The economical and high-throughput detection and quantitation of disease-relevant nucleic acid sequences is a key goal in the road to widespread adoption of precision medicine, wherein optimal individualized treatment is provided to each patient based on his or her unique genetic and disease profile. Current widely used technology platforms such as microarray, NGS, and PCR are either expensive and time-consuming, or difficult to scale up to multiplexed assays. Additionally, highly specific and sensitive detection of small nucleotide variants is still challenging using conventional methods. During my PhD, I have developed several novel molecular approaches to improve the specificity and / or multiplexibility of existing technology platforms, and further validated them using biological and clinical samples. The philosophy behind these works is to pursue reliable in silico assay design and thus less empirical optimization, to develop methods that are generalizable to any target sequence in the genome, and to make the experimental procedures simple, cheap, and fast.