An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform (Q41313805)

29 September 2017

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform (English)

1 reference

29 September 2017

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11

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29 September 2017

Maléne E Lindholm

3

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Francesco Marabita

Francesco Marabita

1

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Carl Johan Sundberg

Carl J Sundberg

7

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Jesper Tegnér

10

Jesper Tegnér

1 reference

29 September 2017

2

Malin Almgren

1 reference

29 September 2017

8

Tomas J Ekström

1 reference

PMCID

3669124

29 September 2017

Andrew E Teschendorff

9

Andrew E Teschendorff

1 reference

29 September 2017

4

Sabrina Ruhrmann

1 reference

29 September 2017

6

Maja Jagodic

1 reference

29 September 2017

Fredrik Fagerström-Billai

5

1 reference

29 September 2017

19 February 2013

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29 September 2017

1 reference

29 September 2017

8

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29 September 2017

3

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29 September 2017

333-346

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PMCID

3669124

describes a project that uses

29 September 2017

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/3669124

based on heuristic

inferred from PubMed Central ID database lookup

cites work

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

DNA methylation biomarkers and their utility for solid cancer diagnostics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

DNA methylation profiling in the clinic: applications and challenges

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Cancer epigenetics: from mechanism to therapy

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Functions of DNA methylation: islands, start sites, gene bodies and beyond

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Batch effect correction for genome-wide methylation data with Illumina Infinium platform

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Genome-wide DNA methylation profiling using Infinium® assay

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Epigenome-wide association studies for common human diseases

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Mapping and analysis of chromatin state dynamics in nine human cell types

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

DNMT3A Mutations in Acute Myeloid Leukemia

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Epigenomics reveals a functional genome anatomy and a new approach to common disease

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Principles and challenges of genomewide DNA methylation analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Human DNA methylomes at base resolution show widespread epigenomic differences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

CpG islands--'a rough guide'.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Genome-scale DNA methylation maps of pluripotent and differentiated cells

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

lumi: a pipeline for processing Illumina microarray

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Capturing heterogeneity in gene expression studies by surrogate variable analysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Increased methylation variation in epigenetic domains across cancer types

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Comprehensive high-throughput arrays for relative methylation (CHARM).

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Evaluation of diagnostic tests without gold standards.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

High density DNA methylation array with single CpG site resolution

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Epigenetics as a unifying principle in the aetiology of complex traits and diseases.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Methylated DNA immunoprecipitation (MeDIP).

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Random effects models in latent class analysis for evaluating accuracy of diagnostic tests.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

5-Methylcytosine as an Endogenous Mutagen in the Human LDL Receptor and p53 Genes

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3669124

Evaluation of the Infinium Methylation 450K technology

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23422812

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Methylated DNA immunoprecipitation (MeDIP) from low amounts of cells

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23422812

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.4161/EPI.24008

1 reference

29 September 2017

1 reference

29 September 2017

1 reference

PMCID

3669124