Toward engineered processes for sequencing-based analysis of single circulating tumor cells

• A process for sequencing single CTCs involves multiple defined operations.
• Current methods for enrichment fail to capture the entire repertoire of CTCs in blood.
• Cost of sequencing necessitates the identification and selection of candidate single CTCs without degrading DNA.
• Whole-genome amplification introduces biases that hinder sensitivity and specificity.
• Nanoscale technologies could be integrated to improve CTC analysis.

Sequencing-based analysis of single circulating tumor cells (CTCs) has the potential to revolutionize our understanding of metastatic cancer and improve clinical care. Technologies exist to enrich, identify, recover, and sequence single cells, but to enable systematic routine analysis of single CTCs from a range of cancer patients, there is a need to establish processes that efficiently integrate these specific operations. Such engineered processes should address challenges associated with the yield and viability of enriched CTCs, the robust identification of candidate single CTCs with minimal degradation of DNA, the bias in whole-genome amplification, and the efficient handling of candidate single CTCs or their amplified DNA products. Advances in methods for single-cell analysis and nanoscale technologies suggest opportunities to overcome these challenges, and could create integrated platforms that perform several of the unit operations together. Ultimately, technologies should be selected or adapted for optimal performance and compatibility in an integrated process.