To date, circulating tumor DNA (ctDNA) has been most extensively investigated, likely due to recent technological advances in the field of next-generation sequencing (NGS). NGS technologies allow the analysis of custom panels of genes (i.e., targeted gene panels, TGP) [1]) and the detection of mutant alleles presenting with low frequency (<1%; [2-4]), which is mandatory when dealing with ctDNA, i.e., underrepresented among the more abundant cell-free DNA (cfDNA) of hematopoietic origin. Although ctDNA was shown to be effective in the diagnosis of advanced cancer, the use of ctDNA for detection of early-stage tumors is suboptimal, which can be ascribable to the rare amount of ctDNA present in blood samples of stage I disease patients; indeed, the low proliferation/metabolic rate, and/or dismal tumor angiogenesis, and/or lack of necrotic areas of these localized and tiny tumor lesions all contribute to a reduced ctDNA shedding, as recent observations have suggested [5a].

While we recognize the importance that DNA biomarkers play in later stage disease detection, management, and recurrence monitoring, we have chosen to focus our early detection efforts, which we define as stage 0-II disease, on RNA gene expression. The dynamic genomic output in the form of RNA molecules is a fingerprint of the physiological state of cells, and offers unique real-time information about disease progression, making early disease detection possible. Accordingly, gene expression profiles can be used as a surrogate measurement of disease phenotype [5b], offering important information on the biology of the patient, rather than the biology of the tumor, and affording opportunities for innovation for early detection of cancer and even non-oncological diseases and conditions.

SOURCES: 

[1] Van Nimwegen K.J.M., Van Soest R.A., Veltman J.A., Nelen M.R., Van Der Wilt G.J., Vissers L.E.L.M., Grutters J.P.C. Is the $1000 genome as near as we think? A cost analysis of next-generation sequencing. Clin. Chem. 2016;62:1458–1464. 

[2] ewman A.M., Bratman S.V., To J., Wynne J.F., Eclov N.C., Modlin L.A., Liu C.L., Neal J.W., Wakelee H.A., Merritt R.E., et al. An ultrasensitive method for quantitating circulating tumor dna with broad patient coverage. Nat. Med. 2014;20:548–554. 

[3] Ståhlberg A., Krzyzanowski P.M., Jackson J.B., Egyud M., Stein L., Godfrey T.E. Simple, multiplexed, PCR-based barcoding of dna enables sensitive mutation detection in liquid biopsies using sequencing. Nucleic Acids Res. 2016;44:e105.

[4] Ståhlberg A., Krzyzanowski P.M., Egyud M., Filges S., Stein L., Godfrey T.E. Simple multiplexed PCR-based barcoding of dna for ultrasensitive mutation detection by next-generation sequencing. Nat. Protoc. 2017;12:664–682. 

[5a] Chabon J.J., Hamilton E.G., Kurtz D.M., Esfahani M.S., Moding E.J., Stehr H., Schroers-Martin J., Nabet B.Y., Chen B., Chaudhuri A.A., et al. Integrating genomic features for non-invasive early lung cancer detection. Nature. 2020;580:245–251.

[5b] Mansoori, B. et al. miR-142-3p as tumor suppressor miRNA in the regulation of tumorigenicity, invasion and migration of human breast cancer by targeting Bach-1 expression. J. Cell. Physiol. 234, 9816–9825.