A systematic assessment of normalization approaches for the Infinium 450K methylation platform

Wu, Michael C.; Joubert, Bonnie R.; Kuan, Pei Fen; Håberg, Siri E.; Nystad, Wenche; Peddada, Shyamal D.; London, Stephanie J.

doi:10.4161/epi.27119

Cited by 61 publications

(58 citation statements)

References 22 publications

(42 reference statements)

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“…These results are similar to those reported by other researchers. [12][13][14] However, for SQN, although the bias is reduced, the correlation/difference between the WGBS and its normalized 450K data, and that between technical replicates, is severely compromised, which was already shown in the above analyses. Hence, PBC and QN.…”

Section: 13mentioning

confidence: 54%

“…To address this issue, several comparisons of different preprocessing approaches have been conducted, [12][13][14] mostly assessing reproducibility of technical replicates, reduction of probe design bias and the influence of downstream differential methylation analysis. As a result, BMIQ was the most recommended method, and Marabita et al even preferred a QN plus BMIQ (QN.BMIQ) analysis pipeline, which first quantile-normalized the intensities of methylation signals among all arrays and then used BMIQ to normalize the b-values within each array.…”

mentioning

confidence: 99%

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A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

Wang

Guan²,

Lin

et al. 2015

Epigenetics

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Section: 13mentioning

confidence: 54%

mentioning

confidence: 99%

A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

Wang

Guan²,

Lin

et al. 2015

Epigenetics

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“…There is consensus that Infinium 450K β-values should be normalized (28, 29) and several methods have been proposed. We considered three normalization methods (minfi-Illumina, SWAN and DASEN) in addition to using raw (un-normalized) β-values.…”

Section: Resultsmentioning

confidence: 99%

Expanding Epigenomics to Archived FFPE Tissues: An Evaluation of DNA Repair Methodologies

Siegel

Berglund

Riggs

et al. 2014

Cancer Epidemiology, Biomarkers &Amp; Prevention

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Background Epigenome-wide association studies are emerging in the field of cancer epidemiology with the rapid development of large-scale methylation array platforms. Until recently, these methods were only valid for DNA from fresh frozen (FF) tissues. Novel techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) have emerged; however, a direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched FF tissues has not been conducted. Methods We conducted a systematic performance comparison of two DNA repair methods (REPLI-g Ligase vs. Infinium HD Restore Kit) on FFPE-DNA compared to matched FF tissues on the Infinium 450K array. A threshold of discordant methylation between FF-FFPE pairs was set at Δβ>0.3. The correlations of β-values from FF-FFPE pairs were compared across methods and experimental conditions. Results The Illumina Restore kit outperformed the REPLI-g ligation method with respect to reproducibility of replicates(R2>0.970), highly correlated β-values between FF-FFPE(R2>0.888), and fewest discordant loci between FF-FFPE(≤0.61%). The performance of the Restore kit was validated in an independent set of 121 FFPE tissues. Conclusions The Restore kit outperformed RELPI-g ligation in restoring FFPE-derived DNA prior to analysis on the Infinium 450K methylation array. Our findings provide critical guidance that may significantly enhance the breadth of diseases that can be studied by methylomic profiling. Impact Epigenomic studies using FFPE tissues should now be considered among cancers that have not been fully characterized from an epigenomic standpoint. These findings promote novel epigenome-wide studies focused on cancer etiology, identification of novel biomarkers, and developing targeted therapies.

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“…In addition to the BMIQ performed for this analysis, we evaluated various normalization methods in this dataset and observed little impact on the results (31). …”

Section: Discussionmentioning

confidence: 99%

Maternal Smoking and DNA Methylation in Newborns: In Utero Effect or Epigenetic Inheritance?

Joubert

Håberg

Bell

et al. 2014

Cancer Epidemiology, Biomarkers &Amp; Prevention

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111

104

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Background Maternal smoking in pregnancy is associated with adverse health outcomes in children, including cancers; underlying mechanisms may include epigenetic modifications. Using Illumina’s 450K array, we previously identified differential DNA methylation related to maternal smoking during pregnancy at 26 CpG sites (CpGs) in 10 genes in newborn cord bloods from the Norwegian Mother and Child Cohort Study (MoBa). Whether these methylation signals in newborns reflect in utero exposure only or possibly epigenetic inheritance of smoking-related modifications is unclear. Methods We therefore evaluated the impact of the timing of mother’s smoking (before or during pregnancy using cotinine measured at 18 weeks gestation), the father’s smoking before conception, and the grandmother’s smoking during her pregnancy with the mother on methylation at these 26 CpGs in 1,042 MoBa newborns. We used robust linear regression, adjusting for covariates, applying Bonferroni correction. Results The strongest and only statistically significant associations were observed for sustained smoking by the mother during pregnancy through at least gestational week 18 (p<1.6×10−5 for all 26 CpGs). We observed no statistically significant differential methylation due to smoking by the mother prior to pregnancy or that ceased by week 18, father’s smoking before conception, or grandmother’s smoking while pregnant with the mother. Conclusions Differential methylation at these CpGs in newborns appears to reflect sustained in utero exposure rather than epigenetic inheritance. Impact Smoking cessation in early pregnancy may negate effects on methylation. Analyses of maternal smoking during pregnancy and offspring health outcomes, including cancer, limited to ever smoking might miss true associations.

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A systematic assessment of normalization approaches for the Infinium 450K methylation platform

Cited by 61 publications

References 22 publications

A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

Expanding Epigenomics to Archived FFPE Tissues: An Evaluation of DNA Repair Methodologies

Maternal Smoking and DNA Methylation in Newborns: In Utero Effect or Epigenetic Inheritance?

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