An Ultra-High Discrimination Y Chromosome Short Tandem Repeat Multiplex DNA Typing System

Abstract

In forensic casework, Y chromosome short tandem repeat markers (Y-STRs) are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12–17 loci are currently used in forensic casework (Promega's PowerPlex® Y and Applied Biosystems' AmpFlSTR® Yfiler®). Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used ‘core’ Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD) multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572) indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR® Yfiler® kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary genetics and genetic genealogy.

Y-STR diversity in the Himalayas

“…Ychromosome short tandem repeats (Y-STRs), on the other hand, mutate rapidly and are more suitable for reconstructing the phylogeny of relatively recent demographic events as well as for forensic casework and paternity testing [2,[4][5][6]. Recently, Y-STR data have been increasingly used to investigate the evolution, migration, and genetic diversity of modern human populations [2,[6][7][8][9][10][11].…”

The Applicability of Autosomal Short Tandem Repeats Genotyping for Minor Contributor DNA Profiling from Mixed Saliva Samples

“…Mixed sample resolution based on Y-STR analysis in male/female mixed samples is relatively straightforward but its applicability in direct personal identification is limited [7]. In our previous study based on Y-chromosome sequence identification and Y-STR profiling we showed that salivary samples gained from females could be a useful source of forensic evidence in specific cases of sexual assaults in which the victim (female) was constrained to kissing by the perpetrator (male) [10].…”

“…In such cases, Y-chromosomal short tandem repeats (Y-STR) profiling is of great help, because it is possible to successfully profile the male Y-STR haplotype that could be used for identification of the perpetrator [4,5]. However, Y-STR profiling has insufficient discrimination power and is usually not widely used for individual identification [6], although a recent study focused on ultrahigh discrimination multiplex DNA typing based on Y-STR profiling showed its applicability for personal identification [7]. Satisfactory resolution is typical for widely used autosomal STR (a-STR) profiling kits.…”

Y Chromosome STR Typing: A Distinguishing Tool for Exclusion in a Casework of Sexual Assault

“…It is because autosomal STRs allow the detection of minor components only if they account for more than 5% of the mixture, as the rule of thumb [7,8]. Sex-typing based on amelogenin is an integral part of most identifiler PCR multiplex kits widely used for gender determination and plays an important role in forensic casework and creating DNA database [9].…”