scholarly journals Detection of Circulating Tumor DNA in Patients With Uterine Leiomyomas

2019 ◽  
pp. 1-9
Author(s):  
Joanna Przybyl ◽  
Lien Spans ◽  
Deirdre A. Lum ◽  
Shirley Zhu ◽  
Sujay Vennam ◽  
...  
Keyword(s):  
Lactate Dehydrogenase ◽  
Tumor Suppressor Genes ◽  
Uterine Leiomyoma ◽  
Benign Lesion ◽  
Point Mutations ◽  
Circulating Tumor Dna ◽  
Copy Number Alterations ◽  
Plasma Dna ◽  
Tumor Dna ◽  
Targeted Detection

PURPOSE The preoperative distinction between uterine leiomyoma (LM) and leiomyosarcoma (LMS) is difficult, which may result in dissemination of an unexpected malignancy during surgery for a presumed benign lesion. An assay based on circulating tumor DNA (ctDNA) could help in the preoperative distinction between LM and LMS. This study addresses the feasibility of applying the two most frequently used approaches for detection of ctDNA: profiling of copy number alterations (CNAs) and point mutations in the plasma of patients with LM. PATIENTS AND METHODS By shallow whole-genome sequencing, we prospectively examined whether LM-derived ctDNA could be detected in plasma specimens of 12 patients. Plasma levels of lactate dehydrogenase, a marker suggested for the distinction between LM and LMS by prior studies, were also determined. We also profiled 36 LM tumor specimens by exome sequencing to develop a panel for targeted detection of point mutations in ctDNA of patients with LM. RESULTS We identified tumor-derived CNAs in the plasma DNA of 50% (six of 12) of patients with LM. The lactate dehydrogenase levels did not allow for an accurate distinction between patients with LM and patients with LMS. We identified only two recurrently mutated genes in LM tumors ( MED12 and ACLY). CONCLUSION Our results show that LMs do shed DNA into the circulation, which provides an opportunity for the development of ctDNA-based testing to distinguish LM from LMS. Although we could not design an LM-specific panel for ctDNA profiling, we propose that the detection of CNAs or point mutations in selected tumor suppressor genes in ctDNA may favor a diagnosis of LMS, since these genes are not affected in LM.

scholarly journals Analytical and Clinical Validation of an Amplicon-based Next Generation Sequencing Assay for Ultrasensitive Detection of Circulating Tumor DNA

2021 ◽  
Author(s):  
Jonathan Poh ◽  
Kao Chin Ngeow ◽  
Michelle Pek ◽  
Kian-Hin Tan ◽  
Jing Shan Lim ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Point Mutations ◽  
Circulating Tumor Dna ◽  
Clinical Validation ◽  
Gene Fusions ◽  
Copy Number Alterations ◽  
Next Generation ◽  
Tumor Dna ◽  
Generation Sequencing

Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA. The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (EBV and HBV) and microsatellite instability. Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF, with high specificity even at 0.1% VAF (99.11% per-base). The limit of detection for copy number alterations, EBV, HBV, and microsatellite instability were also empirically determined. Orthogonal comparison of EGFR variant calls made by LiquidHALLMARK and a reference allele-specific PCR method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% alteration-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.

scholarly journals Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anaïs Prouteau ◽  
Jérôme Alexandre Denis ◽  
Pauline De Fornel ◽  
Edouard Cadieu ◽  
Thomas Derrien ◽  
...  
Keyword(s):  
Residual Disease ◽  
Specific Antigen ◽  
Point Mutations ◽  
Antigen Receptor ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Histiocytic Sarcoma ◽  
Oncology Research ◽  
Tumor Dna

AbstractCirculating tumor DNA (ctDNA) has become an attractive biomarker in human oncology, and its use may be informative in canine cancer. Thus, we used droplet digital PCR or PCR for antigen receptor rearrangement, to explore tumor-specific point mutations, copy number alterations, and chromosomal rearrangements in the plasma of cancer-affected dogs. We detected ctDNA in 21/23 (91.3%) of histiocytic sarcoma (HS), 2/8 (25%) of oral melanoma, and 12/13 (92.3%) of lymphoma cases. The utility of ctDNA in diagnosing HS was explored in 133 dogs, including 49 with HS, and the screening of recurrent PTPN11 mutations in plasma had a specificity of 98.8% and a sensitivity between 42.8 and 77% according to the clinical presentation of HS. Sensitivity was greater in visceral forms and especially related to pulmonary location. Follow-up of four dogs by targeting lymphoma-specific antigen receptor rearrangement in plasma showed that minimal residual disease detection was concordant with clinical evaluation and treatment response. Thus, our study shows that ctDNA is detectable in the plasma of cancer-affected dogs and is a promising biomarker for diagnosis and clinical follow-up. ctDNA detection appears to be useful in comparative oncology research due to growing interest in the study of natural canine tumors and exploration of new therapies.

Treatment and relapse in breast cancer show significant correlations to noninvasive testing using urinary and plasma DNA

2020 ◽  
Vol 16 (13) ◽  
pp. 849-858
Author(s):  
Jinling Zhang ◽  
Xueli Zhang ◽  
Shuwei Shen
Keyword(s):  
Breast Cancer ◽  
Circulating Tumor Dna ◽  
Noninvasive Testing ◽  
Plasma Dna ◽  
Operating Characteristics ◽  
Risk Profiling ◽  
Routine Monitoring ◽  
Plasma And Urine Samples ◽  
Serial Time Point ◽  
Tumor Dna

Aim: Circulating tumor DNA is promising for routine monitoring of breast cancer. Noninvasive testing allows regular probing using plasma and urine samples. Methods: Peripheral blood and simultaneous urine collection from patients were quantified. Concordance between methods were made. Serial time-point measurements were correlated to disease outcome. Results: Index measurements demonstrate over 90% concordance with biopsy. Receiver operating characteristics curves showed over 0.95 for both plasma and urine results comparing with controls. Patients with lower risk of relapse experienced greater declines in detected DNA levels. Maximal declines were registered at 4.0- and 6.8-fold for plasma and urine results, respectively. Conclusion: Measuring and monitoring DNA levels complement existing testing regimes and provides better risk profiling of patients for possible relapse.

Circulating tumor DNA in plasma of breast cancer patients from India

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e22213-e22213
Author(s):  
S. Bhattacharyya ◽  
V. Raina ◽  
N. K. Shukla ◽  
S. Shukla ◽  
R. Kumar ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Early Diagnosis ◽  
Cancer Patients ◽  
Circulating Tumor Dna ◽  
Genome Equivalent ◽  
Breast Cancer Patients ◽  
Plasma Dna ◽  
Dna Concentration ◽  
Free Plasma ◽  
Tumor Dna

e22213 Background: Recently, breast cancer has become the most common cancer among women in all urban population in India. Annually about 80000 new cases and 40000 deaths occur and majority of breast cancers are pre-menopausal. Conventional diagnostic methods are not very sensitive especially in early stages of cancer. This necessitated a more sensitive and reliable method for early diagnosis leading to effective treatment, better prognosis and survival. Recently, the level of cell free circulating tumor DNA in blood plasma or serum of patients with variety of tumors are being considered as reliable non-invasive diagnostic tool but no study has been done in India. The present study has therefore been undertaken to evaluate clinical utility of cell free DNA as potential biomarkers for early diagnosis and management of breast cancer. Methods: 25 newly diagnosed untreated breast cancer patients and 25 healthy subjects having no sign of significant medical illness with informed consent were enrolled for the study. 9 patients after chemotherapy were also included in the study. Blood plasma collected from both patients and controls were employed for DNA isolation, using Qiagen kit. Concentration of cell free plasma DNA was analyzed by 3 methods viz. nanodrop spectro-photometry, integrated density value (IDV) of PCR products of Exon 7 of p53 gene and quantitative real time PCR (cycles threshold converted to genome equivalent). All values of DNA concentration obtained by three methods used as continuous variables and receiver operating characteristic (ROC) were plotted and the cut-of value was determined at 90% sensitivity and 100% specificity level of ROC. Results: Mean free plasma DNA concentration as determined by both Q-RT PCR and IDV in cancer patients was found to be significantly higher in advanced stage breast cancer patients than in controls (genome equivalent 18850 vs 431; IDV 17912 vs 4197; p=0.001). However, no significant difference could be observed in early stage disease as compared to controls possibly due small sample size. Conclusions: Free Plasma DNA concentration is a reliable molecular marker for detection of breast cancer and can serve as a prognostic indicator leading to its potential clinical application either alone or in combination with other conventional methods. No significant financial relationships to disclose.

scholarly journals Circulating Tumor DNA as a Liquid Biopsy for Cancer

2015 ◽  
Vol 61 (1) ◽  
pp. 112-123 ◽  
Author(s):  
Ellen Heitzer ◽  
Peter Ulz ◽  
Jochen B Geigl
Keyword(s):  
Liquid Biopsy ◽  
Dna Analysis ◽  
Clonal Evolution ◽  
Cost Effective ◽  
Circulating Tumor Dna ◽  
Analytical Sensitivity ◽  
Plasma Dna ◽  
Multicenter Studies ◽  
Almost All ◽  
Tumor Dna

Abstract BACKGROUND Targeted therapies have markedly changed the treatment of cancer over the past 10 years. However, almost all tumors acquire resistance to systemic treatment as a result of tumor heterogeneity, clonal evolution, and selection. Although genotyping is the most currently used method for categorizing tumors for clinical decisions, tumor tissues provide only a snapshot, or are often difficult to obtain. To overcome these issues, methods are needed for a rapid, cost-effective, and noninvasive identification of biomarkers at various time points during the course of disease. Because cell-free circulating tumor DNA (ctDNA) is a potential surrogate for the entire tumor genome, the use of ctDNA as a liquid biopsy may help to obtain the genetic follow-up data that are urgently needed. CONTENT This review includes recent studies exploring the diagnostic, prognostic, and predictive potential of ctDNA as a liquid biopsy in cancer. In addition, it covers biological and technical aspects, including recent advances in the analytical sensitivity and accuracy of DNA analysis as well as hurdles that have to be overcome before implementation into clinical routine. SUMMARY Although the analysis of ctDNA is a promising area, and despite all efforts to develop suitable tools for a comprehensive analysis of tumor genomes from plasma DNA, the liquid biopsy is not yet routinely used as a clinical application. Harmonization of preanalytical and analytical procedures is needed to provide clinical standards to validate the liquid biopsy as a clinical biomarker in well-designed and sufficiently powered multicenter studies.

Identification of putative germline mutations in 10,288 patients undergoing circulating tumor DNA testing.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 1514-1514 ◽  
Author(s):  
Thomas Paul Slavin ◽  
Kimberly Banks ◽  
Darya Chudova ◽  
Geoffrey R. Oxnard ◽  
Justin I. Odegaard ◽  
...  
Keyword(s):  
Point Mutations ◽  
Read Depth ◽  
Circulating Tumor Dna ◽  
Tumor Burden ◽  
Hereditary Cancer Syndrome ◽  
Dna Testing ◽  
Sequencing Data ◽  
Advanced Cancer Patients ◽  
Cancer Syndrome ◽  
Tumor Dna

1514 Background: No studies have yet described incidental detection of germline cancer predisposition mutations using circulating cell-free DNA (cfDNA). Methods: Deidentified cfDNA sequencing data from 10288 advanced cancer patients (pts) undergoing clinical circulating tumor DNA testing (Guardant360, 73 genes) were included in this study. CfDNA was extracted from plasma and quantified. A DNA library was prepared and sequenced to 15,000X average read depth. Using Ingenuity Variant Analysis, point mutations and small indels suspicious for germline origin (allele fraction 40-60%) were classified following American College of Medical Genetics and Genomics guidelines. Results: More than 50 cancer types were studied, including lung (40%), breast (20%), CRC (8%), prostate (6%), and pancreas (3%). Average age was 63.6 years (range:18-95), 42% were male. Of 34,873 putative germline variants identified, 520 (1.5%) were pathogenic or likely pathogenic (PV), 16,939 (49%) were of uncertain significance, and 17,414 (50%) were benign or likely benign. Of the 250 pts (2.4%) with hereditary cancer syndrome gene PVs, 83 were excluded due to high level of somatic tumor burden leaving 167 (1.6%) with putative germline PVs; rates were higher in pts <50 vs >50 overall (3.3% vs 1.4%, p=0.02) and in breast cancer pts (4.3% vs 1.5%, p=0.03). Conclusions: The observed frequency of incidentally identified putative germline PVs is expectedly lower than the true germline rate; however, these findings illustrate that detection from cfDNA is clinically feasible. Importantly, incidental germline findings could impact oncology treatment planning (e.g. PARP inhibitors for BRCA1/2 mutations) and could benefit families via increased surveillance/primary prevention. Further research is needed to explore how to report potential germline results to clinicians using a systems-based approach. [Table: see text]

Acquired genomic alterations in circulating tumor DNA from patients receiving abemaciclib alone or in combination with endocrine therapy.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 3519-3519
Author(s):  
Matthew P. Goetz ◽  
Erika Paige Hamilton ◽  
Mario Campone ◽  
Sara A. Hurvitz ◽  
Javier Cortes ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Endocrine Therapy ◽  
Acquired Resistance ◽  
Unmet Need ◽  
Point Mutations ◽  
Metastatic Breast ◽  
Circulating Tumor Dna ◽  
Mechanisms Of Resistance ◽  
Genomic Alterations ◽  
Tumor Dna

3519 Background: An understanding of the mechanisms of acquired resistance to CDK4 & 6 inhibitors, either alone or with endocrine therapy (ET), is an unmet need. Abemaciclib is a CDK4 & 6 inhibitor approved for treatment of HR+, HER2- advanced breast cancer (ABC). Here we evaluated acquired genomic alterations detected in circulating tumor DNA (ctDNA) from patients (pts) treated with abemaciclib + nonsteroidal aromatase inhibitor (AI) or placebo + AI in MONARCH 3 or abemaciclib monotherapy in nextMONARCH 1. Methods: MONARCH 3 randomized postmenopausal women with HR+, HER2- ABC with no prior systemic therapy in the advanced setting to abemaciclib (150 mg Q12H) or placebo + AI. nextMONARCH 1 randomized women with HR+, HER2- metastatic breast cancer who had progressed on or after prior ET and CT to abemaciclib (150 mg Q12H) + tamoxifen, abemaciclib (150 mg Q12H), or abemaciclib (200 mg Q12H) + loperamide. Plasma from pts in the abemaciclib or placebo + AI arms (MONARCH 3) or abemaciclib monotherapy arms (nextMONARCH 1) was analyzed by the Guardant360 assay to identify potential tumor-related genomic alterations including point mutations, indels, amplifications, and fusions acquired at EOT in comparison with baseline. Results: For MONARCH 3, commonly acquired alterations at EOT included ESR1 (17%), TP53 (10%), EGFR (8%), FGFR1 (7%), and PDGFRA (7%) in the abemaciclib + AI arm, and ESR1 (31%), TP53 (10%), and BRCA1 (7%) in the placebo + AI arm. Acquired alterations more frequent for abemaciclib + AI pts included RB1 (6%), MYC (5%), and AR (5%), compared to 0% in the placebo + AI arm (p = 0.008 RB1; p = 0.015 MYC or AR). In contrast, acquired ESR1 alterations were less frequent with abemaciclib + AI vs placebo + AI (17% vs 31%, p = 0.038). In nextMONARCH 1, the most commonly acquired alterations with abemaciclib monotherapy were in TP53 (10%), EGFR (9%), RB1 (9%), MYC (9%), and MET (8%). In addition, acquired alterations in ESR1 (6%) and AR (3%) were also found. PIK3CA alterations were not frequently acquired (abemaciclib + AI 1%, placebo + AI 6%, abemaciclib monotherapy 5%). Conclusions: Acquired genomic alterations potentially associated with emerging mechanisms of resistance to abemaciclib alone or in combination with AI may include RB1, MYC, or AR alterations, while the acquisition of ESR1 alterations was less common in pts treated with abemaciclib + AI compared to placebo + AI. These findings are hypothesis-generating and provide insight into mechanisms of resistance to abemaciclib vs ET. Clinical trial information: NCT02246621, NCT02747004 .

Clonal Heavy and Light Chain Immunoglobulin DNA in Plasma/Serum of AIDS Lymphoma Patients.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1579-1579
Author(s):  
Nina D. Wagner-Johnston ◽  
Dilber Nurmemet ◽  
Christopher Gocke ◽  
Lan Lin ◽  
Victor M. Lemas ◽  
...  
Keyword(s):  
Tumor Suppressor Genes ◽  
Point Mutations ◽  
Dna Rearrangements ◽  
Healthy Donors ◽  
Stage Disease ◽  
Pcr Products ◽  
Light Chain Immunoglobulin ◽  
Viral Sequences ◽  
Tumor Dna ◽  
Aids Related Lymphoma

Abstract Background DNA tumor markers in plasma and serum such as point mutations, hypermethylation of tumor suppressor genes, and viral sequences have attracted much interest. We investigated clonal Ig DNA rearrangements in the plasma of AIDS-related lymphoma (ARL) patients (pts). Methods We evaluated specimens for Ig rearrangements from pts with ARL using fluorescently-labeled multiplex primers targeting IgH and IgK. PCR products were analyzed by capillary electrophoresis. Re-amplified PCR products from plasma and tumor were cloned and sequenced. Results Clonal IgH DNA spikes were seen in plasma at baseline in 5 of 10 pts. Clonal DNA was detected in plasma in pts with either early or advanced stage disease, with or without marrow involvement. Presence of a plasma clone was associated with high LDH. Serial specimens were available from 4 pts. In 2 pts who died with primary refractory disease, clonal peaks remained present after the administration of chemotherapy. In a pt with disease that initially responded and then relapsed, clonal DNA disappeared with chemotherapy, then reappeared presaging relapse and death. In 4 pts, matching serum specimens were available. Results were similar in both types of specimens with identical sized rearrangements amplified from matched specimens. Furthermore in 2 pts, the IgH amplification products from plasma and tumor were sequenced and confirmed to be identical. Two pts with positive IgH amplification products were also screened for light chains in the plasma and in both, clonal IgK rearrangements were detected. For purposes of comparison, plasma from healthy donors (n=20) and AIDS pts with Kaposi’s sarcoma (KS) (n=10) were also surveyed. Clonal Ig DNA rearrangements were not detected in any of these. Conclusions These results are consistent with observations suggesting that free tumor DNA can often be detected in plasma or serum of cancer pts. The absence of clonal Ig DNA in plasma from healthy donors and pts with AIDS KS suggests that detection of such DNA may be highly specific. Identification of the same Ig rearrangement and sequence in plasma and tumor is consistent with this interpretation. Serial monitoring of circulating clonal DNA appears to track—and perhaps anticipate—clinical evidence of disease. These approaches may be especially valuable in ARL where FDG uptake reflective of inflammatory disease or benign lymphoproliferation detected by PET scan often renders interpretation of imaging ambiguous. Similarly, elevated LDH in this population is relatively non-specific.

scholarly journals Signed in Blood: Circulating Tumor DNA in Cancer Diagnosis, Treatment and Screening

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3600
Author(s):  
Jacob J. Adashek ◽  
Filip Janku ◽  
Razelle Kurzrock
Keyword(s):  
Point Mutations ◽  
Circulating Tumor Dna ◽  
Molecular Testing ◽  
Dynamic Changes ◽  
Tissue Acquisition ◽  
Polymerase Chain ◽  
Molecular Landscape ◽  
Metastatic Sites ◽  
Next Generation Sequencing Ngs ◽  
Tumor Dna

With the addition of molecular testing to the oncologist’s diagnostic toolbox, patients have benefitted from the successes of gene- and immune-directed therapies. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. An important advance in the application of molecular testing is the liquid biopsy, wherein circulating tumor DNA (ctDNA) is analyzed for point mutations, copy number alterations, and amplifications by polymerase chain reaction (PCR) and/or next-generation sequencing (NGS). The advantages of evaluating ctDNA over tissue DNA include (i) ctDNA requires only a tube of blood, rather than an invasive biopsy, (ii) ctDNA can plausibly reflect DNA shedding from multiple metastatic sites while tissue DNA reflects only the piece of tissue biopsied, and (iii) dynamic changes in ctDNA during therapy can be easily followed with repeat blood draws. Tissue biopsies allow comprehensive assessment of DNA, RNA, and protein expression in the tumor and its microenvironment as well as functional assays; however, tumor tissue acquisition is costly with a risk of complications. Herein, we review the ways in which ctDNA assessment can be leveraged to understand the dynamic changes of molecular landscape in cancers.

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