Tumor biopsies remain the gold standard for evaluating genetic changes in cancers either at diagnosis or following treatment with targeted therapies. However, this is not always feasible and can seldom be performed more than once. Noninvasive techniques, so-called “liquid biopsies” that measure the allelic burden in blood promise to realize the full potential of genotype-directed cancer therapy. These technologies can be potentially used for non-invasive tumor genotyping and in addition also provide an opportunity for disease monitoring and as a tool for pharmacodynamic assessment of drug efficacy. These features offer the ability to gain real-time dynamic biological insights into the benefits and failures of cancer therapies. Several publications have demonstrated the potential of plasma cell-free DNA (cfDNA) genotyping. While historical studies focused on measuring total cfDNA concentrations for diagnosis and prognosis of disease, recent technologic advances now enable the ability to obtain novel molecular insights non-invasively 1-4. First, monitoring response to treatment, i.e., does one observe a reduction (or increase) in a population of tumor derived mutant alleles from cfDNA that track with treatment response observed by radiographic imaging? Second, monitoring of known, actionable resistance clones that arise, as a result, of selective pressure from targeted therapy. The latter is particularly interesting as there are now several drugs in the clinic that specifically target cancers harboring such resistance mechanisms. In addition one might learn when the resistant clone will become detectable in cases where re-biopsy is difficult or not possible. In a study examining the mechanism of resistance to epidermal growth factor receptor (EGFR) inhibition using monoclonal antibodies in colorectal cancer, investigators performed genotyping on cfDNA specimens from 24 patients and demonstrated that clinical resistance arose through acquisition of KRAS mutations, which were detectable in cfDNA up to 10 months prior to radiographic progression2. Similarly, Oxnard et al. demonstrated the presence of EGFR activating mutations in cfDNA prior to initiation of erlotinib therapy in EGFR mutant lung cancer patients, its reduction or disappearance during therapy and its subsequent re-emergence along with the drug resistance EGFR T790M mutation following continued erlotinib treatment5. The appearance of the EGFR T790M mutation was observed up to 3 months prior to the development of disease progression defined by radiographic (RECIST) criteria. Several different technologies for analyses of cfDNA are currently under evaluation. Allele-Specific Polymerase Chain Reaction (ASPCR) allows for the detection of pre-specified mutations in DNA and exploits the transcription initiation requirements of DNA polymerase. DNA polymerase requires a homology between the 3′ sequence of the primer and the DNA sequence to be transcribed. As such, mutation-specific primers can be designed, fluorescently tagged, and measured and will only be detectable if the correct homology, in this case mutant specific DNA fragment, exists. In cases of a sequence mismatch, extension will not be initiated, and the result would be read as a negative. Advantages of this approach include a low background signal,high sensitivity, and the ability to multiplex the detection of multiple pre-specified mutations at one time. Roche's cobas™ EGFR test is an example of an FDA approved allele-specific tissue based test, which measures 42 EGFR mutations simultaneously. In the current issue of Cancer, Sorensen at al applied a modified version of the cobas™ Tissue EGFR test (cobas™ EGFR blood test) on serially collected plasma from 23 advanced non-small cell lung cancer (NSCLC) patients that were known to have an EGFR sensitizing mutation6. In 22 out of 23 patients a reduction of the original EGFR sensitizing mutation was observed in plasma after 4 weeks of erlotinib treatment. There was considerable variation in the kinetics of the reduction with some patients demonstrating no residual detectable EGFR mutation in cfDNA after 4 weeks of erlotinib treatment. During the course of treatment, the reappearance of the EGFR activating mutation was detected from cfDNA in 17/23 patients. These differences in the kinetics of the mutant alleles may have long term clinical implications and need to be studied in a prospective clinical trial of EGFR mutant NSCLC patients. The current study is a subset of a larger cohort of lung cancer patients, some of whom harbor EGFR mutations, who were treated with erlotinib. In 9 out of 23 patients the known acquired resistance EGFR T790M mutation, which was not detectable in plasma at treatment initiation, was detected in plasma samples at progression. In some cases, the emergence of EGFR T790M was detected months ahead of radiographic progression6. While this study is not the first that investigate plasma genotyping as a way of noninvasively detecting EGFR T790M 7,8, nor to demonstrate that serial assessment of plasma genotype allows detection of resistance weeks (and sometimes months) prior to clinical development of resistance5, it does provide further evidence that plasma genotyping, particularly to monitor acquired resistance, may have clinical utility. It should be noted that the FDA approved version of the cobas™ EGFR test is qualitative and is only approved for using tumor tissue. The present study uses a cobas™ EGFR blood test in a research setting and uses a proprietary and still in development EGFR blood software analysis package. The analytical performance characteristics of this test are not provided. In general, ASPCR tests are best when used qualitative, and at-best are semi-quantitative. The sensitivity and specificity of this test are not provided, and it may be that these parameters vary for each of the alleles being examined. Emulsion PCR is an alternative allele-specific genotyping assays for the detection of mutations in the circulation of cancer patients. It is inherently sensitive, offers improvements in precision of detecting small changes in template DNA, and is highly quantitative. Emulsion PCR, a family of techniques that include droplet digital PCR or BEAMing (beads, emulsion, amplification and magnetics)9,10, involves partitioning input DNA into thousands of oil-aqueous emulsion droplets which can subsequently be evaluated as individual PCR reactions. On average each vessel contains one copy of your DNA template, which are PCR amplified to end-point, and read in a flow cytometer. Each droplet is assigned a positive and negative (1 or 0) value based on their fluorescent intensity, which then is used to calculate the allelic concentration and the 95% Poisson confidence levels. Emulsion PCR is currently being explored for its clinical utility in several diseases, including lung cancer, colon cancer, and melanoma. The quantitative nature of emulsion PCR allows one to define a diagnostically relevant concentration of mutant alleles that will minimize false positives and provides a straightforward path for assay performance characterization (i.e. sensitivity, specificity, reproducibility) across different laboratories. While the assay validation path is the same for ASPCR, and equally achievable, its' semi-quantitative nature may make it more difficult to compare the kinetic characteristics of the assay. The analytic landscape for these technologies is undergoing rapid change. However, platforms, such as ASPCR, emulsion PCR and more recently Next Generation Sequencing (NGS) 11,12 have become sufficiently analytically robust to support hypothesis-based, multi-institutional, and adequately powered prospective evaluation in lung cancer patients. Their true value in replacing or augmenting tissue based genomic analyses, either at diagnosis, or following the development of acquired resistance to targeted therapies needs to be evaluated in prospective clinical trials. For EGFR mutant lung cancer patients, the detection of the emergence of the EGFR T790M drug resistance mutation non-invasively using cfDNA, prior to the development of clinically or radiographically defined EGFR inhibitor resistance, at present time, has limited clinical utility due to the lack of effective treatments. However, this will likely change in the near future with the ongoing clinical development of third generation mutant selective EGFR kinase inhibitors including AZD9291 and CO-168613,14. To date, this class of agents appears to be more effective in patients with EGFR T790M mediated resistance compared to those with non-T790M mediated resistance. The ability to rapidly and non-invasively identify appropriate patients for treatment with new EGFR inhibitors highlights an important clinical application of analyzing cfDNA. However, before implementing such an approach clinically, the ability of cfDNA detected EGFR T790M to predict response to third generation EGFR inhibitor, will first need to be evaluated in a prospective clinical trial.