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  • Oxford University Press (OUP)  (2)
  • Bai, Liangliang  (2)
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  • Oxford University Press (OUP)  (2)
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  • 1
    Online Resource
    Online Resource
    Novel Assay for Quantitative Analysis of DNA Methylation at Single-Base Resolution
    Oxford University Press (OUP) ; 2019
    In:  Clinical Chemistry Vol. 65, No. 5 ( 2019-05-01), p. 664-673
    Details
    In: Clinical Chemistry, Oxford University Press (OUP), Vol. 65, No. 5 ( 2019-05-01), p. 664-673
    Abstract: The DNA methylation profile provides valuable biological information with potential clinical utility. Several methods, such as quantitative methylation-specific PCR (qMSP), have been developed to examine methylation of specific CpG sites. Existing qMSP-based techniques fail to examine the genomic methylation at a single-base resolution, particularly for loci in gene bodies or extensive CpG open seas lacking flanking CpGs. Therefore, we established a novel assay for quantitative analysis of single-base methylation. METHODS To achieve a robust single-base specificity, we developed a PCR-based method using paired probes following bisulfite treatment. The 6-carboxyfluorescein- and 2′-chloro-7′phenyl-1,4-dichloro-6-carboxy-fluorescein-labeled probes conjugated with minor groove binder were designed to specifically bind to the methylated and unmethylated allele of targeted single CpGs at their 3′ half regions, respectively. The methylation percentage was calculated by values of methylation / (methylation + unmethylation). RESULTS In the detection of single CpGs within promoters or bodies of 4 human genes, the quantitative analysis of the single-base methylation assay showed a detection capability in the 1 to 1:10000 dilution experiments with linearity over 4 orders of magnitude (R2 = 0.989–0.994; all P & lt; 0.001). In a cohort of 10 colorectal cancer samples, the assay showed a comparable detection performance with bisulfite pyrosequencing (R2 = 0.875–0.990; all P & lt; 0.001), which was better than conventional qMSP methods normalized by input control reaction (R2 = 0.841 vs 0.769; P = 0.002 vs 0.009). CONCLUSIONS This assay is highly specific and sensitive for determining single-base methylation and, thus, is potentially useful for methylation-based panels in diagnostic and prognostic applications.
    Type of Medium: Online Resource
    ISSN: 0009-9147 , 1530-8561
    URL: Article
    DOI: 10.1373/clinchem.2018.298570
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
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  • 2
    Online Resource
    Online Resource
    DNA methylation profile in CpG-depleted regions uncovers a high-risk subtype of early-stage colorectal cancer
    Oxford University Press (OUP) ; 2023
    In:  JNCI: Journal of the National Cancer Institute Vol. 115, No. 1 ( 2023-01-10), p. 52-61
    Details
    In: JNCI: Journal of the National Cancer Institute, Oxford University Press (OUP), Vol. 115, No. 1 ( 2023-01-10), p. 52-61
    Abstract: The current risk stratification system defined by clinicopathological features does not identify the risk of recurrence in early-stage (stage I-II) colorectal cancer (CRC) with sufficient accuracy. We aimed to investigate whether DNA methylation could serve as a novel biomarker for predicting prognosis in early-stage CRC patients. Methods We analyzed the genome-wide methylation status of CpG loci using Infinium MethylationEPIC array run on primary tumor tissues and normal mucosa of early-stage CRC patients to identify potential methylation markers for prognosis. The machine-learning approach was applied to construct a DNA methylation–based prognostic classifier for early-stage CRC (MePEC) using the 4 gene methylation markers FAT3, KAZN, TLE4, and DUSP3. The prognostic value of the classifier was evaluated in 2 independent cohorts (n = 438 and 359, respectively). Results The comprehensive analysis identified an epigenetic subtype with high risk of recurrence based on a group of CpG loci in the CpG-depleted region. In multivariable analysis, the MePEC classifier was independently and statistically significantly associated with time to recurrence in validation cohort 1 (hazard ratio = 2.35, 95% confidence interval = 1.47 to 3.76, P  & lt; .001) and cohort 2 (hazard ratio = 3.20, 95% confidence interval = 1.92 to 5.33, P  & lt; .001). All results were further confirmed after each cohort was stratified by clinicopathological variables and molecular subtypes. Conclusions We demonstrated the prognostic statistical significance of a DNA methylation profile in the CpG-depleted region, which may serve as a valuable source for tumor biomarkers. MePEC could identify an epigenetic subtype with high risk of recurrence and improve the prognostic accuracy of current clinical variables in early-stage CRC.
    Type of Medium: Online Resource
    ISSN: 0027-8874 , 1460-2105
    URL: Article
    DOI: 10.1093/jnci/djac183
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2992-0
    detail.hit.zdb_id: 1465951-7
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