Impact of Sample Heterogeneity on Methylation Analysis

M. Loh; N. Liem; P.L. Lim; A. Vaithilingam; C.L. Cheng; Manuel Salto-Tellez; W.P. Yong; R. Soong

doi:10.1097/PDM.0b013e3181de4396

Impact of Sample Heterogeneity on Methylation Analysis

M. Loh, N. Liem, P.L. Lim, A. Vaithilingam, C.L. Cheng, Manuel Salto-Tellez, W.P. Yong, R. Soong

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

6 Citations (Scopus)

Abstract

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

Original language	English
Pages (from-to)	243-247
Number of pages	5
Journal	Diagnostic Molecular Pathology
Volume	19
Issue number	4
DOIs	https://doi.org/10.1097/PDM.0b013e3181de4396
Publication status	Published - Dec 2010

ASJC Scopus subject areas

Pathology and Forensic Medicine
Cell Biology
Molecular Biology

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title = "Impact of Sample Heterogeneity on Methylation Analysis",

abstract = "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",

author = "M. Loh and N. Liem and P.L. Lim and A. Vaithilingam and C.L. Cheng and Manuel Salto-Tellez and W.P. Yong and R. Soong",

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AU - Loh, M.

AU - Liem, N.

AU - Lim, P.L.

AU - Vaithilingam, A.

AU - Cheng, C.L.

AU - Salto-Tellez, Manuel

AU - Yong, W.P.

AU - Soong, R.

PY - 2010/12

Y1 - 2010/12

N2 - 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

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

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DO - 10.1097/PDM.0b013e3181de4396

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SP - 243

EP - 247

JO - Diagnostic Molecular Pathology

JF - Diagnostic Molecular Pathology

SN - 1052-9551

IS - 4

ER -

Impact of Sample Heterogeneity on Methylation Analysis

Abstract

ASJC Scopus subject areas

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