Clearance of plasma cell free DNA in metastatic uveal melanoma with radiographic response to immune checkpoint inhibitors

Purpose

To report a case of metastatic uveal melanoma treated with immune checkpoint inhibition in which serial circulating tumor DNA (ctDNA) was assessed throughout treatment.

Observations

A 33-year-old man was diagnosed with metastatic uveal melanoma and initially had progression of disease following hepatic embolization and nivolumab/ipilimumab. At the time, plasma ctDNA GNA11 and SF3B1 were measurable and repeat ctDNA showed increased variant allele frequency following further progression of disease on vorinostat. Following additional nivolumab/ipilimumab, radiographic response was noted and repeat ctDNA became undetectable and remained so at 27 months follow up.

Conclusions and importance

Clearance of cell free DNA in metastatic uveal melanoma may be associated with radiographic response to immune checkpoint inhibitors.

Trace DNA and its persistence on various surfaces: A long term study investigating the influence of surface type and environmental conditions - Part one, metals

It is imperative for proper evidence triage that forensic biologists understand what kind of results to expect from certain evidence types submitted for DNA analysis. The persistence of trace DNA has been insufficiently investigated and there is little data available pertaining to the persistence of DNA in different environmental conditions and on different materials. The goal of this study is to increase the available data on this topic which would, in turn, help forensic biologists manage expectations when submitting specific evidence types for DNA testing. The work presented herein is a large-scale persistence project aimed to identify trends in the persistence of trace DNA and indicate how different environmental storage conditions and target surface characteristics influence the persistence of cellular and cell free DNA (cfDNA) over time. To eliminate variation within the experiment we used a proxy DNA deposit consisting of a synthetic fingerprint solution, cellular DNA, and/or cfDNA. Samples were collected and analysed from 7 metals over the course of 1 year (27 time points) under 3 different environmental storage conditions. The results of this experiment show that metal type greatly influences DNA persistence. For instance, copper exhibited an expected poor DNA persistence (up to 4 h) which a purification step did not help increase the DNA yield. Alternatively, DNA can persist for up to a year on lead at levels potentially high enough to allow for forensic DNA testing. Additionally, this study showed that the sample storage environment had no impact on DNA persistence in most cases. When considering DNA type, cfDNA was shown to persist for longer than cellular DNA and persistence as a whole appears to be better when DNA is deposited as mixtures over when deposited alone. Unsurprisingly, it can be expected that DNA recovery rates from trace deposits will decrease over time. However, DNA decay is highly dependent on the metal surface and extremely variable at short time points but slightly less variable as time since deposition increases. This data is intended to add to our understanding of DNA persistence and the factors which affect it.

Methylation signatures as biomarkers for non-invasive early detection of breast cancer: A systematic review of the literature

BACKGROUND

Early detection of breast cancer would help alleviate the burden of treatment for early-stage breast cancer and help patient prognosis. There is currently no established gene panel that utilizes the potential of DNA methylation as a molecular signature for the early detection of breast cancer. This systematic review aims to identify the optimal methylation biomarkers for a non-invasive liquid biopsy assay and the gaps in knowledge regarding biomarkers for early detection of breast cancer.

METHODS

Following the PRISMA-ScR method, Pubmed and Google Scholar was searched for publications related to methylation biomarkers in breast cancer over a five-year period. Eligible publications were mined for key data fields such as study aims, cohort demographics, types of breast cancer studied, technologies used, and outcomes. Data was analyzed to address the objectives of the review.

RESULTS

Literature search identified 112 studies of which based on eligibility criteria, 13 studies were included. 28 potential methylation gene targets were identified, of which 23 were methylated at the promoter region, 1 was methylated in the body of the gene and 4 were methylated at yet to be identified locations.

CONCLUSIONS

Our evaluation shows that at minimum APC, RASSFI, and FOXA1 genes would be a promising set of genes to start with for the early detection of breast cancer, based on the sensitivity and specificity outlined in the studies. Prospective studies are needed to optimize biomarkers for broader impact in early detection of breast cancer.

Management of a complete mole and coexisting fetus in post-dobbs world

BACKGROUND

Twin pregnancies consisting of a complete hydatidiform mole and a coexistent fetus (CMCF) are rare and associated with a high rate of maternal-fetal morbidity and mortality. Management of these pregnancies remains controversial and increasingly challenging following the Dobbs versus Jackson Women's Health decision given the viability of the coexisting twin fetus.

CASE

This case looks at the diagnosis, management, and maternal-fetal outcomes of a viable fetus coexisting molar pregnancy at a large academic center in an abortion-restricted state.

CONCLUSION

CMCF pregnancies are associated with a high risk of morbidity and mortality and are increasingly difficult to manage following the Dobbs decision. Testing platforms, which identify genetic abnormalities in the first trimester, are increasingly important as access to abortion care in the United States is restricted.

Cell-free DNA as a potential diagnostic biomarker in academic stress: A case-control study in young adults

Background

Stress is a pervasive issue in modern life, affecting both physical and mental health. Identifying biomarkers like cell-free DNA (cfDNA) could provide insights into stress response and help detect individuals at risk for stress-related disorders.

Objective

The aim of this study is to investigate the potential use of cfDNA as a diagnostic biomarker in individuals experiencing stress.

Methodology

A case-control analysis was conducted using convenient sampling on university participants (N = 285 cases, N = 500 controls) aged 18-24. The study assessed haematological and lipid profile parameters using the Sysmex XP-300TM automated analyzer and an automated biochemistry analyzer, and cfDNA was extracted using a standardized in house developed Phenol-Chloroform protocol and estimated using Agarose Gel Electrophoresis and Nanodrop. Statistical analysis was performed using SPSS ver. 21.0.

Results

The results indicated a significant difference between stressed individuals and healthy controls in demographic, haematological and biochemical parameters. Specifically, stressed cases had significantly higher levels of cholesterol, LDL cholesterol, triglycerides, glucose, VLDL cholesterol, and lower levels of HDL compared to healthy controls. Stressed cases also showed significantly elevated levels of circulating cfDNA relative to healthy controls.

Conclusion

These findings suggest that cfDNA may have potential as a diagnostic biomarker for stress.

Cationic brush hybrid nanoparticles scavenge cell-free DNA to enhance rheumatoid arthritis treatment

Abnormally high level of cell-free DNA (cfDNA) is one of the important causes of autoimmune diseases, which aggravate the symptoms of rheumatoid arthritis (RA). Recently, the utilization of cationic polymeric nanoparticles for scavenging cfDNA has emerged as a promising therapeutic strategy for the treatment of RA. However, the intravenous introduction of cationic polymeric nanoparticles into the circulation carries a risk of dissociation, causing toxicity. To realize the potential clinical translation, we employed a series of silica particles grafted with poly(2-(dimethylamino) ethyl methacrylate) (PDMA) (SiNP@PDMA) brush, which possess adjustable PDMA content (100, 200, and 300 degree of polymerization (DP)) and particle size (50, 100, and 200 nm diameter), to selectively scavenge cfDNA in inflamed joint cavity. We demonstrate that the binding affinity for cfDNA, cytotoxicity, circulation time in vivo and retention in the inflamed joint cavity are influenced by the core-shell structure of SiNP@PDMA, ultimately impacting therapeutic efficacy. Among them, SiNP@PDMA with 100 nm size and 200 DP of PDMA exhibit enhanced accumulation and prolonged retention time in inflammatory joint cavity, resulting in superior therapeutic effect. Therefore, in this study, applying the precisely tuning size and cation content of SiNP@PDMA, we demonstrated the factors to matter the therapeutic effect of cationic nanoparticles, which deepened the understanding of the anti-inflammatory therapies based on cfDNA scavenger for RA. STATEMENT OF SIGNIFICANCE: Inspired by the discovery that cfDNA would induce inappropriate immune responses to exacerbate the progress of RA, we innovatively employed SiNP@PDMA as a cfDNA scavenger to inhibit cfDNA-induced inflammation in RA. Increase in the cation content efficiently strengthened the binding between SiNP@PDMA and cfDNA, leading to an improvement in inhibitory effect of inflammation. In addition, we compared the behaviors of 50, 100 and 200 nm SiNP@PDMA in RA symptom suppression, local cfDNA scavenging and inflammation inhibition. The results demonstrated that SiNP100-PDMA200 outperformed other analogues, corresponding to their more favorable distribution in inflammatory articular cavity. Together, this study revealed the structure-property relationship of cfDNA scavengers for further development of safe and effective cfDNA scavenging system.

Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study

Background

COVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group.

Methods

Lithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19).

Results

Plasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the "WHO clinical progression scale". D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels.

Conclusion

The results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomarker of disease severity in COVID-19.

Rejection markers in kidney transplantation: do new technologies help children?

Recent insights in allorecognition and graft rejection mechanisms revealed a more complex picture than originally considered, involving multiple pathways of both adaptive and innate immune response, supplied by efficient inflammatory synergies. Current pillars of transplant monitoring are serum creatinine, proteinuria, and drug blood levels, which are considered as traditional markers, due to consolidated experience, low cost, and widespread availability. The most diffuse immunological biomarkers are donor-specific antibodies, which are included in routine post-transplant monitoring in many centers, although with some reproducibility issues and interpretation difficulties. Confirmed abnormalities in these traditional biomarkers raise the suspicion for rejection and guide the indication for graft biopsy, which is still considered the gold standard for rejection monitoring. Rapidly evolving new "omic" technologies have led to the identification of several novel biomarkers, which may change the landscape of transplant monitoring should their potential be confirmed. Among them, urinary chemokines and measurement of cell-free DNA of donor origin are perhaps the most promising. However, at the moment, these approaches remain highly expensive and cost-prohibitive in most settings, with limited clinical applicability; approachable costs upon technology investments would speed their integration. In addition, transcriptomics, metabolomics, proteomics, and the study of blood and urinary extracellular vesicles have the potential for early identification of subclinical rejection with high sensitivity and specificity, good reproducibility, and for gaining predictive value in an affordable cost setting. In the near future, information derived from these new biomarkers is expected to integrate traditional tools in routine use, allowing identification of rejection prior to clinical manifestations and timely therapeutic intervention. This review will discuss traditional, novel, and invasive and non-invasive biomarkers, underlining their strengths, limitations, and present or future applications in children.

A synthetic fingerprint solution and its importance in DNA transfer, persistence and recovery studies

A review of the literature on DNA transfer and persistence highlights many difficulties that are encountered when conducting research of this nature. One of the main problems highlighted repeatedly in the literature is the prevalence of inherent uncontrolled variation that accompany these studies, and in turn, the results obtained. This work aims to decrease the amount of intrinsic variability associated with DNA transfer and persistence experiments using a realistic proxy solution which is adaptable, of known composition, reproducible, and capable of being standardised. This proxy is composed of three parts: a synthetic fingerprint solution, cellular DNA, and cell free DNA. In this proof-of-concept study the proxy was tested with a small-scale DNA transfer and recovery experiment and the data obtained suggests that the use of a solution that mimics real fingerprint secretions, over an alternative (such as buffer or a body fluid), is important when working with non-donor provided trace DNA samples. This is because the DNA deposit solution likely impacts the transfer of DNA from fingers/hands to a surface as well as the ability to recover the biological material once deposited.

IL-6 and cfDNA monitoring throughout COVID-19 hospitalization are accurate markers of its outcomes

BACKGROUND

Severe COVID-19 entails a dysregulated immune response, most likely inflammation related to a lack of virus control. A better understanding of immune toxicity, immunosuppression balance, and COVID-19 assessments could help determine whether different clinical presentations are driven by specific types of immune responses. The progression of the immune response and tissular damage could predict outcomes and may help in the management of patients.

METHODS

We collected 201 serum samples from 93 hospitalised patients classified as moderately, severely, and critically ill. We differentiated the viral, early inflammatory, and late inflammatory phases and included 72 patients with 180 samples in separate stages for longitudinal study and 55 controls. We studied selected cytokines, P-selectin, and the tissue damage markers lactate dehydrogenase (LDH) and cell-free DNA (cfDNA).

RESULTS

TNF-α, IL-6, IL-8, and G-CSF were associated with severity and mortality, but only IL-6 increased since admission in the critical patients and non-survivors, correlating with damage markers. The lack of a significant decrease in IL-6 levels in the critical patients and non-survivors in the early inflammatory phase (a decreased presence in the other patients) suggests that these patients did not achieve viral control on days 10-16. For all patients, lactate dehydrogenase and cfDNA levels increased with severity, and cfDNA levels increased in the non-survivors from the first sample (p = 0.002) to the late inflammatory phase (p = 0.031). In the multivariate study, cfDNA was an independent risk factor for mortality and ICU admission.

CONCLUSIONS

The distinct progression of IL-6 levels in the course of the disease, especially on days 10-16, was a good marker of progression to critical status and mortality and could guide the start of IL-6 blockade. cfDNA was an accurate marker of severity and mortality from admission and throughout COVID-19 progression.

Fragment length profiles of cancer mutations enhance detection of circulating tumor DNA in patients with early-stage hepatocellular carcinoma

BACKGROUND

Late detection of hepatocellular carcinoma (HCC) results in an overall 5-year survival rate of less than 16%. Liquid biopsy (LB) assays based on detecting circulating tumor DNA (ctDNA) might provide an opportunity to detect HCC early noninvasively. Increasing evidence indicates that ctDNA detection using mutation-based assays is significantly challenged by the abundance of white blood cell-derived mutations, non-tumor tissue-derived somatic mutations in plasma, and the mutational tumor heterogeneity.

METHODS

Here, we employed concurrent analysis of cancer-related mutations, and their fragment length profiles to differentiate mutations from different sources. To distinguish persons with HCC (PwHCC) from healthy participants, we built a classification model using three fragmentomic features of ctDNA through deep sequencing of thirteen genes associated with HCC.

RESULTS

Our model achieved an area under the curve (AUC) of 0.88, a sensitivity of 89%, and a specificity of 82% in the discovery cohort consisting of 55 PwHCC and 55 healthy participants. In an independent validation cohort of 54 PwHCC and 53 healthy participants, the established model achieved comparable classification performance with an AUC of 0.86 and yielded a sensitivity and specificity of 81%.

CONCLUSIONS

Our study provides a rationale for subsequent clinical evaluation of our assay performance in a large-scale prospective study.

Liquid Biopsy Screening for Early Detection of Lung Cancer: Current State and Future Directions

Liquid biopsy (LB) is clinically utilized to detect minute amounts of genetic material or protein shed by cancer cells, most commonly cell free DNA (cfDNA), as a noninvasive precision oncology tool to assess genomic alterations to guide cancer therapy or to detect the persistence of tumor cells after therapy. LB is also being developed as a multi-cancer screening assay. The use of LB holds great promise as a tool to detect lung cancer early. Although lung cancer screening (LCS) with low-dose computed tomography (LDCT) substantially reduces lung cancer mortality in high-risk individuals, the ability of current LCS guidelines to reduce the public health burden of advanced lung cancer through early detection has been limited. LB may be an important tool to improve early lung cancer detection among all populations at risk for lung cancer. In this systematic review, we summarize the test characteristics, including sensitivity and specificity of individual tests, as they pertain to the detection of lung cancer.  We also address critical questions in the use of liquid biopsy for early detection of lung cancer including: 1. How might liquid biopsy be used to detect lung cancer early; 2. How accurate is liquid biopsy in detecting lung cancer early; and 3. Does liquid biopsy perform as well in never and light-smokers compared with current and former smokers.

The role of the first trimester screen in the face of normal cell free DNA

OBJECTIVE

There is no consensus for the method of aneuploidy screening in pregnancy. Cell free DNA (cfDNA) is the most sensitive screen for trisomies 21, 13, and 18, however the first trimester screen (FTS) is a marker for other adverse outcomes, such as structural anomalies, growth restriction, and preeclampsia. In 2019, we offered FTS (nuchal translucency (NT) and analytes) with or without cfDNA. The purpose of this study was to assess clinical relevance of abnormal FTS in women with normal cfDNA.

METHODS

We retrospectively reviewed women undergoing screening in our Fetal Evaluation Unit in 2019. Women included had normal cfDNA and abnormal FTS; consisting of NT >95%, PAPP-A < 0.4 MoM, beta-HCG >2.5 MoM, or overall increased risk of trisomies.

RESULTS

195 patients had abnormal FTS and normal cfDNA. 41 (21%) had adverse maternal outcomes including hypertension, abnormal placentation, and placental abruption. 34 (17%) had adverse fetal outcomes including growth restriction, structural anomalies, fetal demise, polyhydramnios, previable PPROM, necrotizing enterocolitis after a preterm birth, and a balanced translocation.

CONCLUSION

Abnormal FTS predicts adverse outcomes in 33% of women with normal cfDNA. Our data suggests that offering universal FTS with cfDNA may have clinical benefit.

The implications of gene mutations in salivary DNA for noninvasive diagnosis of head and neck cancer with a focus on oral cancer

DNA-based liquid biopsy as a diagnostic strategy of head and neck squamous cell carcinoma (HNSCC) has emergingly gained momentum. In this letter, we identified 6 studies contained 274 patients with HNSCC focused on gene mutations in salivary DNA. We observe that the incidence of DNA mutations with at least one gene mutated ranges from 63% to 95.9%, and the most frequently examined gene mutations are TP53, CDKN2A, PIK3CA, FAT1, and NOTCH1. Meanwhile, studies have demonstrated that saliva had a greater sensitivity and much higher quantitative values than plasma in both tumor DNA count and variant allele frequency. Interestingly, more tumor-derived mutations were detected in salivary DNA among patients with tumors arising in oral cavity compared to in oropharynx, larynx, and hypopharynx. Collectively, it is feasibility to identify somatic mutations in driver genes using saliva samples to noninvasively diagnose HNSCC, especially in oral cavity cancer and even at early stages of the disease. Larger well-designed studies are needed to consolidate the evidence.

Computational challenges in detection of cancer using cell-free DNA methylation

Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.

Noninvasive prenatal diagnosis of duchenne muscular dystrophy in five Chinese families based on relative mutation dosage approach

Background

Relative haplotype dosage (RHDO) approach has been applied in noninvasive prenatal diagnosis (NIPD) of Duchenne muscular dystrophy (DMD). However, the RHDO procedure is relatively complicated and the parental haplotypes need to be constructed. Furthermore, it is not suitable for the diagnosis of de novo mutations or mosaicism in germ cells. Here, we investigated NIPD of DMD using a relative mutation dosage (RMD)-based approach—cell-free DNA Barcode-Enabled Single-Molecule Test (cfBEST), which has not previously been applied in the diagnosis of exon deletion.

Methods

Five DMD families caused by DMD gene point mutations or exon deletion were recruited for this study. After the breakpoints of exon deletion were precisely mapped with multiple PCR, the genotypes of the fetuses from the five DMD families were inferred using cfBEST, and were further validated by invasive prenatal diagnosis.

Results

The cfBEST results of the five families indicated that one fetus was female and did not carry the familial molecular alteration, three fetuses were carriers and one was male without the familial mutation. The invasive prenatal diagnosis results were consistent with those of the cfBEST procedure.

Conclusion

This is the first report of NIPD of DMD using the RMD-based approach. We extended the application of cfBEST from point mutation to exon deletion mutation. The results showed that cfBEST would be suitable for NIPD of DMD caused by different kinds of mutation types.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-021-01128-1.

Unique genomic alterations of cerebrospinal fluid cell-free DNA are critical for targeted therapy of non-small cell lung cancer with leptomeningeal metastasis

We reported unique molecular features of cerebrospinal fluid (CSF) of NSCLC patients with leptomeningeal metastasis (LM), suggesting to establish CSF as a better liquid biopsy in clinical practices. We performed next-generation panel sequencing of primary tumor tissue, plasma and CSF from 131 NSCLC patients with LM, and observed high somatic copy number variations (CNV) in CSF of NSCLC patients with LM. The status of EGFR-activating mutations was highly concordant between CSF, plasma, and primary tumors. ALK translocation was detected in 8.3% of tumor tissues, but only 2.4% in CSF and 2.7% in plasma. Others such as ROS1 rearrangement, RET fusion, HER2 mutation, NTRK1 fusion, and BRAF V600E mutation were detected in 7.9% of CSF and 11.1% of tumor tissues, but only 4% in plasma. Our study has shed light on the unique genomic variations of CSF and demonstrated that CSF may represent better liquid biopsy for NSCLC patients with LM.

Cell-free DNA diagnostics in transplantation utilizing next generation sequencing

The use of Next Generation Sequencing (NGS) to interrogate cell-free DNA (cfDNA) as a transplant diagnostic provides a crucial step in improving the accuracy of post-transplant monitoring of allograft health. cfDNA interrogation provides a powerful, yet minimally invasive, biomarker for disease and tissue injury. cfDNA can be isolated from a variety of body fluids and analyzed using bioinformatics to unlock its origins. Furthermore, cfDNA characteristics can reveal the mechanisms and conditions under which it was generated and released. In transplantation, donor-derived cfDNA monitoring provides a tool for identifying active allograft injury at the time of transplant, infection, and rejection. Multiple detection and interrogation methods for cfDNA detection are now being evaluated for clinical validity and hold the promise to provide minimally invasive, quantitative, and reproducible measures of allograft injury across organ types.

Validation of a next-generation sequencing assay for the detection of EGFR mutations in cell-free circulating tumor DNA

Detection of EGFR mutations from blood plasma represents a gentle, non-invasive alternative to rebiopsy and can therefore be used for therapy monitoring of non-small-cell lung cancer (NSCLC) patients. The aim of this project was to investigate whether the Reveal ctDNA™ 28 NGS assay (ArcherDX, Boulder, CO), has a comparable sensitivity and specificity to droplet digital PCR (ddPCR, gold-standard) and is therefore suitable for therapy monitoring of progressing lung cancer patients. First, we validated the NGS assay with a commercially available reference material (SeraCare, Massachusetts, US). Using an input of 22 ng, a sensitivity of 96% and a specificity of 100% could be achieved for variant allele frequencies (VAF) of 0.5%. For variants at a VAF of 0.1% the sensitivity was substantially reduced. Next, 28 plasma samples from 16 patients were analyzed and results were compared to existing ddPCR data. This comparative analysis of patient samples revealed a concordance of 91% between NGS and ddPCR. These results confirm that the Reveal ctDNA™ 28 NGS assay can be used for therapy monitoring of patients under TKI therapy. However, due to the slightly superior sensitivity of ddPCR, a combination of NGS (with broad coverage of a large number of genomic loci) and ddPCR (with targeted highly sensitive detection of specific mutations) might be the ideal approach.

Potential utility of liquid biopsies in the management of patients with biliary tract cancers: A review

Biliary tract cancer, comprising gallbladder cancer, cholangiocarcinoma and ampullary cancer, represents a more uncommon entity outside high-endemic areas, though global incidence is rising. The majority of patients present at a late stage, and 5-year survival remains poor. Advanced stage disease is incurable, and though palliative chemotherapy has been shown to improve survival, further diagnostic and therapeutic options are required in order to improve patient outcomes. Although certain subtypes of biliary tract cancer are relatively rich in targetable mutations, attaining tumour tissue for histological diagnosis and treatment monitoring is challenging due to locoregional anatomical constraints and patient fitness. Liquid biopsies offer a safe and convenient alternative to invasive procedures and have great potential as diagnostic, predictive and prognostic biomarkers. In this review, the current standard of care for patients with biliary tract cancer, future treatment horizons and the possible utility of liquid biopsies within a variety of contexts will be discussed. Circulating tumour DNA, circulating microRNA and circulating tumour cells are discussed with an overview of their potential applications in management of biliary tract cancer. A summary is also provided of currently recruiting clinical trials incorporating liquid biopsies within biliary tract cancer research.

Characterizing circulating nucleosomes in the plasma of dogs with lymphoma

BACKGROUND

Nucleosomes consist of DNA wrapped around a histone octamer core like beads on a string so that DNA can be condensed as chromatin into chromosomes. Diseases such as cancer or inflammation lead to cell death where chromatin is fragmentated and released as mononucleosomes into the blood. The Nu.Q™ H3.1 assay measures total nucleosome concentration in plasma of humans and has been used to detect and identify cancer even at early stages. The objectives of this study were to determine if nucleosome levels could be used to distinguish between healthy dogs and dogs with various stages of lymphoma (LSA) using the Nu.Q™ H3.1 assay. A total of 126 dogs diagnosed with LSA and 134 healthy controls were recruited for this study. Plasma was collected from each dog and stored in K2-EDTA tubes. The LSA patient samples were recruited from TAMU or purchased from various biobanks. All control cases were recruited from TAMU.

RESULTS

Dogs with LSA had an approximately 7-fold increase in their plasma nucleosome concentrations compared to controls (AUC 87.8%). Nucleosome concentrations increased with cancer stage and dogs with B cell lymphomas had significantly higher nucleosome concentrations than dogs with T cell lymphomas.

CONCLUSIONS

The Nu.Q™ H3.1 assay was able to reliably detect elevated nucleosome concentrations in the plasma of dogs with LSA. Furthermore, it appears that nucleosomes are useful for differentiating cancer from healthy individuals in canines.

Topical cationic hairy particles targeting cell free DNA in dermis enhance treatment of psoriasis

Abnormal high level of cell free DNA (cfDNA) triggers chronic inflammation to exacerbate psoriasis symptoms. Scavenging cfDNA by topical cationic polymeric nanoparticles has been certified as an effective therapeutic strategy for treating psoriasis. However, cationic cfDNA scavengers have a great potential risk to organs after entering systemic circulation through skin barrier. For better transformation to clinical application, herein a series of poly(2-(dimethylamino)ethyl methacrylate) (PDMA) grafted hairy silica particles (cSPs) with tunable PDMA length and particle size are applied to scavenge cfDNA in dermis. We reveal that the structure of cSPs correlates with the permeation ability across stratum corneum, retention time in dermis, binding affinity to cfDNA, and toxicity tolerance, which in turn affect the therapeutic effect. Especially, the cSPs of 700 nm show more accumulation and longer retention in psoriatic lesions, leading to excellent treatment results. They also outperform the cSPs of 200 nm at a lower administration frequency. Thus, we address the issues of size, cationic content of cSPs to open a potential new avenue to topically treatment of psoriasis by targeting cfDNA in dermis.

Characterizing circulating nucleosomes in the plasma of dogs with hemangiosarcoma

Background

Nucleosomes consist of DNA wrapped around a histone octamer core like thread on a spool to condense DNA as chromatin into chromosomes. Diseases such as cancer or inflammation lead to cell death, chromatin fragmentation and release of nucleosomes into the blood. The Nu.Q™ platform measures circulating nucleosomes in the blood of humans that result from disease and has been used to detect and identify cancer even at early stages. The objectives of this study are to quantify and better characterize nucleosomes in dogs with various stages of hemangiosarcoma (HSA) using this ELISA-based assay.

Samples from 77 dogs with a confirmed diagnosis of hemangiosarcoma and 134 healthy controls were utilized for this study. The HSA samples were recruited from the Texas A&M University Small Animal Clinic (TAMU-SAC) or purchased from biobanks. All control samples were recruited from the TAMU-SAC.

Results

Dogs with hemangiosarcoma had a 6.6-fold increase in their median plasma nucleosome concentrations compared to controls (AUC 92.9 %). Elevated nucleosome concentrations were seen at all stages of disease and nucleosome concentrations increased with the stage of the disease.

Conclusions

Plasma nucleosome concentrations are a reliable way to differentiate dogs with hemangiosarcoma from healthy dogs. Further testing is underway to better characterize cancer associated HSA circulating nucleosomes and optimize future diagnostics for canine HSA detection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02934-6.

Targeted Liquid Biopsy Using Irradiation to Facilitate the Release of Cell-Free DNA from a Spatially Aimed Tumor Tissue

Purpose

We investigated the feasibility of using an anatomically localized, target-enriched liquid biopsy (TLB) in mouse models of lung cancer.

Materials and Methods

After irradiating xenograft mouse with human lung cancer cell lines, H1299 (NRAS proto-oncogene, GTPase [NRAS] Q61K) and HCC827 (epidermal growth factor receptor [EGFR] E746–750del), circulating (cell-free) tumor DNA (ctDNA) levels were monitored with quantitative polymerase chain reaction on human long interspersed nuclear element-1 and cell line-specific mutations. We checked dose-dependency at 6, 12, or 18 Gy to each tumor-bearing mouse leg using 6-MV photon beams. We also analyzed ctDNA of lung cancer patients by LiquidSCAN, a targeted deep sequencing to validated the clinical performances of TLB method.

Results

Irradiation could enhance the detection sensitivity of NRAS Q61K in the plasma sample of H1299-xenograft mouse to 4.5-fold. While cell-free DNA (cfDNA) level was not changed at 6 Gy, ctDNA level was increased upon irradiation. Using double-xenograft mouse with H1299 and HCC827, ctDNA polymerase chain reaction analysis with local irradiation in each region could specify mutation type matched to transplanted cell types, proposing an anatomically localized, TLB. Furthermore, when we performed targeted deep sequencing of cfDNA to monitor ctDNA level in 11 patients with lung cancer who underwent radiotherapy, the average ctDNA level was increased within a week after the start of radiotherapy.

Conclusion

TLB using irradiation could temporarily amplify ctDNA release in xenograft mouse and lung cancer patients, which enables us to develop theragnostic method for cancer patients with accurate ctDNA detection.

Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology

Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.

Probing of breast cancer using a combination of plasma and urinary circulating cell-free DNA

Monitoring of early-stage breast cancer is critical in promptly addressing disease relapse. Circulating cell-free DNA provides a minimally invasive and sensitive means to probing the disease. In a longitudinal analysis of 250 patients with early breast cancer, we compared the circulating cell-free DNA recovered from both plasma and urine specimens. For comparison, 50 healthy controls were also recruited. Specific mutations associated with the disease were profiled to determine the clinical sensitivity and specificity. Correlations of recovered concentrations of cell-free DNA with outcomes were examined to address early prognostication. PIK3CA mutation profiling in both plasma and urinary cell-free DNA showed an agreement of 97.2% compared with the results obtained for tumor tissues. The analysis of healthy controls revealed that cell-free DNA measurements were stable and consistent over time. Over the short 6-month period of monitoring, our analyses showed declines in recovered cell-free DNA; these findings may aid physicians in stratifying patients at higher risk for relapse. Similar results were observed in both plasma and urine specimens (hazard ratios: 2.16 and 2.48, respectively). Cell-free DNA presents a novel and sensitive method for the monitoring of early-stage breast cancer. In the present study, serial measurements of both plasma and urine specimens were useful in probing the disease.

Causes of aberrant non-invasive prenatal testing for aneuploidy: A systematic review

Non-invasive prenatal testing (NIPT) is performed worldwide to detect common chromosomal aneuploidies. The analysis of cell-free DNA (cfDNA) in maternal blood for NIPT is highly accurate for the detection of the main fetal trisomies: 21,18, and 13. However, false-positive, false-negative, and non-reportable results can occur, and these can have biological causes. Understanding the causes of unexpected NIPT results is essential to enable clinicians and genetic counselors to counsel patients comprehensively and appropriately, both prior to testing as well as after receiving the test results. The classification of non-reportable results from cfDNA analysis is important in order to provide women with precise information. In addition to technical issues, there are biological reasons for discordant results, which can be either fetal or maternal in origin. Contributing fetal factors include insufficient or absent fetal fraction, fetoplacental mosaicism, and the presence of a vanishing twin. In some pregnant women that test positive for NIPT, multiple chromosome aneuploidy has been reported as a result of suspected malignancy, and cancer has been found. False-positive and false-negative results may be the result of placental biology and not a failure in the actual test platform. Explaining the placental origin of cfDNA provides the patient with a clear view of the abilities and limitations of cfDNA-based prenatal screening.

Intestinal schistosomiasis: Can a urine sample decide the infection?

Intestinal schistosomiasis, one of the neglected tropical diseases whose control depends on accurate diagnosis of the disease prevalence. The use of low sensitive Kato Katz (KK) fecal egg detection method as a reference gold standard is not an accurate indication especially in low transmission areas. Latent class analysis frameworks especially the Bayesian could be used instead to compare between different diagnostic tests without the use of a gold standard method as a reference. Thus, this study compared two urine-based tests for the detection of circulating antigen and cell free DNA of Schistosoma mansoni versus KK method using the Bayesian latent class analytical framework and in two models where the trace results of point of contact - assay of circulating cathodic antigen (POC-CCA) were once estimated as positive, and as negative in the other model. The Bayesian framework in the trace CCA positive model showed an estimate of disease prevalence of 26% (95% BCI:0 to 60%). POC-CCA showed the highest sensitivity (74% with BCI: 9 to 91%) and lowest specificity for (20% with BCI: 0% to 37%) and the reverse for KK. For POC-CCA with traces considered negative, it was found that results between the three tests were moderated where the positivity for infection by Schistosoma antigen detection and PCR for cell free DNA approached that estimated by the Bayesian framework (44%), and the specificity for point of contact assay(81%; 95%BCI: 59% to 100%) rose in hand with its sensitivity(77%, 95% BCI:53% to 100%) and with results for PCR test (sensitivity = 80%; 95% BCI: 61% to 100%, specificity = 69%; 95% BIC: 47% to 100%). KK remains with the highest specificity while its sensitivity in the two models never exceeded 22%. Thus, we conclude that the use of a single urine sample could be very sensitive and highly specific in the diagnosis of intestinal schistosomiasis using either the trace negative model of point of contact assay, or conventional PCR, when compared to the fecal egg detection using duplicate KK. However, the use of a single tool restricts the management of the disease in areas of low endemicity.

A novel pathway for the induction of DNA damage in human spermatozoa involving extracellular cell-free DNA

DNA damage is a common feature of human spermatozoa associated with an impaired capacity to fertilize the oocyte and an increased mutational load in the offspring. However, the etiology of this damage remains poorly defined. In this study we demonstrate that a major pathway for the induction of DNA damage in mammalian spermatozoa is triggered by exposure to exogenous cell free DNA (cfDNA). Exposure of human and mouse spermatozoa to cfDNA (calf thymus, mouse liver and salmon testes) in vitro induced a dose-dependent increase in sperm DNA damage that could be effectively suppressed by the concomitant presence of DNase. The induction of such damage was not accompanied by any concomitant change in sperm motility or vitality and was not directly associated with the induction of oxidative stress. In vivo the injection of exogenous DNA again precipitated an increase in sperm DNA fragmentation that could be reversed by the prior administration of DNase. Similarly, the induction of a transient unilateral testicular ischemia induced an increase in DNA fragmentation that was evident within 24 h and sustained for at least 14 days via mechanisms that could be completely suppressed by the prior administration of DNase. We conclude that exogenous cfDNA activates a defensive response in human spermatozoa associated with the nuclease-mediated induction of DNA fragmentation, possibly involving the participation of TLR9 and CD4. These novel insights have significant implications for our understanding of DNA fragmentation in the male germ line and open up new pathways for the remediation of this condition.

Monitoring of urothelial cancer disease status after treatment by digital droplet PCR liquid biopsy assays

OBJECTIVES

Real-time monitoring of disease status would be beneficial for timely decision making in the treatment of urothelial cancer (UC), and may accelerate the evaluation of clinical trials. Use of cell free tumor DNA (cftDNA) as a biomarker in liquid biopsy is minimally invasive and its successful use has been reported in various cancer types, including UC. The objective of this study was to evaluate the use of digital droplet PCR (ddPCR)-based assays to monitor UC after treatment.

METHOD AND MATERIALS

Blood, urine and matching formalin fixed, paraffin embedded diagnostic specimens were collected from 20 patients diagnosed with stage T1 (n = 2) and T2/T3 (n = 18) disease. SNaPshot assays, Sanger sequencing and whole exome sequencing were used to identify tumor-specific mutations, and somatic mutation status was confirmed using patient-matched DNAs extracted from buffy coats and peripheral blood mononucleocytes. The ddPCR assays of the tumor-specific mutations were used to detect the fractional abundance of cftDNA in plasma and urine.

RESULTS

SNaPshot and Sanger sequencing identified point mutations in 70% of the patients that were assayable by ddPCR. Cases of remission and relapse monitored by assays for PIK3CA E542K and TP53 Y163C mutations in plasma and urine concurred with clinical observations up to 48 months from the start of chemotherapy. A new ddPCR assay for the telomerase reverse transcriptase (TERT) promoter (-124) mutation was developed. The TERT assay was able to detect mutations in cases below the limit of detection by SNaPshot. Whole exome sequencing identified a novel mutation, CNTNAP4 G727*. A ddPCR assay designed to detect this mutation was able to distinguish mutant from wild-type alleles.

CONCLUSIONS

The study demonstrated that ddPCR assays could be used to detect cftDNA in liquid biopsy monitoring of the post-therapy disease status in patients with UC. Overall, 70% of the patients in our study harbored mutations that were assayable by ddPCR.

Association between low fetal fraction of cell free DNA at the early second-trimester and adverse pregnancy outcomes

OBJECTIVE

The purpose of this study was to examine whether low fetal fraction (FF) of cell free DNA is associated with risks of adverse pregnancy outcomes.

METHODS

This was a historical cohort study of 2191 women with singleton pregnancies who had non-invasive prenatal test (NIPT) at 13 to 26 weeks of gestation. Data were collected from prenatal screening system and hospital records. Main outcome was the subsequent diagnosis of gestational diabetes mellitus (GDM), intrahepatic cholestasis of pregnancy (ICP), preeclampsia (PE), pregnancy induced hypertension (PIH) and preterm birth (PTB). Logistic regression analysis was performed to evaluate the association between LFF and adverse pregnancy outcomes.

RESULTS

The prevalence of GDM, ICP, PE, PIH and PTB was 23.87% (523), 4.02% (88), 2.92% (64), 2.83% (62) and 6.85% (150), respectively. Low FF, defined as less than the 10th percentile, was associated with an increased risk of PE (adjusted OR = 2.06, 95% CI: 1.07-3.98) and early PTB (<34 weeks' gestation: adjusted OR = 3.09, 95% CI: 1.21-7.92). In addition, low FF, defined as less than the 5th percentile, was associated with an increased risk of low birth weight babies (<2500 g: adjusted OR = 2.50, 95% CI: 1.01-6.17). However, there was no significant association between low FF and GDM, as well as ICP and PIH.

CONCLUSION

Our study provides evidence that low FF is associated with PE and early PTB. Further exploration of the clinical significance of low FF is warranted.

Cell-free Chromatin Immunoprecipitation (cfChIP) from blood plasma can determine gene-expression in tumors from non-small-cell lung cancer patients

OBJECTIVES

Lung cancer is the leading cause of cancer related death worldwide. Accurate molecular diagnostics from a tumor biopsy is paramount for correct diagnosis, treatment strategy, and prediction of outcome. However, a tumor biopsy can be misleading due to tumor heterogeneity and consecutive biopsies are rarely achievable. Importantly, tumor-specific genetic information concerning mutations and translocations, can also be obtained from liquid biopsies, e.g. blood plasma, containing cell-free DNA (cfDNA) with both systemic and tumor origin. Tumor-specific gene-expression information can also be determined from liquid biopsies using cfDNA methylation and cell-free RNA analyses. However, supplementary methodologies that can determine gene-expression patterns in lung tumors from liquid biopsies could also have diagnostic impact.

MATERIALS AND METHODS

We here present the method cell-free chromatin Immunoprecipitation (cfChIP), which for genes having high expression specifically in the tumor, can determine such gene-expression from blood plasma. In cfChIP cell-free nucleosomes modified with histone H3 lysine 36 tri-methylation (H3K36me3), a mark quantitatively correlated with the transcription of the underlying gene, are isolated, and associated cfDNA quantified.

RESULTS

We demonstrate that cfChIP from lung cancer patient blood plasma can successfully quantify the level of H3K36me3 associated with circulating cell-free nucleosomes and thereby quantify the transcriptional level of genes associated with these nucleosomes. Moreover, as a proof-of-principle we show that in blood plasma from 14 lung cancer patients, H3K36me3 cfChIP can replicate the expected higher expression of KRT6 in lung squamous cell carcinoma relative to adenocarcinoma.

CONCLUSION

This work shows that for genes with a high expression specifically in tumor, cfChIP can determine this gene-expression pattern from blood plasma. cfChIP is a method that determine gene-expression at the transcriptional level and accordingly can supplement cfDNA methylation and cell-free RNA analyses.

Cell-free DNA for genomic profiling and minimal residual disease monitoring in Myeloma- are we there yet?

OBJECTIVE

Multiple myeloma (MM), a plasma cell neoplasm, afflicts elder individuals accounting for 10% of hematologic malignancies. The MM plasma cells largely reside within the bone marrow niche and are accessible through an invasive bone marrow biopsy, which is challenging during serial monitoring of patients. In this setting, cell free DNA (cfDNA) may have a role to ascertain the molecular aberrations at diagnosis and in assessment of residual disease during therapy. The aim of this review was to explore the utility and current status of cfDNA in MM.

METHOD

PubMed was searched with terms including cell-free DNA, circulating-tumor DNA, Multiple Myeloma, diagnosis, genomic profiling, Minimal Residual Disease individually or in combination to shortlist the relevant studies.

RESULT

cfDNA serves as a non-invasive source of tumor-specific molecular biomarker, ctDNA that has immense potential in facilitating management of cancer patients. The mutation detection platforms for ctDNA include hybrid capture and ultra-deep sequencing. Hybrid capture allows full length gene sequencing for mutation and CNV detection. The disease progression can be monitored by profiling prognostic somatic copy number alterations by ultra-low pass whole genome sequencing of ctDNA cost-effectively. Evolution of both the laboratory protocols and bioinformatics tools may further improve the sensitivity of ctDNA detection for better disease management. Only a limited number of studies were available in MM exploring the potential utility of cfDNA.

CONCLUSION

In this review, we discuss the nuances and challenges associated with molecular evaluation of cfDNA and its potential role in diagnosis and monitoring of treatment response in MM.

Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing

OBJECTIVE

Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT.

STUDY DESIGN

We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up.

RESULTS

A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality.

CONCLUSION

When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.

Non-invasive prenatal test to screen common trisomies in twin pregnancies

Objectives

Recent years have witnessed a shift from invasive methods of prenatal screening to non-invasive strategies. Accordingly, non-invasive prenatal testing (NIPT) using cell-free fetal DNA in maternal plasma has gained a considerable deal of interest from both geneticists and obstetricians. Efficacy of this method in identification of common aneuploidies has been extensively assessed in singleton pregnancies. However, a limited number of studies have addressed the twin pregnancies. In this context, the present study is aimed at identification of the efficacy of NIPT in twin pregnancies.

Methods

NIPT was performed on twin pregnancies to screen trisomies 13, 18 and 21. Pregnant women referring to Nilou Clinical Laboratory between March 2016 and December 2018 were included in this research.

Results

In the current study, a total 356 twin pregnancies were screened in search for trisomies 13, 18 and 21. 6 cases exhibited positive NIPT results in which the presence of trisomies 13, 18 and 21 was confirmed by fetal karyotype in 1, 2 and 2 cases, respectively. One twin pregnancy showed normal karyotype. The combined false-positive rate for these trisomies was 0.28%. No false negative case was observed. The combined sensitivity and specificity of NIPT in twin pregnancies were 100 and 99.7%, respectively.

Conclusion

The results of the current study verify the feasibility, sensitivity and specificity of NIPT in twin pregnancies.

Rapid response of stage IV colorectal cancer with APC/TP53/KRAS mutations to FOLFIRI and Bevacizumab combination chemotherapy: a case report of use of liquid biopsy

Background

Liquid biopsies of blood plasma cell free DNA can be used to monitor treatment response and potentially detect mutations that are present in resistant clones in metastatic cancer patients.

Case presentation

In our non-interventional liquid biopsy study, a male patient in his fifties diagnosed with stage IV colorectal cancer and polytope liver metastases rapidly progressed after completing chemotherapy and deceased 8 months after diagnosis. Retrospective cell free DNA testing showed that the APC/TP53/KRAS major clone responded quickly after 3 cycles of FOLFIRI + Bevacizumab. Retrospective exome sequencing of pre-chemotherapy and post-chemotherapy tissue samples including metastases confirmed that the APC/TP53/KRAS and other major clonal mutations (GPR50, SLC5A, ZIC3, SF3A1 and others) were present in all samples. After the last chemotherapy cycle, CT imaging, CEA and CA19–9 markers validated the cfDNA findings of treatment response. However, 5 weeks later, the tumour had rapidly progressed.

Conclusion

As FOLFIRI+Bevacizumab has recently also been associated with sustained complete remission in a APC/TP53/KRAS triple-mutated patient, these driver genes should be tested and monitored in a more in-depth manner in future patients. Patients with metastatic disease should be monitored more closely during and after chemotherapy, ideally using cfDNA.

An automated high throughput solution for DNA extraction and bisulfite-conversion from high volume liquid biopsy specimens: sample preparation for epigenetic analysis

Objective

DNA methylation analysis via real-time PCR or other analytical techniques requires purified bisulfite converted DNA. We report on an automated high throughput solution for DNA extraction, bisulfite-conversion, and purification of 96 samples with an input volume of up to 3.5 mL of plasma or urine, using reagents from the commercially available Epi BisKit.

Results

Magnetic bead-based DNA extraction, bisulfite conversion at high temperature, and efficient DNA purification was conducted on a customized commercially available liquid-handling platform. A highly interlaced 4 × 24 sample protocol was implemented for DNA extraction, elution in a 96-well plate, efficient bisulfite-conversion and extensive purification. The resulting bisulfite-converted DNA was stored in a 96-well format, ready for PCR set-up or other down-stream applications. The automated method is a walk-away solution for processing 96 samples in 7 h 30 min. Performance of the method was validated by comparison with the standard manual method of the Epi BiSKit using technical and biological samples. Overall DNA yield was assessed with a standardized β-actin assay. The automated workflow demonstrated equivalent performance to the manual method for technical, plasma and urine samples. It may provide a new standard for effective high-throughput preparation of bisulfite-converted DNA from a variety of high volume liquid biopsy specimens.

Use of cell free DNA as a prognostic biomarker in non-small cell lung cancer patients with bone metastasis

BACKGROUND

Non-small cell lung cancer (NSCLC) is difficult to treat when metastasis has occurred. This study explores the use of cell-free DNA in the clinical management of NSCLC patients who have Kirsten rat sarcoma viral oncogene homolog (KRAS)-positive mutations and as a marker for prognosis.

METHODS

Peripheral blood collected from advanced NSCLC patients was examined with digital droplet polymerase chain reaction and ultraviolet spectrometry. KRAS mutations were analyzed and quantitated. The specificity and sensitivity of the proposed assay was computed by associating the results with tumor tissue specimens. Comparison against different sub-groups of patients with different metastatic sites and healthy volunteers were made. Patients were subsequently followed up and survival analysis was conducted.

RESULTS

Among the 186 patients recruited, 150 had concordant KRAS mutational profiles using cell-free DNA with tumor tissues. The assay sensitivity and specificity were 80.6% and 100%, respectively. For the 150 patients with concordant results, the range of cell-free DNA quantities in peripheral blood was 5.3 to 115 ng. Among the patient groups with different metastatic sites, we observed that patients with bone metastasis had higher concentrations of cell-free DNA. Survival analysis showed that these patients had worse survival outcome. Patients with higher KRAS counts in peripheral blood also had worse outcome.

CONCLUSION

The use of cell-free DNA presents opportunities for risk stratification of patients and possibly aids in the clinical management of the disease. In the current study for NSCLC, patients with bone metastases showed higher cell-free DNA concentrations. Quantitating the concentrations of cell-free DNA presents a noninvasive biomarker capable of prognostic utility.

Comparison of Roche Cell-Free DNA collection Tubes ® to Streck Cell-Free DNA BCT ® s for sample stability using healthy volunteers

Objectives

To compare the Roche Cell-Free DNA Collection Tubes^® against the Streck Cell-Free DNA BCT^®s for sample stability using Cell Free DNA (cfDNA) from healthy volunteers (n = 20).

Design & methods

Whole blood was drawn into five Roche and five Streck tubes per volunteer, stored at room temperature and processed at five different time points (Days 0, 4, 7, 10 and 14). One volunteer had blood drawn into ×10 K₃EDTA tubes to observe the effect of no preservation buffer on White Blood Cell (WBC) lysis. DNA was extracted from the plasma and the concentration (ng/μL) measured using the Qubit Fluorometer^® at each time point. The eluted DNA was further analysed by capillary electrophoresis to determine the proportion of cfDNA and gDNA contamination in the samples over the 14 days.

Results

There was no difference in individual (p = 0.097) and median paired (p = 0.26) DNA concentration across the five time points between the two tubes. However, a difference was observed for samples in the Roche tubes for pair days 0-7 (p = 0.01), 0 to 10 (p = 0.046) and 0 to 14 (p = 0.0016) in contrast to the Streck tubes after adjustment for multiple testing.

Conclusion

The findings of this study indicate that the Roche Cell-Free DNA Collection Tubes^® are a suitable alternative for sample collection and storage at room temperature, albeit for a duration of less than 7 days.

Profile of HBV Integration in the Plasma DNA of Hepatocellular Carcinoma Patients

Background:

Hepatitis B Viral (HBV) infection is one of the major causes of Hepatocellular Carcinoma (HCC). Mounting evidence had provided that the HBV integration might be a critical con-tributor of HCC carcinogenesis.

Objective and Methods:

To explore the profile of HBV integration in the plasma DNA, the method of next-generation sequencing, HBV capture and bioinformatics had been employed to screen for HBV in-tegration sites in the plasma samples.

Results:

In the initial experiment, a total of 87 breakpoints were detected in the 20 plasma samples. The distribution of breakpoints showed that there was significant enrichment of breakpoints in the region of intron. Furthermore, the HBV breakpoints were prone to occur in the region of X protein (1,700-2,000bp) in the plasma samples. The pathway analysis had revealed that the HBV integrations sites were specifically enriched in the cancer pathway.

Conclusion:

Altogether, our results had provided direct evidence for the HBV integration in plasma DNA, and they might be potentially useful for future HCC prognosis and diagnosis.

The First ongoing Pregnancy Following Comprehensive Aneuploidy Assessment Using a Combined Blastocenetesis, Cell Free DNA and Trophectoderm Biopsy Strategy

BACKGROUND

The exact origin of cell-free DNA found in spent culture media or blastocoel fluid is currently unknown but with the potential to become an improved source of DNA for chromosomal analysis than trophectoderm biopsy samples, it provides a superior representation of the fetal genetic status. However, the genetic material contained within the blastocoel cavity may be more reliable to assessment of embryo euploidy in a clinical context than trophectoderm of cell-free DNA.

CASE PRESENTATION

This is the first UK case report where all three sources of DNA were analyzed in a clinical setting on 29 th January 2018 at the Centre for Reproductive and Genetic Health, London, leading to an ongoing clinical pregnancy.

CONCLUSION

The experience from this case report suggests that removal of blastocoel fluid, sampling of spent culture media and trophectoderm biopsy can be carried out in parallel. Gathering genetic information from two to three independent samples of embryo DNA may provide enhanced diagnostic accuracy and may clarify cytogenetic status of mosaic embryos.

Clinical Interest of Circulating Tumor DNA in Oncology

Genetic alterations in tumors, as predictor of response to targeted-therapies or as prognostic markers, are clinically relevant to determine adequate therapeutic management. Tumor biopsy is currently the golden standard for somatic alterations assessment, but this approach is invasive and does not consider tumor heterogeneity. In various body fluids like plasma, somatic mutations have been identified. Circulating tumor DNA (ctDNA) holds promises in tumor burden monitoring or malignancies early detection. Since allele frequencies of circulating somatic mutations are low, highly sensitive novel assays have been developed to allow the investigation of the tumor genome, leading to the emergence of the "liquid biopsy" concept. Despite these technological advances, other assays for identifying intratumor and intermetastases heterogeneity need to be developed. Before being applied to clinic, ctDNA analyses need to be harmonized and validated with well-powered, well-designed studies. One of the primary prerequisite to incorporation of ctDNA analysis in the follow-up strategy of malignancies is the checking of the concordance with golden standard detection methods, imaging, circulating proteins and biopsy. This review focuses on the clinical interest of ctDNA in solid tumors and hematological malignancies.

Methodological development and biological observations of cell free DNA with a simple direct fluorescent assay in colorectal cancer

BACKGROUND

Cell free DNA (cfDNA) has shown promising utility as prognostic biomarker for patients with colorectal cancer (CRC), with an ongoing need to optimize and validate the laboratory methodology. Here, we report our optimization and validation of a direct fluorescent assay and display the potential utility in patients with colorectal cancer.

METHODS

Plasma cfDNA was analyzed by a direct fluorescent assay (DFA) and compared to quantification by droplet digital PCR (ddPCR). For clinical validation, baseline blood samples were available for a total of 273 patients from six different Nordic trials, covering patients with locally advanced rectal cancer (n = 176, cohorts A + B), liver limited metastatic CRC (n = 75C + D) and wide spread metastatic CRC (n = 22 E + F).

RESULTS

Validating the DFA analysis with ddPCR revealed a strong correlation with an R2 of 0.81. For the clinical cohorts, the levels of cfDNA were: 0.8 ng/uL (95%CI 0.75-0.83) (A + B), 0.93 ng/uL (95%CI 0.86-1.02) (C + D) and 1.2 ng/uL (95%CI 0.85-1.47) (E + F), respectively (p < 0.01). All cohorts of colorectal cancer had higher levels of cell free DNA than healthy individuals (n = 94) (p < 0.01).

CONCLUSION

Analysis of cell free DNA by a direct fluorescent assay could be an attractive laboratory option for a rapid inexpensive quantification of cell free DNA.

Correlations of Circulating Cell-Free DNA With Clinical Manifestations in Acute Myocardial Infarction

BACKGROUND

The objective of the study was to examine the potential use of circulating cell free DNA (cfDNA) in acute myocardial infarction (AMI) patients and correlate it with clinical features. Serial monitoring was conducted to assess any associations to disease.

METHODS

Quantification of cfDNA was performed on 130 cardiovascular disease (CVD) patients as well as 30 healthy volunteers. Serial samplings were conducted using PicoGreen dsDNA assay. Of the 130 patients with CVD, 100 had an AMI and measurements were taken during treatment. Short and medium intervals serial sampling of patients' blood were undertaken.

RESULTS

The results were highly correlative of CVD disease status. The mean concentration of cfDNA in patients with AMI was 5 folds higher during the onset of disease compared with healthy volunteers. The cfDNA content was also higher than other patients with CVD. Interestingly, short term monitoring of patients with AMI showed distinct trends that highlighted the severity of the disease and linked to complication events. Medium term monitoring showed 2 distinctive groups with 1 that had their cfDNA returned to basal levels and the other with persistently elevated cfDNA levels.

CONCLUSIONS

Measuring cfDNA in patients with CVD offers an alternative approach to monitor the disease and has potential clinical applications to identify high-risk individuals.

Cell free DNA: A Novel Predictor of Neurological Outcome after Intravenous Thrombolysis and/or Mechanical Thrombectomy in Acute Ischemic Stroke Patients

PURPOSE

Several blood markers have been evaluated in stroke patients, but their role remains limited in clinical practice. This study was designed to evaluate the utility of cell free DNA (cf DNA) in stroke patients undergoing therapeutic intervention in the form of mechanical thrombectomy in acute ischemic stroke patients.

MATERIALS AND METHODS

Twenty-six patients with ischemic stroke who were managed with interventions like intravenous thrombolysis (IVT) and mechanical thrombectomy were recruited consecutively in this study. The cf DNA was extracted by using circulating nucleic acid kit and measured by real-time quantitative PCR assay for β-globin gene. The neurological outcome was measured by modified Rankin scale (mRS) score at three months after the onset of symptoms.

RESULTS

Cf DNA levels correlated with severity of stroke at the time of admission (r=0.421, P=0.032) and poor outcome at three months (r=0.606, P=0.001). Therapeutic intervention in the form of mechanical thrombectomy or IVT was associated with improved outcome in patients with cf DNA <10,000 kilogenome-equivalents/L (P=<0.05).

CONCLUSION

Cf DNA level correlated well with the 3 month outcome in acute ischemic stroke patients. It can be a potential supplementary marker to predict neurological outcome after therapeutic intervention.

Detection of fusion gene in cell-free DNA of a gastric synovial sarcoma

Synovial sarcoma (SS) is genetically characterized by chromosomal translocation, which generates SYT-SSX fusion transcripts. Although SS can occur in any body part, primary gastric SS is substantially rare. Here we describe a detection of the fusion gene sequence of gastric SS in plasma cell-free DNA (cfDNA). A gastric submucosal tumor was detected in the stomach of a 27-year-old woman and diagnosed as SS. Candidate intronic primers were designed to detect the intronic fusion breakpoint and this fusion sequence was confirmed in intron 10 of SYT and intron 5 of SSX2 by genomic polymerase chain reaction (PCR) and direct sequencing. A locked nucleic acid (LNA) probe specific to the fusion sequence was designed for detecting the fusion sequence in plasma and the fusion sequence was detected in preoperative plasma cfDNA, while not detected in postoperative plasma cfDNA. This technique will be useful for monitoring translocation-derived diseases such as SS.

Multiplex identification of sepsis-causing Gram-negative pathogens from the plasma of infected blood

Early and accurate detection of bacterial pathogens in the blood is the most crucial step for sepsis management. Gram-negative bacteria are the most common organisms causing severe sepsis and responsible for high morbidity and mortality. We aimed to develop a method for rapid multiplex identification of clinically important Gram-negative pathogens and also validated whether our system can identify Gram-negative pathogens with the cell-free plasm DNA from infected blood. We designed five MLPA probe sets targeting the genes specific to major Gram-negative pathogens (uidA and lacY for E. coli, ompA for A. baumannii, phoE for K. pneumoniae, and ecfX for P. aeruginosa) and one set targeting the CTX-M group 1 to identify the ESBL producing Gram-negative pathogens. All six target-specific peaks were clearly separated without any non-specific peaks in a multiplex reaction condition. The minimum detection limit was 100 fg of pathogen DNA. When we tested 28 Gram-negative clinical isolates, all of them were successfully identified without any non-specific peaks. To evaluate the clinical applicability, we tested seven blood samples from febrile patients. Three blood culture positive cases showed E. coli specific peaks, while no peak was detected in the other four culture negative samples. This technology can be useful for detection of major sepsis-causing, drug-resistant Gram-negative pathogens and also the major ESBL producing Gram-negatives from the blood of sepsis patients in a clinical setting. This system can help early initiation of effective antimicrobial treatment against Gram-negative pathogens for sepsis patients, which is very crucial for better treatment outcomes.

The Natural History and Outcome Predictors of Metastatic Castration-resistant Prostate Cancer

CONTEXT

Biomarkers for the treatment of metastatic castration-resistant prostate cancer (mCRPC) are urgently needed by clinicians to facilitate treatment decisions.

OBJECTIVE

To review current prognostic and predictive biomarkers in mCRPC.

EVIDENCE ACQUISITION

We performed a nonsystematic review of the literature from 2004 to August 2016 by searching in Medline. Cross-matching references were used to search for additional articles. We reviewed clinical research and review articles written in the English language.

EVIDENCE SYNTHESIS

Nomograms of prognostic factors (eg, albumin, lactate dehydrogenase) enable clinicians to estimate the prognosis of men with mCRPC. These prognostic tools may aid with when to trigger treatment, therapeutic monitoring, and follow-up. However, validated predictive biomarkers in mCRPC are still lacking. Androgen receptor (AR) splice variants (ie, AR-V7), gene fusions, and point mutations determined using liquid biopsies such as circulating tumor cells (CTCs) or cell-free DNA (cfDNA) are promising biomarkers that are the subject of ongoing research. Patient biomarkers (eg, neutrophil-to-lymphocyte ratio) are readily available and come with no extra cost but need further validation before their implementation in clinical practice.

CONCLUSIONS

Determination of AR-V7 in CTCs is a big step towards a more personalized treatment approach in mCRPC. Genomic characterization of liquid biopsies such as CTCs, cfDNA, and circulating RNA are noninvasive tools to further personalize treatment in prostate cancer. Clinical parameters are readily available, but are derived from retrospective studies and should be interpreted with care. Only by conducting biomarker-driven studies, rather than large one-size-fits-all trials, will we be able to improve prostate cancer treatment.

PATIENT SUMMARY

Several biomarkers are currently under investigation that may predict which patients will respond to specific therapies in the future of metastatic castration-resistant prostate cancer treatment.

Non-invasive urine testing of EGFR activating mutation and T790M resistance mutation in non-small cell lung cancer

Background

The increasing understanding of non-small cell lung cancer (NSCLC) biology over the last two decades has led to the identification of multiple molecular targets. This led to the development of multiple targeted therapies in the primary and secondary resistance setting and the epidermal growth factor receptor (EGFR) gene remains the most frequently observed molecular target in NSCLC. Tissue biopsies remain the standard for the identification of such EGFR mutations. Obtaining serial tissue biopsies, especially in the secondary resistance setting is associated with multiple medical and logistical challenges. Utilizing circulating tumor DNA (ctDNA) fragments for molecular analysis can overcome these challenges and aid in therapeutic decision-making.

Case presentation

Here we present a present a 72-year-old Korean woman with metastatic, EGFR L858R mutated bronchogenic adenocarcinoma. She developed skeletal progression on treatment with first and second generation tyrosine kinase inhibitors (TKIs). Repeated biopsies failed to provide informative molecular test results. A novel urine ctDNA assay was utilized and confirmed T790M positive status. The patient was started on a third generation TKI, which led to a measurable clinical response.

Conclusions

Utilization of urine liquid biopsies for EGFR diagnostics are feasible and provided critical clinical information in this patient’s case. Urine liquid biopsy represents a viable alternative to tissue biopsy, particularly in the secondary resistance setting, when tissue is not available for molecular testing.

DNA integrity as biomarker in pancreatic cyst fluid

Identification of pancreatic cysts with malignant potential is important to prevent pancreatic cancer development. Integrity of cell free DNA (cfDNA) has been described as tumor biomarker, but its potential for pancreatic cancer is unclear. While normal apoptotic cells release uniformly truncated DNA, malignant tissues release long fragments of cell free DNA (cfDNA). We measured 247 base pair (bp) and 115 bp DNA fragments of ALU repeats by qPCR in serum from healthy controls and pancreatic cancer patients, and in cyst fluid from pancreatic cyst patients. No differences in total cfDNA (ALU115) and cfDNA integrity (ALU247/115) were observed between sera from healthy controls (n=19) and pancreatic cancer patients (n=19). Although elevated as compared to serum, but no differences in cfDNA were found in cyst fluid from high risk (n=10) and low risk (n=20) cyst patients. We conclude that cfDNA integrity is not a useful marker to identify (pre)malignant pancreatic lesions.