# Tackling somatic DNA contamination in sperm epigenetic studies

## TL;DR

This study presents a comprehensive method to eliminate somatic DNA contamination in sperm epigenetic research, ensuring accurate and reliable results.

## Contribution

A detailed plan combining quality checks, CpG biomarkers, and data analysis cutoffs to address somatic DNA contamination in sperm epigenetics.

## Key findings

- 9564 CpG sites were identified as markers for somatic DNA contamination in sperm samples.
- A 15% cutoff during data analysis effectively eliminates contamination influence.
- Combining microscopic evaluation and SCLB treatment improves sample quality assessment.

## Abstract

Recent 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.

In 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.

The 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.