

Selection of potential disease-specific biomarkers from saliva or epithelial tissues through next generation sequencing (NGS)-based protein studies has recently become possible. The early diagnosis of oral squamous cell carcinoma (OSCC) has been difficult, if not impossible, until now due to the lack of an effective OSCC biomarker and efficient molecular validation method. The aim of this study was to summarize the advances in the application of NGS in cancer research and to propose potential proteomic and genomic saliva biomarkers for NGS-based study in OSCC screening and diagnosis programs. We have reviewed four categories including definitions and use of NGS, salivary biomarkers and OSCC, current biomarkers using the NGS-based technique, and potential salivary biomarker candidates in OSCC using NGS.

Construction of miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma

BACKGROUND

Oral squamous cell carcinoma (OSCC) severely affects the quality of life and the 5-year survival rate is low. Exploring the potential miRNA-mRNA regulatory network and analyzing hub genes and clinical data can provide a theoretical basis for further elucidating the pathogenesis of OSCC.

METHODS

The miRNA expression datasets of GSE113956 and GSE124566 and mRNA expression datasets of GSE31056, GSE37991 and GSE13601 were obtained from the Gene Expression Omnibus databases. The differentially expressed miRNAs (DEMs) and mRNAs (DEGs) were screened using GEO2R. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by DAVID database. The PPI network was established through STRING database and the hub genes were preliminarily screened out by Cytoscape software. After identifying the hub genes in the TCGA database, we predicted the potential DEM transcription factors, constructed a miRNA-mRNA regulatory network, and analyzed the relationship between the hub genes and clinical data.

RESULTS

A total of 28 DEMs and 764 DEGs were screened out, which were composed of 285 up-regulated genes and 479 down-regulated genes. Enrichment analysis showed that up-regulation of DEGs were mainly enriched in extracellular matrix organization and cancer-related pathway, while down-regulation of DEGs were mainly enriched in muscular system process and adrenaline signal transduction. After preliminary screening by PPI network and identification in TCGA, the up-regulated FN1, COL1A1, COL1A2, AURKA, CCNB1, CCNA2, SPP1, CDC6, and down-regulated ACTN2, TTN, IGF1, CAV3, MYL2, DMD, LDB3, CSRP3, ACTA1, PPARG were identified as hub genes. The miRNA-mRNA regulation network showed that hsa-miR-513b was the DEM with the most regulation, and COL1A1 was the DEG with the most regulation. In addition, CDC6, AURKA, CCNB1 and CCNA2 were related to overall survival and tumor differentiation.

CONCLUSIONS

The regulatory relationship of hsa-miR-513b/ CDC6, CCNB1, CCNA2 and the regulatory relationship of hsa-miR-342-5p /AURKA were not only verified in the miRNA-mRNA regulatory network but also related to overall survival and tumor differentiation. These results indicated that they participated in the cellular regulatory process, and provided a molecular mechanism model for the study of pathogenesis.

The emerging roles of NGS in clinical oncology and personalized medicine

Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.

Overview of oral cavity squamous cell carcinoma: Risk factors, mechanisms, and diagnostics

Oral cavity squamous cell carcinoma (OCSCC) is the most common malignancy of the oral cavity. The substantial risk factors for OCSCC are the consumption of tobacco products, alcohol, betel quid, areca nut, and genetic alteration. However, technological advancements have occurred in treatment, but the survival decreases with late diagnosis; therefore, new methods are continuously being investigated for treatment. In addition, the rate of secondary tumor formation is 3-7% yearly, which is incomparable to other malignancies and can lead to the disease reoccurrence. Oral cavity cancer (OCC) arises from genetic alterations, and a complete understanding of the molecular mechanism involved in OCC is essential to develop targeted treatments. This review aims to update the researcher on oral cavity cancer, risk factors, genetic alterations, molecular mechanism, classification, diagnostic approaches, and treatment.

Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience

Dental caries are one of the chronic diseases caused by organic acids made from oral microbes. However, there was a lack of knowledge about the oral microbiome of Korean children. The aim of this study was to analyze the metagenome data of the oral microbiome obtained from Korean children and to discover bacteria highly related to dental caries with machine learning models. Saliva and plaque samples from 120 Korean children aged below 12 years were collected. Bacterial composition was identified using Illumina HiSeq sequencing based on the V3-V4 hypervariable region of the 16S rRNA gene. Ten major genera accounted for approximately 70% of the samples on average, including Streptococcus, Neisseria, Corynebacterium, and Fusobacterium. Differential abundant analyses revealed that Scardovia wiggsiae and Leptotrichia wadei were enriched in the caries samples, while Neisseria oralis was abundant in the non-caries samples of children aged below 6 years. The caries and non-caries samples of children aged 6-12 years were enriched in Streptococcus mutans and Corynebacterium durum, respectively. The machine learning models based on these differentially enriched taxa showed accuracies of up to 83%. These results confirmed significant alterations in the oral microbiome according to dental caries and age, and these differences can be used as diagnostic biomarkers.

Next Generation Sequencing for Detecting Somatic FAS Mutations in Patients With Autoimmune Lymphoproliferative Syndrome

Autoimmune lymphoproliferative syndrome (ALPS) is a primary immune regulatory disorder clinically defined by chronic and benign lymphoproliferation, autoimmunity and an increased risk of lymphoma due to a genetic defect in the FAS-FASL apoptotic pathway. Genetic defects associated with ALPS are germinal and somatic mutations in FAS gene, in addition to germinal mutations in FASLG, FADD, CASP8 and CASP10 genes. The accumulation of CD3+TCRαβ+CD4-CD8- double negative T-cells (DNT) is a hallmark of the disease and 20-25% of ALPS patients show heterozygous somatic mutations restricted to DNT in the FAS gene (ALPS-sFAS patients). Nowadays, somatic mutations in the FAS gene are detected through Sanger sequencing in isolated DNT. In this study, we report an ALPS-sFAS patient fulfilling clinical and laboratory ALPS criteria, who was diagnosed through NGS with a targeted gene panel using DNA from whole blood. Data analysis was carried out with Torrent Suite Software and variant detection was performed by both germinal and somatic variant caller plugin. The somatic variant caller correctly detected other six ALPS-sFAS patients previously diagnosed in the authors’ laboratories. In summary, this approach allows the detection of both germline and somatic mutations related to ALPS by NGS, avoiding the isolation of DNT as the first step. The reads of the somatic variants could be detected even in patients with DNT in the cut off limit. Thus, custom-designed NGS panel testing may be a faster and more reliable method for the diagnosis of new ALPS patients, including those with somatic FAS mutations (ALPS-sFAS).