Method development and verification using cell-free DNA
Recently, we have been applying a library preparation technique from paleogenomics to cell-free DNA (cfDNA) studies. We found that such a method (adapting all cfDNA as single-strands rather than double-strands) allows us to collect forms that are more degraded in blood. Our analysis has lead to much higher capture rates of microbial and mitochondrial cell-free DNA, which we apply to the case of lung transplant patients. Other groups have applied the technique to create better tests for fetal abnormalities and to determine tissue-specific origins of the cfDNA. Check out our group's first paper in Scientific Reports.
We recently applied an extension of this method to determine the efficacy of utilizing cell-free DNA as a replacement for urine culture, urinalysis, and viruria qPCR detection. In this pilot study, we profiled the urinary cell-free DNA of several dozen kidney transplant patients with urinary tract infections from standard uropathogens (E. coli and Enterococcus) as well as rarer infections (BK polyomavirus and parvovirus B19). We also showed that that reactions of the host to infections can be observed (such as graft damage and immune activation). Work is continuing in this area to more sensitively probe the tissue-of-origin of cell-free DNA to determine host tropism.