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Indonesian Journal of Medical Chemistry and Bioinformatics

Abstract

Background: The rs4944946 variant, located in the 5’UTR of the DHCR7 gene and upstream of NADSYN1, is biologically implicated in vitamin D and cholesterol metabolism pathways closely linked to cancer pathogenesis. This study aimed to experimentally validate the association between the rs4944946 polymorphism and breast cancer susceptibility in an independent cohort of Indonesian women. Method: A case-control study was conducted involving 36 breast cancer patients and 39 healthy adult females. Genotyping of the rs4944946 variant was performed using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). The genetic association was evaluated across codominant, dominant, and recessive models. Luminal B was the predominant molecular subtype (36.1%) within the case group. Results: Validation results demonstrated no significant association between the rs4944946 variant and breast cancer susceptibility across all tested genetic models. The discordance between our validation cohort and prior in silico predictions is likely attributable to the low frequency of the mutant allele, limited sample size, and the "winner’s curse" phenomenon. Furthermore, technical constraints inherent to PCR-RFLP, such as the risk of incomplete enzymatic digestion, may have influenced genotyping accuracy. Conclusion: This experimental validation did not establish a significant association between the rs4944946 variant and breast cancer in the studied cohort. Future multicenter studies utilizing larger cohorts and more advanced, precise genotyping technologies (e.g., Next-Generation Sequencing) are required to definitively determine the clinical significance of this variant.

Bahasa Abstract

Latar Belakang: Varian rs4944946, yang terletak di daerah 5’UTR pada gen DHCR7 dan upstream dari NADSYN1, secara biologis terlibat dalam jalur metabolisme vitamin D dan kolesterol yang berkaitan erat dengan patogenesis kanker. Penelitian ini bertujuan untuk memvalidasi secara eksperimental asosiasi antara polimorfisme rs4944946 dengan kerentanan kanker payudara pada kohort independen wanita Indonesia. Metode: Studi kasus-kontrol dilakukan dengan melibatkan 36 pasien kanker payudara dan 39 wanita dewasa sehat. Genotiping varian rs4944946 dilakukan menggunakan metode Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). Asosiasi genetik dievaluasi melalui model kodominan, dominan, dan resesif. Luminal B merupakan subtipe molekuler yang paling dominan (36,1%) pada kelompok kasus. Hasil: Hasil validasi menunjukkan tidak adanya asosiasi yang signifikan antara varian rs4944946 dengan kerentanan kanker payudara pada semua model genetik yang diuji. Diskordansi antara hasil in vitro ini dengan prediksi in silico sebelumnya kemungkinan besar disebabkan oleh rendahnya frekuensi alel mutan, ukuran sampel yang terbatas, dan fenomena "winner’s curse". Lebih lanjut, keterbatasan teknis yang melekat pada metode PCR-RFLP, seperti risiko digesti enzimatik yang tidak sempurna, kemungkinan turut memengaruhi akurasi genotiping. Kesimpulan: Validasi eksperimental ini tidak menetapkan adanya asosiasi yang signifikan antara varian rs4944946 dan kanker payudara pada kohort yang diteliti. Studi multisentris di masa depan yang menggunakan kohort lebih besar serta teknologi genotiping yang lebih mutakhir dan presisi (misalnya, Next-Generation Sequencing) diperlukan untuk memastikan signifikansi klinis dari varian ini.

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