Amended FBI Allele Frequencies


REFERENCE: Budowle B, Moretti TR, Baumstark AL, Defenbaugh DA, Keys KM. Population data 2 on the thirteen CODIS core short tandem repeat loci in African Americans, US Caucasians, Hispanics, 3 Bahamians, Jamaicans and Trinidadians. J Forensic Sci 1999;44(6):1277-86. 4


Since the development in the late 1990s of the original short tandem repeat (STR) typing systems that 6 included the 13 CODIS core loci, new amplification kits that expand the number of loci to 24 in a 7 multiplex reaction are now commercially available. To establish allele distributions for the additional 8 loci, population samples that were originally genotyped using AmpFlSTR Profiler Plus, COfiler, 9 Identifiler (Thermo Fisher Scientific, South San Francisco, CA) and/or GenePrint PowerPlex 10 (Promega Corp., Madison, WI) (1,2) were retyped using GlobalFiler (Thermo Fisher Scientific) and 11 PowerPlex Fusion (Promega Corp.). For any sample where a given locus is typed with different 12 amplification kits, concordant genotypes should be obtained irrespective of the kit(s) used, with the 13 exception of genotype differences due to rare primer binding site variants and improvements in allelic 14 ladders that expand allele identification capabilities (e.g., an allele may be designated as <11 in one 15 system and as 9 in another). 16

During a comparison of the 1100 profiles from African Americans, Caucasians, Southwest Hispanics, 17 Bahamians, Jamaicans, Trinidadians, Filipinos and Chamorros in the original (3,4)1 and new studies, 18 genotyping discrepancies were revealed. Discrepancies were attributable to (a) human error, typically 19 due to the limited software capabilities for genotyping with manual data editing and recording, and (b) 20 technological limitations (e.g., insufficient resolution for distinguishing microvariants by 21 polyacrylamide gel electrophoresis). The published genotype data (3,4) from which allele frequencies 22 were calculated also includes data or sample processing errors (e.g., known genotype duplications). 23

1Electronic genotype data corresponding to the published allele frequencies are not available for the Southeast Hispanic, Apache, Navaho and Minnesota Native American populations (6), as well as Filipino and Chamorro populations (except for D2S1338 and D19S433) (7), and could not be assessed for concordance with GlobalFiler and Fusion genotypes.

Genotyping errors were made in 27 samples, affecting the reported frequencies of 51 alleles. 24 Additionally, 6 samples exhibited full or partial genotype duplications, which affected all allele 25 frequencies at the duplicated loci in the respective populations due to the change in N that resulted 26 from removal of duplicate genotypes. The minimum allele frequency (5/2N) was amended 27 accordingly. For alleles requiring a frequency correction, the magnitude of the change in frequencies 28 ranged from 0.000012 to 0.018 (average 0.0020 ± 0.0025). See Table 1. 29

The published allele frequencies (1,2) have been used in the past to generate profile probabilities for 30 autosomal STR typing results using FBI PopStats software. Empirical testing suggests that any 31 discrepancy between profile probabilities calculated using the original and corrected data is expected 32 to be less than a factor of two in a full profile. The actual minimum ratio that we could obtain for a 33 constructed profile in the direction of the profile probability being more rare in the original as 34 compared to the amended data was for a highly homozygous partial profile in the Jamaica dataset. It 35 was 0.76, which is well within the factor of 10 suggested by previous studies and the National 36 Research Council (7-10). See Figure 1 and Table 2. Amended data will be available at and 37 through FBI PopStats. The authors are of the view that these discrepancies require acknowledgement 38 but are unlikely to materially affect any assessment of evidential value. 39

Pre-Publication Copy Released with Permission of the Journal of Forensic Sciences


References 40

1. Budowle B, Moretti TR, Baumstark AL, Defenbaugh DA, Keys KM. Population data on the 41 thirteen CODIS core short tandem repeat loci in African Americans, US Caucasians, 42 Hispanics, Bahamians, Jamaicans and Trinidadians. J Forensic Sci 1999;44:1277-86. 43

2. Budowle B, Collins P, Dimsoski P, Ganong C, Hennessy L, Leibelt C, Rao-Coticone S, 44 Shadravan F, Reeder D. Population data on the STR loci D2S1338 and D19S433. Forensic 45 Science Communications 2001;3(3). 46

3. Budowle B, Moretti TR. Genotype profiles for six population groups at the 13 CODIS short 47 tandem repeat core loci and other PCR based loci. Forensic Science Communications 48 1999;1(2). 49

4. Budowle B. Genotype profiles for five population groups at the short tandem repeat loci 50 D2S1338 and D19S433. Forensic Science Communications 2001;3(3). 51

5. Budowle B, Shea B, Niezgoda S, Chakraborty R. CODIS STR loci data from 41 sample 52 populations. J Forensic Sci 2001;46:453-89. 53

6. Budowle B, Defenbaugh DA, Keys KM. Genetic variation at nine short tandem repeat loci in 54 Chamorros and Filipinos from Guam. Legal Medicine 2000;2:26-30. 55

7. National Research Council. The evaluation of forensic DNA evidence. Washington, DC: 56 National Academy Press, 1996. 57

8. Monson KL, Budowle B. Effect of reference database on frequency estimates of polymerase 58 chain reaction (PCR) – based DNA profiles. J Forensic Sci 1998;43:483-8. 59

9. Budowle B, Monson KL, Giusti AM, Brown B. The assessment of frequency estimates of 60 Hae III-generated VNTR profiles in various reference databases. J Forensic Sci 1994;39:319-61 52. 62

10. Budowle B, Monson KL, Giusti AM, Brown B. Evaluation of Hinf I-generated VNTR profile 63 frequencies determined using various ethnic databases. J Forensic Sci 1994;39:988-1008. 64


Tamyra R. Moretti, Ph.D. 66

DNA Support Unit 67

Federal Bureau of Investigation Laboratory 68

Quantico, VA 69


Bruce Budowle, Ph.D. 71

Institute of Applied Genetics 72

University of North Texas Health Science Center 73

Fort Worth, TX 74


John S. Buckleton, Ph.D. 76

Institute of Environmental Science and Research 77

Auckland, New Zealand 78