RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip.
BMC Genomics
; 18(1): 4, 2017 01 03.
Article
en En
| MEDLINE
| ID: mdl-28049437
ABSTRACT
BACKGROUND:
The Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in epigenome-wide association studies. Both arrays use two fluorescent dyes (Cy3-green/Cy5-red) to measure methylation level at CpG sites. However, performance difference between dyes can result in biased estimates of methylation levels.RESULTS:
Here we describe a novel method, called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels. We evaluate the method in several datasets against other widely used dye-bias correction methods. Results on data quality improvement showed that RELIC correction statistically significantly outperforms alternative dye-bias correction methods. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website ( https//www.bioconductor.org/packages/release/bioc/html/ENmix.html ).CONCLUSIONS:
RELIC is an efficient and robust method to correct for dye-bias in Illumina Methylation BeadChip data. It outperforms other alternative methods and conveniently implemented in R package ENmix to facilitate DNA methylation studies.Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Biología Computacional
/
Metilación de ADN
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Análisis de Secuencia por Matrices de Oligonucleótidos
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Secuenciación de Nucleótidos de Alto Rendimiento
Límite:
Humans
Idioma:
En
Revista:
BMC Genomics
Asunto de la revista:
GENETICA
Año:
2017
Tipo del documento:
Article
País de afiliación:
Estados Unidos