HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data

Mancuso, Francesco; Montfort, Magda; Carreras, Anna; Alibés, Andreu; Roma, Guglielmo

doi:10.1186/1756-0500-4-546

Cited by 21 publications

(19 citation statements)

References 18 publications

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“…We conducted genome-wide analysis of DNA methylation using Infinium HumanMethylation450 BeadChips (Illumina, San Diego, CA, USA), which contain 485,764 probes (> 99% with CpG dinucleotides), following the manufacturer’s recommendations. We preprocessed the data with the GenomeStudio (version 2011.1) Methylation module (version 1.9; Illumina) and evaluated them using an adaptation of HumMeth27QCReport (Mancuso et al 2011). We used Gene ARMADA (Chatziioannou et al 2009) for within- and between-array normalization (linear LOESS and A-quantile, respectively) and imputation of missing values ( k nearest neighbors approach).…”

Section: Methodsmentioning

confidence: 99%

Performance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research

Hebels

Georgiadis

Keun

et al. 2013

Environ Health Perspect

136

133

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Background: The suitability for omic analysis of biosamples collected in previous decades and currently stored in biobanks is unknown.Objectives: We evaluated the influence of handling and storage conditions of blood-derived biosamples on transcriptomic, epigenomic (CpG methylation), plasma metabolomic [UPLC-ToFMS (ultra performance liquid chromatography–time-of-flight mass spectrometry)], and wide-target proteomic profiles.Methods: We collected fresh blood samples without RNA preservative in heparin, EDTA, or citrate and held them at room temperature for ≤ 24 hr before fractionating them into buffy coat, erythrocytes, and plasma and freezing the fractions at –80oC or in liquid nitrogen. We developed methodology for isolating RNA from the buffy coats and conducted omic analyses. Finally, we analyzed analogous samples from the EPIC-Italy and Northern Sweden Health and Disease Study biobanks.Results: Microarray-quality RNA could be isolated from buffy coats (including most biobank samples) that had been frozen within 8 hr of blood collection by thawing the samples in RNA preservative. Different anticoagulants influenced the metabolomic, proteomic, and to a lesser extent transcriptomic profiles. Transcriptomic profiles were most affected by the delay (as little as 2 hr) before blood fractionation, whereas storage temperature had minimal impact. Effects on metabolomic and proteomic profiles were noted in samples processed ≥ 8 hr after collection, but no effects were due to storage temperature. None of the variables examined significantly influenced the epigenomic profiles. No systematic influence of time-in-storage was observed in samples stored over a period of 13–17 years.Conclusions: Most samples currently stored in biobanks are amenable to meaningful omics analysis, provided that they satisfy collection and storage criteria defined in this study.

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Section: Methodsmentioning

confidence: 99%

Performance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research

Hebels

Georgiadis

Keun

et al. 2013

Environ Health Perspect

136

133

View full text Add to dashboard Cite

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“…Normalized M values were generated from primary HumanMethylation27 beadchip beta values using the R package HumMeth27KQCReport function, including the X chromosome data and using an average probe p-value of 0.03 as the cutoff for sample inclusion (16). The resulting normalized M values represent a continuous variable from −6 (unmethylated) to 6 (methylated).…”

Section: Methodsmentioning

confidence: 99%

Unique DNA Methylation Loci Distinguish Anatomic Site and HPV Status in Head and Neck Squamous Cell Carcinoma

Lleras

Smith

Adrien

et al. 2013

Clinical Cancer Research

104

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Purpose: We have utilized a genome-wide approach to identify novel differentially methylated CpG dinucleotides that are seen in different anatomic sites of head and neck squamous cell carcinoma (HNSCC), as well as those that might be related to HPV status in the oropharynx. Experimental Design: We performed genome-wide DNA methylation profiling of primary tumor samples and corresponding adjacent mucosa from 118 HNSCC patients undergoing treatment at Montefiore Medical Center, Bronx, NY using the Illumina HumanMethylation27 beadchip. For each matched tissue set, we measured differentially methylated CpG loci using a change in methylation level (M-value). Results: When datasets were individually analyzed by anatomic site of the primary tumor, we identified 293 differentially methylated CpG loci in oral cavity SCC, 219 differentially methylated CpG loci in laryngeal SCC, and 460 differentially methylated in oropharyngeal SCC. A subset of these differentially methylated CpG loci was common across all anatomic sites of HNSCC. Stratification by HPV status revealed a significantly higher number of differentially methylated CpG loci in HPV-positive patients. Conclusion: Novel epigenetic biomarkers derived from clinical HNSCC specimens can be used molecular classifiers of this disease, revealing many new avenues of investigation for this disease.

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“…The second workflow demonstrates usage of an R package for quality control and primary analysis of Illumina Infinium methylation data [18]. …”

Section: Resultsmentioning

confidence: 99%

BIFI: a Taverna plugin for a simplified and user-friendly workflow platform

et al. 2014

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BackgroundHeterogeneity in the features, input-output behaviour and user interface for available bioinformatics tools and services is still a bottleneck for both expert and non-expert users. Advancement in providing common interfaces over such tools and services are gaining interest among researchers. However, the lack of (meta-) information about input-output data and parameter prevents to provide automated and standardized solutions, which can assist users in setting the appropriate parameters. These limitations must be resolved especially in the workflow-based solution in order to ease the integration of software.FindingsWe report a Taverna Workbench plugin: the XworX BIFI (Beautiful Interfaces for Inputs) implemented as a solution for the aforementioned issues. BIFI provides a Graphical User Interface (GUI) definition language used to layout the user interface and to define parameter options for Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF) directly or discover appropriate instances from a configured repository. In the absence of a GDF, BIFI generates a default interface.ConclusionThe Taverna Workbench is an open source software providing the ability to combine various services within a workflow. Nevertheless, users can supply input data to the workflow via a simple user interface providing only a text area to enter the input in text form. The workflow may contain meta-information in human readable form such as description text for the port and an example value. However, not all workflow ports are documented so well or have all the required information.BIFI uses custom user interface components for ports which give users feedback on the parameter data type or structure to be used for service execution and enables client-side data validations. Moreover, BIFI offers user interfaces that allow users to interactively construct workflow views and share them with the community, thus significantly increasing usability of heterogeneous, distributed service consumption.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-0500-7-740) contains supplementary material, which is available to authorized users.

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HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data

Cited by 21 publications

References 18 publications

Performance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research

Performance in Omics Analyses of Blood Samples in Long-Term Storage: Opportunities for the Exploitation of Existing Biobanks in Environmental Health Research

Unique DNA Methylation Loci Distinguish Anatomic Site and HPV Status in Head and Neck Squamous Cell Carcinoma

BIFI: a Taverna plugin for a simplified and user-friendly workflow platform

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