|
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
Introduction.......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.
Top of the page |
Research and Technology
