Completion of the Human Genome Project(1) and the HapMap Project(2) has led to increasing demands for mapping complex traits in humans to understand the aetiology of diseases(3). Identifying variations in the DNA sequence, which affect how we develop disease and respond to pathogens and drugs, is important for this purpose, but it is difficult to identify these variations in large sample sets(3-5). Here we show that through a combination of capillary sequencing and polymerase chain reaction assisted by gold nanoparticles, it is possible to identify several DNA variations that are associated with age-related macular degeneration(6-8) and psoriasis(9) on significant regions of human genomic DNA. Our method is accurate and promising for large-scale and high-throughput genetic analysis of susceptibility towards disease and drug resistance(10-12).