(109d) Block Optical DNA Sequencing and Content Scoring for Rapid Genetic Biomarker Identification
The BOS technique uses surface-enhanced Raman spectroscopy for label-free identification of DNA nucleobases from multiplexed three-dimensional plasmonic nanofocusing and characterization of molecular vibrations within the fingerprinting region of ~400-1400 cm-1. While nanometer-scale mode volumes prevent resolution of single nucleobases, our block optical technique can identify relative A-G-C-T content in DNA k-mers (where k ~10 nucleotides). Our robust bioinformatics algorithm, BOCS, uses content-based sequence alignment for probabilistic mapping of k-mer content measurements to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes from pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and > 90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes.
These results pave the way for a novel, high-throughput sequencing method with inherent lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. Combined with the BOCS algorithm, this potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases.
 Korshoj, Sagar, Hanson, Chowdhury, Otoupal, Chatterjee, Nagpal, Small 14 (4), 1703165 (2018).