Development and Validation of the AmpFℓSTR^® Yfiler™ PCR Amplification Kit: A Male Specific, Single Amplification 17 Y‐STR Multiplex System^*

Abstract

In the past 5 years, there has been a substantial increase in the use of Y-short tandem repeat loci (Y-STRs) in forensic laboratories, especially in cases where typing autosomal STRs has met with limited success. The AmpFlSTR Yfiler PCR amplification kit simultaneously amplifies 17 Y-STR loci including the loci in the "European minimal haplotype" (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393), the Scientific Working Group on DNA Analysis Methods (SWGDAM) recommended Y-STR loci (DYS438 and DYS439), and the highly polymorphic loci DYS437, DYS448, DYS456, DYS458, Y GATA H4, and DYS635 (formerly known as Y GATA C4). The Yfiler kit was validated according to the FBI/National Standards and SWGDAM guidelines. Our results showed that full profiles are attainable with low levels of male DNA (below 125 pg) and that under optimized conditions, no detectable cross-reactive products were obtained on human female DNA, bacteria, and commonly encountered animal species. Additionally, we demonstrated the ability to detect male specific profiles in admixed male and female blood samples at a ratio of 1:1000.

Analysis of mutations in father–son pairs with 17 Y-STR loci

“…Paternity was confirmed by the paternity index value of 5.2 Â 10 3 for 45A and 2.6 Â 10 3 for 52A in the Asian population when the mothers' alleles are included. Thus far, in the four other published studies describing mutation rates with the 17 Yfiler loci [5][6][7][8] there have been no reports of a double mutation or a two repeat loss within a single father/son sample pair. However, previous studies involving fewer Y-STR loci have identified more than one mutation in a father/son pair.…”

“…The paternity index (PI) value for sample pair 16B is 3.8 Â 10 7 in the African American population and for sample pair 101A is 5.5 Â 10 4 in the Asian population using the 15 autosomal Identifiler STR loci genotyping results. When the mothers' profile is included for sample pair 16B, the PI is 1.8 Â 10 9 and for 101A is 4.3 Â 10 6 .…”

“…Reliable estimations of mutation rates for these loci are a valuable asset to assist in the interpretation of Y-STR test results [4]. While there are a large number of articles reporting mutation rates for the minimal haplotype loci, only a few articles [5][6][7][8] have reported results with the 17 Y-STR loci in the AmpF'STR 1 Yfiler TM PCR amplification kit (Applied Biosystems, Foster City, CA). These studies primarily involved samples from populations outside of the U.S.…”

The relationship between surname frequency and Y chromosome variation in Spain

“…Y chromosome STR genotyping was conducted using the Yfiler PCR Amplification kit (Applied Biosystems, Foster City, CA, USA), 10 which co-amplifies a total of 17 Y chromosome STRs (DYS19, DYS385a,b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATAH4). Further information on the loci can be found on the YHRD and NIST webpages (www.yhrd.org; www.cstl.nist.gov/strbase/y_strs.htm).…”

Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data

“…However, reliable locus-specific mutation rates are needed to carefully choose loci to minimize the error rate in kinship analysis and sample identification 2 while obtaining the maximum discriminatory power (eg, Mulero et al, Lim et al and Vermeulen et al [3][4][5]. Also in population genetics and evolutionary studies, correct inferences on the timing of major demographic events, the age of the most common ancestor, as well as dating Y-lineages and tracing disease evolution are based on the knowledge of mutation rates (eg, Shi et al, Zerjal et al and Xue et al [6][7][8] ).…”