Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA

Shen, Shu Yi; Burgener, Justin M.; Bratman, Scott V.; Carvalho, Daniel D. De

doi:10.1038/s41596-019-0202-2

Cited by 140 publications

(105 citation statements)

References 32 publications

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“…Previous methylation-based detection methods have typically either targeted a small number of regions at high depth through PCR 41 , or a large number of regions at low depth through whole genome bisulfite sequencing (WGBS) or RRBS 42 . More recently, techniques have been described to target a large number of regions at higher sequencing depth [43][44][45] . The PanSeer assay interrogates 595 regions at high depth; this reduces the effects of patient variability or target dropout.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Resultsmentioning

confidence: 99%

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

et al. 2020

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“…Ligated cfDNA (5–10 ng) was applied for methylome profiling following the previously published cfMeDIP-seq protocol [ 21 , 22 ] with minor modifications. We used the spike-in controls mentioned above to roughly assess the 5mC enrichment ratio instead of the methylated DNA (meDNA) and unmethylated DNA (unDNA) spike-in controls used in cfMeDIP-seq.…”

Section: Methodsmentioning

confidence: 99%

“…Considering the low mutation frequency of tumor-related somatic mutations and the limited detection sensitivity, 5mC and 5hmC in cfDNA could serve as parallel or even more valuable biomarkers [ 20 ]. Recent technological improvements in 5mC and 5hmC detection from cfDNA, including the cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) method [ 21 , 22 ] and cell-free 5hmC sequencing methods reported recently [ 20 , 23 ], offer substantial advantages over previous ctDNA 5mC and 5hmC detection methods. Therefore, 5mC detection and 5hmC characterization in cfDNA are anticipated to be robust and cost-effective methods for clinical application in cancer diagnosis and therapy [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer

Cao

Wei

et al. 2020

Clin Epigenet

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Background: The high lethal rate of pancreatic cancer is partly due to a lack of efficient biomarkers for screening and early diagnosis. We attempted to develop effective and noninvasive methods using 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) markers from circulating cell-free DNA (cfDNA) for the detection of pancreatic ductal adenocarcinoma (PDAC). Results: A 24-feature 5mC model that can accurately discriminate PDAC from healthy controls (area under the curve (AUC) = 0.977, sensitivity = 0.824, specificity = 1) and a 5hmC prediction model with 27 features demonstrated excellent detection power in two distinct validation sets (AUC = 0.992 and 0.960, sensitivity = 0.786 and 0.857, specificity = 1 and 0.993). The 51-feature model combining 5mC and 5hmC markers outperformed both of the individual models, with an AUC of 0.997 (sensitivity = 0.938, specificity = 0.955) and particularly an improvement in the prediction sensitivity of PDAC. In addition, the weighted diagnosis score (wd-score) calculated with the 5hmC model can distinguish stage I patients from stage II-IV patients. Conclusions: Both 5mC and 5hmC biomarkers in cfDNA are effective in PDAC detection, and the 5mC-5hmC integrated model significantly improve the detection sensitivity.

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“…• Determining the threshold for difference will be vital for early detection. 41,42 Cancer detection Cancer origin/ localization Epigenetic changes, particularly methylation changes, are another unique signature like mutations that can be analyzed and measured in DNA. Methyl groups can be identified using bisulfite conversion or captured using biotin labels or antibody-coated magnetic beads.…”

Section: Capp-seq 33mentioning

confidence: 99%

Considerations for the use of circulating tumor DNA sequencing as a screening tool in cancer predisposition syndromes

Paramathas

Guha

Pugh

et al. 2020

Pediatric Blood & Cancer

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Liquid biopsy, specifically circulating tumor DNA (ctDNA) detection, has started to revolutionize the clinical management of patients with cancer by surpassing many limitations of traditional tissue biopsies, particularly for serial testing. ctDNA sequencing has been successfully utilized for cancer detection, prognostication, and assessment of disease response and evolution. While the applications of ctDNA analysis are growing, the majority of studies to date have primarily evaluated its use as a tool for tracking a known cancer, and in most cases at advanced stage. Herein, we discuss the potential application of ctDNA for surveillance and early cancer detection in patients with a cancer predisposition syndrome.

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Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA

Cited by 140 publications

References 32 publications

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

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

Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer

Considerations for the use of circulating tumor DNA sequencing as a screening tool in cancer predisposition syndromes

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