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Nucleic Acids Research 2006 34(2):555-563; doi:10.1093/nar/gkj468
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Published online 23 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer

Zhiqing Huang1, Yaqing Wen1, Ruby Shandilya1, Jeffrey R. Marks2,3, Andrew Berchuck1,3 and Susan K. Murphy1,3,*

1Division of Gynecologic Oncology, Duke University Medical Center Durham, NC 27708, USA 2Department of Surgery, Duke University Medical Center Durham, NC 27708, USA 3Duke Institute for Genome Sciences and Policy, Duke University Medical Center Durham, NC 27708, USA

*To whom correspondence should be addressed. Tel: +1 919 681 3423; Fax: +1 919 684 5336; Email: murph035{at}mc.duke.edu

Received November 7, 2005. Revised January 9, 2006. Accepted January 9, 2006.

Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploited the normal allele-specific differential methylation of the M6P/IGF2R intron 2 CpG island to rapidly evaluate potential LOH in ovarian cancers, since every normal individual is informative. To this end, we developed a method for bisulfite modification of genomic DNA in 96-well format that allows for rapid methylation profiling. We identified ovarian cancers with M6P/IGF2R LOH, but unexpectedly also found frequent abnormal acquisition of methylation on the paternally inherited allele at intron 2. These results demonstrate the utility of our high-throughput method of bisulfite modification for analysis of large sample numbers. They further show that the methylation status of the intron 2 CpG island may be a useful indicator of LOH and biomarker of disease.


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L. Goh, S. K. Murphy, S. Muhkerjee, and T. S. Furey
Genomic sweeping for hypermethylated genes
Bioinformatics, February 1, 2007; 23(3): 281 - 288.
[Abstract] [Full Text] [PDF]


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