Whole-genome bisulfite sequencing with improved accuracy and cost

Masako Suzuki, Will Liao, Frank Wos, Andrew D. Johnston, Justin DeGrazia, Jennifer Ishii, Toby Bloom, Michael C. Zody, Soren Germer, John M. Greally

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopu-lations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples. We have optimized a new transposase-based library preparation assay for the Illumina HiSeq X platform suitable for limited amounts of DNA and providing a major cost reduction for WGBS. By incorporating methylated cytosines during fragment end repair, we reveal an end-repair artifact affecting 1%–2% of reads that we can remove analytically. We show that the use of a high (G + C) content spike-in performs better than PhiX in terms of bisulfite sequencing quality. As expected, the loci with transposase-accessible chromatin are DNA hypomethylated and enriched in flanking regions by post-translational modifications of histones usually associated with positive effects on gene expression. Using these transposase-accessible loci to represent the cis-regulatory loci in the genome, we compared the representation of these loci between WGBS and other genome-wide DNA methylation assays, showing WGBS to outperform substantially all of the alternatives. We conclude that it is now technologically and financially feasible to perform WGBS in larger numbers of samples with greater accuracy than previously possible.

Original languageEnglish (US)
Pages (from-to)1364-1371
Number of pages8
JournalGenome Research
Volume28
Issue number9
DOIs
StatePublished - Sep 1 2018

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Genome
Costs and Cost Analysis
DNA Methylation
Transposases
Chromatin
hydrogen sulfite
Cytosine
DNA
Base Composition
Post Translational Protein Processing
Histones
Artifacts
Libraries
Alleles
Gene Expression

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Whole-genome bisulfite sequencing with improved accuracy and cost. / Suzuki, Masako; Liao, Will; Wos, Frank; Johnston, Andrew D.; DeGrazia, Justin; Ishii, Jennifer; Bloom, Toby; Zody, Michael C.; Germer, Soren; Greally, John M.

In: Genome Research, Vol. 28, No. 9, 01.09.2018, p. 1364-1371.

Research output: Contribution to journalArticle

Suzuki, M, Liao, W, Wos, F, Johnston, AD, DeGrazia, J, Ishii, J, Bloom, T, Zody, MC, Germer, S & Greally, JM 2018, 'Whole-genome bisulfite sequencing with improved accuracy and cost', Genome Research, vol. 28, no. 9, pp. 1364-1371. https://doi.org/10.1101/gr.232587.117
Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J et al. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Research. 2018 Sep 1;28(9):1364-1371. https://doi.org/10.1101/gr.232587.117
Suzuki, Masako ; Liao, Will ; Wos, Frank ; Johnston, Andrew D. ; DeGrazia, Justin ; Ishii, Jennifer ; Bloom, Toby ; Zody, Michael C. ; Germer, Soren ; Greally, John M. / Whole-genome bisulfite sequencing with improved accuracy and cost. In: Genome Research. 2018 ; Vol. 28, No. 9. pp. 1364-1371.
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