Cell-free DNA In Patients Research Articles

241P Genomic analysis of plasma cell-free DNA in patients with heavily pretreated HER-2+ metastatic breast cancer (MBC)

We explored the accumulated genomic alterations and their clinical significance through circulating tumor DNA (ctDNA) analysis in patients who were enrolled in the KCSG BR18-14/KM10B trial. This trial investigated the efficacies of trastuzumab biosimilar with cytotoxic chemotherapy in HER2+ MBC patients who had failed 2 or more HER2 directed chemotherapies.

Plasma metagenomic next-generation sequencing of microbial cell-free DNA detects pathogens in patients with suspected infected pancreatic necrosis

BackgroundInfected pancreatic necrosis (IPN) is a life-threatening complication of acute pancreatitis (AP). Timely diagnosis of IPN could facilitate appropriate treatment, but there is a lack of reliable non-invasive screening tests. In this study, we aimed to evaluate the diagnostic value of plasma metagenomic next-generation sequencing (mNGS) based on circulating microbial cell-free DNA in patients with suspected IPN.MethodsFrom October 2020 to October 2021, 44 suspected IPN patients who underwent plasma mNGS were reviewed. Confirmatory diagnosis of IPN within two weeks after the index blood sampling was considered the reference standard. The confirmation of IPN relied on the microbiological results of drains obtained from the necrotic collections. The distribution of the pathogens identified by plasma mNGS was analyzed. Positive percent agreement (PPA) and negative percent agreement (NPA) were evaluated based on the conformity between the overall mNGS results and culture results of IPN drains. In addition, the clinical outcomes were compared between mNGS positive and negative patients.ResultsAcross all the study samples, thirteen species of bacteria and five species of fungi were detected by mNGS. The positivity rate of plasma mNGS was 54.55% (24/44). Of the 24 mNGS positive cases, twenty (83.33%, 95% CI, 68.42–98.24%) were consistent with the culture results of IPN drains. The PPA and NPA of plasma mNGS for IPN were 80.0% (20/25; 95% CI, 64.32–95.68%) and 89.47% (17/19; 95% CI, 75.67–100%), respectively. Compared with the mNGS negative group, patients in the positive group had more new-onset septic shock [12 (50.0%) vs. 4 (20.0%), p = 0.039].ConclusionIPN relevant pathogens can be identified by plasma mNGS, potentially facilitating appropriate treatment. The clinical application of mNGS in this cohort appears feasible.

Markers of neutrophil activation and neutrophil extracellular traps in diagnosing patients with acute venous thromboembolism: A feasibility study based on two VTE cohorts.

BackgroundVenous thromboembolism (VTE) diagnosis would greatly benefit from the identification of novel biomarkers to complement D-dimer, a marker limited by low specificity. Neutrophil extracellular traps (NETs) have been shown to promote thrombosis and could hypothetically be used for diagnosis of acute VTE.ObjectivesTo assess the levels of specific markers of neutrophil activation and NETs and compare their diagnostic accuracy to D-dimer.MethodsWe measured plasma levels of neutrophil activation marker neutrophil elastase (NE), the NET marker nucleosomal citrullinated histone H3 (H3Cit-DNA) and cell-free DNA in patients (n = 294) with suspected VTE (pulmonary embolism and deep vein thrombosis) as well as healthy controls (n = 30). A total of 112 VTE positive and 182 VTE negative patients from two prospective cohort studies were included.ResultsHigher levels of H3Cit-DNA and NE, but not cell-free DNA, were associated with VTE. Area under receiver operating curves (AUC) were 0.90 and 0.93 for D-dimer, 0.65 and 0.68 for NE and 0.60 and 0.67 for H3Cit-DNA in the respective cohorts. Adding NE and H3Cit-DNA to a D-dimer based risk model did not improve AUC.ConclusionsOur study demonstrates the presence of neutrophil activation and NET formation in VTE using specific markers. However, the addition of NE or H3Cit-DNA to D-dimer did not improve the discrimination compared to D-dimer alone. This study provides information on the feasibility of using markers of NETs as diagnostic tools in acute VTE. Based on our findings, we believe the potential of these markers are limited in this setting.

Detection and Significance of Cell-Free DNA Mutation in Pleural Effusion in Patients with Advanced NSCLC.

Objective To detect EGFR/KRAS genes in pleural effusion cell-free DNA in patients with advanced non-small-cell lung cancer (NSCLC) and to explore the clinical significance of EGFR/KRAS mutation status in pleural effusion. Methods A retrospective collection was performed on the specimens of pleural effusion and matched tissues from 50 patients with advanced NSCLC admitted to the hospital between January 2019 and January 2021. DNA mutation status of EGFR/KRAS in different specimens was detected and compared by pyrosequencing. The clinicopathological data and follow-up data of survival were collected. The relationship between DNA mutation and clinicopathological characteristics and prognosis was analyzed. Results In the 50 pleural effusion specimens, there were 22 cases (44.00%) with EGFR mutations (19/21 exon mutations), including 12 cases with EGFR19 deletion mutation and 10 cases with EGFR21 exon L858R mutation. There were 6 cases (12.00%) with KRAS mutations (single-base substitution mutations), including 4 cases with 12-codon mutation and 2 cases with 13-codon mutation. In the 50 tissue specimens, there were 24 cases (48.00%) with EGFR mutations and 4 cases (8.00%) with KRAS mutations. There was no significant difference between pleural effusion specimens and tissue specimens, with good consistency (kappa = 0.920–0.779, P > 0.05). EGFR mutation in pleural effusion was related to smoking history, types of pathological tissues, and lymph node metastasis (P < 0.05). The incidence of EGFR mutation was higher in nonsmokers, patients with lung adenocarcinoma, and patients with lymph node metastasis. The carcinoembryonic antigen (CEA) in patients with EGFR mutation was higher than that with wild-type EGFR, while the level of cytokeratin 19 fragment (Cy21-1) was lower than that with wild-type EGFR (P < 0.05). The 1-year overall survival rate in the EGFR mutation group was significantly higher than that in the EGFR wild group (68.18% vs. 42.86%) (HR = 0.419, 95% CI = 0.178–0.989, and P < 0.001). Conclusion For the detection of EGFR gene mutation, the results of the pleural effusion specimens and the tumor pathological tissue specimens were well consistent and the detection of pleural effusion could be used as an alternative method when tissue specimens cannot be obtained. EGFR gene mutations are present in majority in patients with advanced NSCLC. The incidence of EGFR mutation is higher in nonsmokers, patients with lung adenocarcinoma, those with lymph node metastasis, those with high-expression CEA, and those with low-expression Cy21-1. The prognosis is better in patients with EGFR mutation.

Genetic alterations in tumor tissue and cell-free DNA in patients with papillary thyroid carcinoma at initial surgery.

e18083 Background: The value of sequencing cell-free DNA (cfDNA) from patients with papillary carcinoma of the thyroid (PTC) is controversial. Studies utilizing whole-exome sequencing (WES) or single-gene detection methods have reported lower mutational yield in cfDNA in PTC compared with other cancers. Alternatively, mutational analyses of anaplastic thyroid carcinoma (ATC), which is thought to evolve from PTC, demonstrate high levels of mutated cfDNA. We report on mutations in tumor and cfDNA at initial surgery for PTC, correlate with clinicopathologic status and further characterize the mutational landscape of these tumors in tissue and blood utilizing deep-sequencing panel testing. Methods: 50 patients were enrolled 2017-2020. Tempus xT (648 genes) and xF (105 genes) panels were used to prepare next generation sequencing libraries from tissue and blood samples, respectively. Cell-free DNA (cfDNA) sequencing depth average is 20,000x (raw reads)/5,000x (unique reads). Results: More than half of the patients had pT3-T4 tumors and/or local metastases and one had distant metastasis. 47/47 (100%) of processable tissue samples and 40/49 (81.6%) of blood samples yielded at least one relevant mutation. BRAF V600E was found in 77% of tissue and 8% of cfDNA, while mutated TERT was detected in 17% of tissue and none of the blood samples. The most frequently mutated genes in cfDNA were KMT2A (18% of blood samples, 6 % tissue), ATM (12% blood, 6% tissue), and TP53 (12% blood, 2 % tissue). There was marked mutational heterogeneity among samples, and a range of alterations representing multiple oncogenic pathways. Conclusions: Patients at initial surgery demonstrated highly mutated tissue DNA, including BRAF, TERT and other mutations known to be found in PTC. The most frequent tissue mutations were found at higher rates than previously reported by WES, which may reflect the sensitivity of targeted deep sequencing versus WES, and possibly a selection bias of more advanced PTC. A high percentage of cfDNA samples yielded mutations relevant to thyroid cancer, and the absence of TERT is consistent with prior studies. Mutations and co-mutations associated with de-differentiation and worse outcomes were demonstrated in both tissue and cfDNA. Interestingly, mutations more common in ATC than PTC, such as TP53, were detected in cfDNA, often without primary tumor correlate. Since mutations associated with aggressive behavior may be found in metastatic foci while not detected in the primary tumor, we conclude that cfDNA may reveal prognostic information important for the development of surveillance strategies in selected patients with residual PTC after surgery who may be at risk for poor outcomes.

Utilization and financial coverage of blood based next generation sequencing for solid tumors: A study from Augusta-Georgia.

e18592 Background: There is an increasing trend of integrating molecular profiling to devise treatment plans for solid malignancies. Tumor testing for specific clonal abnormalities is being supplanted by broad multigene panel testing from blood specimen, aptly labelled liquid biopsy. Due to varying utility across malignancies in differing contexts and issues of access and affordability, their adoption is not uniform. We attempt to characterize the pattern of utilization across tumor types and financial coverage schemes in an academic cancer institute in southeastern United States. Methods: All blood based next generation testing samples ordered by providers affiliated to Georgia Cancer center between January 1, 2017, and December 31, 2021, via Guardant platform for all solid tumors was included in this analysis. Guardant360 and Guardant360CDx assays tested for upto 83 cancer related genes in circulating cell-free DNA in patients of solid tumors. Primary cancer diagnosis, insurance information and turnaround time was obtained from Guardant. Results: 296 tests were sent from January 1, 2017, through December 31, 2021. The total number of tests performed in year 2017, 2018, 2019, 2020 and 2021 were 1, 3, 28, 99 and 165 respectively. Billing information was available for all cases, clinical information was available for 262 cases. Average turnaround time was 8.5 days overall. 221 Guardant360 was sent with average turnaround time of 10 days. 41 Guardant360CDx was sent with average turnaround time of 7 days. The frequency of malignancies in the order of dimensioning frequency were lung 50.7%, prostate 12.1%, breast 6.9%, kidney 3.8% and colorectal 3.4%. The remaining 22.1% comprised of pancreatic, melanoma, glioblastoma, and bladder malignancies. The test was covered by private insurance/employee health plan in 53.4% (158/296), Medicare in 31.1% (92/296) and Medicaid in 10.5% (31/296) (table). 4.7% (14/296) qualified for free of charge testing (financial indigent) and 0.3% (1/296) were self-pay (table). Conclusions: There is an increase in the utilization of liquid biopsy to perform comprehensive genomic analysis. The distribution of tumor types is not entirely explained by the incidence and availability of targeted therapies for each type. Private insurers accounted for most of the tests being done. The disparities in utilization of this platform across different tumor types and payment models deserve further exploration. T[Table: see text]

Diagnostic Value of Circulating Cell-free DNA in Patients With Papillary Thyroid Cancer.

We investigated whether the occurrence and development of papillary thyroid cancer (PTC) might be predicted using levels of circulating cell-free DNA (cfDNA). The peripheral blood samples were collected from 68 patients with PTC, 31 patients with nodular goiter (NG), and 86 healthy controls (HC). The concentration of cfDNA was measured by qPCR using three primer sets: β-actin99, β-actin394 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in plasma samples. It was demonstrated that plasma β-actin99 and β-actin394 in the PTC group were significantly higher compared to HC (p<0.05 and p<0.001, respectively). The cfDNA integrity index was significantly higher in the PTC patients compared to HC and NG (p<0.001, p<0.05, respectively). The cfDNA concentration in the NG group was significantly higher than in the PTC (p<0.05 and p<0.001, respectively). Moreover, in most PTC patients with suppressed thyroglobulin, the β-actin394 and cfDNA integrity index was significantly decreased after surgery (p<0.05 and p<0.001, respectively). ROC analysis revealed that cfDNA integrity index can be used as a potential marker in distinguishing PTC from HC (AUC 0.901, p<0.001) and NG (AUC 0.629, p<0.05). Increased concentration of cfDNA β-actin99 and β-actin394 may be a valuable biomarker that differentiates PTC patients from HC. Also, an increased cfDNA integrity index may be a suitable parameter which differentiates PTC patients from NG and HC.

Detection of MDM2 amplification by shallow whole genome sequencing of cell-free DNA of patients with dedifferentiated liposarcoma.

High-level amplification of MDM2 and other genes in the 12q13–15 locus is a hallmark genetic feature of well-differentiated and dedifferentiated liposarcomas (WDLPS and DDLPS, respectively). Detection of this genomic aberration in plasma cell-free DNA may be a clinically useful assay for non-invasive distinction between these liposarcomas and other retroperitoneal tumors in differential diagnosis, and might be useful for the early detection of disease recurrence. In this study, we performed shallow whole genome sequencing of cell-free DNA extracted from 10 plasma samples from 3 patients with DDLPS and 1 patient with WDLPS. In addition, we studied 31 plasma samples from 11 patients with other types of soft tissue tumors. We detected MDM2 amplification in cell-free DNA of 2 of 3 patients with DDLPS. By applying a genome-wide approach to the analysis of cell-free DNA, we also detected amplification of other genes that are known to be recurrently affected in DDLPS. Based on the analysis of one patient with DDLPS with longitudinal plasma samples available, we show that tracking MDM2 amplification in cell-free DNA may be potentially useful for evaluation of response to treatment. The patient with WDLPS and patients with other soft tissue tumors in differential diagnosis were negative for the MDM2 amplification in cell-free DNA. In summary, we demonstrate the feasibility of detecting amplification of MDM2 and other DDLPS-associated genes in plasma cell-free DNA using technology that is already routinely applied for other clinical indications. Our results may have clinical implications for improved diagnosis and surveillance of patients with retroperitoneal tumors.

Circulating tumour cells and circulating cell-free DNA in patients with lung cancer: a comparison between thoracotomy and video-assisted thoracoscopic surgery

IntroductionThe type of lung cancer surgery impacts on tumour manipulation during surgery and may drive dissemination of cancer cells into the vasculature, thus facilitating metastatic spread. The aim of this...

Characterization and Clinical Utility of BRAFV600 Mutation Detection Using Cell-Free DNA in Patients with Advanced Melanoma.

Simple SummaryThe choice of cancer drug(s) for the treatment of advanced melanoma is based on the types of gene alterations that are present in the patient’s tumor(s). Sometimes, the tumor sample that is obtained from surgery may be degraded, and the test does not provide a reliable result, leading to the selection of the wrong treatment, and, consequently, poor outcomes for the patient. Surgery to obtain fresh tumor samples is inconvenient. In recent years, scientists have learned that fragments of genes from dying cells, including tumors, are constantly being released into the blood. This study shows that the presence of altered genes can be reliably determined using easy-to-obtain blood samples. The study also shows that, while there is a small rate of error with the commonly used tests based on the tumor tissue sample, retests using blood samples may be a less invasive and rapid alternative for identifying the BRAF mutation status and selecting the right treatment for these patients.Tissue-based tests for BRAFV600 mutation-positive melanoma involve invasive biopsy procedures, and can lead to an erroneous diagnosis when the tumor samples degrade. Herein, we explored a minimally invasive, cell-free deoxyribonucleic acid (cfDNA)-based platform, to retest patients for BRAFV600 mutations. This phase 2 study enrolled adult patients with unresectable/metastatic melanoma. A prescreening testing phase evaluated the concordance between a prior tissue-based BRAFV600 mutation test result and a subsequent plasma cfDNA-based test result. A treatment phase evaluated the patients who were confirmed as BRAFV600 mutation-positive, and were treated with cobimetinib plus vemurafenib. It was found that 35/54 patients (64.8%) with a mutant BRAF status by prior tissue test had a positive BRAFV600 mutation with the cfDNA test. Further, 7/118 patients (5.9%) with a wild-type BRAF status had a positive BRAFV600 mutation cfDNA test; tissue retests on archival samples confirmed BRAFV600 mutation positivity in 5/7 patients (71.4%). One of these patients received BRAF pathway-targeted therapy (cobimetinib plus vemurafenib), and had progression-free survival commensurate with previous experience. In the overall cobimetinib plus vemurafenib-treated population, 29/36 patients (80.6%) had an objective response. The median progression-free survival was 13.6 months (95% confidence interval, 9.5–16.5). Cell-free DNA–based tests may be a fast and convenient option to identify BRAF mutation status in melanoma patients, and help inform treatment decisions.

Mycobacterium tuberculosis-derived circulating cell-free DNA in patients with pulmonary tuberculosis and persons with latent tuberculosis infection.

ObjectivesThe timely diagnosis of pulmonary tuberculosis (PTB) is challenging. Although pathogen-derived circulating cell-free DNA (cfDNA) has been detected in humans, the significance of Mycobacterium tuberculosis (MTB)-cfDNA detection in patients with PTB remains unclear.MethodsThis study enrolled patients with PTB and persons with latent tuberculosis infection (LTBI) as the study and control groups, respectively, from 2018 to 2020. We measured interferon-γ levels and calculated blood monocyte-to-lymphocyte ratio (MLR). We conducted plasma cfDNA extraction, quantitative polymerase chain reaction (qPCR), and droplet digital PCR targeting the IS6110 gene of MTB. We calculated the sensitivity and specificity of using MTB-cfDNA to identify PTB and analyzed the factors associated with PTB diagnosis and MTB-cfDNA positivity.ResultsWe enrolled 24 patients with PTB and 57 LTBI controls. The sensitivity of using MTB-cfDNA to identify PTB was 54.2%(13/24) in total and 46.2%(6/13) in smear-negative cases. Two LTBI controls (3.5%) tested positive for MTB-cfDNA, indicating a specificity of 96.5%(55/57). By using MTB-cfDNA positivity and an MLR ≥0.42 to identify PTB, sensitivity increased to 79.2%(19/24). Among patients with PTB, MTB-specific interferon-γ levels were higher in MTB-cfDNA positive participants than in those who tested negative (7.0 ±2.7 vs 2.7±3.0 IU/mL, p<0.001). MTB-cfDNA levels declined after 2 months of anti-tuberculosis therapy (p<0.001).ConclusionThe sensitivity of using MTB-cfDNA to identify PTB in participants was 54.2%, which increased to 79.2% after incorporating an MLR ≥0.42 into the analysis. MTB-cfDNA positivity was associated with MTB-specific immune response, and MTB-cfDNA levels declined after treatment. The clinical value of MTB-cfDNA in PTB management necessitates further investigation.

Spectrum of FGFR2/3 Alterations in Cell-Free DNA of Patients with Advanced Urothelial Carcinoma.

Detecting genomic alterations (GAs) in advanced urothelial carcinoma (aUC) can expand treatment options by identifying candidates for targeted therapies. Erdafitinib is FDA-approved for patients with platinum-refractory aUC with activating mutation or fusion in FGFR2/3. We explored the prevalence and spectrum of FGFR2/3 GAs identified with plasma cfDNA NGS testing (Guardant360) in 997 patients with aUC. FGFR2/3 GAs were detected in 201 patients (20%) with characterized activating GAs in 141 (14%). Our results indicate the Guardant360-based FGFR2/3 GA detection rate is similar to those described from previous studies employing tumor tissue testing, suggesting that plasma-based cfDNA NGS may non-invasively identify candidates for anti-FGFR targeted therapies.

The diagnostic accuracy of digital PCR, ARMS and NGS for detecting KRAS mutation in cell-free DNA of patients with colorectal cancer: A systematic review and meta-analysis.

Before anti-EGFR therapy is given to patients with colorectal cancer, it is required to determine KRAS mutation status in tumor. When tumor tissue is not available, cell-free DNA (liquid biopsy) is commonly used as an alternative. Due to the low abundance of tumor-derived DNA in cell-free DNA samples, methods with high sensitivity were preferred, including digital polymerase chain reaction, amplification refractory mutation system and next-generation sequencing. The aim of this systemic review and meta-analysis was to investigate the accuracy of those methods in detecting KRAS mutation in cell-free DNA sample from patients with colorectal cancer. Literature search was performed in Pubmed, Embase, and Cochrane Library. After removing duplicates from the 170 publications found by literature search, eligible studies were identified using pre-defined criteria. Quality of the publications and relevant data were assessed and extracted thereafter. Meta-DiSc and STATA softwares were used to pool the accuracy parameters from the extracted data. A total of 33 eligible studies were identified for this systemic review and meta-analysis. After pooling, the overall sensitivity, specificity, and diagnostic odds ratio were 0.77 (95%CI: 0.74-0.79), 0.87 (95%CI: 0.85-0.89), and 23.96 (95%CI: 13.72-41.84), respectively. The overall positive and negative likelihood ratios were 5.55 (95%CI: 3.76-8.19) and 0.29 (95%CI: 0.21-0.38), respectively. Area under curve of the summarized ROC curve was 0.8992. Digital polymerase chain reaction, amplification refractory mutation system, and next-generation sequencing had overall high accuracy in detecting KRAS mutation in cell-free DNA sample. Large prospective randomized clinical trials are needed to further convince the accuracy and usefulness of KRAS mutation detection using cfDNA/liquid biopsy samples in clinical practice. PROSPERO CRD42020176682; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=176682.

Utility of Cerebrospinal Fluid Cell-Free DNA in Patients with EGFR-Mutant Non-Small-Cell Lung Cancer with Leptomeningeal Metastasis.

Leptomeningeal metastasis (LM) is a fatal complication of advanced non-small-cell lung cancer (NSCLC). The aim of this study was to evaluate the utility of cerebrospinal fluid (CSF) as a medium for epidermal growth factor receptor (EGFR) mutation testing in clinical practice. We prospectively enrolled patients with EGFR-mutant NSCLC who underwent CSF sampling for suspected LM. The supernatant of CSF after routine cytology examination was collected. The diagnosis of LM was established according to EANO-ESMO criteria. CSF and plasma cell-free DNA (cfDNA) were retrieved for EGFR mutation testing. Fifty-one patients with a median age of 62.7 years were enrolled. The median duration from initial diagnosis to CSF sampling was 23.0 months and most patients (94.1%) had received at least one EGFR-tyrosine kinase inhibitor. Adenocarcinoma cells were found in 37 CSF samples (72.5%), and 48 (94.1%) patients had confirmed or probable LM. Thirty-five of these 48 patients (72.9%) had valid EGFR mutation-testing results using CSF cfDNA and tended to have higher white blood cell counts and positive cytology in their CSF compared to those with invalid mutation testing results. The overall detection rate of EGFR mutation in CSF cfDNA was 68.8%, and the T790M detection rate was 14.6%. In 37 patients with paired CSF and plasma samples, the concordance rate of the EGFR mutation results was 29.7%. For patients with EGFR-mutant NSCLC with LM, CSF supernatant is a valuable source for EGFR mutation testing and may provide important information.

Circulating Cell-free DNA in Patients With Acute Biliary Pancreatitis: Association With Disease Markers and Prolonged Hospitalization Time-A Prospective Cohort Study.

To evaluate cfDNA as an indicator of pancreatitis severity. Acute pancreatitis severity scores have limited proficiency, and are complex and challenging to use clinically. Elevation of circulating cfDNA concentration has been shown to be associated with hospital length of stay (LOS) and mortality. In a prospective study, cfDNA concentration was measured by a simple fluorometric test, at admission and for 2 consecutive days, in patients with acute biliary pancreatitis (ABP). Ranson and APACHE II scores were used as measures of pancreatitis severity. Hospital LOS and mortality were used as outcome measures. Seventy-eight patients were included. Patients with severe disease according to Ranson's Criteria (n = 24) had elevated median admission cfDNA compared to patients with mild disease (n = 54, 2252ng/ml vs 1228 ng/ml, P < 0.05 ). Admission cfDNA levels correlated with Ranson and APACHE II scores and markers of bile duct obstruction. LOS did not differ between patients with mild and severe disease according to Ranson and APACHE II scores. Patients with cfDNA at 24 hours concentrations above the cutoff value of healthy patients (>850 ng/ml) had a significantly longer LOS compared to those with normal cfDNA levels ( P < 0.001 ). cfDNA, measured by a rapid simple assay, proved a valuable early marker of severity in ABP with clear advantages for prediction of LOS over Ranson and APACHE II. Measurement of cfDNA has the potential to be an effective practical approach to predict the course of ABP and should be further evaluated in larger trials.

Next Generation Sequencing-Based Profiling of Cell Free DNA in Patients with Advanced Non-Small Cell Lung Cancer: Advantages and Pitfalls.

Simple SummaryGenomic profiling of non-small cell lung cancer (NSCLC) patients offers the possibility of therapeutic intervention with target-based agents. The analysis of circulating free DNA (cfDNA) through next generation sequencing (NGS) technologies is emerging as a powerful tool to assess the whole tumor molecular landscape of NSCLC patients and characterize spatial and temporal tumor heterogeneity. Moreover, cfDNA NGS testing allows the monitoring of therapy response and the early identification of resistance mechanisms. In this review, we describe the importance of implementation of cfDNA NGS testing in routine clinical practice to improve targeted diagnostic procedures and personalized therapies in NSCLC patients.Lung cancer (LC) is the main cause of death for cancer worldwide and non-small cell lung cancer (NSCLC) represents the most common histology. The discovery of genomic alterations in driver genes that offer the possibility of therapeutic intervention has completely changed the approach to the diagnosis and therapy of advanced NSCLC patients, and tumor molecular profiling has become mandatory for the choice of the most appropriate therapeutic strategy. However, in approximately 30% of NSCLC patients tumor tissue is inadequate for biomarker analysis. The development of highly sensitive next generation sequencing (NGS) technologies for the analysis of circulating cell-free DNA (cfDNA) is emerging as a valuable alternative to assess tumor molecular landscape in case of tissue unavailability. Additionally, cfDNA NGS testing can better recapitulate NSCLC heterogeneity as compared with tissue testing. In this review we describe the main advantages and limits of using NGS-based cfDNA analysis to guide the therapeutic decision-making process in advanced NSCLC patients, to monitor the response to therapy and to identify mechanisms of resistance early. Therefore, we provide evidence that the implementation of cfDNA NGS testing in clinical research and in the clinical practice can significantly improve precision medicine approaches in patients with advanced NSCLC.

Response to CAR-T Therapy Can be Monitored Using Genome-Wide Sequencing of Cell-Free DNA in Patients with DLBCL

Response to CAR-T Therapy Can be Monitored Using Genome-Wide Sequencing of Cell-Free DNA in Patients with DLBCL

Longitudinal Genomic Characterization Using Cell-Free DNA in Patients with Idiopathic Aplastic Anemia

The molecular profile of clonal hematopoiesis in patients (pts) with idiopathic aplastic anaemia (iAA) has been shown to predict response to immunosuppressive therapy (IST). Moreover, clonal evolution is associated with transformation of iAA to aggressive myeloid malignancies such as myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). Detection of somatic mutations may help identify pts more likely to respond to IST and also those at increased risk of transformation however the predictive value of detecting mutations at a single timepoint is limited. Longitudinal detection of changes in mutation profile over time may improve prediction of transformation risk, however due to bone marrow hypocellularity DNA quality and quantity from pts with iAA is frequently suboptimal. Serial mutation analysis of cell-free DNA (cfDNA) is one approach that may overcome this problem as the majority of cfDNA originates from hematopoietic cells and mutations detected in this compartment have been shown to closely resemble those detected from peripheral blood (PB) / bone marrow (BM) analysis in other haematological malignancies. We aimed to characterise longitudinal genomic changes in pts with iAA and contrast mutation detection in the cellular compartment with those detected in cfDNA. Fifteen pts (10 female and 5 male) with a diagnosis of iAA were included (median age 35 years (range 17 - 78)); eleven were newly diagnosed (within six months of diagnosis) and four were two or more years post diagnosis. Cellular DNA (PB or BM aspirate) and cfDNA were collected upon study enrolment and cfDNA samples were collected longitudinally for each pt. Somatic mutations in cellular samples were assessed using custom targeted next generation sequencing panels with an analytical sensitivity of ~1%. cfDNA samples were assessed using a custom anchored multiplex PCR panel with molecular barcodes with an analytical sensitivity of ~0.5%. Twenty-nine genes were assessed in both cellular and cfDNA. Somatic mutations were detected in 13 of 15 (87%) pts at the first sampled timepoint, with two or more mutations detected in seven pts. Overall 27 mutations were detected in seven genes including PIGA (n=12), DNMT3A (n=5), ASXL1 (n=5), BCOR (n=2), BCORL1, NPM1 and RUNX1 (n=1 each) with a higher proportion detected in cfDNA (25 of 27) compared to cellular DNA (22 of 27). Mutations unique to cfDNA were in PIGA (n=3), ASXL1 (n=1) and DNMT3A (n=1) and those unique to cellular DNA were in NPM1 (n=1) and PIGA (n=1). The variant allele frequency (VAF) was &amp;lt;10% for 26 of 27 mutations (median cellular and cfDNA VAF 1.78% and 1.19% respectively), highlighting the need for sensitive mutation detection approaches in the setting of iAA regardless of the compartment tested. We next assessed the mutation dynamics in cfDNA over time by analysing a median of 3 (range 2 - 4) sequential samples per pt (median follow-up interval 670 days, range 249 - 923). 20 of 25 cfDNA mutations were detected in longitudinal cfDNA at similar VAF, including PIGA (n=9), BCOR (n=2), DNMT3A (n=5), ASXL1 (n=3) and RUNX1 (n=1). Five mutations in PIGA (n=2), ASXL1 (n=2) and BCORL1 (n=1) became undetectable over time. Importantly, acquisition of new mutations during follow-up was observed in four pts (total of 13 new cfDNA mutations detected). Three out of these four pts experienced disease transformation to hematological malignancy (MDS n=2, AML n=1), with acquired mutations in SETBP1, NPM1, NRAS, KRAS, WT1 and KIT. Importantly, these mutations often went from undetectable to relatively high VAF within a short interval (5 - 13 months) which is important to consider when designing molecular screening schedules to potentially pre-empt transformation. In summary, our data shows that cfDNA mutation profiling in pts with iAA is technically feasible and is able to detect additional mutations not detectable in the cellular compartment. Importantly, we demonstrate the limitations of analysis of both compartments in the context of low VAF mutations, suggesting that concurrent testing of both cellular and cfDNA may increase the sensitivity for detecting low frequency events. Our data also suggests that longitudinal changes in mutation profile may improve identification of pts at high risk of transformation to hematological malignancy. The optimal frequency of monitoring and the magnitude of increased risk requires validation in prospective trials. GLR and LCF contributed equally to this work Disclosures Szer: Alexion Pharmaceuticals Inc.: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Apellis: Consultancy; Pfizer: Honoraria, Speakers Bureau; Takeda: Honoraria, Speakers Bureau; Novartis: Consultancy, Honoraria, Speakers Bureau; Prevail Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees. Bajel:Astellas: Honoraria; Novartis: Honoraria; Amgen: Honoraria, Speakers Bureau; Pfizer: Honoraria; Abbvie: Honoraria. Blombery:Novartis: Consultancy; Invivoscribe: Honoraria; Amgen: Consultancy; Janssen: Honoraria.

Colon and liver tissue damage detection using methylated SESN3 and PTK2B genes in circulating cell-free DNA in patients with acute graft-versus-host disease

Cell-free DNA (cfDNA) has been investigated in acute graft-versus-host disease (aGvHD) following allogeneic cell transplantation (HSCT). Identifying the tissue of origin of cfDNA in patients with aGvHD is relevant particularly when a biopsy is not feasible. We investigate the cfDNA tissue of origin in patients with aGvHD using methylated gene biomarkers. Patients with liver, colon, or skin aGvHD (n = 28) were analyzed. Liver- and colon-derived cfDNA was measured using a colon- (SESN3) and liver (PTK2B)-specific methylation marker with digital droplet PCR. A statistically significant difference (p < 0.001) in PTK2B and SESN3 concentration was observed between patients with colon or liver GvHD and the control group. For SESN3 and PTK2B the area under the curve in the receiver-operating characteristic (ROC) space was 0.952 (95% CI, 0.888–1 p < 0.001) and 0.971 (95% CI, 0.964–1 p < 0.001), respectively. Thresholds to differentiate aGvHD from non-aGvHD in colon were 0 (sensitivity: 0.905; specificity: 0.989) and liver 1.5 (sensitivity: 0.928; specificity: 0.910). Clinical improvement of liver or colon aGvHD resulted in PTK2B and SESN3 reduced concentration. Whereas, in those patients without improvement the PTK2B and SESN3 level remained stable or increased. The PTK2B liver-specific marker and the SESN3 colon-specific marker and their longitudinal analysis might improve aGvHD detection.

Circulating cell-free DNA in patients with newly diagnosed and recurrent cervical cancer

Objective: Sequencing analysis of circulating cell-free DNA (cfDNA) has been shown to play a role in the diagnosis, prognosis, and disease-monitoring of cancer. Its potential in cervical cancer, however, has yet to be defined. We sought to determine whether the levels of cfDNA correlate with stage, histologic type, or both in cervical cancer patients.