Accessing Genetic Information with Liquid Biopsies

Recent scientific advances in understanding circulating tumor cells, cell-free DNA/RNA, and exosomes in blood have laid a solid foundation for the development of routine molecular ‘liquid biopsies’. This approach provides non-invasive access to genetic information – somatic mutations, epigenetic changes, and differential expression – about the physiological conditions of our body and diseases. It opens a valuable avenue for future genetic studies and human disease diagnosis, including prenatal and neurodegenerative disease diagnosis, as well as for cancer screening and monitoring. With the rapid development of highly sensitive and accurate technologies such as next-generation sequencing, molecular ‘liquid biopsies’ will quickly become a central piece in the future of precision medicine.

exosome rna

Unique Molecular Identifiers (UMIs). (A) Each unique original molecule is represented in different color; a true variant (red circle) presents in one of the unique original molecules. After PCR amplification and sequencing, additional errors (blue circle) are introduced. However, the true variant can be found in the majority of PCR progenies from the original ‘yellow’ molecule that carries the true variant. Conversely, the ‘variants’ caused by amplification/sequencing errors are not shared by the other PCR progenies of the same original molecule. Therefore, true variants can be differentiated from errors by making census variant call after grouping the PCR progenies of the same original molecule. (B) UMIs can be incorporated into each original molecule by either PCR or ligation. After PCR amplification, each original molecule contains the same UMI ‘tag’ and thus can be grouped together after sequencing. (C) PCR and sequencing errors (pink asterisk) can also happen within the UMI sequences, making the subsequent grouping inefficient, and therefore lead to difficulties in census variant calling. (D) Amplification errors introduced during the first cycle of PCR would present in a significant portion of PCR progenies of the original molecule. Therefore, it can sometimes cause ambiguities in census variant calling. This type of amplification error is called ‘jackpot mutation’.

Cai X, Janku F, Zhan Q, Fan JB. (2015) Accessing Genetic Information with Liquid Biopsies. Trends Genet 31(10):564-75. [abstract]

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