Advancements in Next-Generation Sequencing for Detecting Minimal Residual Disease

For decades, cytogenetic markers have played a major role in the diagnosis and classification of pediatric and adult cancers. However, many chromosomal lesions less than 50,000 base pairs (bp) are not typically detected by traditional cytogenetic studies, and these alterations are currently an area of active focus to determine the relationship with disease severity and outcome. Recent advancements in DNA sequencing technology have aided in our ability to detect numerous genomic alterations, ranging from a single-nucleotide to chromosomal-scale lesions, from a single genome. However, the routine implementation of sequencing-based strategies for the detection of minimal residual disease (MRD) has been limited because of the inherent error rate of the NGS platforms. With error rates of 0.5–2.0%, the ability to detect clinical significant remaining disease at lesser frequencies is limited. However, a variety of strategies and platforms are rapidly advancing, which will enable sequencing with the sensitivity and specificity to not only detect very rare levels of refractory or residual disease but also guide oncologists in precision therapeutic selection. This chapter details key considerations, limitations, and advancements in next-generation sequencing technologies, with a focus on error-corrected sequencing using unique molecular indexing, in the application of accurately detecting minimal residual disease.