Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.

Genome Research
Katherine E Varley, Robi David Mitra

Abstract

Aberrant DNA methylation frequently occurs at gene promoters during cancer progression. It is important to identify these loci because they are often misregulated and drive tumorigenesis. Bisulfite sequencing is the most direct and highest resolution assay for identifying aberrant promoter methylation. Recently, genomic capture methods have been combined with next-generation sequencing to enable genome-scale surveys of methylation in individual samples. However, it is challenging to validate candidate loci identified by these approaches because an efficient method to bisulfite sequence more than 50 differentially methylated loci across a large number of samples does not exist. To address this problem, we developed Bisulfite Patch PCR, which enables highly multiplexed bisulfite PCR and sequencing across many samples. Using this method, we successfully amplified 100% of 94 targeted gene promoters simultaneously in the same reaction. By incorporating sample-specific DNA barcodes into the amplicons, we analyzed 48 samples in a single run of the 454 Life Sciences (Roche) FLX sequencer. The method requires small amounts of starting DNA (250 ng) and does not require a shotgun library construction. The method was highly specific; 90% o...Continue Reading

References

Mar 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·M FrommerC L Paul
Jul 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·M L VeiglS D Markowitz
Mar 29, 2000·Nucleic Acids Research·C A EadsP W Laird
Nov 9, 2000·The New England Journal of Medicine·M EstellerJ G Herman
Feb 19, 2005·Nature Reviews. Cancer·Toshikazu Ushijima
Apr 6, 2005·Human Molecular Genetics·Peter W Laird
Oct 20, 2005·Journal of the National Cancer Institute·Frank Lyko, Robert Brown
Oct 26, 2005·Proceedings of the National Academy of Sciences of the United States of America·Mathias EhrichDirk van den Boom
Feb 7, 2006·BMC Biology·Jung Yeon KimDarryl Shibata
Sep 9, 2006·Science·Tobias SjöblomVictor E Velculescu
Nov 11, 2006·International Journal of Cancer. Journal International Du Cancer·Kunitoshi TomiiNobuyoshi Shimizu
Apr 19, 2007·Nucleic Acids Research·Kristofer MunsonSteven S Smith
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Oct 13, 2007·Science·Laura D WoodBert Vogelstein
Oct 16, 2007·Nature Methods·Gregory J PorrecaJay Shendure
Nov 6, 2007·Nature Genetics·Emily HodgesW Richard McCombie
Feb 20, 2008·British Journal of Cancer·H SuzukiS B Baylin
Apr 10, 2008·Epigenetics : Official Journal of the DNA Methylation Society·George J KlarmannWilliam L Farrar
Jul 5, 2008·Nature·Alexander MeissnerEric S Lander
Sep 6, 2008·Nature·UNKNOWN Cancer Genome Atlas Research Network
Oct 14, 2008·Genome Research·Katherine Elena Varley, Robi David Mitra
Mar 31, 2009·Nature Biotechnology·Madeleine P BallGeorge M Church
Apr 14, 2009·Oncogene·N H NabilsiD S Loose

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Citations

Aug 12, 2014·Epigenomics·Timo WittenbergerMartin Widschwendter
Aug 28, 2014·Nature Reviews. Genetics·Nongluk PlongthongkumKun Zhang
Apr 11, 2014·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Elizabeth J DuncanPeter K Dearden
Aug 27, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Hassan AshktorabHassan Brim
Dec 4, 2012·Cancer Letters·Eun-Joon LeeHuidong Shi
Aug 1, 2012·Biochimie·Alexandre How KitJörg Tost
Jun 16, 2016·Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry·Kazuki HasegawaMizuo Maeda
Jul 28, 2016·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Zibo LiJun Wang
Jan 24, 2012·American Journal of Botany·Corrinne E GroverJonathan F Wendel
Jun 23, 2018·Journal of the National Cancer Institute·Miguel R OssandonJames V Tricoli
May 7, 2011·Expert Review of Molecular Diagnostics·Rachael Natrajan, Jorge S Reis-Filho
Jan 13, 2018·GeroScience·Dustin R MasserWillard M Freeman
Apr 20, 2018·Nature Communications·Yu Amanda GuoAnders Jacobsen Skanderup
Oct 24, 2018·BMC Genomics·Timothy G JenkinsDouglas T Carrell
Jul 16, 2011·Genome Research·H Kiyomi KomoriDaniel R Salomon

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