ChAMP: updated methylation analysis pipeline for Illumina BeadChips

Tian, Yuan; Morris, Tiffany; Webster, Amy P; Yang, Zhen; Beck, Stephan; Feber, Andrew; Teschendorff, Andrew E.

doi:10.1093/bioinformatics/btx513

Cited by 722 publications

(577 citation statements)

References 14 publications

Supporting

Mentioning

574

Contrasting

Unclassified

Order By: Relevance

“…Methylation array raw data from S:CORT cohorts 1 and 3 was processed with the R-package ChAMP (35). CIMP classification was generated by recursively partitioned mixture model as previously done in TCGA (36)…”

Section: Cimp Classificationmentioning

confidence: 99%

Image-based consensus molecular subtype classification (imCMS) of colorectal cancer using deep learning

Verrill

Sirinukunwattana

Domingo

et al. 2019

Preprint

View full text Add to dashboard Cite

Image analysis is a cost-effective tool to associate complex features of tissue organisation with molecular and outcome data. Here we predict consensus molecular subtypes (CMS) of colorectal cancer (CRC) from standard H&E sections using deep learning. Domain adversarial training of a neural classification network was performed using 1,553 tissue sections with comprehensive multiomic data from three independent datasets. Image-based consensus molecular subtyping (imCMS) accurately classified CRC whole-slide images and preoperative biopsies, spatially resolved intratumoural heterogeneity and provided accurate secondary calls with higher discriminatory power than bioinformatic prediction. In all three cohorts imCMS established sensible classification in CMS unclassified samples, reproduced expected correlations with (epi)genomic alterations and effectively stratified patients into prognostic subgroups. Leveraging artificial intelligence for the development of novel biomarkers extracted from histological slides with molecular and biological interpretability has remarkable potential for clinical translation.

show abstract

Section: Cimp Classificationmentioning

confidence: 99%

Image-based consensus molecular subtype classification (imCMS) of colorectal cancer using deep learning

Verrill

Sirinukunwattana

Domingo

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…We provide for each microarray and each species two files: one containing the whole set of CS-valid or MM-valid probes (filtered for probes with a mismatch at 1 or 2 bp from the CpG) and another file containing only perfectly matched probes. These annotation files retain the format of the original Illumina manifest and can thus be used without further modifications in analysis pipelines for BeadChips such as SQN [40] or the widely used ChAMP pipeline [42]. All columns of the respective manifest files are described in detail in the supporting file (manifest header descriptions file included in the compressed Supplementary Material).…”

Section: K and Epic Manifest Files For Chlorocebus Sabaeus And Macmentioning

confidence: 99%

Analysis and annotation of genome-wide DNA methylation patterns in two nonhuman primate species using the Infinium Human Methylation 450K and EPIC BeadChips

Pichon

Busato

Jochems

et al. 2020

Preprint

View full text Add to dashboard Cite

The Infinium Human Methylation450 and Methylation EPIC BeadChips are useful tools for the study of the methylation state of hundreds of thousands of CpG across the human genome at affordable cost. However, in a wide range of experimental settings in particular for studies in infectious or brain-related diseases, human samples cannot be easily obtained. Hence, due to their close developmental, immunological and neurological proximity with humans, nonhuman primates are used in many research fields of human diseases and for preclinical research. Few studies have used DNA methylation microarrays in simian models. Microarrays designed for the analysis of DNA methylation patterns in the human genome could be useful given the genomic proximity between human and nonhuman primates. However, there is currently information lacking about the specificity and usability of each probe for many nonhuman primate species, including rhesus macaques (Macaca mulatta), originating from Asia, and African green monkeys originating from West-Africa (Chlorocebus sabaeus).Rhesus macaques and African green monkeys are among the major nonhuman primate models utilized in biomedical research. Here, we provide a precise evaluation and reannotation of the probes of the two microarrays for the analysis of genome-wide DNA methylation patterns in these two Cercopithecidae species. We demonstrate that up to 162,000 of the 450K and 255,000 probes of the EPIC BeadChip can be reliably used in Macaca mulatta or Chlorocebus sabaeus. The annotation files are provided in a format compatible with a variety of preprocessing, normalization and analytical pipelines designed for data analysis from 450K/EPIC arrays, facilitating high-throughput DNA methylation analyses in Macaca mulatta and Chlorocebus sabaeus. They provide the opportunity to the research community to focus their analysis only on those probes identified as reliable. The described analytical workflow leaves the choice to the user to balance coverage versus specificity and can also be applied to other Cercopithecidae species.

show abstract

“…The raw .idat files were imported into R (version 3.5.1) 83 , using the minfi 84 Bioconductor (version 3.7) 85,86 package, for all subsequent data processing and analyses. After quality control (QC) 84,87,88 , data pre-processing [89][90][91][92][93][94] was conducted on all QC'ed samples (DNHS: n = 187; GTP: n = 390). This included duplicates in the DNHS and participants with missing data in the GTP.…”

Section: Quality Control and Pre-processing Of 450k Datamentioning

confidence: 99%

“…After within-array background correction and dye-bias equalization using out-of-band control probes (ssNoob 90,95 ; minfi), probes with detection p-value > 0.001 in more than 10% of samples 87 and cross-reactive probes 91 (i.e., cross-hybridized between autosomes and sex chromosomes) were removed. Beta-mixture quantile (BMIQ) normalization (ChAMP 93,94 ) was used to correct for type II probe bias 92 .…”

Section: Quality Control and Pre-processing Of 450k Datamentioning

confidence: 99%

Methylomic profiles reveal sex-specific shifts in leukocyte composition associated with post-traumatic stress disorder

Kim

Smith

et al. 2019

Preprint

View full text Add to dashboard Cite

Post-traumatic stress disorder (PTSD) is a debilitating mental disorder precipitated by trauma exposure. However, only some persons exposed to trauma develop PTSD. There are sex differences in risk; twice as many women as men, develop a lifetime diagnosis of PTSD.Methylomic profiles derived from peripheral blood are well-suited for investigating PTSD because DNA methylation (DNAm) encodes individual response to trauma and may play a key role in the immune dysregulation characteristic of PTSD pathophysiology. In the current study, we leveraged recent methodological advances to investigate sex-specific shifts in DNAm-based leukocyte composition that are associated with lifetime PTSD. We estimated leukocyte composition on a combined methylation array dataset (483 participants, ~450k CpG sites) consisting of two civilian cohorts, the Detroit Neighborhood Health Study and Grady Trauma Project. Sex-stratified Mann-Whitney U test and two-way ANCOVA revealed that lifetime PTSD was associated with a small but significant elevation in monocyte proportions in males, but not in females (Holm-adjusted p-val < 0.05). No difference in monocyte proportions was observed between current and remitted PTSD cases in males, suggesting that this sex-specific peak shift reflects a long-standing trait of lifetime history of PTSD, rather than current state of PTSD. Associations with lifetime PTSD or PTSD status were not observed in any other leukocyte subtype and our finding in monocytes was confirmed using cell estimates based on a different deconvolution algorithm, suggesting that our sex-specific findings are robust across cell estimation approaches. Overall, our main finding of elevated monocyte proportions in males, but not in females with lifetime history of PTSD provides evidence for a sex-specific shift in peripheral blood leukocyte composition that is detectable in methylomic profiles and that reflects long-standing changes associated with PTSD diagnosis.University of North Carolina at Chapel Hill. The GTP, based in Atlanta, GA, was approved by the institutional review boards Hospital. All participants provided written informed consent prior to data collection. Details regarding the DNHS 43,67,68 and GTP 69-71 were published previously. While neither study excluded participants based on illness, women known to be pregnant (in the GTP) were excluded from estimation and analyses, due to well-known/known significant differences in leukocyte composition during pregnancy 72 . Collected demographic data included self-reported gender, race, age, and current smoking, which was defined as any cigarette smoking in the past 30 days. Assessment of PTSDStudy participants were assessed for PTSD, as defined by the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) 1 . In the DNHS, study participants were assessed for PTSD using the well-validated self-report PTSD Checklist, Civilian Version (PCL-C) [73][74][75][76] and additional questions about duration, timing, and impairment due to symptoms, via structured telepho...

show abstract

ChAMP: updated methylation analysis pipeline for Illumina BeadChips

Cited by 722 publications

References 14 publications

Image-based consensus molecular subtype classification (imCMS) of colorectal cancer using deep learning

Image-based consensus molecular subtype classification (imCMS) of colorectal cancer using deep learning

Analysis and annotation of genome-wide DNA methylation patterns in two nonhuman primate species using the Infinium Human Methylation 450K and EPIC BeadChips

Methylomic profiles reveal sex-specific shifts in leukocyte composition associated with post-traumatic stress disorder

Contact Info

Product

Resources

About