Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

Liu, L.; Toung, Jonathan; Jassowicz, Adam; Vijayaraghavan, Raakhee; Kang, Hee Jung; Zhang, Ruoyu; Kruglyak, Kristina M.; Huang, Helen J.; Hinoue, Toshinori; Shen, Hui; Salathia, Neeraj; Hong, David S.; Naing, Aung; Subbiah, Vivek; Piha-Paul, Sarina A.; Bibikova, Marina; Granger, Gale A.; Barnes, Bret; Shen, Richard; Gutekunst, Karen; Fu, Siqing; Tsimberidou, Apostolia M.; Lu, Charles; Eng, Cathy; Moulder, Stacy L.; Kopetz, E. Scott; Amaria, R.; Meric‐Bernstam, Funda; Laird, Peter W.; Fan, Jian‐Bing; Janků, Filip

doi:10.1093/annonc/mdy119

Cited by 112 publications

(100 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Furthermore, most studies complement their method of choice by enlarging their panel of cancer-related genes further including the detection of methylation patterns or circulating proteins, resulting in a more robust approach toward earlier cancer detection and disease monitoring. 25,26 In our case, we strongly recommend the use of CTCs and cfDNA as complementary biomarkers as we successfully detected circulating tumor cells in 29 of 54 patients (54%) independently of tumor burden. Inter-and intratumoral heterogeneity remains a challenge in cancer treatment, emphasizing the importance of individualized therapy.…”

Section: Discussionmentioning

confidence: 80%

“…Those challenges highlight the urgent need of standard operating protocols to guarantee optimal sample management regarding storage, processing and analysis of plasma samples. Furthermore, most studies complement their method of choice by enlarging their panel of cancer‐related genes further including the detection of methylation patterns or circulating proteins, resulting in a more robust approach toward earlier cancer detection and disease monitoring . In our case, we strongly recommend the use of CTCs and cfDNA as complementary biomarkers as we successfully detected circulating tumor cells in 29 of 54 patients (54%) independently of tumor burden.…”

Section: Discussionmentioning

confidence: 89%

See 1 more Smart Citation

Detection of mutations in circulating cell‐free DNA in relation to disease stage in colorectal cancer

et al. 2019

View full text Add to dashboard Cite

Enthusiasm has emerged for the potential of liquid biopsies to provide easily accessible genetic biomarkers for early diagnosis and mutational cancer characterization. We here systematically investigated the suitability of circulating cell‐free DNA (cfDNA) analysis for mutation detection in colorectal cancer (CRC) patients with respect to clinicopathological disease stage. Droplet Digital PCR (ddPCR) was performed to detect common point mutations in the KRAS and BRAF oncogenes in cfDNA from 65 patients and compared to mutations in tumor tissue. Stage of disease was classified according to UICC (Union for International Cancer Control) criteria. In tumor tissue, KRAS or BRAF mutations were present in 35 of 65 cases (44% UICC stage I, 50% stage II, 47% stage III, and 62% stage IV). Although cfDNA was detected in 100% of patients, ddPCR displayed the tumor tissue mutation in only 1 of 6 (17%) stage II patients, whereas 10 of 18 (56%) reported variants were verified in cfDNA samples of the stage IV cohort. No BRAF or KRAS mutation was detected in cfDNA from patients with wild‐type tumor tissue. In one case of mutant stage II colon cancer ( KRAS ‐G12C), the G12D variant was detected in cfDNA instead. Further workup revealed that circulating tumor‐derived DNA and liver metastases originated from a synchronous KRAS ‐mutated cancer of the pancreas. Our results demonstrate that ddPCR‐based analysis is highly specific and useful for mutation monitoring, but the sensitivity limits its usefulness for early cancer detection.

show abstract

Section: Discussionmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 89%

Detection of mutations in circulating cell‐free DNA in relation to disease stage in colorectal cancer

et al. 2019

View full text Add to dashboard Cite

show abstract

“…PanSeer assay development. We defined a set of differentially methylated CpG sites using publicly available microarray and Whole Genome Bisulfite Sequencing (WGBS) data from The Cancer Genome Atlas (TCGA) 28 and genomic regions known to be cancer-related in the literature [29][30][31][32][33][34][35] , as well as internal Reduced Representation Bisulfite Sequencing (RRBS) data from a variety of cancer tissues. From these sources, we compiled a targeted panel of 595 genomic regions (Supplementary Data 1) for further interrogation in plasma samples.…”

Section: Resultsmentioning

confidence: 99%

Non-invasive early detection of cancer four years before conventional diagnosis using a blood test

et al. 2020

View full text Add to dashboard Cite

Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long-term storage and were then monitored for cancer occurrence. Here we report the preliminary results of PanSeer, a noninvasive blood test based on circulating tumor DNA methylation, on TZL plasma samples from 605 asymptomatic individuals, 191 of whom were later diagnosed with stomach, esophageal, colorectal, lung or liver cancer within four years of blood draw. We also assay plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. We show that PanSeer detects five common types of cancer in 88% (95% CI: 80-93%) of post-diagnosis patients with a specificity of 96% (95% CI: 93-98%), We also demonstrate that PanSeer detects cancer in 95% (95% CI: 89-98%) of asymptomatic individuals who were later diagnosed, though future longitudinal studies are required to confirm this result. These results demonstrate that cancer can be non-invasively detected up to four years before current standard of care.

show abstract

“…Although SEPT9 and PTGER4 / SHOX2 methylation-based non- or minimally invasive tests are already commercially available for CRC and LC detection, respectively [ 19 , 20 ], they have limited sensitivity. Furthermore, a recent study using methylation scores displayed 87% sensitivity for advanced cancer detection (BrC, CRC, non-small cell LC and melanoma) with 100% specificity, predicting also the cancer type in 76% of cases [ 21 ]. Thus, we aimed to develop a sensitive and specific methylation-based test enabling the simultaneous detection of BrC, CRC and LC in women using ccfDNA.…”

Section: Introductionmentioning

confidence: 99%

Cell-Free DNA Methylation of Selected Genes Allows for Early Detection of the Major Cancers in Women

Nunes

Moreira-Barbosa

Salta

et al. 2018

Cancers

View full text Add to dashboard Cite

Background: Breast (BrC), colorectal (CRC) and lung (LC) cancers are the three most common and deadly cancers in women. Cancer screening entails an increase in early stage disease detection but is hampered by high false-positive rates and overdiagnosis/overtreatment. Aberrant DNA methylation occurs early in cancer and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable biomarker and enabling non-invasive testing for cancer detection. We aimed to develop a ccfDNA methylation-based test for simultaneous detection of BrC, CRC and LC. Methods: CcfDNA from BrC, CRC and LC patients and asymptomatic controls were extracted from plasma, sodium-bisulfite modified and whole-genome amplified. APC, FOXA1, MGMT, RARβ2, RASSF1A, SCGB3A1, SEPT9, SHOX2 and SOX17 promoter methylation levels were determined by multiplex quantitative methylation-specific PCR. Associations between methylation and standard clinicopathological parameters were assessed. Biomarkers’ diagnostic performance was also evaluated. Results: A “PanCancer” panel (APC, FOXA1, RASSF1A) detected the three major cancers with 72% sensitivity and 74% specificity, whereas a “CancerType” panel (SCGB3A1, SEPT9 and SOX17) indicated the most likely cancer topography, with over 80% specificity, although with limited sensitivity. Conclusions: CcfDNA’s methylation assessment allows for simultaneous screening of BrC, CRC and LC, complementing current modalities, perfecting cancer suspects’ triage, increasing compliance and cost-effectiveness.

show abstract

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

Abstract: Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.

Cited by 112 publications

References 33 publications

Detection of mutations in circulating cell‐free DNA in relation to disease stage in colorectal cancer

Detection of mutations in circulating cell‐free DNA in relation to disease stage in colorectal cancer

Non-invasive early detection of cancer four years before conventional diagnosis using a blood test

Cell-Free DNA Methylation of Selected Genes Allows for Early Detection of the Major Cancers in Women

Contact Info

Product

Resources

About