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Challenges in the analysis of epigenetic biomarkers in clinical samples

  • José Luis García-Giménez EMAIL logo , Salvador Mena-Mollá , Jesús Beltrán-García und Fabian Sanchis-Gomar
Veröffentlicht/Copyright: 16. März 2017
Clinical Chemistry and Laboratory Medicine (CCLM)
Aus der Zeitschrift Clinical Chemistry and Laboratory Medicine (CCLM) Band 55 Heft 10

Abstract

Epigenetic modifications represent an interesting landscape which can describe relevant features of human disease. Epigenetic biomarkers show several advantages as disease biomarkers because they provide information about gene function, specific endophenotypes and can even incorporate information from the environment and the natural history of disease. The improvement in genomic and epigenomic technologies has revolutionized the current comprehension of biological processes underlying health and disease. However, now is the time to adopt these new technologies to improve human health, thus converting this information into reliable biomarkers. This endeavor should be focused on improving methodologies to analyze gene methylation, histone modifications and microRNAs. Ideally, epigenetic biomarkers should be robust, routine, accurate and inexpensive in order to provide better information for patient diagnosis, prognosis, stratification and treatment monitoring. Here we describe some challenges and provide strategies to improve the adoption of epigenetic biomarkers into clinical routine. Furthermore, we summarize the recommended properties for clinical epigenetic biomarkers.

Keywords: ChIP assay; DNA methylation; formalin-fixed paraffin-embedded (FFPE); liquid biopsy; microRNAs (miRNAs)
Corresponding author: José Luis García Giménez, PhD, Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Av/ Blasco Ibañez, 15, 46010, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain; and The Biomedical Research Network on Rare Diseases (CIBERER), Valencia, Spain

Acknowledgments

José Luis García-Giménez thanks INCLIVA for the starting grants, the Ministry of Economy and Competitiveness, ISCIII through CIBERer (Biomedical Network Research Center for Rare Diseases and INGENIO2010) and AES2016 (ISCIII) for grant number PI16/01036, co-financed by the European Regional Development Fund (ERDF). Fabian Sanchis-Gomar is supported by a post-doctoral contract (APOSTD/2016/140) granted by the Regional Ministry of Education, Research, Culture and Sport (Valencia). Salvador Mena Molla thanks “Generalitat Valenciana” for starting grant number GV2016-109.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: AES2016 (ISCIII) PI16/01036; Generalitat Valenciana GV2016-109; Regional Ministry of Education, Research, Culture and Sport (Valencia) APOSTD/2016/140.

  3. Employment or leadership: None declared.

  4. Honorarium: None declared.

  5. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

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Received: 2016-12-20
Accepted: 2017-1-20
Published Online: 2017-3-16
Published in Print: 2017-8-28

©2017 Walter de Gruyter GmbH, Berlin/Boston

Artikel in diesem Heft

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  4. The challenges of genetic risk scores for the prediction of coronary heart disease
  5. Reviews
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https://doi.org/10.1515/cclm-2016-1162
Schlagwörter für diesen Artikel
ChIP assay; DNA methylation; formalin-fixed paraffin-embedded (FFPE); liquid biopsy; microRNAs (miRNAs)

Artikel in diesem Heft

  1. Frontmatter
  2. Editorials
  3. Reporting LDL-cholesterol levels in the era of intensive lipid management: a clarion call
  4. The challenges of genetic risk scores for the prediction of coronary heart disease
  5. Reviews
  6. Advanced lipoprotein testing for cardiovascular diseases risk assessment: a review of the novel approaches in lipoprotein profiling
  7. A review of the challenge in measuring and standardizing BCR-ABL1
  8. Mini Review
  9. Challenges in the analysis of epigenetic biomarkers in clinical samples
  10. Opinion Paper
  11. Defining a roadmap for harmonizing quality indicators in Laboratory Medicine: a consensus statement on behalf of the IFCC Working Group “Laboratory Error and Patient Safety” and EFLM Task and Finish Group “Performance specifications for the extra-analytical phases”
  12. Genetics and Molecular Diagnostics
  13. Assessment of EGFR mutation status using cell-free DNA from bronchoalveolar lavage fluid
  14. General Clinical Chemistry and Laboratory Medicine
  15. A survey of patients’ views from eight European countries of interpretive support from Specialists in Laboratory Medicine
  16. Verification of examination procedures in clinical laboratory for imprecision, trueness and diagnostic accuracy according to ISO 15189:2012: a pragmatic approach
  17. Expressing analytical performance from multi-sample evaluation in laboratory EQA
  18. A candidate reference method for serum potassium measurement by inductively coupled plasma mass spectrometry
  19. Practical motives are prominent in test-ordering in the Emergency Department
  20. Technical and clinical validation of the Greiner FC-Mix glycaemia tube
  21. Comparison of pneumatic tube system with manual transport for routine chemistry, hematology, coagulation and blood gas tests
  22. Accuracy of cerebrospinal fluid Aβ1-42 measurements: evaluation of pre-analytical factors using a novel Elecsys immunosassay
  23. Evaluation of cannabinoids concentration and stability in standardized preparations of cannabis tea and cannabis oil by ultra-high performance liquid chromatography tandem mass spectrometry
  24. Analytical performance and diagnostic accuracy of six different faecal calprotectin assays in inflammatory bowel disease
  25. Novel immunoassays for detection of CUZD1 autoantibodies in serum of patients with inflammatory bowel diseases
  26. Hematology and Coagulation
  27. Critical appraisal of discriminant formulas for distinguishing thalassemia from iron deficiency in patients with microcytic anemia
  28. Reference Values and Biological Variations
  29. Reference ranges of thromboelastometry in healthy full-term and pre-term neonates
  30. Cancer Diagnostics
  31. Immunoparesis in IgM gammopathies as a useful biomarker to predict disease progression
  32. Cardiovascular Diseases
  33. Assessment of the clinical utility of adding common single nucleotide polymorphism genetic scores to classical risk factor algorithms in coronary heart disease risk prediction in UK men
  34. Time and age dependent decrease of NT-proBNP after septal myectomy in hypertrophic obstructive cardiomyopathy
  35. Infectious Diseases
  36. Higher serum caspase-cleaved cytokeratin-18 levels during the first week of sepsis diagnosis in non-survivor patients
  37. Letters to the Editor
  38. Data mining for age-related TSH reference intervals in adulthood
  39. Intra-laboratory variation and its effect on gestational diabetes diagnosis
  40. Evaluation of long-term imprecision of automated complete blood cell count on the Sysmex XN-9000 system
  41. Sensitivity of the Sysmex XN9000 WPC-channel for detection of monoclonal B-cell populations
  42. Evaluation of biotin interference on immunoassays: new data for troponin I, digoxin, NT-Pro-BNP, and progesterone
  43. Stability of procalcitonin in cerebrospinal fluid
  44. Between-laboratory analysis of IgG antibodies against Aspergillus fumigatus in paired quality control samples
  45. Mass spectrometry vs. immunoassay in clinical and forensic toxicology: qui modus in rebus est?
  46. Great need for changes in higher education in Greece
  47. A note from the Editor in Chief regarding the Letter to the Editor “Great need for changes in higher education in Greece”
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