The development and validation of a novel targeted methylation sequencing technology detecting 0.003 percent tumor signal in early-stage cancer plasma.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 4092-4092
Author(s):  
Grace Q. Zhao ◽  
Yun Bao ◽  
Heng Wang ◽  
Jianmin Wang ◽  
Shengrong Lin
Keyword(s):  
Early Stage ◽  
Methylation Status ◽  
Gc Content ◽  
Stage I ◽  
Healthy Population ◽  
Current Sensitivity ◽  
High Background ◽  
Early Stage Cancer ◽  
Depth Analysis ◽  
Low Efficiency

4092 Background: Methylation analysis in cell-free DNA holds great potential for early cancer detection. In the plasma of early stage cancer patient, the tumor content is estimated to be less than 0.1%, therefore demands a highly sensitive assay. Targeted Methylation Sequencing (TMS) is the most promising approach; however, the current sensitivity and specificity are compromised by low efficiency and low recovery of target enrichment, and further hampered by background noise associated with large panels. The ideal solution would be an in-depth analysis using a focused small cancer-specific methylation biomarker panel, but is not supported by existing technologies. Methods: Here we present a new technology designed for TMS analysis in cfDNA: Point-n-Seq, featuring an enrichment of target molecules directly from cfDNA before bisulfite conversion and amplification. Particularly, this technology enables small focused panel that interrogates the methylation status of 1 to ~1000 markers. We designed a CRC panel covering 100 methylation markers in 3 steps: identify ~1000 CRC-specific markers from public databases; eliminate makers with high background signal in baseline cfDNA of healthy population; finalize the list with the most differentiating markers between patient and healthy cfDNA. Results: The capture of Point-n-Seq CRC panel is highly efficient resulting in high uniformity (94% > 0.5X) and on-target rate ( > 80%). For 20 ng cfDNA input, more than 1000 deduped informative reads were obtained for each marker on average, despite the high GC content ( > 80%). The output of informative reads was linear to the cfDNA input ranging from 1 ng to 40 ng. In titration studies, 0.6 pg (0.2X genome equivalent) methylated DNA in 20 ng cfDNA (0.003%) was reliably detected over cfDNA background. Using plasma samples from patients with CRC - early stage (I, n = 7; II, n = 7), late stage (III, n = 11; IV, n = 3), and control individuals (n = 105), the average fractions of methylated signal are 0.0034%, 0.013%, 0.09%, 0.17%, 0.29% for control, stage I, II, III, IV accordingly. With a simple cut-off using methylation fraction, Point-n Seq CRC panel achieved a sensitivity of 86% for stage I, 100% for stage (II-IV) at a specificity of 91%, with AUC = 0.96. Conclusions: Point-n-Seq TMS is the first hybridization based NGS technology enables the small focused methylation panel (e.g. 100 markers) sequencing using cfDNA, and it will greatly facilitate the development of practical and cost-effective methylation assays for clinical use.

Prognostic role of promoter hypermethylation of death-associated protein (DAP) kinase and p16 genes in early-stage non-small cell lung cancer

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 7216-7216
Author(s):  
C. Lu ◽  
I. Wistuba ◽  
X. Zhou ◽  
B. N. Bekele ◽  
J. B. Putnam ◽  
...  
Keyword(s):  
Promoter Methylation ◽  
Early Stage ◽  
Methylation Status ◽  
Promoter Hypermethylation ◽  
Stage I ◽  
Prognostic Role ◽  
Early Stage Nsclc ◽  
Dap Kinase ◽  
Nsclc Patients

7216 Background: Promoter hypermethylation is an epigenetic mechanism of gene silencing commonly observed in malignancies. Prior studies suggest that hypermethylation of DAP kinase and p16, genes involved in apoptosis and cell cycle regulation, respectively, are associated with poorer survival in NSCLC patients. In this study we investigate the prognostic role of DAP kinase and p16 promoter hypermethylation in a large cohort of early-stage NSCLC patients. Methods: Pathologic stage I and II NSCLC patients who underwent complete surgical resection between 1/97 and 12/01 at our institution and did not receive adjuvant therapy were identified. Formalin-fixed, paraffin-embedded tissue blocks were retrieved, and p16 and DAP kinase promoter methylation status was determined by methylation specific PCR. Two-sided statistical analyses were performed to determine associations between methylation status, clinicopathologic characteristics, and survival. Results: DAP kinase and p16 methylation status was observed in 36.3% (97 of 267) and 36.4% (95 of 261) cases, respectively. Subject characteristics: 55% female, 77% former/current smokers, 81% stage I, 19% stage II, 61% adenocarcinoma, 29% squamous carcinoma, 63% performance status (PS) 0, 37% PS 1,93% < 5% weight loss. Recurrent NSCLC and death occurred in 21.3% and 38% of cases, respectively. No significant associations were observed between DAP kinase methylation status and subject characteristics. P16 methylation was associated with moderate/high grade (p = 0.03). A higher frequency of p16 methylation was observed in ever vs never smokers (39% vs 28%, p = 0.17). Preliminary analyses do not demonstrate significant associations between methylation status and overall survival (p16 p = 0.13; DAP kinase p = 0.56) or disease-free survival (p16 p = 0.36; DAP kinase p = 0.71). Conclusions: In this relatively large cohort of early-stage NSCLC patients, we did not detect significant associations between p16 and DAP kinase promoter methylation and clinical outcome. Further subset analyses stratified by gender and histology will be performed. The prognostic role of these biomarkers in NSCLC remains unclear. No significant financial relationships to disclose.

A novel biophysical based marker with multilevel, multiparameter expression for early stage cancer detection.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e20673-e20673
Author(s):  
Junjie Wu ◽  
Gengxi Jiang ◽  
Jiansong Ji ◽  
Xuedong Du ◽  
Yue Lin ◽  
...  
Keyword(s):  
Sensitivity And Specificity ◽  
Cancer Detection ◽  
Early Stage ◽  
Physical Property ◽  
Stage I ◽  
Potential Candidate ◽  
Healthy Individuals ◽  
Blind Test ◽  
Early Stage Cancer ◽  
Multi Level

e20673 Background: Early stage cancer detection remains to be elusive despite of many years of efforts. In this work, a bio-physical based marker (named Cancer Differentiation Analysis (CDA)) with multi-level and multi-parameter expression features has been developed which has shown a number of clear advantages over the traditional approaches such as bio-chemistry based marker, circulating tumor cell (CTC) and circuiting DNA (ct-DNA). In stage I non-small cell lung cancer (NSCLC), sensitivity and specificity reached a record high of 85.2% and 93.0%, respectively. Methods: In this study, 832 NSCLC cancer samples with pathological information and 642 samples from healthy individuals were measured in a single blind test. Peripheral blood of each individual was drawn in EDTA tubes. One class of bio-physical property in blood samples was utilized for CDA tests. The CDA data were first processed using an algorithm built from data base and subsequently analyzed using SPSS. The results were shown in the table. Results: The results indicated that CDA technology has a very good sensitivity and specificity even at stage I (85% and 93%, respectively), which is much better than those previously reported results by other methods. Conclusions: Initial results showed that CDA technology could effectively screen NSCLC patients from healthy individuals. As a novel bio-physical based cancer detection approach with multi-level and multi-parameter expressions, CDA technology could be a potential candidate for early stage cancer screening. [Table: see text]

A multiplex methylation-specific PCR assay for detection of early-stage ovarian cancer using cell-free serum DNA.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 5535-5535
Author(s):  
Beihua Kong ◽  
Qing Zhang ◽  
Guohong Hu ◽  
Qifeng Yang ◽  
Ruifen Dong ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Early Detection ◽  
Early Stage ◽  
Methylation Status ◽  
Stage I ◽  
Methylation Specific Pcr ◽  
Specific Pcr ◽  
Preoperative Serum ◽  
Serum Dna ◽  
Free Serum

5535 Background: Epithelial ovarian cancer (EOC) remains the most lethal disease among gynecological malignancies. Prompt diagnosis is challenging because of the non-specific symptoms exhibited during the early stage of the disease. So there is an urgent need for better detection methods. Here we performed this work to build up a platform of multiplex methylation-specific PCR (MSP) assay to improve the early detection of ovarian cancer, via identifying the methylation status of cell-free serum DNA. Methods: After screening, we chose seven genes (APC, RASSF1A, CDH1, RUNX3, TFPI2, SFRP5 and OPCML) with a high frequency of methylation as candidate genes to construct the multiplex-MSP assay. When methylation of at least one of the seven genes was observed, the multiplex-MSP assay was considered positive. We performed the retrospective and screening study to verify its specificity and sensitivity in the detection of EOC. Results: The methylation status of cell-free serum DNA was examined in the preoperative serum of 202 patients, including 87 EOC cases (stage I, n=41, stage II-IV, n=46), 53 benign ovarian tumors and 62 healthy controls. As expected, multiplex MSP assay achieved a sensitivity of 85.3% and a specificity of 90.5% in stage I EOC, strikingly higher than that of single CA125, producing a sensitivity of 56.1% at 64.15% specificity [p=0.0036](Table). Conclusions: Multiplex MSP assay analyzing the methylation status of cell-free serum DNA is a suitable and reliable approach to improve the early detection of ovarian cancer, potentially benefiting a broad range of applications in clinical oncology. [Table: see text]

LOW-DOSE COMPUTED TOMOGRAPHY IN MOSCOW FOR LUNG CANCER SCREENING (LDCT-MLCS): BASELINE RESULTS

2019 ◽  
Vol 65 (2) ◽  
pp. 224-233
Author(s):  
Sergey Morozov ◽  
Viktor Gombolevskiy ◽  
Anton Vladzimirskiy ◽  
Albina Laypan ◽  
Pavel Kononets ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Lung Cancer ◽  
Cancer Screening ◽  
Low Dose ◽  
Early Stage ◽  
Lung Cancer Screening ◽  
Stage I ◽  
Malignant Neoplasms ◽  
Number Needed To Screen ◽  
Low Dose Computed Tomography

Study aim. To justify selective lung cancer screening via low-dose computed tomography and evaluate its effectiveness. Materials and methods. In 2017 we have concluded the baseline stage of “Lowdose computed tomography in Moscow for lung cancer screening (LDCT-MLCS)” trial. The trial included 10 outpatient clinics with 64-detector CT units (Toshiba Aquilion 64 and Toshiba CLX). Special low-dose protocols have been developed for each unit with maximum effective dose of 1 mSv (in accordance with the requirements of paragraph 2.2.1, Sanitary Regulations 2.6.1.1192-03). The study involved 5,310 patients (53% men, 47% women) aged 18-92 years (mean age 62 years). Diagnosis verification was carried out in the specialized medical organizations via consultations, additional instrumental, laboratory as well as pathohistological studies. The results were then entered into the “National Cancer Registry”. Results. 5310 patients (53% men, 47% women) aged 18 to 92 years (an average of 62 years) participated in the LDCT-MLCS. The final cohort was comprised of 4762 (89.6%) patients. We have detected 291 (6.1%) Lung-RADS 3 lesions, 228 (4.8%) Lung- RADS 4A lesions and 196 (4.1%) Lung-RADS 4B/4X lesions. All 4B and 4X lesions were routed in accordance with the project's methodology and legislative documents. Malignant neoplasms were verified in 84 cases (1.76% of the cohort). Stage I-II lung cancer was actively detected in 40.3% of these individuals. For the first time in the Russian Federation we have calculated the number needed to screen (NNS) to identify one lung cancer (NNS=57) and to detect one Stage I lung cancer (NNS=207). Conclusions. Based on the global experience and our own practices, we argue that selective LDCT is the most systematic solution to the problem of early-stage lung cancer screening.

scholarly journals Adjuvant brachytherapy for FIGO stage I serous or clear cell endometrial cancer

2021 ◽  
pp. ijgc-2020-002217
Author(s):  
Elizabeth B Jeans ◽  
William G Breen ◽  
Trey C Mullikin ◽  
Brittany A Looker ◽  
Andrea Mariani ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Clear Cell ◽  
Early Stage ◽  
Figo Stage ◽  
Stage I ◽  
High Dose ◽  
Vaginal Cuff ◽  
Locoregional Failure ◽  
Platinum Based Chemotherapy ◽  
Increased Risk

ObjectivesOptimal adjuvant treatment for early-stage clear cell and serous endometrial cancer remains unclear. We report outcomes for women with surgically staged International Federation of Gynecology and Obstetrics (FIGO) stage I clear cell, serous, and mixed endometrial cancers following adjuvant vaginal cuff brachytherapy with or without chemotherapy.MethodsFrom April 1998 to January 2020, women with FIGO stage IA–IB clear cell, serous, and mixed endometrial cancer underwent surgery and adjuvant vaginal cuff brachytherapy. Seventy-six patients received chemotherapy. High-dose rate vaginal cuff brachytherapy was planned to a total dose of 21 gray in three fractions using a multichannel vaginal cylinder. The primary objective was to determine the effectiveness of adjuvant vaginal cuff brachytherapy and to identify surgicopathological risk factors that could portend towards worse oncological outcomes.ResultsA total of 182 patients were included in the analysis. Median follow-up was 5.3 years (2.3–12.2). Ten-year survival was 73.3%. Five-year cumulative incidence (CI) of vaginal, pelvic, and para-aortic relapse was 1.4%, 2.1%, and 0.9%, respectively. Five-year locoregional failure, any recurrence, peritoneal relapse, and other distant recurrence was 4.4%, 11.6%, 5.3%, and 6.7%, respectively. On univariate analysis, locoregional failure was worse for larger tumors (per 1 cm) (HR 1.9, 95% CI 1.2 to 3.0, p≤0.01). Any recurrence was worse for tumors of at least 3.5 cm (HR 3.8, 95% CI 1.3 to 11.7, p=0.02) and patients with positive/suspicious cytology (HR 4.4, 95% CI 1.5 to 12.4, p≤0.01). Ten-year survival for tumors of at least 3.5 cm was 56.9% versus 86.6% for those with smaller tumors (HR 2.9, 95% CI 1.4 to 5.8, p≤0.01). Ten-year survival for positive/suspicious cytology was 50.9% versus 77.4% (HR 2.2, 95% CI 0.9 to 5.4, p=0.09). Multivariate modeling demonstrated worse locoregional failure, any recurrence, and survival with larger tumors, as well as any recurrence with positive/suspicious cytology. Subgroup analysis demonstrated improved outcomes with the use of adjuvant chemotherapy in patients with large tumors or positive/suspicious cytology.ConclusionAdjuvant vaginal cuff brachytherapy alone without chemotherapy is an appropriate treatment for women with negative peritoneal cytology and small, early-stage clear cell, serous, and mixed endometrial cancer. Larger tumors or positive/suspicious cytology are at increased risk for relapse and worse survival, and should be considered for additional upfront adjuvant treatments, such as platinum-based chemotherapy.

scholarly journals Surgery in Small-Cell Lung Cancer

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 390
Author(s):  
Nicola Martucci ◽  
Alessandro Morabito ◽  
Antonello La Rocca ◽  
Giuseppe De Luca ◽  
Rossella De Cecio ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Early Stage ◽  
Small Cell ◽  
Stage I ◽  
Phase Iii ◽  
Small Cell Lung ◽  
Early Stage Disease ◽  
Stage Disease

Small-cell lung cancer (SCLC) is one of the most aggressive tumors, with a rapid growth and early metastases. Approximately 5% of SCLC patients present with early-stage disease (T1,2 N0M0): these patients have a better prognosis, with a 5-year survival up to 50%. Two randomized phase III studies conducted in the 1960s and the 1980s reported negative results with surgery in SCLC patients with early-stage disease and, thereafter, surgery has been largely discouraged. Instead, several subsequent prospective studies have demonstrated the feasibility of a multimodality approach including surgery before or after chemotherapy and followed in most studies by thoracic radiotherapy, with a 5-year survival probability of 36–63% for patients with completely resected stage I SCLC. These results were substantially confirmed by retrospective studies and by large, population-based studies, conducted in the last 40 years, showing the benefit of surgery, particularly lobectomy, in selected patients with early-stage SCLC. On these bases, the International Guidelines recommend a surgical approach in selected stage I SCLC patients, after adequate staging: in these cases, lobectomy with mediastinal lymphadenectomy is considered the standard approach. In all cases, surgery can be offered only as part of a multimodal treatment, which includes chemotherapy with or without radiotherapy and after a proper multidisciplinary evaluation.

scholarly journals Platelets as messengers of early-stage cancer

2021 ◽  
Author(s):  
Siamack Sabrkhany ◽  
Marijke J. E. Kuijpers ◽  
Mirjam G. A. oude Egbrink ◽  
Arjan W. Griffioen
Keyword(s):  
Tumor Angiogenesis ◽  
Blood Test ◽  
Early Stage ◽  
Human Studies ◽  
Early Stage Cancer ◽  
Reciprocal Interaction ◽  
Early Stages ◽  
New Strategy ◽  
Mrna Content

AbstractPlatelets have an important role in tumor angiogenesis, growth, and metastasis. The reciprocal interaction between cancer and platelets results in changes of several platelet characteristics. It is becoming clear that analysis of these platelet features could offer a new strategy in the search for biomarkers of cancer. Here, we review the human studies in which platelet characteristics (e.g., count, volume, protein, and mRNA content) are investigated in early-stage cancer. The main focus of this paper is to evaluate which platelet features are suitable for the development of a blood test that could detect cancer in its early stages.

Simple and fast isolation of circulating exosomes with chitosan modified shuttle flow microchip towards breast cancer diagnosis

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Wenwen Chen ◽  
Rongkai Cao ◽  
Wentao Su ◽  
xu zhang ◽  
Yuhai Xu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Medical Treatment ◽  
Cancer Diagnosis ◽  
Biological Samples ◽  
Early Stage ◽  
Breast Cancer Diagnosis ◽  
Early Stage Cancer ◽  
Tumor Prognosis ◽  
Huge Challenge

Tumor-derived exosomes have been recognized as promising biomarkers for early-stage cancer diagnosis, tumor prognosis monitoring and individual medical treatment. However, separating exosomes from trace biological samples is a huge challenge...

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