Amelogenin-Based Sex Identification as a Strategy to Control the Identity of DNA Samples in Genetic Association Studies

Abstract

Misassignment between DNA samples and clinical or epidemiological data may compromise the results of genetic association studies. Genotyping in replicates or controlling for Hardy–Weinberg equilibrium cannot identify misassignments caused by sample mix-ups. DNA-based sex identification (sex typing) is currently the best strategy to identify mix-ups. Here we review the available methods and present validated protocols for sex typing. The protocols are based on single-nucleotide differences between the human amelogenin genes, AMELX and AMELY, and are optimized for real-time PCR (TaqMan^®), primer-extension (SNaPshot™) and PCR-RFLP genotyping platforms. In addition, we review the limitations of the sex-typing strategy, including a limited ability to identify single sample mix-ups, the dependence of the power of this approach on the sex distribution in the study population, and rare genetic conditions. Alternative strategies for mix-up identification and possible consequences of mix-up identification are also discussed.

KEYWORDS::

• amelogenin
• AMELX
• AMELY
• association studies
• PCR-RFLP
• quality control
• sample mix-up
• sample swap
• sex typing
• SNaPshot™
• TaqMan^®

Acknowledgements

We acknowledge Karoline Jobst for her excellent technical support.

Financial & competing interests disclosure

This project was financially supported by a DFG GRK1034 grant to Mladen Tzvetkov. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This project was financially supported by a DFG GRK1034 grant to Mladen Tzvetkov. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.