The BisPCR 2 method for targeted bisulfite sequencing

Epigenetics & Chromatin

Klaus H Kaestner¹  Karyn L Sheaffer¹  John E Le Lay¹  Vasumathi Kameswaran¹  Diana L Bernstein¹ 

[1] Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia 19104, PA, USA

关键词: Next-generation sequencing;    DNA methylation;    Targeted bisulfite sequencing;   

Others  :  1223307
DOI  :  10.1186/s13072-015-0020-x

 received in 2015-06-16, accepted in 2015-07-23,  发布年份 2015

【 摘 要 】

Background

DNA methylation has emerged as an important regulator of development and disease, necessitating the design of more efficient and cost-effective methods for detecting and quantifying this epigenetic modification. Next-generation sequencing (NGS) techniques offer single base resolution of CpG methylation levels with high statistical significance, but are also high cost if performed genome-wide. Here, we describe a simplified targeted bisulfite sequencing approach in which DNA sequencing libraries are prepared following sodium bisulfite conversion and two rounds of PCR for target enrichment and sample barcoding, termed BisPCR ² .

Results

We have applied the BisPCR ²technique to validate differential methylation at several type 2 diabetes risk loci identified in genome-wide studies of human islets. We confirmed some previous findings while not others, in addition to identifying novel differentially methylated CpGs at these genes of interest, due to the much higher depth of sequencing coverage in BisPCR ²compared to prior array-based approaches.

Conclusion

This study presents a robust, efficient, and cost-effective technique for targeted bisulfite NGS, and illustrates its utility by reanalysis of prior findings from genome-wide studies.

【 授权许可】

   
2015 Bernstein et al.

【 图 表 】

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