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Apolipoprotein E (APOE) genotyping is important for assessing the risk of late-onset Alzheimer's disease. We developed a DNA amplification-free method to perform APOE genetic analysis based on the high sensitivity of fiber optic particle plasmon resonance (FOPPR) biosensor and the specificity of ligase reaction. The method employed the dual-functional gold-iron oxide core-satellite hybrid nanoparticles (HNPs), which was modified with a single-stranded DNA (ssDNA) probe-P1, and a ssDNA probe-P2 modified with biotin to form a nanoplasmonic detection probe. Ligation of a ssDNA target complementary to the P1–P2 pair results in a ligation product with the HNP at one end and the biotin group at the other end, which can be captured by a streptavidin-functionalized sensor fiber, leading to an increase of nanoplasmonic absorption with magnitude useful for APOE genotype determination. Using synthetic ssDNA targets as standards, we achieved limits of detection in the range of 16–38 fM and the sensor responses from the mimic homozygous samples were about two times of that from mimic heterozygous samples at the same ssDNA concentration. For proof-of-principle, three genomic samples extracted from blood were analyzed and the results favorably agree with that by DNA sequencing. • Amplification-free biosensor for genotyping of Apolipoprotein E (APOE) using ligase reaction for specificity. • High sensitivity with detection limits in the range of 16–38 fM. • Allow discrimination between homozygous DNA and heterozygous DNA. • Good correlation with DNA sequencing for genomic samples extracted from blood. • Require very small amount of sample and thus provide an opportunity to develop a POCT device for APOE genotyping. [ABSTRACT FROM AUTHOR]