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Nasopharyngeal Cancer Whole Genome Sequencing: Identification Of Clinically Meaningful Genes.

Latar Belakang: Kanker nasofaring (KNF) merupakan keganasan yang memiliki distribusi geografis dan etnis yang khas serta sering dikaitkan dengan mutasi genetik dan faktor lingkungan. Penelitian ini berfokus pada whole genome dan sekuensing metilasi KNF menggunakan teknologi sekuensing Nanopore untuk mengeksplorasi perubahan genetik dan epigenetik yang signifikan secara klinis yang berkontribusi pada karsinogenesis KNF. Metode: Sebanyak tujuh sampel biopsi KNF disekuensing menggunakan teknologi Nanopore. Proses ini meliputi ekstraksi DNA, library preparation, dan analisis bioinformatika, termasuk basecalling, alignment, dan variant calling. Penelitian ini menilai small nucleotide variants (SNVs), copy number variations (CNVs), structural variants (SVs), short tandem repeat (STR), dan pola metilasi menggunakan berbagai software bioinformatika. Selain itu, data kelangsungan hidup, respons terhadap pengobatan, dan karakteristik klinis juga dievaluasi. Hasil: Studi ini mengidentifikasi berbagai varian genetik yang diprediksi memberikan dampak fungsional tinggi pada semua sampel, misalnya pada tumour suppressor gene seperti LIMD1 dan CNDP2, yang menunjukkan potensi kehilangan fungsi. Onkogen potensial juga teridentifikasi di studi ini. Kami juga mengidentifikasi beberapa mutasi patogenik sesuai ClinVar seperti mutasi pada gen PERM1 dan APOA2. Varian struktural ditemukan lebih sering pada sampel S1, dengan banyak kelainan pada gen DNA repair tetapi tidak ditemukan di sample lain, kelainan ini menunjukkan korelasi prognosis klinis yang buruk. Analisis metilasi juga menunjukkan pola hiper metilasi secara global pada KNF, terutama melibatkan jalur sinyal seperti PI3K-Akt, aktivitas GTPase, dan sinyal Ras. Tumour suppressor gene, termasuk PRKCB, ITGB3, EPHA2, dan CDKN2A, juga mengalami hiper metilasi, dan menunjukkan potensi keterlibatan dalam perkembangan KNF. Kesimpulan: Studi ini menemukan mutasi pada gen DNA repair berkaitan dengan prognosis yang buruk pada KNF. Berbagai mutasi pada tumour suppressor gene dan onkogen ditemukan yang berpotensi berkaitan dengan karsinogenesis KNF.
Kata kunci: Kanker nasofaring, whole genome sequencing, epigenom, metilasi, driver mutation


Background: Nasopharyngeal carcinoma (NPC) is a malignancy with distinct geographical and ethnic distribution, often linked to genetic mutations and environmental factors. The current study focuses on the whole genome and methylation sequencing of NPC using Nanopore sequencing technology to explore clinically significant genetic and epigenetic alterations contributing to NPC carcinogenesis. Method: A total of seven NPC biopsy samples were sequenced using Nanopore technology. DNA extraction and library preparation followed by bioinformatics analysis, including basecalling, alignment, and variant calling, were performed. The study assessed small nucleotide variants (SNVs), copy number variations (CNVs), structural variants (SVs), short tandem repeat (STR) and methylation patterns using advanced bioinformatic tools. Additionally, survival data, treatment response, and clinical characteristics were evaluated. Results: The study identified various high-impact genetic variants across all samples, in tumour suppressor genes such as LIMD1 and CNDP2, suggesting potential loss of function. Potential oncogenes were also identified. Furthermore, we identified several ClinVar pathogenic mutation such as mutation in gene PERM1 and APOA2. Structural variants were notably more frequent in sample S1, with aberrant multiple DNA repair genes, not found in other samples, which correlated with poor clinical prognosis. Methylation analysis revealed global hypermethylation patterns in NPC, particularly involving key signalling pathways like PI3K-Akt, GTPase activity, and Ras signalling. Tumour suppressor genes including PRKCB, ITGB3, EPHA2, and CDKN2A were also frequently hypermethylated in our NPC. Conclusion: This study found aberrant DNA repair genes to be associated with ppor prognosis in NPC. Furthermore, various mutation in tumour suppressor genes and oncogens were identified which were potential driver carcinogenesis in NPC.
Keywords: Nasopharyngeal cancer, whole genome sequencing, epigenome, methylation, driver mutation.