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Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison.

De Meyer T, Bady P, Trooskens G, Kurscheid S, Bloch J, Kros JM, Hainfellner JA, Stupp R, Delorenzi M, Hegi ME, Van Criekinge W - Sci Rep (2015)

Bottom Line: In addition, genome-wide characteristics were compared, revealing that HM450 probes identified substantially fewer regions compared to MethylCap-seq.Although results indicated that the latter method can detect more potentially relevant DNA-methylation, this did not translate into the discovery of more differentially methylated loci between tumours and controls compared to HM450.Our results therefore indicate that both methodologies are complementary, with a higher sensitivity for HM450 and a far larger genome-wide coverage for MethylCap-seq, but also that a more comprehensive character does not automatically imply more significant results in biomarker studies.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.

ABSTRACT
Two cost-efficient genome-scale methodologies to assess DNA-methylation are MethylCap-seq and Illumina's Infinium HumanMethylation450 BeadChips (HM450). Objective information regarding the best-suited methodology for a specific research question is scant. Therefore, we performed a large-scale evaluation on a set of 70 brain tissue samples, i.e. 65 glioblastoma and 5 non-tumoral tissues. As MethylCap-seq coverages were limited, we focused on the inherent capacity of the methodology to detect methylated loci rather than a quantitative analysis. MethylCap-seq and HM450 data were dichotomized and performances were compared using a gold standard free Bayesian modelling procedure. While conditional specificity was adequate for both approaches, conditional sensitivity was systematically higher for HM450. In addition, genome-wide characteristics were compared, revealing that HM450 probes identified substantially fewer regions compared to MethylCap-seq. Although results indicated that the latter method can detect more potentially relevant DNA-methylation, this did not translate into the discovery of more differentially methylated loci between tumours and controls compared to HM450. Our results therefore indicate that both methodologies are complementary, with a higher sensitivity for HM450 and a far larger genome-wide coverage for MethylCap-seq, but also that a more comprehensive character does not automatically imply more significant results in biomarker studies.

No MeSH data available.


Related in: MedlinePlus

Fractions of CpG-island and functional location context assessed by both methodologies.Fractions of loci corresponding to CpG-islands, shores, shelves and open sea and fractions of promoter, exon, intron, pseudogene and intergenic loci assessed by HM450 (A,B) and detected by MethylCap-seq (C,D) and their genome-wide distribution (E,F).
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f4: Fractions of CpG-island and functional location context assessed by both methodologies.Fractions of loci corresponding to CpG-islands, shores, shelves and open sea and fractions of promoter, exon, intron, pseudogene and intergenic loci assessed by HM450 (A,B) and detected by MethylCap-seq (C,D) and their genome-wide distribution (E,F).

Mentions: This confirmed that the HM450 probe locations have specifically been selected towards CpG-islands and associated shores and shelves (Fig. 4A), as described elsewhere14. Also for MethylCap-based results (Fig. 4C), in comparison with the genome-wide occurrence of these features (Fig. 4E), there is apparent enrichment for CpG-islands, shores and shelves. For MethylCap-seq, variation in function of sequencing depth were very limited, with a slight decrease in CpG-island, shore and shelve fractions and an increase for the open sea fraction for higher sequencing depths (Supplementary Fig. S2, panel A), in line with the slightly decreasing specificity for increasing sequencing depths. When evaluating absolute numbers of detected methylated loci, using a beta-value threshold of 0.3 for HM450, the latter method detects more methylated loci in CpG-islands, but clearly less methylated loci in CpG-island shore and shelve regions (Table 2). Only considering MethylCap-seq samples with high sequencing depths did not alter these conclusions, nor did the application of other beta-value thresholds for presence of methylation (data not shown).


Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison.

De Meyer T, Bady P, Trooskens G, Kurscheid S, Bloch J, Kros JM, Hainfellner JA, Stupp R, Delorenzi M, Hegi ME, Van Criekinge W - Sci Rep (2015)

Fractions of CpG-island and functional location context assessed by both methodologies.Fractions of loci corresponding to CpG-islands, shores, shelves and open sea and fractions of promoter, exon, intron, pseudogene and intergenic loci assessed by HM450 (A,B) and detected by MethylCap-seq (C,D) and their genome-wide distribution (E,F).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4612737&req=5

f4: Fractions of CpG-island and functional location context assessed by both methodologies.Fractions of loci corresponding to CpG-islands, shores, shelves and open sea and fractions of promoter, exon, intron, pseudogene and intergenic loci assessed by HM450 (A,B) and detected by MethylCap-seq (C,D) and their genome-wide distribution (E,F).
Mentions: This confirmed that the HM450 probe locations have specifically been selected towards CpG-islands and associated shores and shelves (Fig. 4A), as described elsewhere14. Also for MethylCap-based results (Fig. 4C), in comparison with the genome-wide occurrence of these features (Fig. 4E), there is apparent enrichment for CpG-islands, shores and shelves. For MethylCap-seq, variation in function of sequencing depth were very limited, with a slight decrease in CpG-island, shore and shelve fractions and an increase for the open sea fraction for higher sequencing depths (Supplementary Fig. S2, panel A), in line with the slightly decreasing specificity for increasing sequencing depths. When evaluating absolute numbers of detected methylated loci, using a beta-value threshold of 0.3 for HM450, the latter method detects more methylated loci in CpG-islands, but clearly less methylated loci in CpG-island shore and shelve regions (Table 2). Only considering MethylCap-seq samples with high sequencing depths did not alter these conclusions, nor did the application of other beta-value thresholds for presence of methylation (data not shown).

Bottom Line: In addition, genome-wide characteristics were compared, revealing that HM450 probes identified substantially fewer regions compared to MethylCap-seq.Although results indicated that the latter method can detect more potentially relevant DNA-methylation, this did not translate into the discovery of more differentially methylated loci between tumours and controls compared to HM450.Our results therefore indicate that both methodologies are complementary, with a higher sensitivity for HM450 and a far larger genome-wide coverage for MethylCap-seq, but also that a more comprehensive character does not automatically imply more significant results in biomarker studies.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.

ABSTRACT
Two cost-efficient genome-scale methodologies to assess DNA-methylation are MethylCap-seq and Illumina's Infinium HumanMethylation450 BeadChips (HM450). Objective information regarding the best-suited methodology for a specific research question is scant. Therefore, we performed a large-scale evaluation on a set of 70 brain tissue samples, i.e. 65 glioblastoma and 5 non-tumoral tissues. As MethylCap-seq coverages were limited, we focused on the inherent capacity of the methodology to detect methylated loci rather than a quantitative analysis. MethylCap-seq and HM450 data were dichotomized and performances were compared using a gold standard free Bayesian modelling procedure. While conditional specificity was adequate for both approaches, conditional sensitivity was systematically higher for HM450. In addition, genome-wide characteristics were compared, revealing that HM450 probes identified substantially fewer regions compared to MethylCap-seq. Although results indicated that the latter method can detect more potentially relevant DNA-methylation, this did not translate into the discovery of more differentially methylated loci between tumours and controls compared to HM450. Our results therefore indicate that both methodologies are complementary, with a higher sensitivity for HM450 and a far larger genome-wide coverage for MethylCap-seq, but also that a more comprehensive character does not automatically imply more significant results in biomarker studies.

No MeSH data available.


Related in: MedlinePlus