Cargando…

Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use

In this study, our goal was to determine probe-specific thresholds for identifying aberrant, or outlying, DNA methylation and to provide guidance on the relative merits of using continuous or outlier methylation data. To construct a reference database, we downloaded Illumina Human 450K array data fo...

Descripción completa

Detalles Bibliográficos
Autores principales:	Downs, Bradley M., Thursby, Sara-Jayne, Cope, Leslie
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Taylor & Francis 2023
Materias:	Research Paper
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10208159/ https://www.ncbi.nlm.nih.gov/pubmed/37218167 http://dx.doi.org/10.1080/15592294.2023.2213874

Ejemplares similares

MethylToSNP: identifying SNPs in Illumina DNA methylation array data
por: LaBarre, Brenna A., et al.
Publicado: (2019)

Low-level processing of Illumina Infinium DNA Methylation BeadArrays
por: Triche, Timothy J., et al.
Publicado: (2013)

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
por: Fortin, Jean-Philippe, et al.
Publicado: (2014)

Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array
por: Mansell, Georgina, et al.
Publicado: (2019)

Evaluating DNA methylation age on the Illumina MethylationEPIC Bead Chip
por: Dhingra, Radhika, et al.
Publicado: (2019)

Identification of methylation states of DNA regions for Illumina methylation BeadChip
por: Luo, Ximei, et al.
Publicado: (2020)

Reliability of DNA methylation measures using Illumina methylation BeadChip
por: Xu, Zongli, et al.
Publicado: (2020)

Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array
por: Grant, Olivia A., et al.
Publicado: (2022)

Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc.
por: Roessler, Jessica, et al.
Publicado: (2012)

Agreement in DNA methylation levels from the Illumina 450K array across batches, tissues, and time
por: Forest, Marie, et al.
Publicado: (2018)

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays
por: Mah, Clarence K., et al.
Publicado: (2018)

DNA-methylation for the detection and distinction of 19 human malignancies
por: Danilova, Ludmila, et al.
Publicado: (2021)

An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays
por: Mallik, Saurav, et al.
Publicado: (2018)

Detecting differentially methylated loci for Illumina Array methylation data based on human ovarian cancer data
por: Chen, Zhongxue, et al.
Publicado: (2013)

Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array
por: Lee, Yunsung, et al.
Publicado: (2020)

Aberrant DNA Methylation in Keratoacanthoma
por: Nobeyama, Yoshimasa, et al.
Publicado: (2016)

DNA Methylation Aberrant in Atherosclerosis
por: Dai, Yao, et al.
Publicado: (2022)

CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes
por: Thursby, Sara-Jayne, et al.
Publicado: (2020)

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip
por: Watkins, Sarah Holmes, et al.
Publicado: (2022)

Differential Methylation Analysis of Suicidal Ideation Severity in Schizophrenia with the Illumina MethylationEPIC Array
por: Wang, Kevin Z., et al.
Publicado: (2022)

Comparison of methylation patterns generated from genomic and cell-line derived DNA using the Illumina Infinium MethylationEPIC BeadChip array
por: Smyth, L. J., et al.
Publicado: (2019)

Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays
por: Zhang, Wei, et al.
Publicado: (2023)

Aberrant DNA Methylation and Prostate Cancer
por: Majumdar, Sunipa, et al.
Publicado: (2011)

Aberrant DNA Methylation in ES Cells
por: Ludwig, Guy, et al.
Publicado: (2014)

Aberrant DNA methylation in cervical Carcinogenesis
por: Yang, Hui-Juan
Publicado: (2013)

Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data
por: Ross, Jason P., et al.
Publicado: (2022)

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
por: Fortin, Jean-Philippe, et al.
Publicado: (2017)

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
por: Pidsley, Ruth, et al.
Publicado: (2016)

Seven-CpG DNA Methylation Age Determined by Single Nucleotide Primer Extension and Illumina’s Infinium MethylationEPIC Array Provide Highly Comparable Results
por: Vetter, Valentin Max, et al.
Publicado: (2022)

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data
por: Maksimovic, Jovana, et al.
Publicado: (2015)

Aberrant DNA methylation patterns in diabetic nephropathy
por: Maghbooli, Zhila, et al.
Publicado: (2014)

Aberrant DNA Methylation of ABC Transporters in Cancer
por: Zappe, Katja, et al.
Publicado: (2020)

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform
por: Marabita, Francesco, et al.
Publicado: (2013)

Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray
por: Gujar, Hemant, et al.
Publicado: (2018)

A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip
por: Wang, Zhenxing, et al.
Publicado: (2018)

“Gap hunting” to characterize clustered probe signals in Illumina methylation array data
por: Andrews, Shan V., et al.
Publicado: (2016)

Aberrant DNA Methylation in Acute Myeloid Leukemia and Its Clinical Implications
por: Yang, Xianwen, et al.
Publicado: (2019)

Comparative analysis of Illumina Mouse Methylation BeadChip and reduced-representation bisulfite sequencing for routine DNA methylation analysis
por: Fennell, Lochlan J., et al.
Publicado: (2022)

Osteoponin Promoter Controlled by DNA Methylation: Aberrant Methylation in Cloned Porcine Genome
por: Shen, Chih-Jie, et al.
Publicado: (2014)

A data-driven approach to preprocessing Illumina 450K methylation array data
por: Pidsley, Ruth, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_p4i7ab00mciaf2mabpe8nejdgl