Merck

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants.

Nature communications (2015-05-30)
Fiona Allum, Xiaojian Shao, Frédéric Guénard, Marie-Michelle Simon, Stephan Busche, Maxime Caron, John Lambourne, Julie Lessard, Karolina Tandre, Åsa K Hedman, Tony Kwan, Bing Ge, Lars Rönnblom, Mark I McCarthy, Panos Deloukas, Todd Richmond, Daniel Burgess, Timothy D Spector, André Tchernof, Simon Marceau, Mark Lathrop, Marie-Claude Vohl, Tomi Pastinen, Elin Grundberg
RESUMEN

Most genome-wide methylation studies (EWAS) of multifactorial disease traits use targeted arrays or enrichment methodologies preferentially covering CpG-dense regions, to characterize sufficiently large samples. To overcome this limitation, we present here a new customizable, cost-effective approach, methylC-capture sequencing (MCC-Seq), for sequencing functional methylomes, while simultaneously providing genetic variation information. To illustrate MCC-Seq, we use whole-genome bisulfite sequencing on adipose tissue (AT) samples and public databases to design AT-specific panels. We establish its efficiency for high-density interrogation of methylome variability by systematic comparisons with other approaches and demonstrate its applicability by identifying novel methylation variation within enhancers strongly correlated to plasma triglyceride and HDL-cholesterol, including at CD36. Our more comprehensive AT panel assesses tissue methylation and genotypes in parallel at ∼4 and ∼3 M sites, respectively. Our study demonstrates that MCC-Seq provides comparable accuracy to alternative approaches but enables more efficient cataloguing of functional and disease-relevant epigenetic and genetic variants for large-scale EWAS.

MATERIALES
Referencia del producto
Marca
Descripción del producto

SAFC
HEPES
Sigma-Aldrich
L-Ascorbic acid, FCC, FG
Sigma-Aldrich
Magnesium chloride solution, PCR Reagent, 25 mM MgCI2 solution for PCR
Sigma-Aldrich
Magnesium chloride solution, for molecular biology, 1.00 M±0.01 M
Sigma-Aldrich
HEPES, BioXtra, pH 5.0-6.5 (1 M in H2O), ≥99.5% (titration)
Sigma-Aldrich
HEPES, BioPerformance Certified, ≥99.5% (titration), suitable for cell culture
Sigma-Aldrich
HEPES, BioXtra, suitable for mouse embryo cell culture, ≥99.5% (titration)
Sigma-Aldrich
HEPES, ≥99.5% (titration)
Sigma-Aldrich
L-Ascorbic acid, ACS reagent, ≥99%
Sigma-Aldrich
L-Ascorbic acid, puriss. p.a., ACS reagent, reag. ISO, Ph. Eur., 99.7-100.5% (oxidimetric)
Sigma-Aldrich
L-Ascorbic acid, BioUltra, ≥99.5% (RT)
Sigma-Aldrich
Magnesium chloride solution, BioUltra, for molecular biology, ~0.025 M in H2O
Sigma-Aldrich
HEPES buffer solution, 1 M in H2O
Sigma-Aldrich
L-Ascorbic acid, puriss. p.a., ≥99.0% (RT)
Sigma-Aldrich
L-Ascorbic acid, BioXtra, ≥99.0%, crystalline
Sigma-Aldrich
L-Ascorbic acid, reagent grade, crystalline
Sigma-Aldrich
L-Ascorbic acid, meets USP testing specifications
Sigma-Aldrich
L-Ascorbic acid, reagent grade
Sigma-Aldrich
L-Ascorbic acid, suitable for plant cell culture
Sigma-Aldrich
L-Ascorbic acid, suitable for cell culture, suitable for plant cell culture, ≥98%
Sigma-Aldrich
L-Ascorbic acid, powder, suitable for cell culture, γ-irradiated
Sigma-Aldrich
Magnesium chloride solution, BioUltra, for molecular biology, 2 M in H2O
Sigma-Aldrich
L-Ascorbic acid, 99%
Sigma-Aldrich
HEPES, BioUltra, for molecular biology, ≥99.5% (T)
Sigma-Aldrich
Magnesium chloride solution, BioUltra, for molecular biology, ~1 M in H2O
Sigma-Aldrich
HEPES, anhydrous, free-flowing, Redi-Dri, ≥99.5%
Sigma-Aldrich
Magnesium chloride solution, 0.1 M
SAFC
HEPES
Sigma-Aldrich
Potassium phosphate dibasic solution, 1.0 M
Sigma-Aldrich
Ethylenediaminetetraacetic acid, anhydrous, crystalline, BioReagent, suitable for cell culture