Analysis of eight STR loci in two Hungarian populations

An optimized protocol for forensic application of the PreCR™ Repair Mix to multiplex STR amplification of UV-damaged DNA

Damage to the DNA molecule can occur through exposure to environmental conditions such as ultraviolet light, heat and humidity. Forensic samples are particularly prone to such damage due to their prolonged exposure after deposition at crime scenes or mass disasters. Current methods for typing such samples rely heavily on the intact DNA template, and can be adversely affected by damage that is present. Proposed solutions center around increased access to the smaller remaining fragments and/or increased sensitivity. However, all rely on the polymerase chain reaction to copy the starting material; the required polymerase can be impeded by certain types of damage such as dimer-formation after ultraviolet light exposure, resulting in stochastic effects that can complicate interpretation. In vitro repair of such damage offers the ability to generate high quality profiles using traditional methods without changes to the current amplification reagents or conditions. Typically, repair reactions required large quantities of starting material and a separate repair reaction. Forensic samples, however, usually consist of small quantities, and quality control measures necessitate laboratory procedures that minimize sample manipulation. Here, an optimized protocol for forensic application of the PreCR™ Repair Mix to current typing methods is demonstrated for samples damaged by ultraviolet light exposure.

A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.

STR sequence analysis for characterizing normal, variant, and null alleles

DNA sequence variation is known to exist in and around the repeat region of short tandem repeat (STR) loci used in human identity testing. While the vast majority of STR alleles measured in forensic DNA laboratories worldwide type as "normal" alleles compared with STR kit allelic ladders, a number of variant alleles have been reported. In addition, a sequence difference at a polymerase chain reaction (PCR) primer binding site in the DNA template can cause allele drop-out (i.e., a "null" or "silent" allele) with one set of primers and not with another. Our group at the National Institute of Standards and Technology (NIST) has been sequencing variant and null alleles supplied by forensic labs and cataloging this information on the NIST STRBase website for the past decade. The PCR primer sequences and strategy used for our STR allele sequencing work involving 23 autosomal STRs and 17 Y-chromosome STRs are described along with the results from 111 variant and 17 null alleles.

Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing

Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

Population genetic study in two Transylvanian populations using forensically informative autosomal and Y-chromosomal STR markers

Our study provides population genetic data on two population samples collected in a Hungarian speaking region of Transylvania, Romania. Allele frequency and profile databases were generated on 17 autosomal STR loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, VWA, FGA, TH01, TPOX, CSF1PO, Penta E and Penta D) as well as at the 12 European Y-STR extended haplotype loci (DYS19, DYS389-I/II, DYS390, DYS391, DYS392, DYS393, DYS385 loci, DYS437, DYS438 and DYS439). Data were compared to a Central Hungarian (Budapest region) population sample [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27] that was used as a reference group of the Hungarian population. Calculating the F(ST) indices and with the pairwise comparisons of interpopulation molecular variance (AMOVA) the two populations from Transylvania could be fit into the Hungarian population data showing less substructuring effects as compared to the previous findings in Hungary [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27; B. Egyed, S. Füredi, M. Angyal, I. Balogh, L. Kalmar, Z. Padar, Analysis of the population heterogeneity in Hungary using fifteen forensically informative STR markers, Forensic Sci. Int. 158 (2005) 244-249].