Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA

被引:92
作者
Korshunova, Yalia [1 ]
Maloney, Rebecca K. [1 ]
Lakey, Nathan [1 ]
Citek, Robert W. [1 ]
Bacher, Blaire [1 ]
Budiman, Arief [1 ]
Ordway, Jared M. [1 ]
McCombie, W. Richard [2 ]
Leon, Jorge [1 ]
Jeddeloh, Jeffrey A. [1 ,4 ]
McPherson, John D. [3 ]
机构
[1] Orion Genom LLC, St Louis, MO 63108 USA
[2] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11723 USA
[3] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA
[4] Roche NimbleGen, Madison, WI 53719 USA
关键词
D O I
10.1101/gr.6883307
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Cytosine-methylation changes are stable and thought to be among the earliest events in tUrnorigenesis. Theoretically, DNA carrying tumor-specifying methylation patterns escape the tumors and may be found circulating in the sera from cancer patients, thus providing the basis for development of noninvasive clinical tests for early cancer detection. Indeed, using methylation-specific PCR-based techniques, several groups reported the detection of tumor-associated methylated DNA in the sera from cancer patients with varying clinical success. However, by design, such analytical approaches allow assessment of the presence of molecules with only one rnethylation pattern, leaving the bigger Picture unexplored. The limited knowledge about circulating DNA methylation patterns hinders the efficient development of clinical methylation tests and testing platforms. Here, we report the results of a comprehensive methylation pattern analysis from breast cancer clinical tissues and sera obtained using massively parallel bisulphite pyrosequencing. The four loci studied were recently discovered by Our group, and demonstrated to be powerful epigenetic biomarkers of breast cancer. The detailed analysis of more than 700,000 DNA fragments derived from more than 50 individuals (cancer and cancer-free) revealed all unappreciated complexity of genomic cytosine-methylation patterns in both tissue derived and Circulating DNAs. Both tumor and cancer-free tissues (as well as sera) contained molecules with nearly every conceivable cytosine-methylation pattern at each locus. Tumor samples displayed more variation in methylation level than normal samples. Importantly, by establishing the rnethylation landscape within circulating DNA, this Study has better defined the development challenges facing DNA methylation-based cancer-detection tests.
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页码:19 / 29
页数:11
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