Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses

Shijie C Zheng^{1

2}, Stephan Beck³, Andrew E Jaffe^{4

5}, Devin C Koestler⁶, Kasper D Hansen^{7

8

4}, Andres E Houseman⁹, Rafael A Irizarry^{10

11}, Andrew E Teschendorff^{1

12

13}

Affiliations

¹ CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
² University of Chinese Academy of Sciences, Beijing, China.
³ Medical Genomics, UCL Cancer Institute, University College London, London, UK.
⁴ Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
⁵ Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA.
⁶ Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA.
⁷ Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
⁸ McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
⁹ School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, USA.
¹⁰ Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
¹¹ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
¹² Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
¹³ Department of Women's Cancer, University College London, London, UK.

PMID: 28245219
PMCID: PMC6659733
DOI: 10.1038/nmeth.4187

Comment

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses

Shijie C Zheng et al. Nat Methods. 2017.

. 2017 Feb 28;14(3):216-217.

doi: 10.1038/nmeth.4187.

Authors

Shijie C Zheng^{1

2}, Stephan Beck³, Andrew E Jaffe^{4

5}, Devin C Koestler⁶, Kasper D Hansen^{7

8

4}, Andres E Houseman⁹, Rafael A Irizarry^{10

11}, Andrew E Teschendorff^{1

12

13}

Affiliations

¹ CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
² University of Chinese Academy of Sciences, Beijing, China.
³ Medical Genomics, UCL Cancer Institute, University College London, London, UK.
⁴ Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
⁵ Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA.
⁶ Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA.
⁷ Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
⁸ McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
⁹ School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, USA.
¹⁰ Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
¹¹ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
¹² Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
¹³ Department of Women's Cancer, University College London, London, UK.

PMID: 28245219
PMCID: PMC6659733
DOI: 10.1038/nmeth.4187

No abstract available

PubMed Disclaimer

Comment in

Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation.
Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E. Rahmani E, et al. Nat Methods. 2017 Feb 28;14(3):218-219. doi: 10.1038/nmeth.4190. Nat Methods. 2017. PMID: 28245214 Free PMC article. No abstract available.
Editor's note on Zheng et al. and Rahmani et al.
[No authors listed] [No authors listed] Nat Methods. 2017 Feb 28;14(3):219. doi: 10.1038/nmeth.4208. Nat Methods. 2017. PMID: 28245216 No abstract available.

Comment on

Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.
Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E. Rahmani E, et al. Nat Methods. 2016 May;13(5):443-5. doi: 10.1038/nmeth.3809. Epub 2016 Mar 28. Nat Methods. 2016. PMID: 27018579 Free PMC article.

References

1. Jaffe AE & Irizarry RA Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome biology 15, R31 (2014). - PMC - PubMed
1. Houseman EA et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC bioinformatics 13, 86 (2012). - PMC - PubMed
1. Houseman EA, Molitor J & Marsit CJ Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics 30, 1431–1439 (2014). - PMC - PubMed
1. Leek JT & Storey JD Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS genetics 3, 1724–1735 (2007). - PMC - PubMed
1. Zou J, Lippert C, Heckerman D, Aryee M & Listgarten J Epigenome-wide association studies without the need for cell-type composition. Nature methods 11, 309–311 (2014). - PubMed

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Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses

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Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses

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