The presence of sequence variation in the flanking region of commonly used STR loci along with the use of different PCR primers for typing these STR repeats can result in failure to amplify one or both of the alleles present at the particular locus. These "null" or "silent" alleles due to allele dropout are typically surmised with concordance studies where more than one PCR primer set is used to test the STR locus of interest.
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Results from Concordance Studies
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|
Locus |
STR Kits/Assays Compared |
Results |
Frequency of Primer Binding Site Mutation |
Source |
|
MF: 11,11 and ID: 11,11.1 One base insertion in Identifiler amplicon outside of MiniFiler and PP16 primers |
1/1308 |
|||
|
Loss of allele 14 with COfiler; fine with PP16 |
2/1537 |
Budowle et al. (2001) |
||
|
|
SGM vs SGM Plus |
Loss of allele 26 with SGM Plus; weak amp of same allele with SGM |
|
Cotton et al. (2000) |
|
Loss of allele 22 with ProPlus; fine with PP16 |
|
Budowle and Sprecher (2001) |
||
| FGA | PP16 vs SGM Plus/ProPlus | Loss of allele 22 with PP16; fine with SGM Plus | 1/2055 | Delamoye et al. (2004) |
| FGA | PP16 vs SGM Plus/ProPlus | Loss of allele 21 with SGM Plus; fine with PP16 | 1/2055 | Delamoye et al. (2004) |
| FGA | ID vs PP16 | Loss of allele 24 with Identifiler; fine with PP16 | Ricci et al. (2007) | |
|
Loss of allele 9 with COfiler; fine with PP16 |
1/1537 |
Budowle et al. (2001) |
||
|
|
SGM vs SGM Plus |
Loss of allele 6 with SGM Plus; fine with SGM |
1/4245 |
Clayton et al. (2004) |
| TH01 | PP16 vs SGM Plus | Loss of allele 7 with SGM Plus; fine with PP16 | 2/1377 | Vanderheyden et al. (2007) |
|
|
Loss of allele 19 with ProPlus; fine with PP1.1 |
2/1483 |
Kline et al. (1998) and Walsh (1998) |
|
|
Loss of alleles 15 and 17 with ProPlus; fine with PP16 |
2/1537 |
Budowle et al. (2001) |
||
|
ID vs miniplexes |
Loss of alleles 12, 13, and 14 with miniplex assay; fine with ID |
9/532 |
|
|
|
SGM vs SGM Plus |
Loss of allele 17 with SGM Plus; fine with SGM |
1/4245 |
Clayton et al. (2004) |
|
| VWA | ProPlus vs CTTv | Loss of alleles 17, 18, and 19 with ProPlus; fine with CTTv | 4/434 | Alves et al. (2001) |
| VWA | PP16 vs SGM Plus/ProPlus | Loss of alleles 17, 18, and 21 with SGM Plus; fine with PP16 | 5/2055 | Delamoye et al. (2004) |
| VWA | PP16 vs SGM Plus | Loss of allele 17 and 18 with SGM Plus; fine with PP16 | 4/1377 | Vanderheyden et al. (2007) |
|
|
Loss of alleles 10 and 11 with PP16; fine with ProPlus |
3/110 |
Alves et al. (2003) |
|
|
ID vs miniplexes |
Loss of allele 12 with miniplex assay; fine with ID |
1/532 |
||
| D5S818 | PP16 vs SGM Plus/ProPlus | Loss of allele 10 with PP16; fine with SGM Plus | 2/2055 | Delamoye et al. (2004) |
|
MF: 8,11 and ID: 8,9.3 5 base deletion in Identifiler amplicon outside of MiniFiler and PP16 primers |
1/1308 |
|||
|
|
Loss of alleles 15, 16, 17, and 18 with ProPlus; fine with PP16 |
13/1537 |
Budowle et al. (2001) |
|
| D8S1179 | PP16 vs ProPlus | Loss of allele 16 with ProPlus; fine with PP16 | 1/110 | Alves et al. (2003) |
|
SGM vs SGM Plus |
Loss of allele 16 with SGM Plus; fine with SGM |
1/4245 |
Clayton et al. (2004) |
|
| D8S1179 | PP16 vs SGM Plus/ProPlus | Loss of alleles 10, 16, and 18 with SGM Plus; fine with PP16 | 3/2055 | Delamoye et al. (2004) |
|
ID vs miniplexes |
Shift of alleles 10 and 11 due to deletion outside of miniplex assay but internal to ID |
5/532 |
||
|
MF: 11,11 and ID: 9,11 4 base deletion in the reverse MiniFiler primer binding region |
14/1308 |
|||
|
MF: 9,9 and ID: 9,11 caused by SNP in the MiniFiler primer binding site |
10/1308 |
|||
|
|
Loss of alleles with PP1.1; fine with PP16 and COfiler |
|
Nelson et al. (2002) |
|
|
Loss of allele 12 with PP16; fine with COfiler |
1/1537 |
Budowle et al. (2001) |
||
|
MF: 13,15 and ID: 15,15 caused by SNP in the Identifiler primer binding site |
1/1308 |
|||
|
|
SGM vs SGM Plus |
Loss of alleles 17, 18, 19, and 20 with SGM Plus (in Kuwaiti individuals); fine with SGM |
9/4245 |
Clayton et al. (2004) |
| D18S51 | PP16 vs SGM Plus/ProPlus | Loss of allele 16 with PP16; fine with SGM Plus | 1/2055 | Delamoye et al. (2004) |
| D18S51 | PP16 vs SGM Plus/ProPlus | Loss of alleles 16 and 18 with SGM Plus; fine with PP16 | 2/2055 | Delamoye et al. (2004) |
| D18S51 | PP16 vs SGM Plus | Loss of allele 19 with SGM Plus; fine with PP16 | 2/1377 | Vanderheyden et al. (2007) |
| D18S51 | PP16 vs SGM Plus | Loss of allele 14 with PP16; fine with SGM Plus | 1/1377 | Vanderheyden et al. (2007) |
|
Loss of allele 32.2 with PP16; fine with ProPlus |
1/1537 |
Budowle et al. (2001) |
||
| D19S433 | SGM Plus vs SGM | Loss of allele 11 with SGM Plus; fine with SGM | 1/4245 | Clayton et al. (2004) |
***Some information from Table 6.2 of Forensic DNA Typing, 2nd Edition (J.M. Butler, 2005)
Non-published variant alleles are being observed on a regular basis as STR typing becomes more wide-spread. To save duplication and to confirm suspicious alleles, the putative variant alleles are being cataloged. When variants are confirmed by sequencing or are published, we include them with the STR fact sheets.
Reference List:
Alves, C., Gusmao, L., Pereira, L., Amorim, A. (2003) Multiplex STR genotyping: comparison study, population data and new sequence information. Progress in Forensic Genetics 9 Int Congress Ser 1239:131-135.
Budowle, B. and Sprecher, C. J. (2001) Concordance study on population database samples using the PowerPlex 16 kit and AmpFlSTR Profiler Plus kit and AmpFlSTR COfiler kit. J. Forensic Sci. 46(3): 637-641.
Budowle, B., Masibay, A., Anderson, S. J., Barna, C., Biega, L., Brenneke, S., Brown, B. L., Cramer, J., DeGroot, G. A., Douglas, D., Duceman, B., Eastman, A., Giles, R., Hamill, J., Haase, D. J., Janssen, D. W., Kupferschmid, T. D., Lawton, T., Lemire, C., Llewellyn, B., Moretti, T., Neves, J., Palaski, C., Schueler, S., Sgueglia, J., Sprecher, C., Tomsey, C., and Yet, D. (2001) STR primer concordance study. Forensic Sci. Int. 124(1): 47-54.
Clayton, T. M., Hill, S. M., Denton, L. A., Watson, S. K., and Urquhart, A. J. (2004) Primer binding site mutations affecting the typing of STR loci contained within the AMPFlSTR SGM Plus kit. Forensic Sci. Int. 139(2-3): 255-259.
Cotton, E. A., Allsop, R. F., Guest, J. L., Frazier, R. R., Koumi, P., Callow, I. P., Seager1 A, and Sparkes, R. L. (2000) Validation of the AMPFlSTR SGM Plus system for use in forensic casework. Forensic Sci. Int. 112(2-3): 151-161.
Delamoye, M., Duverneuil, C., Riva, K., Leterreux, M., Taieb, S., and de Mazancourt, P. (2004) False homozygosities at various loci revealed by discrepancies between commercial kits: implications for genetic databases. Forensic Sci. Int. 143(1): 47-52.
Drabek, J., Chung, D.T., Butler, J.M., McCord, B.R. (2004) Concordance study between miniplex STR assays and a commercial STR typing kit. J. Forensic Sci. 49(4): 859-860.
Hill, C.R., Kline, M.C., Mulero, J.J., Lagace, R.E., Chang, C.-W., Hennessy, L.K., Butler, J.M. (2007) Concordance study between the AmpFlSTR MiniFiler PCR Amplification Kit and conventional STR typing kits. J. Forensic Sci. 52(4): 870-873.
Kline, M. C., Jenkins, B., and Rodgers.S. (1998) Non-Amplification of a vWA Allele. J. Forensic Sci. 43(1): 250.
Leibelt, C., Budowle, B., Collins, P., Daoudi, Y., Moretti, T., Nunn, G., Reeder, D., and Roby, R. (5-5-2003) Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles. Forensic Sci.Int. 133(3): 220-227.
Nelson, M. S., Levedakou, E. N., Matthews, J. R., Early, B. E., Freeman, D. A., Kuhn, C. A., Sprecher, C. J., Amin, A. S., McElfresh, K. C., and Schumm, J. W. (2002) Detection of a primer-binding site polymorphism for the STR locus D16S539 using the Powerplex 1.1 system and validation of a degenerate primer to correct for the polymorphism. J. Forensic Sci. 47(2): 345-349.
Ricci, U., Melean, G., Robino, C., and Genuardi, M. (2007) A Single Mutation in the FGA Locus Responsible for False Homozygosities and Discrepancies Between Commercial Kits in an Unusual Paternity Test Case. J Forensic Sci. 52(2): 393-396.
Vanderheyden, N., Mai, A., Gilissen, A., Cassiman, J. J., and Decorte, R. (2007) Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus and PowerPlex 16. Int. J Legal Med. 121(4): 297-301.
Walsh, S. (1998) Commentary on Kline MC, Jenkins B, Rogers S. Non-amplification of a vWA allele. J Forensic Sci 1998 Jan;43(1):250. J. Forensic Sci. 43: 1103-1104.
See also Butler, J.M. (2006) Genetics and genomics of core STR loci used in human identity testing. J. Forensic Sci. 51(2): 253-265.
Last Updated: 07/05/2007