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Population Data on the STR Loci D2S1338 and D19S433 by Budowle et al. (Forensic Science Communications, July 2001)

Population Data on the STR Loci D2S1338 and D19S433 by Budowle et al. (Forensic Science Communications, July 2001)

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July 2001 - Volume 3 - Number 3

Research and Technology

Population Data on the STR Loci D2S1338 and D19S433

Bruce Budowle
Senior Scientist
Laboratory Division
Federal Bureau of Investigation
Washington, DC

Patrick J. Collins
Scientist

Pero Dimsoski
Senior Scientist

Constance K. Ganong
Scientist

Lori K. Hennessy
Senior Scientist

Craig S. Leibelt
Senior Scientist

Sulekha Rao-Coticone
Senior Scientist

Farideh Shadravan
Senior Scientist

Dennis J. Reeder
Manager

Human Identity Group
Applied Biosystems
Foster City, California

Materials and Methods | Results and Discussion | References

Allele distributions for two tetrameric short tandem repeat (STR) loci, D2S1338 and D19S433, were determined in African Americans, U.S. Caucasians, southwestern Hispanics, Chamorros, and Filipinos. These two loci are highly polymorphic in the five datasets analyzed. There were no detectable departures from Hardy–Weinberg expectations (HWE) in any of the sample populations. In a pairwise comparison of these two loci with the CODIS core STR loci previously typed in these sample populations, there was little evidence for association of alleles between the loci in these five databases. Departures from expectations of independence were observed at D5S818 / D2S1338 (p = 0.039) in African Americans; at FGA / D2S1338 (p = 0.043), D8S1179 / D2S1338 (p = 0.045), and D21S11 / D2S1338 (p = 0.022) in Hispanics; and at CSF1PO / D2S1338 (p = 0.024) in Chamorros.

Introduction

A new multiplex kit—AmpFlSTR® Identifiler™ PCR Amplification kit (Applied Biosystems, Foster City, California)—has been developed that enables simultaneous amplification of the 13 core CODIS STR loci, two additional STR loci (D2S1338 and D19S433), and the amelogenin locus. As part of the requirement for CODIS acceptance of the identifiler kit, a primer concordance study was performed to compare typing results obtained on samples analyzed using the identifiler kit with those obtained using the AmpFlSTR® Profiler Plus™ PCR Amplification kit and AmpFlSTR® COfiler™ PCR Amplification kit (Applied Biosystems, Foster City, California). There were no differences in typing results (manuscript in preparation). An ancillary benefit of the study was that allele distribution data were generated for the loci D2S1338 and D19S433 in African Americans, U.S. Caucasians, southwestern Hispanics, Chamorros, and Filipinos. This article reports those data so that the weight of evidence can be estimated for DNA profiles that contain these loci.

Materials and Methods

The source and preparation of the samples have been described previously (Budowle et al. 2000; Budowle et al. 1999; Budowle et al. 1998; Budowle et al. 1995; Budowle et al. 2001; Comey et al. 1994; Waye et al. 1989). The DNA samples were amplified simultaneously at the loci CSF1PO, FGA, TPOX, TH01, VWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, and D21S11 using the AmpFlSTR® Identifiler™ PCR Amplification kit (Applied Biosystems, Foster City, California). A targeted input of 0.5-1.25ng of template DNA was used in each PCR. Either an Applied Biosystems GeneAmp PCR System 9600 or a 9700 thermal cycler (Applied Biosystems, Foster City, California) was used for the PCR amplifications.

The amplified products were separated by capillary electrophoresis using an ABI Prism® 3700 DNA Analyzer (Applied Biosystems, Foster City, California) and separation medium POP 6™ Performance Optimized Polymer (Applied Biosystems, Foster City, California) or an ABI Prism® 310 Genetic Analyzer with separation medium POP 4™ (Applied Biosystems, Foster City, California) according to the manufacturer's recommended protocols. Amplified samples that were not typeable with the 3700 were subjected to electrophoresis in an ABI Prism® 310 Genetic Analyzer with separation medium POP 4™. Allele designations were determined by comparison of the amplicon fragments with those of the allelic ladders and internal lane standards using Applied Biosystems Genotyper® software.

Statistical Analysis: The frequency of each allele for each locus was calculated from the numbers of each genotype in the sample set (i.e., the gene count method). Unbiased estimates of expected heterozygosity were computed as described by Edwards et al. (1992). Possible divergence from Hardy–Weinberg expectations (HWE) was tested by calculating the unbiased estimate of the expected homozygote/heterozygote frequencies (Chakraborty et al. 1991; Chakraborty et al. 1988; Nei 1978; Nei and Roychoudhury 1974) and the exact test (Guo and Thompson 1992), on the basis of 2000 shuffling experiments. An interclass correlation criterion (Karlin et al. 1981) for two-locus associations was used for detecting disequilibrium between the STR loci.

Results and Discussion

Because the allele data for the 13 CODIS STR loci on these five sample populations have been reported previously (Budowle et al. 1999; Budowle et al. 2001), only allele distributions for the loci D2S1338 and D19S433 are described in this article.

The distributions of observed alleles are shown in Tables 1 and 2. The observed and expected homozygosities, exact test for departures from HWE, discrimination probability (PD), and probability of exclusion (PE) are also provided. Both loci are highly polymorphic in all five sample populations. Although the sample size for Chamorros and Filipinos is smaller than the other sample populations, the data support that these loci are highly polymorphic in these groups as well. In fact, the PD for the D2S1338 locus is one of the highest of any of the 15 STR loci typed using the identifiler kit, and the D19S433 locus is comparable in PD with that of the more polymorphic CODIS core loci (Budowle et al. 1999; Budowle et al. 2001). No detectable departures from HWE were detected.

An interclass correlation test analysis was performed to detect any correlations between alleles at any of the pairwise comparisons of the 15 STR loci. Thus for each sample population, there was a total of 105 pairwise comparisons performed. For the two loci, D2S1338 and D19S433, the only departures from expectations that were observed are D5S818 / D2S1338 (p = 0.039) in African Americans; FGA / D2S1338 (p = 0.043), D8S1179 / D2S1338 (p = 0.045), and D21S11 / D2S1338 (p = 0.022) in Hispanics; and CSF1PO / D2S1338 (p = 0.024) in Chamorros. Combining these data with previously reported STR data (Budowle et al. 2000; Budowle et al. 1999; Budowle et al. 2001), the number of significant departures is 2 for African Americans (1.9%), 9 for Caucasians (8.6%), 5 for Hispanics (4.8%), 5 for Chamorros (4.8%), and 4 for Filipinos (3.8%). Only the Caucasian sample population exceeds the expected value of 5%. However, after the Bonferroni correction (Weir 1990), these observations are not significant.

In conclusion, African American, U.S. Caucasian, southwestern Hispanic, Chamorro, and Filipino databases have been established for the loci D2S1338 and D19S433. The results of independence testing support the use of these data for estimating the rarity of a DNA profile containing these two STR loci.

Genotype profile data for this study are available at http://www.fbi.gov/hq/lab/fsc/backissu/july2001/budowle.txt

We thank Indira Sohel of Applied Biosystems for providing valuable technical assistance with sample preparation.

References

Budowle, B. Genotype profiles for five population groups at the short tandem repeat loci D2S1338 and D19S433, Forensic Science Communications [Online]. (July 2001). Available: http://www.fbi.gov/hq/lab/fsc/backissu/july2001/budowle1.htm

Budowle, B., Baechtel, F. S., Comey, C. T., Giusti, A. M., and Klevan, L. Simple protocols for typing forensic biological evidence: Chemiluminescent detection for human DNA quantitation and RFLP analyses and manual typing of PCR amplified polymorphisms, Electrophoresis (1995) 16:1559–1567.

Budowle, B., Baechtel, F. S., and Fejeran, R. Polymarker, HLA-DQA1, and D1S80 allele frequency data in Chamorro and Filipino populations in Guam, Journal of Forensic Sciences (1998) 43:1195–1198.

Budowle B., Defenbaugh, D. A., and Keys, K. M. Genetic variation at nine short tandem repeat loci in Chamorros and Filipinos from Guam, Legal Medicine (2000) 2(1):26–30.

Budowle, B., Moretti, T. R., Baumstark, A. L., Defenbaugh, D. A., and Keys K. M. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians, Journal of Forensic Sciences (1999) 44:1277–1286.

Budowle, B., Shea, B., Niezgoda, S., and Chakraborty, R. CODIS STR loci data from 41 sample populations, Journal of Forensic Sciences (2001) 46:453–489.

Chakraborty, R., Fornage, M., Guegue, R., and Boerwinkle, E. Population genetics of hypervariable loci: Analysis of PCR-based VNTR polymorphism within a population. In: DNA Fingerprinting: Approaches and Applications, T. Burke, G. Dolf, A. J. Jeffreys, and R. Wolff, eds. Birkhauser Verlag, Berlin, 1991, pp. 127–143.

Chakraborty, R., Smouse, P. E., and Neel, J. V. Population amalgamation and genetic variation: Observations on artificially agglomerated tribal populations of Central and South America, American Journal of Human Genetics (1988) 43:709–725.

Comey, C. T., Koons, B. W., Presley, K. W., Smerick, J. B., Sobieralski, C. A., Stanley, D. M., and Baechtel, F. S. DNA extraction strategies for amplified fragment length polymorphism analysis, Journal of Forensic Sciences (1994) 39:1254–1269.

Edwards, A., Hammond, H. A., Jin, L., Caskey, C. T., and Chakraborty, R. Genetic variation at five trimeric and tetrameric repeat loci in four human population groups, Genomics (1992) 12:241–253.

Guo, S. W. and Thompson, E. A. Performing the exact test of Hardy–Weinberg proportion for multiple alleles, Biometrics (1992) 48:361–372.

Karlin, S., Cameron, E. C., and Williams, P. T. Sibling and parent-offspring correlation estimation with variable family size, Proceedings of the National Academy of Sciences USA (1981) 78:2664–2668.

Nei, M. Estimation of average heterozygosity and genetic distance from a small number of individuals, Genetics (1978) 89:583–590.

Nei, M. and Roychoudhury, A. K. Sampling variances of heterozygosity and genetic distance, Genetics (1974) 76:379–390.

Waye, J. S., Presley, L., Budowle, B., Shutler, G. G., and Fourney, R. M. A simple method for quantifying human genomic DNA in forensic specimen extracts, BioTechniques (1989) 7:852–855.

Weir, B. S. Multiple tests. In: Genetic Data Analysis, Sinauer Associates, Sunderland, Massachusetts, 1990, pp. 109–110.


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