Adventitious Match of AmpFlSTR® Yfiler® Profiles Between Individuals from Two Ethnic Groups

Mahamud Hasan1, Tania Hossain1, Ashish Kumar Majumder1, Abu Sufian1, Pilu Momtaz1 and Sharif Akhteruzzaman2
1National Forensic DNA Profiling Laboratory, Dhaka Medical College, Dhaka-1000, Bangladesh 2Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh
Publication Date: 2015

Abstract

In this study we report an adventitious match between Bengali and Santal individuals from Bangladesh for the Yfiler® loci in spite of their different paternal lineages and ethnic affiliations. Further typing of these two individuals using the PowerPlex® Y23 System yielded different haplotypes consisting of three mismatches out of six additional loci included in the kit. Supplementary analysis using the AmpFlSTR® Identifiler® PCR Amplification Kit (Life Technologies, USA), PowerPlex® Fusion System (Promega Corporation, USA) and Investigator® DIPplex Kit (Qiagen, Germany) confirmed their individual identities as the two men yielded different profiles. Thus, the 17 Y-STR loci included in the Yfiler® Kit may be inadequate in extraordinary situations despite overwhelming statistical odds. The importance of increasing the number of loci in a Y-STR profile panel therefore cannot be neglected solely based on statistical grounds.

Introduction

For the past two and a half decades, short tandem repeats (STRs) have been the mainstay in most forensic labs in the world (1) (2) . Due to their high abundance in the human genome, low mutation rate, smaller amplicon size and multiplexing capability, these loci have become very useful markers in personal identification, parentage testing and population genetics studies (3) (4) (5) . In routine casework, autosomal STRs are usually used for paternity and identity testing along with a gender marker. However, in complex kinship situations, Y-chromosome and X-chromosome-specific STRs also provide vital information (6) (7) . The human identity testing community has developed different sets of core STR loci for autosomal, Y-chromosome and X-chromosome analyses; these loci are available as commercial kits from different sources (6) (8) (9) (10) .

As for Y-STRs, two commercial kits, the Yfiler® PCR Amplification Kit (Life Technologies, USA) and PowerPlex® Y System (Promega Corporation, USA) predominate the market. The PowerPlex® Y System shares all of its 12 loci with the Yfiler® Kit. In recent years, there has been an increase in the use of Y-STRs by forensic laboratories, especially in sexual assault cases, to detect male DNA in male-female mixtures and in deficiency paternity cases involving a male offspring. In addition, absence of sperm in azoospermia and amelogenin Y-deficient males can be detected by Y-STR profiling. Because of the unique paternal inheritance, Y-STR analysis is now widely used as an important tool for evolution and migration studies (11) .

The continued technological advances in the area of population genetics have led to the necessity of establishing lineage-specific DNA databases. Today several Y-chromosome-specific databases are available online (12) . Considering this growing need, Promega launched a new Y-STR kit containing all 17 Yfiler® STR loci plus six additional loci. This study emphasizes the need for using more Y-STR loci in relationship testing by describing an adventitious match for all 17 Yfiler® loci between two unrelated individuals.

Materials and Methods

Samples and DNA Extraction

Peripheral blood samples were collected from the donors following procedures that are in accordance with Helsinki declaration of 1964, revised in 1983 (13) . Genomic DNA was extracted from blood samples using the Chelex®-100 method described by Walsh et al. (14) . Extracted DNA was quantified using the NanoDrop®-100 spectrophotometer (NanoDrop Technologies Inc., USA).

PCR Amplification and Genotyping

For PCR amplification 1–2 ng of genomic DNA was used following manufacturer’s recommendation in a Veriti® thermal cycler (Life Technologies, USA). Samples from both individuals were amplified using the Yfiler®, PowerPlex® Y23, Identifiler®, PowerPlex® Fusion and Investigator® DIPplex Kits. Amplified products were separated by capillary electrophoresis on an Applied Biosystems® 3500 Genetic Analyzer (Life Technologies, USA) using POP-4® polymer and Data Collection software version 1.0. Peak sizing and genotyping assignments were done using GeneMapper® ID-X software version 1.2.

Results and Discussion

Since the first recommendation of a minimal haplotype set of nine Y-STR loci, the number of Y-STR markers has grown considerably for routine forensic and population genetics studies. Y-STRs are usually used as a tool in forensic cases for male sex identification, paternity tests involving a male offspring, kinship analysis and detection of male DNA in male-female mixtures. However, despite low mutation rates of commonly used Y-STRs, low discrimination power compared to autosomal STRs and difficulty in differentiating between closely related males, the use of Y-STR markers has grown considerably over the past few years (15) (16) . Commercial manufacturers, therefore, subsequently came up with several partially overlapping Y-STR multiplexes such as 12 loci in the PowerPlex® Y System, 17 loci in the Yfiler® Kit, 23 loci in the PowerPlex® Y23 System and 25 loci in the Yfiler® Plus Kit.

In this article we report an unexpected match for all Yfiler® loci between two individuals who are from two different known ethnic backgrounds. According to our laboratory records, one of them was from the mainstream Bengali population and the other from the Santal ethnic group who live in different districts of Rajshahi division with the highest presence in Dinajpur district. Both of them donated blood samples as references in the disaster victim identification effort of the Rana Plaza building collapse on April 24, 2013. This adventitious match was detected by our CODIS software (FBI, United States) while comparing the DNA profiles between the unknown victims and known relatives.

In spite of being ethnically different, both samples gave a complete match for all Yfiler® loci tested (Table 1). In order to rule out any sampling error, DNA was re-extracted from the samples and amplified, giving the same results. The samples were therefore analyzed using the PowerPlex® Y23 System, which shares all 17 Y-STR loci present in Yfiler® Kit and includes six additional loci (DYS576, DYS481, DYS549, DYS533, DYS570 and DYS643). The PowerPlex® Y23 results are shown in Figures 1 and 2. The analysis yielded the same haplotypes for all 17 Yfiler® loci and three mismatches out of six new loci introduced in the kit (Table 1), providing the first clue that these samples were different. Further typing of these samples with the Identifiler®, PowerPlex® Fusion and DIPplex Kits clearly showed that the samples indeed originated from two different individuals (Table 1).

Akhteruzzaman_Table1Table 1. Y-chromosome, autosomal-STR and insertion/deletion profiles of the Bengali and Santal individuals under study.
Akhteruzzaman_Figure1Figure 1. PowerPlex® Y23 profile of the mainstream Bengali individual sample.
Akhteruzzaman_Figure2Figure 2. PowerPlex® Y23 profile of the mainstream Santal individual sample.

Conclusion

This report demonstrates that the 17 Yfiler® loci may not be adequate to differentiate individuals from different paternal lineages and emphasizes the importance of increasing the number of loci in a Y-STR profile panel for routine laboratory workflow in forensic labs.

Article References

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How to Cite This Article

Scientific Style and Format, 7th edition, 2006

Hasan, M. et al. Adventitious Match of AmpFlSTR® Yfiler® Profiles Between Individuals from Two Ethnic Groups. [Internet] 2015. [cited: year, month, date]. Available from: https://www.promega.com/resources/profiles-in-dna/2015/adventitious-match-of-ampflstr-yfiler-profiles-between-individuals-from-two-ethnic-groups/

American Medical Association, Manual of Style, 10th edition, 2007

Hasan, M. et al. Adventitious Match of AmpFlSTR® Yfiler® Profiles Between Individuals from Two Ethnic Groups. Promega Corporation Web site. https://www.promega.com/resources/profiles-in-dna/2015/adventitious-match-of-ampflstr-yfiler-profiles-between-individuals-from-two-ethnic-groups/ Updated 2015. Accessed Month Day, Year.

Contribution of an article to Profiles in DNA does not constitute an endorsement of Promega products.

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Applied Biosystems, AmpFlSTR, GeneMapper, Identifiler, Veriti and Yfiler are registered trademarks of Applied Biosystems. Chelex is a registered trademark of Bio-Rad Laboratories, Inc. Investigator is a registered trademark of Qiagen GmbH Corp. NanoDrop is a registered trademark of Thermo Fisher Scientific. POP-4 is a registered trademark of Life Technologies Corporation.