Analysis of DNA methylation in cancer: location revisited

Alexander Koch; Sophie C. Joosten; Zheng Feng; Tim C. de Ruijter; Muriel X. Draht; Veerle Melotte; Kim M. Smits; Jurgen Veeck; James G. Herman; Leander Van Neste; Wim Van Criekinge; Tim De Meyer; Manon van Engeland

doi:10.1038/s41571-018-0004-4

Analysis of DNA methylation in cancer: location revisited

Alexander Koch, Sophie C. Joosten, Zheng Feng, Tim C. de Ruijter, Muriel X. Draht, Veerle Melotte, Kim M. Smits, Jurgen Veeck, James G. Herman, Leander Van Neste, Wim Van Criekinge, Tim De Meyer, Manon van Engeland^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Changes in DNA methylation in cancer have been heralded as promising targets for the development of powerful diagnostic, prognostic, and predictive biomarkers. Despite the existence of more than 14,000 scientific publications describing DNA methylation-based biomarkers and their clinical associations in cancer, only 14 of these biomarkers have been translated into a commercially available clinical test. Methodological and experimental obstacles are both major causes of this disparity, but the genomic location of a DNA methylation-based biomarker is an intrinsic and essential property that also has an important and often overlooked role. Here, we examine the importance of the location of DNA methylation for the development of cancer biomarkers, and take a detailed look at the genomic location and other relevant characteristics of the various biomarkers with commercially available tests. We also emphasize the value of publicly available databases for the development of DNA methylation-based biomarkers and the importance of accurate reporting of the full methodological details of research findings.

Original language	English
Pages (from-to)	459-466
Number of pages	8
Journal	Nature Reviews Clinical Oncology
Volume	15
Issue number	7
DOIs	https://doi.org/10.1038/s41571-018-0004-4
Publication status	Published - 1 Jul 2018

Keywords

CPG ISLAND HYPERMETHYLATION
CHRONIC LYMPHOCYTIC-LEUKEMIA
PROSTATE-CANCER
PROMOTER METHYLATION
COLORECTAL-CANCER
GSTP1 METHYLATION
GENE-EXPRESSION
GASTRIC-CANCER
BLADDER-CANCER
CELL CARCINOMA

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10.1038/s41571-018-0004-4

1 Erratum / corrigendum / retractions

Author Correction: Analysis of DNA methylation in cancer: location revisited
Koch, A., Joosten, S., Feng, Z., de Ruijter, T., Draht, M., Melotte, V., Smits, K., Veeck, J., Herman, J. G., van Neste, L., Van Criekinge, W., De Meyer, T. & van Engeland, M., 2018, In: Nature Reviews Clinical Oncology. 15, p. 467
Research output: Contribution to journal › Erratum / corrigendum / retractions › Academic

Open Access

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title = "Analysis of DNA methylation in cancer: location revisited",

abstract = "Changes in DNA methylation in cancer have been heralded as promising targets for the development of powerful diagnostic, prognostic, and predictive biomarkers. Despite the existence of more than 14,000 scientific publications describing DNA methylation-based biomarkers and their clinical associations in cancer, only 14 of these biomarkers have been translated into a commercially available clinical test. Methodological and experimental obstacles are both major causes of this disparity, but the genomic location of a DNA methylation-based biomarker is an intrinsic and essential property that also has an important and often overlooked role. Here, we examine the importance of the location of DNA methylation for the development of cancer biomarkers, and take a detailed look at the genomic location and other relevant characteristics of the various biomarkers with commercially available tests. We also emphasize the value of publicly available databases for the development of DNA methylation-based biomarkers and the importance of accurate reporting of the full methodological details of research findings.",

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author = "Alexander Koch and Joosten, {Sophie C.} and Zheng Feng and {de Ruijter}, {Tim C.} and Draht, {Muriel X.} and Veerle Melotte and Smits, {Kim M.} and Jurgen Veeck and Herman, {James G.} and {Van Neste}, Leander and {Van Criekinge}, Wim and {De Meyer}, Tim and {van Engeland}, Manon",

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AU - Joosten, Sophie C.

AU - Feng, Zheng

AU - de Ruijter, Tim C.

AU - Draht, Muriel X.

AU - Melotte, Veerle

AU - Smits, Kim M.

AU - Veeck, Jurgen

AU - Herman, James G.

AU - Van Neste, Leander

AU - Van Criekinge, Wim

AU - De Meyer, Tim

AU - van Engeland, Manon

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AB - Changes in DNA methylation in cancer have been heralded as promising targets for the development of powerful diagnostic, prognostic, and predictive biomarkers. Despite the existence of more than 14,000 scientific publications describing DNA methylation-based biomarkers and their clinical associations in cancer, only 14 of these biomarkers have been translated into a commercially available clinical test. Methodological and experimental obstacles are both major causes of this disparity, but the genomic location of a DNA methylation-based biomarker is an intrinsic and essential property that also has an important and often overlooked role. Here, we examine the importance of the location of DNA methylation for the development of cancer biomarkers, and take a detailed look at the genomic location and other relevant characteristics of the various biomarkers with commercially available tests. We also emphasize the value of publicly available databases for the development of DNA methylation-based biomarkers and the importance of accurate reporting of the full methodological details of research findings.

KW - CPG ISLAND HYPERMETHYLATION

KW - CHRONIC LYMPHOCYTIC-LEUKEMIA

KW - PROSTATE-CANCER

KW - PROMOTER METHYLATION

KW - COLORECTAL-CANCER

KW - GSTP1 METHYLATION

KW - GENE-EXPRESSION

KW - GASTRIC-CANCER

KW - BLADDER-CANCER

KW - CELL CARCINOMA

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DO - 10.1038/s41571-018-0004-4

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VL - 15

SP - 459

EP - 466

JO - Nature Reviews Clinical Oncology

JF - Nature Reviews Clinical Oncology

IS - 7

ER -

Analysis of DNA methylation in cancer: location revisited

Abstract

Keywords

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Author Correction: Analysis of DNA methylation in cancer: location revisited

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