Optimization and Developmental Validation of 38-plex InDel Panel for Ancestry Inference

Abstract

ObjectiveThe previously established 38-plex InDel system was optimized and its performance was validated according to the Scientific Working Group on DNA Analysis Method （SWGDAM） application guidelines. The ancestry inference accuracy of individuals from East Asian， European， African and mixed populations was verified.MethodsDNA standard sample 9947A was used as the template to establish the optimal amplification conditions by adjusting primer balance， Mg2+ final concentration and optimizing PCR thermal cycle parameters and amplification volume. The allelic dropout， nonspecific amplification and whether the origin of the inferred samples matched the known information were compared to evaluate the performance of this system.ResultsThe optimal dosage of this system was 0.125-2 ng DNA template. The results of InDel typing were accurate， the amplification equilibrium was good， and the species specificity was good. This system showed certain tolerance to DNA samples including the inhibitor such as hemoglobin （≤80 μmol/L）， indigo （≤40 mmol/L）， calcium ion （≤1.0 mmol/L）， and humic acid （≤90 ng/μL）. The system enabled the direct amplification of DNA from saliva and blood on filter paper， and the results of ethnic inference were accurate. The system successfully detected the mixed DNA sample from two individuals. The test results of the system for common biological materials in practical cases were accurate.ConclusionThe results of the 38-plex InDel system are accurate and reliable， and the performance of the system meets the requirement of the SWGDAM guidelines. This system can accurately differentiate the ancestry origins of individuals from African， European， East Asian， and Eurasian populations and can be implemented in forensic practice.

Keywords

• forensic genetics
• ancestry inference
• indel polymorphism
• multiplex amplification
• developmental validation