The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
Open accessAbstract
We report a new class of artifacts in DNA methylation measurements from Illumina HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed hybridization to target DNA, often due to germline or somatic deletions and manifest as incorrectly reported intermediate methylation. The artifacts often survive existing preprocessing pipelines, masquerade as epigenetic alterations and can confound discoveries in epigenome-wide association studies and studies of methylation-quantitative trait loci. We implement a solution, P-value with out-of-band (OOB) array hybridization (pOOBAH), in the R package SeSAMe. Our method effectively masks deleted and hyperpolymorphic regions, reducing or eliminating spurious reports of epigenetic silencing at oft-deleted tumor suppressor genes such as CDKN2A and RB1 in cases with somatic deletions. Furthermore, our method substantially decreases technical variation whilst retaining biological variation, both within and across HM450 and EPIC platform measurements. SeSAMe provides a light-weight, modular DNA methylation data analysis suite, with a performant implementation suitable for efficient analysis of thousands of samples.
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The Cancer Genome Atlas Research Network (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1301689 · Cited by 5,078
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The landscape of somatic copy-number alteration across human cancers
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Multi-omics approaches to disease
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MethodSelf-citationTackling the widespread and critical impact of batch effects in high-throughput data
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Self-citationUniversal DNA methylation age across mammalian tissues
Lu, A. T., Fei, Z., Haghani, A., Robeck, T. R., Zoller, J. A., Li, C. Z., Lowe, R., Yan, Q., Zhang, J., Vu, H., et al. (2023) · Nature Aging · doi:10.1038/s43587-023-00462-6 · Cited by 386
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Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer
Carrot-Zhang, J., Chambwe, N., Damrauer, J. S., Knijnenburg, T. A., Robertson, A. G., Yau, C., Zhou, W., Berger, A. C., Huang, K.-L., Newberg, J. Y., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.04.012 · Cited by 331
Self-citationMeningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities
Choudhury, A., Magill, S. T., Eaton, C. D., Prager, B. C., Chen, W. C., Cady, M. A., Seo, K., Lucas, C.-H. G., Casey-Clyde, T. J., Vasudevan, H. N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01061-8 · Cited by 293
Metadata
- Authors
- Zhou, W., Triche, T. J., Laird, P. W., & Shen, H.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-07-31
- Volume
- 46
- Issue
- 20
- Pages
- e123-e123
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2887474968
- Cited by
- 521
- References
- 62
- FWCI
- 6.36
- Type
- journal article
- Language
- en
- Open access
- gold
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- Zhou, W., Triche, T. J., Laird, P. W., & Shen, H. (2018). SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Research. https://doi.org/10.1093/nar/gky691
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