Validation of STR typing by capillary electrophoresis.

With the use of capillary electrophoresis (CE), high-resolution electrophoretic separation of short tandem repeat (STR) loci can be achieved in a semiautomated fashion. Laser-induced detection of fluorescently labeled PCR products and multicolor analysis enable the rapid generation of multilocus DNA profiles. In this study, conditions for typing PCR-amplified STR loci by capillary electrophoresis were investigated using the ABI Prism 310 Genetic Analyzer (Applied Biosystems). An internal size standard was used with each run to effectively normalize mobility differences among injections. Alleles were designated by comparison to allelic ladders that were run with each sample set. Multiple runs of allelic ladders and of amplified samples demonstrate that allele sizes were reproducible, with standard deviations typically less than 0.12 bases for fragments up to 317 bases in length (largest allele analyzed) separated in a 47 cm capillary. Therefore, 99.7% of all alleles that are the same length should fall within the measurement error window of +/- 0.36 bases. Microvariants of the tetranucleotide repeats were also accurately typed by the analytical software. Alleles differing in size by one base could be resolved in two-donor DNA mixtures in which the minor component comprised > or = 5% of the total DNA. Furthermore, the quantitative data format (i.e., peak amplitude) can in some instances assist in determining individual STR profiles in mixed samples. DNA samples from previously typed cases (typed for RFLP, AmpliType PM+DQA1, and/or D1S80) were amplified using AmpFlSTR Profiler Plus and COfiler and were evaluated using the ABI Prism 310. Most samples yielded typable results. Compared with previously determined results for other loci, there were no discrepancies as to the inclusion or exclusion of suspects or victims. CE thus provides efficient separation, resolution, sensitivity and precision, and the analytical software provides reliable genotyping of STR loci. The analytical conditions described are suitable for typing samples such as reference and evidentiary samples from forensic casework.

Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples.

The amplification and typing conditions for the 13 core CODIS loci and their forensic applicability were evaluated. These loci are CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11. Results were obtained using the multiplex STR systems AmpFlSTR Profiler Plus and AmpFlSTR COfiler (Applied Biosystems, Foster City, CA), GenePrint PowerPlex (Promega Corporation, Madison, WI), and subsets of these kits. For detection of fluorescently labeled amplified products, the ABI Prism 310 Genetic Analyzer, the ABI Prism 377 DNA Sequencer, the FMBIO II Fluorescent Imaging Device, and the Fluorlmager were utilized. The following studies were conducted: (a) evaluation of PCR parameter ranges required for adequate performance in multiplex amplification of STR loci, (b) determination of the sensitivity of detection of the systems, (c) characterization of non-allelic PCR products, (d) evaluation of heterozygous peak intensities, (e) determination of the relative level of stutter per locus, (f) determination of stochastic PCR thresholds, (g) analysis of previously typed case samples, environmentally insulted samples, and body fluid samples deposited on various substrates, and (h) detection of components of mixed DNA samples. The data demonstrate that the commercially available multiplex kits can be used to amplify and type STR loci successfully from DNA derived from human biological specimens. There was no evidence of false positive or false negative results and no substantial evidence of preferential amplification within a locus. Although at times general balance among loci labeled with the same fluorophore was not observed, the results obtained were still valid and robust. Suggested criteria are provided for determining whether a sample is derived from a single source or from more than one contributor. These criteria entail the following: (a) the number of peaks at a locus, (b) the relative height of stutter products, and (c) peak height ratios. Stochastic threshold levels and the efficiency of non-templated nucleotide addition should be considered when evaluating the presence of mixtures or low quantity DNA samples. Guidelines, not standards, for interpretation should be developed to interpret STR profiles in cases, because there will be instances in which the standards may not apply. These instances include (a) a primer binding site variant for one allele at a given locus, (b) unusually high stutter product, (c) gene duplication, and (d) translocation.

Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians.

Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group.

Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians

Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African-American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departure from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p=0.010, Bahamians); CSF1PO (p=0.014, Trinidadians); TPOX (p=0.011, Jamaicans and p= 0.035, U.S. Caucasians); and D16S539 (p=0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group. (AU)

Subtyping of the HLA-DQA1 locus and independence testing with PM and STR/VNTR loci.

Allele and genotype frequencies for six loci (HLA-DQA1 and PM loci) were determined in African Americans, United States Caucasians, and Southwestern Hispanics. The data include allele frequencies of the HLA-DQA1 4 subtypes. The HLA-DQA1 4 allele subtyping affords greater power of discrimination in African Americans and Southwestern Hispanics than in Caucasians, due to the relatively lower 4.2/4.3 allele frequency in Caucasians. Based on the exact test, all loci, except the GYPA locus in the African American sample (p = 0.011), meet Hardy-Weinberg expectations. There were two examples of significant departures from expectations of independence between alleles of the HLA-DQA1 and PM loci (HBGG/Gc in African Americans, p = 0.30; LDLR/DQA1 in Caucasians, p = 0.023). The HLA-DQA1 and PM loci also were tested for associations with three STR loci and the DIS80 locus. There were four examples of significant departures from expectations of independence (TPOX/D7S8 and THO1/HBGG in African Americans, p = 0.035 and 0.028, respectively; THO1/LDLR in Caucasians, p = 0.028; and GYPA/D1S80 in Hispanics, p = 0.046). The HLA-DQA1 and PM allele frequency data were compared with previously reported data on other sample populations of the same population categories from our laboratory; the allele frequencies at all loci, except the D7S8 locus in Hispanics (p = 0.028), were statistically similar. The frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a multiple locus DNA profile in various general United States populations.

United States population data on the multiplex short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--and the variable number tandem repeat locus D1S80.

Allele frequencies for three tetrameric short tandem repeat (STR) loci HUMTHO1, TPOX, and CSF1PO and a variable number tandem repeat locus D1S80 were determined in United States Caucasian, African American, and Hispanic sample populations. All loci, except the TPOX locus in the Caucasian sample population, meet Hardy-Weinberg expectations. There is no evidence for association of alleles among the four loci. The allelic frequency data are similar to other comparable data within the same major population group.

Validation studies of the CTT STR multiplex system.

Studies were performed to define the typing conditions and evaluate the forensic applicability of multiplex amplification of three STR loci, CSF1PO, TPOX, and THO1. Results were obtained using the GenePrint STR System (Promega Corporation, Madison, WI) Kit. To determine the utility of the GenePrint STR System for forensic casework analyses, the following experiments were conducted: 1) analysis of mixed body fluid; 2) determination of the sensitivity of detection; and 3) evaluation of results from biological samples from casework. In addition, the following simulated forensic conditions were assayed to detect whether or not there may be adverse effects on the ability to type these loci: 1) chemical contaminant effects on the DNA in body fluid samples; 2) the effects on DNA from samples deposited on various substrates; 3) the consequences of micro-organism contamination; and 4) the effect of sunlight and storage conditions on the integrity of the STR profiles/DNA. The data demonstrate that STR typing of biological samples exposed to a variety of environmental insults yields reliable results and that the analysis of the STR loci CSF1PO, TPOX, and THO1 can be applied in a forensic setting.

Zimbabwe black population data on the six short tandem repeat loci--CSF1PO, TPOX, THO1, D3S1358, VWA and FGA.

Allele frequencies for six tetrameric short tandem repeat (STR) loci CSF1PO, TPOX, THO1, D3S1358, VWA, and FGA were determined in a Black African sample population from Zimbabwe. All loci are highly polymorphic and meet Hardy-Weinberg expectations. An inter-class correlation test analysis detected only one departure from independence out of 15 pair-wise comparisons of the six loci (i.e., CSF1PO/VWA loci, P = 0.026). The allele frequency data at four of the six STR loci in the Black African sample population are similar to African American data.

Portuguese population data on the six short tandem repeat loci--CSF1PO, TPOX, THO1, D3S1358, VWA and FGA.

Allele frequencies for six tetrameric short tandem repeat (STR) loci CSF1PO, TPOX, THO1, D3S1358, VWA and FGA were determined in a Caucasian population sample from Portugal. All loci are highly polymorphic and meet Hardy-Weinberg expectations. There is little evidence for association of alleles among the six loci. The three loci D3S1358, VWA and FGA are more polymorphic and, hence, are more informative than the loci CSF1PO, TPOX, and THO1. However, all six loci would be useful for human identification applications. The STR allelic frequency data are similar to other Caucasian data.