Genomic tests: unreliable for cancer? A focus on circulating DNA and lung cancer

Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation

In recent years, there have been major advances in the application of non-invasive techniques to predict pregnancy-related complications, for example by measuring cell-free RNA (cfRNA) in maternal blood. In contrast to cell-free DNA (cfDNA), which is already in clinical use to diagnose fetal aneuploidy, circulating RNA levels can correspond with tissue-specific gene expression and provide a snapshot of prenatal health across gestation. Here, we review the physiologic origins of cfRNA and its novel applications and corresponding challenges to monitor fetal and maternal health and predict pregnancy-related complications.

Genome-Wide Analysis of Circulating Cell-Free DNA Copy Number Detects Active Melanoma and Predicts Survival

BACKGROUND

A substantial number of melanoma patients develop local or metastatic recurrence, and early detection of these is vital to maximise benefit from new therapies such as inhibitors of BRAF and MEK, or immune checkpoints. This study explored the use of novel DNA copy-number profiles in circulating cell-free DNA (cfDNA) as a potential biomarker of active disease and survival.

PATIENTS AND METHODS

Melanoma patients were recruited from oncology and dermatology clinics in Sheffield, UK, and cfDNA was isolated from stored blood plasma. Using low-coverage whole-genome sequencing, we created copy-number profiles from cfDNA from 83 melanoma patients, 44 of whom had active disease. We used scoring algorithms to summarize copy-number aberrations and investigated their utility in multivariable logistic and Cox regression analyses.

RESULTS

The copy-number aberration score (CNAS) was a good discriminator of active disease (odds ratio, 3.1; 95% CI, 1.5–6.2; P = 0.002), and CNAS above or below the 75th percentile remained a significant discriminator in multivariable analysis for active disease (P = 0.019, with area under ROC curve of 0.90). Additionally, mortality was higher in those with CNASs above the 75th percentile than in those with lower scores (HR, 3.4; 95% CI, 1.5–7.9; P = 0.005), adjusting for stage of disease, disease status (active or resected), BRAF status, and cfDNA concentration.

CONCLUSIONS

This study demonstrates the potential of a de novo approach utilizing copy-number profiling of cfDNA as a biomarker of active disease and survival in melanoma. Longitudinal analysis of copy-number profiles as an early marker of relapsed disease is warranted.

Biomarkers of risk to develop lung cancer in the new screening era

Low-dose computed tomography for high-risk individuals has for the first time demonstrated unequivocally that early detection save lives. The currently accepted screening strategy comes at the cost of a high rate of false positive findings while still missing a large percentage of the cases. Therefore, there is increasing interest in developing strategies to better estimate the risk of an individual to develop lung cancer, to increase the sensitivity of the screening process, to reduce screening costs and to reduce the numbers of individuals harmed by screening and follow-up interventions. New molecular biomarkers candidates show promise to improve lung cancer outcomes. This review discusses the current state of biomarker research in lung cancer screening with the primary focus on risk assessment.

Circulating DNA is a useful prognostic factor in patients with advanced non-small cell lung cancer

BACKGROUND

Circulating DNA is observed at higher concentrations in patients with lung cancer than in controls. Qualitative and quantitative analysis of circulating DNA is a promising noninvasive tool. Our aim was to prospectively study the association between the catalytic subunit of telomerase (human telomerase reverse transcriptase [hTERT]) in plasma and clinical variables and survival in a large-scale non-small cell lung cancer (NSCLC) study.

METHODS

Four hundred forty-six patients with stages IIIB and IV NSCLC with a median follow-up of 9.7 months (range, 0.5-45) were analyzed. Blood samples were collected before therapy start (cisplatin/docetaxel). Quantification of baseline circulating DNA was determined as the amount of free hTERT in plasma, by using real-time quantitative polymerase chain reaction.

RESULTS

Patients with hTERT ≤ 49.8 ng/ml (median value) had a median time to progression (TTP) of 6.3 months compared with 4.9 for hTERT more than 49.8 ng/ml (p = 0.001). Overall survival (OS) was significantly higher (10.9 versus 9.3 months) at lower hTERT levels (p = 0.012). When calculations were done using hTERT as continuous variable, we did not observe independent significant differences. Thus, there is an apparent discrepancy in p values when hTERT is considered as a continuous versus dichotomized variable. There was a tendency to differentiate median hTERT levels with respect to response rates (complete response + partial response: 33.1 versus stable disease + progressive disease: 50.7 ng/ml, p = 0.12), but other clinical variables such as age, gender, performance status, stage, histology, and number of metastatic locations were not associated with hTERT. In multivariate analysis, hTERT was an independent prognostic variable for both TTP (hazard ratio: 1.44, p < 0.001) and OS (hazard ratio: 1.33, p = 0.007).

CONCLUSIONS

In advanced NSCLC, high pretreatment circulating hTERT level is an independent poor prognostic marker for TTP and OS. Circulating DNA is a noninvasive marker, which may help to improve the prognostic profile of these patients.

Circulating nucleic acids in cancer and pregnancy

Circulating nucleic acids are present in the blood of humans and other vertebrates. During the last 10 years researchers actively studied cell-free nucleic acids present in plasma or serum with great expectations of their use as potential biomarkers for cancer and other pathologic conditions. In the present manuscript the main findings related to the principal characteristics of circulating nucleic acids, the hypothesis on their origin and some methodological considerations on sample collection and extraction as well as on some innovative assay methods have been summarized. Recent reports on the importance of circulating nucleic acids in the intercellular exchange of genetic information between eukaryotic cells have been reviewed.

Value of quantitative analysis of circulating cell free DNA as a screening tool for lung cancer: a meta-analysis

OBJECTIVE

Quantitative analysis of circulating cell free DNA is considered as a possible aid for lung cancer screening. We aimed to comprehensively review the evidence for use of circulating cell free DNA to screen for lung cancer.

METHODS

After a systematic review of English language studies, sensitivity, specificity, and other measures of accuracy of circulating DNA assay in the diagnosis of lung cancer were pooled using random-effects models. Summary receiver operating characteristic curves were used to summarize overall test performance.

RESULTS

Ten studies met our inclusion criteria. The summary estimates for quantitative analysis of circulating cell free DNA in lung cancer screening in the studies included were as follows: sensitivity, 0.80 (95% confidence interval (CI), 0.77-0.83); specificity, 0.77 (95% CI, 0.74-0.80); positive likelihood ratio, 4.54 (95% CI, 2.66-7.76); negative likelihood ratio, 0.28 (95% CI, 0.19-0.40); and diagnostic odds ratio, 20.33 (95% CI, 10.12-40.86).

CONCLUSIONS

The current evidence suggests that the diagnostic accuracy of quantitative analysis of circulating DNA is not lower than conventional serum biomarkers for lung cancer screening, at least. However, it is not recommend for lung cancer screening alone, because its discrimination power is not very perfect. The value of circulating DNA assay in combination with conventional markers for lung cancer detection deserved further investigation.

Potential for Raman spectroscopy to provide cancer screening using a peripheral blood sample

Cancer poses a massive health burden with incidence rates expected to double globally over the next decade. In the United Kingdom screening programmes exists for cervical, breast, and colorectal cancer. The ability to screen individuals for solid malignant tumours using only a peripheral blood sample would revolutionise cancer services and permit early diagnosis and intervention. Raman spectroscopy interrogates native biochemistry through the interaction of light with matter, producing a high definition biochemical 'fingerprint' of the target material. This paper explores the possibility of using Raman spectroscopy to discriminate between cancer and non-cancer patients through a peripheral blood sample. Forty blood samples were obtained from patients with Head and Neck cancer and patients with respiratory illnesses to act as a positive control. Raman spectroscopy was carried out on all samples with the resulting spectra being used to build a classifier in order to distinguish between the cancer and respiratory patients' spectra; firstly using principal component analysis (PCA)/linear discriminant analysis (LDA), and secondly with a genetic evolutionary algorithm. The PCA/LDA classifier gave a 65% sensitivity and specificity for discrimination between the cancer and respiratory groups. A sensitivity score of 75% with a specificity of 75% was achieved with a 'trained' evolutionary algorithm. In conclusion this preliminary study has demonstrated the feasibility of using Raman spectroscopy in cancer screening and diagnostics of solid tumours through a peripheral blood sample. Further work needs to be carried out for this technique to be implemented in the clinical setting.