Measuring the methylome in clinical samples: improved processing of the Infinium Human Methylation450 BeadChip Array.
Epigenetics
; 7(10): 1173-87, 2012 Oct.
Article
en En
| MEDLINE
| ID: mdl-22964528
ABSTRACT
The Infinium Human Methylation450 BeadChip Array (TM) (Infinium 450K) is an important tool for studying epigenetic patterns associated with disease. This array offers a high-throughput, low cost alternative to more comprehensive sequencing-based methodologies. Here we compare data generated by interrogation of the same seven clinical samples by Infinium 450K and reduced representation bisulfite sequencing (RRBS). This is the largest data set comparing Infinium 450K array to the comprehensive RRBS methodology reported so far. We show good agreement between the two methodologies. A read depth of four or more reads in the RRBS data was sufficient to achieve good agreement with Infinium 450K. However, we observe that intermediate methylation values (20-80%) are more variable between technologies than values at the extremes of the bimodal methylation distribution. We describe careful processing of Infinium 450K data to correct for known limitations and batch effects. Using methodologies proposed by others and newly implemented and combined in this report, agreement of Infinium 450K data with independent techniques can be vastly improved.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Análisis de Secuencia de ADN
/
Metilación de ADN
/
Análisis de Secuencia por Matrices de Oligonucleótidos
/
Epigénesis Genética
Límite:
Humans
Idioma:
En
Revista:
Epigenetics
Asunto de la revista:
GENETICA
Año:
2012
Tipo del documento:
Article
País de afiliación:
Singapur