Imperial College London
Alternate

DrMarieLoh

Faculty of Medicine, School of Public Health

Honorary Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 2885m.loh

 
 
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Location

 

172Praed StreetSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Loh:2010:10.1097/PDM.0b013e3181de4396,
author = {Loh, M and Liem, N and Lim, PL and Vaithilingam, A and Cheng, CL and Salto-Tellez, M and Yong, WP and Soong, R},
doi = {10.1097/PDM.0b013e3181de4396},
journal = {Diagn Mol Pathol},
pages = {243--247},
title = {Impact of sample heterogeneity on methylation analysis.},
url = {http://dx.doi.org/10.1097/PDM.0b013e3181de4396},
volume = {19},
year = {2010}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - The recent emergence of high-throughput arrays for methylation analysis has made the influence of tumor content on the interpretation of methylation levels increasingly pertinent. However, to what degree does tumor content have an influence, and what degree of tumor content makes a specimen acceptable for accurate analysis remains unclear. Taking a systematic approach, we analyzed 98 unselected formalin-fixed and paraffin-embedded gastric tumors and matched normal tissue samples using the Illumina GoldenGate methylation assay. Unsupervised hierarchical clustering showed 2 separate clusters with a significant difference in average tumor content levels. The probes identified to be significantly differentially methylated between the tumors and normals also differed according to the tumor content of the samples included, with the sensitivity of identifying the "top" candidate probes significantly reduced when including samples below 70% tumor content. We also tested whether the removal of the probes featuring single nucleotide polymorphisms and/or DNA repetitive elements, reportedly present in GoldenGate arrays, would significantly affect the study's findings, and found little change in the results with their omission. Our findings suggest that tumor content significantly influences the interpretation of methylation levels and candidate gene identification, and that 70% tumor content may be a suitable threshold for selecting samples for methylation studies.
AU  - Loh,M
AU  - Liem,N
AU  - Lim,PL
AU  - Vaithilingam,A
AU  - Cheng,CL
AU  - Salto-Tellez,M
AU  - Yong,WP
AU  - Soong,R
DO  - 10.1097/PDM.0b013e3181de4396
EP  - 247
PY  - 2010///
SP  - 243
TI  - Impact of sample heterogeneity on methylation analysis.
T2  - Diagn Mol Pathol
UR  - http://dx.doi.org/10.1097/PDM.0b013e3181de4396
UR  - https://www.ncbi.nlm.nih.gov/pubmed/21051995
VL  - 19
ER  -
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