Clustering Haplotypes in Native Papuans Based on Polymorphisms in the Sequence of the LDLR Gene

¹ Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Papua. Jl. Gunung Salju Manokwari 98314, West Papua, Indonesia
² Department of Indonesian Literature, Faculty of Literature and Culture, Universitas Papua. Jl. Gunung Salju Manokwari 98314, West Papua, Indonesia

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Abstract

Single-nucleotide polymorphisms (SNPs) within the LDLR can serve as genetic markers for diagnosing susceptibility to coronary heart disease. The presence of SNPs in this gene can serve as a basis for the formation of haplotype clusters within a population. Papua exhibits significant ethnic diversity, potentially influencing genetic variation within the LDLR gene. This study aimed to cluster the haplotypes of native Papuans based on SNPs in the LDLR gene sequence. In this study, the rear end of the LDLR gene was sequenced in 20 native Papuans from tribes inhabiting different ecological zones. Sequence analysis revealed four SNPs that formed six haplotypes. Two SNPs were located at intron 17, namely IVS17- 80 G>A and VS17-42 A>G, and two SNPs were located at the 3'UTR, namely *52G>A and *504G>A, with a nucleotide diversity of 0.00185. The identified haplotypes were GAGG, GGGG, GGGA, AGGG, GAAA, and AAAA, with a diversity of 0.726 ± 0.075. Four haplotypes (GAGG, GGGG, GGGA and AGGG) were clustered into one group (Cluster A), whereas the remaining two haplotypes (GAAA and AAAA) formed another distinct cluster (Cluster B). These findings highlight the potential of haplotype clustering in characterizing the population structure of Papuan tribes across diverse ecological regions.