{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T02:18:53Z","timestamp":1771294733982,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: DNA cytosine methylation is an important epigenetic regulator, critical for mammalian development and the control of gene expression. Numerous techniques using either restriction enzyme or affinity-based approaches have been developed to interrogate cytosine methylation status genome-wide, however these assays must be validated by a more quantitative approach, such as MALDI-TOF mass spectrometry of bisulphite-converted DNA (commercialized as Sequenom's EpiTYPER assay using the MassArray system). Here, we present an R package (\u2018MassArray\u2019) that assists in assay design and uses the standard Sequenom output file as the input to a pipeline of analyses not available as part of the commercial software. The tools in this package include bisulphite conversion efficiency calculation, sequence polymorphism flagging and visualization tools that combine multiple experimental replicates and create tracks for genome browser viewing.<\/jats:p>\n               <jats:p>Contact: \u00a0jgreally@aecom.yu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp382","type":"journal-article","created":{"date-parts":[[2009,6,27]],"date-time":"2009-06-27T00:24:20Z","timestamp":1246062260000},"page":"2164-2170","source":"Crossref","is-referenced-by-count":67,"title":["A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry"],"prefix":"10.1093","volume":"25","author":[{"given":"Reid F.","family":"Thompson","sequence":"first","affiliation":[{"name":"1 Departments of Genetics and 2 Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"}]},{"given":"Masako","family":"Suzuki","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and 2 Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"}]},{"given":"Kevin W.","family":"Lau","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and 2 Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"}]},{"given":"John M.","family":"Greally","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and 2 Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"},{"name":"1 Departments of Genetics and 2 Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,6,26]]},"reference":[{"key":"2023013112103849600_B1","doi-asserted-by":"crossref","first-page":"e119","DOI":"10.1093\/nar\/gkm662","article-title":"Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements","volume":"35","author":"Coolen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112103849600_B2","first-page":"1","article-title":"A heuristic equipartion model for estimating individual methylation ratios in the case of isobaric CpG units","author":"Deciu","year":"2008","journal-title":"Sequenom Technical Report"},{"key":"2023013112103849600_B3","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.ab.2004.05.007","article-title":"De novo quantitative bisulfite sequencing using the pyrosequencing technology","volume":"333","author":"Dupont","year":"2004","journal-title":"Anal. 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