Prevalence and characterisation of size and sequence-based microvariant alleles at nine autosomal STR markers in the Central Indian population

Abstract

Background

Though microvariant alleles are widely reported in global populations, they are not well characterised to date.

Aim

To study the prevalence and characterisation of size and sequence-based microvariant alleles

Subjects and methods

Next Generation Sequencing (NGS) was used to sequence microvariant alleles at nine autosomal STR markers in 138 samples.

Results

After sequencing 31 STR markers using Precision ID GlobalFilerTM NGS STR panel v2, only nine markers, i.e. D12S391, D19S433, D1S1656, D21S11, D2S441, D7S820, FGA, Penta D, and TH01 showed the prevalence of microvariant alleles. Occurrence of microvariant alleles was positively correlated with Total Possible Alleles (p < 0.005), Power of Discrimination (p < 0.01), Polymorphic Information Content (p < 0.01), and Power of Exclusion (p < 0.05) and negatively correlated with the Matching Probability (p < 0.01). The average allele frequency of the microvariant alleles was found to be significantly less than the allele frequency value of the complete alleles (p = 0.88). Further, sequencing of these microvariant alleles reveals the deletion of nucleotides from the start, end, or middle of the repeat unit is responsible for the generation of a microvariant allele.

Conclusions

Prevalence of microvariant alleles is rare in nature and is limited to 9 STR loci out of 31 STR loci tested in the central Indian population. The occurrence of microvariant alleles in a locus increases its forensic and paternity application.

Keywords:

• Microvariant alleles
• STRs
• sequencing
• forensic and paternity parameters

Acknowledgements

The authors are highly acknowledged to Director, State Forensic Science Laboratory, Sagar, M. P., India, and Joint Director, Regional Forensic Science Laboratory, Bhopal, M. P., India for providing infrastructure to carry out the research work. Our sincere thanks to Dr. Atima Agrawal, Dr. Neeraj Chauhan, Dr. Sanjib Dey, and the entire technical team of Thermo Scientific for their constant technical support during the research work.

Author contributions

HRD conceptualised the study. HRD and KV carried out the experiments and analysis. HRD, AS and SD prepared the manuscript. All authors reviewed and approved the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

Please contact the author for data requests