Y-chromosomal loci have proven useful in forensic investigations where low levels of male DNA are present in a high female DNA background, typically sexual assault cases. The Y-STR loci can also be used in relationship testing cases (e.g., missing person identification, familial searching, etc.) to exclude or confirm the relationship. Moreover, due to the lack of recombination, Y-STR loci can provide information on the paternal biogeographic ancestry origins of a sample, which may provide valuable investigative information in many cases. Many studies indicate that the current commercial Y-STR kits deliver highly accurate inferences about which major population a sample may be belong to.
A study on US Y-STR database based on the Yfiler PCR amplification kit has shown that there is little Y-STR haplotype overlap between the major US populations (i.e., African American, Asian, Caucasian, Native American and Hispanic). Table 1  shows that only a small percentage of haplotypes are shared between US populations, indicating that we can infer the correct paternal biogeographic ancestry with an average confidence of ~99% using the 17-locus Yfiler kit. Inferences may be less accurate in small and/or highly-mixed populations (e.g., the accuracy of inference for Native American may be relatively low due to the sample size). Besides, because of cultural influences in North America in recent centuries, the Native American, African American, Caucasian, and Hispanic populations are more closely admixed with each other than they are admixed with the Indian and Asian populations.
Table 1. Number of shared haplotypes and percentages in parentheses between populations with Yfiler.
Increasing the number of markers in a Y haplotype theoretically increases the Power of Discrimination (PD) for the haplotype. Increasing the PD of a Y haplotype provides higher accuracy when inferring biogeographic ancestry. The population data in the developmental validation study of the Yfiler Plus PCR Amplification kit showed that, with 27-loci Yfiler Plus, biogeographic ancestry was inferred with an average of ~99.9% confidence, which 10 times more accurate than that of Yfiler. Yfiler Plus kit is the most informative Y-STR kit among the kits approved by FBI NDIS; therefore, Yfiler Plus should deliver the highest accuracy for biogeographic ancestry inference, compared with other Y-STR kits on the market.
Table 2. Number of shared haplotypes and percentages in parentheses between populations with Yfiler Plus.
The US Y-STR database and YHRD are two publicly accessible Y-STR databases, which allow a user to upload a Y-STR profile, search the profile against the database, and obtain match results for multiple populations. The following figure shows an example of US Y-STR database search results, in which all 20 matches were observed in the Asian population. These results provide strong evidence that the source of the sample is an Asian individual.
Users should interpret search results with caution. Matches and haplotype frequencies depend on database characteristics, such as database size, sample sizes of targeted populations, and whether samples in the database are truly representative of the targeted populations. Nevertheless, Y-STR databases are useful investigative tools for the forensic community.
In summary, Y-STR typing is a quick and easy way to infer the paternal biogeographic ancestry with high accuracy. An average forensic lab is able to implement it with minimum investment and training.
Unfortunately, Y-STR can only infer the paternal ancestors. For a more comprehensive estimate of the biogeographic ancestry admixture ratio of a sample (i.e., to answer the question “what are the chances a sample may belong to these different populations”), additional markers may need to be considered. To assess biogeographic ancestry using autosomal markers, the best tool would be the Applied Biosystems™ Precision ID Ancestry Panel (used with Converge software). To assess maternal lineage, mitochondrial DNA can be sequenced using the Applied Biosystems Precision ID mtDNA Whole Genome Panel.
- Ge J, Budowle B, Planz JV, Eisenberg AJ, Ballantyne J, Chakraborty R. US forensic Y-chromosome short tandem repeats database. Legal Medicine. 2010 Nov 1;12(6):289-95.
- Gopinath S, Zhong C, Nguyen V, Ge J, Lagacé RE, Short ML, Mulero JJ. Developmental validation of the Yfiler® Plus PCR Amplification Kit: An enhanced Y-STR multiplex for casework and database applications. Forensic Science International: Genetics. 2016 Sep 1;24:164-75.
For Research, Forensic, or Paternity Use Only. Not for use in diagnostic procedures.