Allele Frequencies for 15 Autosomal STR Loci on U.S. Caucasian, African American, and Hispanic Populations*

Abstract

Anonymous liquid blood samples with self-identified ethnicities were purchased from Interstate Blood Bank (Memphis, TN) and Millennium Biotech, Inc. (Ft. Lauderdale, FL) and extracted using a modified salt out procedure (1). The extracted DNA was then quantified using UV spectrophotometry at 260 nm and a PicoGreen assay (2). A 150-µL aliquot of the extracted DNA solution was directly quantified in a Cary 100 double-beam spectrophotometer (Varian Analytical Instruments, Walnut Creek, CA). Low volume micro-cuvettes allowed for accurate absorbance measurements (A = 0.2 to 0.6) without prior dilution of the stock extracted DNA. Sample concentrations were adjusted to 1 ng/µL for typing purposes using the PicoGreen assay values. Fifteen autosomal STR markers (the 13 CODIS core loci and D19S433 and D2S1338) were typed along with amelogenin using the Applied Biosystems AmpF1STR® Identifiler™ kit (3). PCR amplification was carried out on a GeneAmp® 9700 (Applied Biosystems) using 1 ng of DNA according to kit protocols (3) with the exception of reduced volume reactions (5 µL instead of 25 µL) and reduced cycles (26 instead of 28). Amplification products were diluted 1:15 in HiDi™ formamide and GS500-LIZ internal size standard (Applied Biosystems) and analyzed on the 16-capillary ABI Prism® 3100 Genetic Analyzer without prior denaturation of samples. POP™-6 (Applied Biosystems) rather than POP™-4 was utilized for higher resolution separations on a 36 cm array. Samples were injected

Concordance study between the ParaDNA ® Intelligence Test, a Rapid DNA profiling assay, and a conventional STR typing kit (AmpFlSTR ® SGM Plus ® )

“…One reason for discordance between the ParaDNA Intelligence Test and AmpFlSTR SGM Plus is the occurrence of microvariants. The most common microvariant, the 9.3 variant in TH01 [4][5][6], is correctly called as 9.3+ by the ParaDNA Intelligence Test. However due to the lower resolution of melting curve analysis compared with capillary electrophoresis (CE), other microvariants may not be distinguished from full repeat variants by the Para DNA Intelligence Test.…”

“…In a review of studies containing allele frequencies for several of the major ethnic population groups in the UK and US the total frequency of microvariants in all five loci used in the ParaDNA Intelligence Test was less than 0.1% [4][5][6]. In addition the ParaDNA Intelligence Software searching/comparison functions use a series of rules to widen the search criteria, thereby mitigating this potential issue [20].…”

“…Discounting the occurrence of null alleles, the allele range at each locus detected and reported by the ParaDNA Intelligence Test is anticipated to cover 94.13% expected alleles at these loci, based on allele frequencies from sample populations [4][5][6]. A further 5.76% more rare alleles with repeat numbers above these ranges are also detected but cannot be resolved.…”

“…Concordance studies are typically conducted on a number (typically several hundred or more) of samples from individuals in a reference population or population subgroup using one profiling kit for which profiling data has been obtained using another product, thus establishing concordance between the profiles generated by the two products [4,10,11]. In addition, population studies can provide data on allele frequencies anticipated in the reference population or populations [5,6,12].…”

“…This population was chosen as a relevant, well characterised population group upon which to conduct this concordance study [5,6]. Similar studies have sampled similar numbers of individuals from single [13,14] or multiple ethnic groups [4,8,9] represented within their geographical location. Loci were tested for departures from Hardy Weinberg expectations (HWE) using Genepop software [15,16].…”