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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

MethylCap-seq sensitivity reaches a plateau phase for increasing sequencing depths.Conditional sensitivity (squares) and specificity (triangles) are plotted as a function of sequencing depth, for both HM450 type 1 (blue) and type 2 (orange) assay types. Loess regression curves (using span smoothing parameter 0.95) have been added for both sensitivity (solid lines) and specificity (dashed lines) for both HM450 assay types.
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f3: MethylCap-seq sensitivity reaches a plateau phase for increasing sequencing depths.Conditional sensitivity (squares) and specificity (triangles) are plotted as a function of sequencing depth, for both HM450 type 1 (blue) and type 2 (orange) assay types. Loess regression curves (using span smoothing parameter 0.95) have been added for both sensitivity (solid lines) and specificity (dashed lines) for both HM450 assay types.

Mentions: Using a beta-value threshold of 0.3, Fig. 3 (includes 2 low coverage samples for graphical purposes) indicate that this is indeed the case. Of note, sensitivity reaches a plateau phase for sufficiently large sequencing depths. Indeed, a maximal sensitivity of about 65% (type I)/55% (type II assay loci) is obtained for sequencing depths larger than ~8 million fragments. As expected, specificity tended to decrease for higher sequencing depths, but stays clearly above 90%. For beta-value thresholds of 0.2 and 0.4 the same trends were observed, with a little lower (~5%) and marginally higher (~2%) maximal sensitivity values for thresholds 0.2 and 0.4, respectively, and specificities consistently above 90%.


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)

MethylCap-seq sensitivity reaches a plateau phase for increasing sequencing depths.Conditional sensitivity (squares) and specificity (triangles) are plotted as a function of sequencing depth, for both HM450 type 1 (blue) and type 2 (orange) assay types. Loess regression curves (using span smoothing parameter 0.95) have been added for both sensitivity (solid lines) and specificity (dashed lines) for both HM450 assay types.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: MethylCap-seq sensitivity reaches a plateau phase for increasing sequencing depths.Conditional sensitivity (squares) and specificity (triangles) are plotted as a function of sequencing depth, for both HM450 type 1 (blue) and type 2 (orange) assay types. Loess regression curves (using span smoothing parameter 0.95) have been added for both sensitivity (solid lines) and specificity (dashed lines) for both HM450 assay types.
Mentions: Using a beta-value threshold of 0.3, Fig. 3 (includes 2 low coverage samples for graphical purposes) indicate that this is indeed the case. Of note, sensitivity reaches a plateau phase for sufficiently large sequencing depths. Indeed, a maximal sensitivity of about 65% (type I)/55% (type II assay loci) is obtained for sequencing depths larger than ~8 million fragments. As expected, specificity tended to decrease for higher sequencing depths, but stays clearly above 90%. For beta-value thresholds of 0.2 and 0.4 the same trends were observed, with a little lower (~5%) and marginally higher (~2%) maximal sensitivity values for thresholds 0.2 and 0.4, respectively, and specificities consistently above 90%.

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