Elsevier

Legal Medicine

Volume 23, November 2016, Pages 17-20
Legal Medicine

Short Communication
Forensic genetic study of 29 Y-STRs in Korean population

https://doi.org/10.1016/j.legalmed.2016.09.001Get rights and content

Highlights

  • •

    PPY23 and YPlus showed similar sensitivity, but PPY23 showed higher tolerance to humic acid than YPlus.

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    The detection rate of unique minor alleles called from male/male mixtures was higher for PPY23 than for YPlus.

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    Comparing the newly added loci, the mean values of gene diversity for PPY23 and YPlus were 0.6715 and 0.8158, respectively.

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    The discrimination capacity in the 306 unrelated South Korean males for PPY23 was 0.9837, and that for YPlus was 0.9935.

Abstract

In this study, we compared two recently released commercial Y-chromosomal short tandem repeat (Y-STR) kits: the PowerPlex Y23 System (PPY23) and Yfiler® Plus PCR amplification kit (YPlus). We performed validation studies, including sensitivity, tolerance to PCR inhibitors, and mixture analysis, and a population genetics study using 306 unrelated South Korean males. PPY23 and YPlus showed similar sensitivity, but PPY23 showed higher tolerance to humic acid than YPlus. Furthermore, the detection rate of unique minor alleles called from male/male mixtures was higher for PPY23 than for YPlus. Comparing the newly added loci, the mean values of gene diversity for PPY23 and YPlus were 0.6715 and 0.8158, respectively. The discrimination capacity in the 306 unrelated South Korean males for PPY23 was 0.9837, and that for YPlus was 0.9935. These results will inform the selection of suitable Y-STR kits based on the purpose of forensic DNA analysis.

Introduction

Y-chromosomal short tandem repeat (Y-STR) analysis has been a very useful tool both in paternity lineage studies and in forensic genetic analyses, particularly for solving sexual assault cases [1], [2]. As the importance of Y-STR analysis in forensics has increased, the number of Y-STR markers including rapidly mutating (RM) Y-STRs in commercial kits has grown considerably to overcome the low discrimination capacity of Y-STR analysis [3], [4], [5], [6], [7].

The PowerPlex Y23 System (PPY23, Promega, Madison, WI) and the Yfiler® Plus PCR amplification kit (YPlus, Thermo Fisher Scientific, Waltham, MA) were released in 2012 and 2014, respectively. Both PPY23 and YPlus include the 17 Y-STR markers (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, DYS437, DYS438, DYS448, and GATA H4) from the AmpF/STR® Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA, released in 2004) and new loci (PPY23: DYS549 and DYS643; YPlus: DYS449, DYS460, DYS518, DYS627, and DYF387S1) in total 23 and 27 markers, respectively [8], [9]. To facilitate the forensic application of new Y-STR kits, determine which kit is suitable for forensic casework, and provide an overview of population genetic characteristics of Korean males, we carried out internal validation and comparison of the PPY23 and YPlus kits herein. The sensitivity, tolerance to inhibitors, and mixture studies were performed and compared using control DNA. Population genetic parameters were calculated by analyzing the DNA from 306 South Korean Males.

Section snippets

DNA samples

2800 M control DNA (10 ng/μL, Promega, Madison, WI), Control DNA 007 (2 ng/μL, Thermo Fisher Scientific, Waltham, MA), and Human Female Genomic DNA (208 μg/mL, Promega, Madison, WI) were used for validation of PPY23 and YPlus kits. Twofold serial dilutions of 2800 M DNA were made (1, 0.5, 0.25, 0.125, 0.0625, and 0.0313 ng/μL). For the tolerance study, 1 ng 2800 M DNA was added to 500 μg/mL, 250 μg/mL, or 125 μg/mL humic acid or tannic acid (Sigma-Aldrich, St. Louis, MO) respectively [10].

For the mixture

Sensitivity

PPY23 and YPlus exhibited 100% detection rates for 0.0625 ng and 0.125 ng DNA, respectively (Supplementary Fig. 1a). A significant sensitivity difference between the two kits was not found, and the average numbers of alleles called at 0.3125 ng DNA were similar (PPY23: 22; YPlus: 22.3). However, the average peak heights for the PPY23 kit were higher than those of YPlus (Supplementary Fig. 1b).

Tolerance to inhibitors

DNA samples derived from a crime scene might contain PCR inhibitors such as tannic acid and humic acid [10]

Conclusion

We carried out comparative studies of the commercial Y-STR kits PPY23 and YPlus. For forensic application in our institute, laboratory validation and population studies are essential processes before introduction of a new kit. No significant differences were detected between the kits in the sensitivity and mixture studies. However, the tolerance study revealed that PPY23 is more stable in humic acid. Therefore, the PPY23 will be a more suitable kit for analysis of forensic samples that can be

Acknowledgements

This work was supported by the Korean government and by grant (NFS2016DNA03) from the Forensic Research program of the National Forensic Service (NFS). The biospecimens used in this study were provided by the Korea Centers for Disease Control & Prevention, Republic of Korea. The authors would like to thank all the DNA donors that made this study possible.

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