Tackling somatic DNA contamination in sperm epigenetic studies
IntroductionRecent interest in sperm epigenetics has stemmed from its implication in sperm DNA quality, sperm fertility, environmental toxicity, and transgenerational inheritance. Sperm epigenetic data may be significantly affected by somatic DNA contamination, resulting in misleading conclusions. H...
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Frontiers Media S.A.
2025-02-01
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| Series: | Frontiers in Reproductive Health |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/frph.2025.1506117/full |
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| author | Anamika Kumari Anamika Kumari Rajender Singh Rajender Singh |
| author_facet | Anamika Kumari Anamika Kumari Rajender Singh Rajender Singh |
| author_sort | Anamika Kumari |
| collection | DOAJ |
| description | IntroductionRecent interest in sperm epigenetics has stemmed from its implication in sperm DNA quality, sperm fertility, environmental toxicity, and transgenerational inheritance. Sperm epigenetic data may be significantly affected by somatic DNA contamination, resulting in misleading conclusions. However, detecting and dealing with somatic DNA contamination in semen samples can be a challenging task.MethodsIn the present study, we worked out a detailed and robust plan to deal with somatic cell DNA contamination in sperm epigenetic studies in order to draw error-free scientific conclusions. Apart from incorporating simple quality checks, such as microscopic examination and somatic cell lysis buffer (SCLB) treatment, we compared the Infinium Human Methylation 450K BeadChip data for sperm and blood samples to identify the CpG sites that were highly methylated in blood samples in comparison to sperm, but were unrelated to infertility.Results and discussionThe comparison of Infinium Human Methylation 450K BeadChip data for sperm and blood samples identified 9564 CpG sites that can be used as markers for analyzing somatic DNA contamination. We have put together a comprehensive plan including evaluation under a microscope, SCLB treatment, inclusion of CpG biomarkers for sample quality evaluation, and applying a 15% cut off at the time of data analysis to completely eliminate the influence of somatic DNA contamination in sperm epigenetic studies. We conclude that if this comprehensive plan is followed, the influence of somatic DNA contamination in sperm epigenetic studies can be completely eliminated. |
| format | Article |
| id | doaj-art-e6d3e63e29764146be027149ea98bce4 |
| institution | Kabale University |
| issn | 2673-3153 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Reproductive Health |
| spelling | doaj-art-e6d3e63e29764146be027149ea98bce42025-02-05T07:32:39ZengFrontiers Media S.A.Frontiers in Reproductive Health2673-31532025-02-01710.3389/frph.2025.15061171506117Tackling somatic DNA contamination in sperm epigenetic studiesAnamika Kumari0Anamika Kumari1Rajender Singh2Rajender Singh3Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaDivision of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, IndiaAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, IndiaIntroductionRecent interest in sperm epigenetics has stemmed from its implication in sperm DNA quality, sperm fertility, environmental toxicity, and transgenerational inheritance. Sperm epigenetic data may be significantly affected by somatic DNA contamination, resulting in misleading conclusions. However, detecting and dealing with somatic DNA contamination in semen samples can be a challenging task.MethodsIn the present study, we worked out a detailed and robust plan to deal with somatic cell DNA contamination in sperm epigenetic studies in order to draw error-free scientific conclusions. Apart from incorporating simple quality checks, such as microscopic examination and somatic cell lysis buffer (SCLB) treatment, we compared the Infinium Human Methylation 450K BeadChip data for sperm and blood samples to identify the CpG sites that were highly methylated in blood samples in comparison to sperm, but were unrelated to infertility.Results and discussionThe comparison of Infinium Human Methylation 450K BeadChip data for sperm and blood samples identified 9564 CpG sites that can be used as markers for analyzing somatic DNA contamination. We have put together a comprehensive plan including evaluation under a microscope, SCLB treatment, inclusion of CpG biomarkers for sample quality evaluation, and applying a 15% cut off at the time of data analysis to completely eliminate the influence of somatic DNA contamination in sperm epigenetic studies. We conclude that if this comprehensive plan is followed, the influence of somatic DNA contamination in sperm epigenetic studies can be completely eliminated.https://www.frontiersin.org/articles/10.3389/frph.2025.1506117/fullsperm DNADNA methylationsomatic cell contaminationsperm qualityepigenetics |
| spellingShingle | Anamika Kumari Anamika Kumari Rajender Singh Rajender Singh Tackling somatic DNA contamination in sperm epigenetic studies Frontiers in Reproductive Health sperm DNA DNA methylation somatic cell contamination sperm quality epigenetics |
| title | Tackling somatic DNA contamination in sperm epigenetic studies |
| title_full | Tackling somatic DNA contamination in sperm epigenetic studies |
| title_fullStr | Tackling somatic DNA contamination in sperm epigenetic studies |
| title_full_unstemmed | Tackling somatic DNA contamination in sperm epigenetic studies |
| title_short | Tackling somatic DNA contamination in sperm epigenetic studies |
| title_sort | tackling somatic dna contamination in sperm epigenetic studies |
| topic | sperm DNA DNA methylation somatic cell contamination sperm quality epigenetics |
| url | https://www.frontiersin.org/articles/10.3389/frph.2025.1506117/full |
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