Allele Dropout/Null Allele Reports
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.
We welcome your contributions in order to more fully catalog the genetic variation observed in these STR loci. To contribute to these concordance study summaries, click here.
Results from Concordance Studies
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|
Locus |
STR Kits/Assays Compared |
Results |
Frequency of Primer Binding Site Mutation |
Source |
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PowerPlex Fusion 5C vs GlobalFiler |
PowerPlex Fusion 5C: 21,22 and Convicted Offender FTA sample |
Tara Scott, DCI Crime Lab (submitted May 21, 2020) |
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MF: 11,11 and ID: 11,11.1 One base insertion in Identifiler amplicon outside of MiniFiler and PP16 primers |
1/1308 |
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Loss of allele 14 with COfiler; fine with PP16 |
2/1537 |
Budowle et al. (2001) |
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| CSF1PO | PP16 vs ID Plus | Loss of allele 11 with Identifiler Plus; fine with PP16 (10,11) | Elaine Taylor, Oklahoma City Police Forensic DNA (submitted Mar 31, 2014) | |
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SGM vs SGM Plus |
Loss of allele 26 with SGM Plus; weak amp of same allele with SGM |
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Cotton et al. (2000) |
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Loss of allele 22 with ProPlus; fine with PP16 |
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Budowle and Sprecher (2001) |
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| 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) | |
| FGA | PP16 vs ID | Loss of allele 24 with PP, fine with ID, caused by SNP in the PP primer binding site, which is confirmed by sequencing after singleplex amplification. | 1/18314 |
Sun Hongyu, Chen Wenjing, Sun Yat-sen University, China (submitted Apr 22, 2011) |
| FGA | Identifiler Plus vs. Globalfiler | A null allele has been observed for FGA for the 25 allele in the Identifiler Plus kit, whereby a sample presented as 19.2 only in ID+ but as a “19.2,25” in Globalfiler. | Leigh A. Clark, Florida Department of Law Enforcement | |
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Loss of allele 9 with COfiler; fine with PP16 |
1/1537 |
Budowle et al. (2001) |
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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) |
| TH01 | PP16 vs ID | Loss of allele 7 with Identifiler; fine with PP16 | Liz Kopitke, Independent Forensics, Hillside, IL (submitted Jan 6, 2011); (observed again June 3, 2014) | |
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TH01
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PP21 vs ID | Loss of allele 5.2 with PP21; fine with Identifiler | seen in both father and son samples | Lai Li, Fu Jian Academy of Medical Sciences, Fu Zhou, China (submitted Sept 3, 2012) |
| TPOX | PP16 vs ID | Loss of allele 11 with PP, fine with ID, caused by SNP in the PP primer binding site, which is confirmed by sequencing after singleplex amplification | 1/18314 |
Sun Hongyu, Chen Wenjing, Sun Yat-sen University, China (submitted Apr 22, 2011) |
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Loss of allele 19 with ProPlus; fine with PP1.1 |
2/1483 |
Kline et al. (1998) and Walsh (1998) |
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Loss of alleles 15 and 17 with ProPlus; fine with PP16 |
2/1537 |
Budowle et al. (2001) |
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| Loss of allele 16 with ProPlus; fine with PP16 on both mother and child in parentage case |
Sergio Rojas Trujillo Bioquìmico Legista SERVICIO MEDICO LEGAL-VALPARAISO (submitted Jan 11, 2010) |
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ID vs miniplexes |
Loss of alleles 12, 13, and 14 with miniplex assay; fine with ID |
9/532 |
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SGM vs SGM Plus |
Loss of allele 17 with SGM Plus; fine with SGM |
1/4245 |
Clayton et al. (2004) |
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| 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) |
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Loss of alleles 10 and 11 with PP16; fine with ProPlus |
3/110 |
Alves et al. (2003) |
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ID vs miniplexes |
Loss of allele 12 with miniplex assay; fine with ID |
1/532 |
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| D5S818 | PP16 vs SGM Plus/ProPlus | Loss of allele 10 with PP16; fine with SGM Plus | 2/2055 | Delamoye et al. (2004) |
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MF: 8,11 and ID: 8,9.3 5 base deletion in Identifiler amplicon outside of MiniFiler and PP16 primers |
1/1308 |
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Loss of alleles 15, 16, 17, and 18 with ProPlus; fine with PP16 |
13/1537 |
Budowle et al. (2001) |
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| D8S1179 | PP16 vs ProPlus | Loss of allele 16 with ProPlus; fine with PP16 | 1/110 | Alves et al. (2003) |
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SGM vs SGM Plus |
Loss of allele 16 with SGM Plus; fine with SGM |
1/4245 |
Clayton et al. (2004) |
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| 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) |
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ID vs miniplexes |
Shift of alleles 10 and 11 due to deletion outside of miniplex assay but internal to ID |
5/532 |
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MF: 11,11 and ID: 9,11 4 base deletion in the reverse MiniFiler primer binding region |
14/1308 |
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MF: 9,9 and ID: 9,11 caused by SNP in the MiniFiler primer binding site |
10/1308 |
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Loss of alleles with PP1.1; fine with PP16 and COfiler |
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Nelson et al. (2002) |
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Loss of allele 12 with PP16; fine with COfiler |
1/1537 |
Budowle et al. (2001) |
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| D16S659 | ESI-16 vs SGM Plus | Loss of allele 13 with SGM Plus: 9,9; ESI-16 genotype: 9,13 | Revoir et al. (2014) Sci. Justice, 54, 95-97 (submitted Feb 24, 2014) | |
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MF: 13,15 and ID: 15,15 caused by SNP in the Identifiler primer binding site |
1/1308 |
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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) |
| D18S51 | PP16 vs ID | Loss of allele 14 with PP16, fine with ID, caused by a SNP in the PP primer binding site, which is confirmed by sequencing after singleplex amplification | 1/18314 |
Sun Hongyu, Chen Wenjing, Sun Yat-sen University, China (submitted Apr 22, 2011) |
| D18S51 | PP16 vs ID | Loss of allele 18, 20 with PP, fine with ID, caused by a SNP in the PP primer binding site, which is confirmed by sequencing after singleplex amplification | 2/18314 |
Sun Hongyu, Chen Wenjing, Sun Yat-sen University, China (submitted Apr 22, 2011) |
| D18S51 | PP16 vs ID | Loss of allele 18 with PP, fine with ID, caused by a SNP in the PP primer binding site, which is confirmed by sequencing after singleplex amplification | 1/18314 |
Sun Hongyu, Chen Wenjing, Sun Yat-sen University, China (submitted Apr 22, 2011) |
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Loss of allele 32.2 with PP16; fine with ProPlus |
1/1537 |
Budowle et al. (2001) |
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| D21S11 | PP16 vs ID | Loss of allele 31 with PP, fine with ID, caused by a SNP in the PP primer binding site, which is confirmed by sequencing after singleplex amplification | 1/18314 |
Sun Hongyu, Chen Wenjing, Sun Yat-sen University, China (submitted Apr 22, 2011) |
| D21S11 | PP16 vs ID | Loss of allele 29.2 with PP, fine with ID, caused by a SNP in the PP primer binding site, which is confirmed by sequencing after singleplex amplification | 1/18314 |
Sun Hongyu, Chen Wenjing, Sun Yat-sen University, China (submitted Apr 22, 2011) |
| D19S433 | SGM Plus vs SGM | Loss of allele 11 with SGM Plus; fine with SGM | 1/4245 | Clayton et al. (2004) |
| D19S433 | PP ESI 17 vs ID | Loss of allele 15 with Identifiler; fine with PowerPlex ESI 17 on both father and son in a parentage case | Graciela Molina Fuentes, Laboratorio de Genetica Forense, Valparaiso, Chile (submitted Nov 8, 2011) | |
| D19S433 | PP Fusion vs ID | Loss of allele 12.3 with Identifiler on a convicted offender single-source sample; fine with PowerPlex Fusion (12.3, 15 with PHR of 98%) | Lesley Katzilierakis, CODIS Supervisor, Oklahoma State Bureau of Investigation | |
| DYS533 | PowerPlex Y23 vs Yfiler Plus | PowerPlex Y23 demonstrated an allele of 12 repeats, while Yfiler Plus demonstrated a 12.1 allele variant. Two additional PCR's led to the same results (CE = 3500XL). | Nurit Bublil, National Center of Forensic Medicine (submitted Oct. 2, 2020) | |
***Some information from Table 6.2 of Forensic DNA Typing, 2nd Edition (J.M. Butler, 2005)
Missing Regions of the Y-Chromosome
Information is also available on Y-STR null alleles at http://www.yhrd.org/Research/Loci.
|
Locus |
STR Kits/Assays Used |
Results |
Frequency of ChrY Deletion |
Source |
| Amelogenin | Promega Powerplex 21, Powerplex Y-23 | Confirmed by re sampling, repeated PCR and re-electrophoresis, and also confirmed by using male specific Y STR multiplex Amplification kit (Powerplex Y-23 Promega) | 2 | R.K. Kumawat, Rajesh Kumar, Anand Kumar, Hemant Priyadarshi* State Forensic Science Laboratory, Rajasthan, Jaipur-302016 (submitted May 28, 2019) |
| DYS576, DYS481, DYS570, and DYS458 | Promega PowerPlex Y 23 - Genetic Analyzer 3130 (4 capillary, POP-4 | Confirmed by re-sampling, repeated PCR and re-electrophoresis. Notes: In autosomal STR at locus AMEL, we observed AMEL Y deletion, which support our observation. | 2 | R.K. Kumawat, Rajesh Kumar, Anand Kumar, State Forensic Science Laboratory, Rajasthan , Jaipur- 302016 (submitted May 30, 2019) |
| DYS458, DYS576, DYS570, DYS481, DYS522, DYS455, DYS454, DYS449, DYS531, DYS590, DYS425, DYS450, DYS520, DYS568, DYS487, DYS522, DYS575, DYS463, DYS525, DYS532 | Y-111 (Family Tree DNA test) | No confirmation testing done. The 24 samples had a variety of surnames. | 24 | Randall Prouse Administrator of the Multiple Deletion and Prouse/Prowse Project at FTDNA |
| DYF387S1 | Yfiler Plus | Re-amplified with no detected product (Note: some peak height imbalance (48.4% and 41.6%) was also observed in DYS385 alleles) | Todd Lindsey, Oklahoma State Bureau of Investigation | |
| DYS385 | Yfiler | Re-amplified and re-analyzed with no detected product | 4 in 6300 | DNA Forensic Division, Supreme Prosecutor's Office, South Korea |
| DYS390 | Yfiler | Re-amplified and re-analyzed with no detected product | 1 in 6300 | DNA Forensic Division, Supreme Prosecutor's Office, South Korea |
| DYS391 | Yfiler | Re-amplified and re-analyzed with no detected product | 1 in 6300 | DNA Forensic Division, Supreme Prosecutor's Office, South Korea |
| DYS392 | Yfiler | Re-amplified and re-analyzed with no detected product | 6 in 6300 | DNA Forensic Division, Supreme Prosecutor's Office, South Korea |
| DYS438 | Yfiler | Re-amplified and re-analyzed with no detected product | 1 in 6300 | DNA Forensic Division, Supreme Prosecutor's Office, South Korea |
| DYS448 | Yfiler | Re-amplified and re-analyzed with no detected product | 63 in 6300 | DNA Forensic Division, Supreme Prosecutor's Office, South Korea |
| GATA-H4 | Yfiler | Re-amplified and re-analyzed with no detected product | 2 in 6300 | DNA Forensic Division, Supreme Prosecutor's Office, South Korea |
| YGATA-H4, DYS533 | Yfiler Plus | Re-amplified with no detected product | Todd Lindsey, Oklahoma State Bureau of Investigation | |
| DYS390, DYS385, DYS392, GATA H4, and DYS448 | Yfiler | Deletion of the 5 listed Y-STR loci observed in 4 separate case samples and 1 reference sample | Caron Pruiett, Washington State Patrol Crime Lab - Vancouver | |
| DYS385 | PPY, YF Plus | First re-amplified with PPY (allele size: 238.25) and concordance test with YF Plus (allele size: 241.33) - Alleles 10 and 18 were observed in father, but 10 and null in son. | 1 in 1119 | Forensic DNA division, National Forensic Service, Ministry of the Interior and Safety, Republic of Korea |
| DYS458 | PPY, YF Plus, Investigator® Argus Y-28 QS | First re-amplified with PPY and concordance test with YF Plus and Investigator® Argus Y-28 QS - The same was observed between father and son. | 2 related individuals (2 in 1119) | Forensic DNA division, National Forensic Service, Ministry of the Interior and Safety, Republic of Korea |
| DYS448 | YF Plus | Re-injection - DYF387S1 triplication and DYS448 deletion were observed concurrently, and the same was observed between father and 2 son. | 3 related individuals (3 in 1119) | Forensic DNA division, National Forensic Service, Ministry of the Interior and Safety, Republic of Korea |
| DYS448 | Promega Powerplex Y23 - ABI3500 | Deletion in Ref Suspect | Netherlands Forensic Institute | |
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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: 08/04/2016