Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip
Abstract Infinium Methylation BeadChips are widely used to profile DNA cytosine modifications in large cohort studies for reasons of cost-effectiveness, accurate quantification, and user-friendly data analysis in characterizing these canonical epigenetic marks. In this work, we conducted a comprehen...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | Epigenetics Communications |
| Online Access: | https://doi.org/10.1186/s43682-023-00021-5 |
| _version_ | 1797453750965633024 |
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| author | Diljeet Kaur Sol Moe Lee David Goldberg Nathan J. Spix Toshinori Hinoue Hong-Tao Li Varun B. Dwaraka Ryan Smith Hui Shen Gangning Liang Nicole Renke Peter W. Laird Wanding Zhou |
| author_facet | Diljeet Kaur Sol Moe Lee David Goldberg Nathan J. Spix Toshinori Hinoue Hong-Tao Li Varun B. Dwaraka Ryan Smith Hui Shen Gangning Liang Nicole Renke Peter W. Laird Wanding Zhou |
| author_sort | Diljeet Kaur |
| collection | DOAJ |
| description | Abstract Infinium Methylation BeadChips are widely used to profile DNA cytosine modifications in large cohort studies for reasons of cost-effectiveness, accurate quantification, and user-friendly data analysis in characterizing these canonical epigenetic marks. In this work, we conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility. Using EPICv2, we were able to identify epigenome and sequence signatures in cell line models of DNMT and SETD2 loss and/or hypomorphism. Furthermore, we provided probe-wise evaluation and annotation to facilitate the use of new features on this array for studying the interplay between somatic mutations and epigenetic landscape in cancer genomics. In conclusion, EPICv2 provides researchers with a valuable tool for studying epigenetic modifications and their role in development and disease. |
| first_indexed | 2024-03-09T15:27:23Z |
| format | Article |
| id | doaj.art-91917cef90fd4805b040cfcf02235f3b |
| institution | Directory Open Access Journal |
| issn | 2730-7034 |
| language | English |
| last_indexed | 2024-03-09T15:27:23Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Epigenetics Communications |
| spelling | doaj.art-91917cef90fd4805b040cfcf02235f3b2023-11-26T12:26:46ZengBMCEpigenetics Communications2730-70342023-09-013111510.1186/s43682-023-00021-5Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChipDiljeet Kaur0Sol Moe Lee1David Goldberg2Nathan J. Spix3Toshinori Hinoue4Hong-Tao Li5Varun B. Dwaraka6Ryan Smith7Hui Shen8Gangning Liang9Nicole Renke10Peter W. Laird11Wanding Zhou12Center for Computational and Genomic Medicine, The Children’s Hospital of PhiladelphiaCenter for Computational and Genomic Medicine, The Children’s Hospital of PhiladelphiaCenter for Computational and Genomic Medicine, The Children’s Hospital of PhiladelphiaDepartment of Epigenetics, Van Andel InstituteDepartment of Epigenetics, Van Andel InstituteDepartment of Urology, University of Southern California, Norris Comprehensive Cancer CenterTruDiagnostic IncTruDiagnostic IncDepartment of Epigenetics, Van Andel InstituteDepartment of Urology, University of Southern California, Norris Comprehensive Cancer CenterProduct Management Department, Illumina, Inc.Department of Epigenetics, Van Andel InstituteCenter for Computational and Genomic Medicine, The Children’s Hospital of PhiladelphiaAbstract Infinium Methylation BeadChips are widely used to profile DNA cytosine modifications in large cohort studies for reasons of cost-effectiveness, accurate quantification, and user-friendly data analysis in characterizing these canonical epigenetic marks. In this work, we conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility. Using EPICv2, we were able to identify epigenome and sequence signatures in cell line models of DNMT and SETD2 loss and/or hypomorphism. Furthermore, we provided probe-wise evaluation and annotation to facilitate the use of new features on this array for studying the interplay between somatic mutations and epigenetic landscape in cancer genomics. In conclusion, EPICv2 provides researchers with a valuable tool for studying epigenetic modifications and their role in development and disease.https://doi.org/10.1186/s43682-023-00021-5 |
| spellingShingle | Diljeet Kaur Sol Moe Lee David Goldberg Nathan J. Spix Toshinori Hinoue Hong-Tao Li Varun B. Dwaraka Ryan Smith Hui Shen Gangning Liang Nicole Renke Peter W. Laird Wanding Zhou Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip Epigenetics Communications |
| title | Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip |
| title_full | Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip |
| title_fullStr | Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip |
| title_full_unstemmed | Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip |
| title_short | Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip |
| title_sort | comprehensive evaluation of the infinium human methylationepic v2 beadchip |
| url | https://doi.org/10.1186/s43682-023-00021-5 |
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