Identifikasi Varian Genetik Menggunakan Metode Long-Read Sequencing Pada Subjek Suspected Alfa-Thalassemia

Alifia Nur Hidayah, Prof. Dr. Niken Satuti Nur Handayani, M.Sc.

2025 | Skripsi | BIOLOGI

Alfa-thalassemia merupakan salah satu penyakit genetik akibat mutasi pada gen alfa-globin yang berperan penting dalam pembentukkan hemoglobin. Tingkat keparahan alfa-thalassemia bergantung pada jenis dan kombinasi varian mutasi yang dimiliki oleh individu. Penelitian ini dilakukan dengan tujuan menganalisis hasil Long-Read Sequencing (PromethION, Oxford Nanopore Technologies) dari genom subjek suspected alfa-thalassemia menggunakan pendekatan bioinformatika. Selain itu, penelitian ini juga bertujuan untuk mengidentifikasi status varian genetik pada subjek. Berdasarkan hasil analisis pada subjek, teridentifikasi 15 varian pada gen-gen terkait globin yang berkaitan dengan thalassemia, meliputi 14 single nucleotide polymorphism (SNP) dan satu structural variant (SV). Salah satu SNP yang teridentifikasi adalah varian HBA1:c.326C>A (p.Thr109Asn) atau Hb Rogliano, yang diklasifikasikan sebagai likely pathogenic. Hb Rogliano dilaporkan berkontribusi terhadap alfa-thalassemia dengan frekuensi alel global kurang dari 1%. Selain itu, teridentifikasi beberapa varian heterozigot pada subjek berstatus benign atau likely benign yang hanya muncul pada fragmen yang sama dengan Hb Rogliano, yaitu HBA1:c.-41C>G, HBA2:c.-41C>G, HBA2: c.300+55T>G, dan HBA2:c.301-24delinsCTCGGCCC.

Alpha-thalassemia is a genetic disorder caused by mutations in the alpha-globin genes, which play a crucial role in hemoglobin synthesis. The clinical severity of alpha-thalassemia depends on the type and combination of genetic variants present in an individual. This study was conducted to analyze the whole genome of a subject suspected of having alpha-thalassemia using Long-Read Sequencing (PromethION, Oxford Nanopore Technologies) and bioinformatics approaches. In addition, this study was conducted to identify the subject's genetic variant status. Based on the analysis of the subject, 15 variants were identified in globin-related genes associated with thalassemia, including 14 single nucleotide polymorphisms (SNPs) and one structural variant (SV). One of the identified SNPs was variant HBA1:c.326C>A (p.Thr109Asn), also known as Hb Rogliano, which is classified as likely pathogenic. Hb Rogliano has been reported to contribute to alpha-thalassemia and has a global allele frequency of less than 1%. Furthermore, several heterozygous variants classified as benign or likely benign were also identified in the subject, which only appeared in the same fragment as Hb Rogliano, namely HBA1:c.-41C>G, HBA2:c.-41C>G, HBA2: c.300+55T>G, and HBA2:c.301-24delinsCTCGGCCC.

Kata Kunci : alfa-thalassemia, WGS, amplicon sequencing, ONT, Hb Rogliano