The purpose of this retrospective case-control study was to investigate the frequency of Apolipoprotein E (
ApoE) polymorphisms and their influence on antiretroviral therapy (ART)-induced lipodystrophy or dyslipidemia in HIV-infected Thai patients. The clinical characteristics and frequencies of
ApoE genotypes were compared between the case (moderate to severe lipodystrophy,
n = 67) and control (absent to mild lipodystrophy,
n = 18) groups. The
ApoE genotype frequencies among the 85 participants were 2.35% (
n = 2) for
E2/E2, 20% (
n = 17) for
E2/E3, 9.41% (
n = 8) for
E2/E4, 36.47% (
n = 31) for
E3/E3, 30.59% (
n = 26) for
E3/E4, and 1.18% (
n = 1) for
E4/E4. None of the
ApoE genotypes showed association with ART-induced lipodystrophy. However, the levels of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-cholesterol), and ApoB were lower in patients carrying the
E2 allele but higher in
E4 carriers. Interestingly, the ratios between TC and high-density lipoprotein (TC/HDL cholesterol ratio) and ApoB/ApoA-I ratio were significantly higher in the case group. Patients carrying the
E2 allele displayed protective lipid profile, while those carrying
E4 appeared to be at higher risk of dyslipidemia. In conclusion,
ApoE polymorphisms were not associated with lipodystrophy in patients undergoing antiretroviral therapy but influenced lipid alteration.
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