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

To contribute to these concordance study summaries, click here.

Locus

STR Kits/Assays Compared

Results

Frequency of Primer Binding Site Mutation

Source

CSF1PO

MiniFiler vs ID vs PP16

MF: 11,11 and ID: 11,11.1

One base insertion in Identifiler amplicon outside of MiniFiler and PP16 primers

1/1308

Hill et al. (2007)

CSF1PO

PP16 vs COfiler

Loss of allele 14 with COfiler; fine with PP16

2/1537

Budowle et al. (2001)

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)

FGA

 

SGM vs SGM Plus

Loss of allele 26 with SGM Plus; weak amp of same allele with SGM

 

Cotton et al. (2000)

FGA

PP16 vs ProPlus

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)
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)

TH01

PP16 vs COfiler

Loss of allele 9 with COfiler; fine with PP16

1/1537

Budowle et al. (2001)

TH01

 

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)
TH01

 

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)

VWA

 

PP1.1 vs ProPlus

Loss of allele 19 with ProPlus; fine with PP1.1

2/1483

Kline et al. (1998) and Walsh (1998)

VWA

PP16  vs ProPlus

Loss of alleles 15 and 17 with ProPlus; fine with PP16

2/1537

Budowle et al. (2001)

VWA

PP16  vs ProPlus

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)

VWA

ID vs miniplexes

Loss of alleles 12, 13, and 14 with miniplex assay; fine with ID

9/532

Drabek et al. (2004)

 

VWA

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)

D5S818

 

PP16  vs ProPlus

Loss of alleles 10 and 11 with PP16; fine with ProPlus

3/110

Alves et al. (2003)

D5S818

ID vs miniplexes

Loss of allele 12 with miniplex assay; fine with ID

1/532

Drabek et al. (2004)

D5S818 PP16  vs SGM Plus/ProPlus Loss of allele 10 with PP16; fine with SGM Plus 2/2055 Delamoye et al. (2004)

D7S820

MiniFiler vs ID vs PP16

MF: 8,11 and ID: 8,9.3

5 base deletion in Identifiler amplicon outside of MiniFiler and PP16 primers

1/1308

Hill et al. (2007)

D8S1179

 

PP16  vs ProPlus

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)

D8S1179

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)

D13S317

ID vs miniplexes

Shift of alleles 10 and 11 due to deletion outside of miniplex assay but internal to ID

5/532

Drabek et al. (2004)

D13S317

MiniFiler vs ID vs PP16

MF: 11,11 and ID: 9,11

4 base deletion in the reverse MiniFiler primer binding region

14/1308

Hill et al. (2007)

D16S659

MiniFiler vs ID vs PP16

MF: 9,9 and ID: 9,11

caused by SNP in the MiniFiler primer binding site

10/1308

Hill et al. (2007)

D16S659

 

PP1.1 vs PP16  vs COfiler

Loss of alleles with PP1.1; fine with PP16 and COfiler

 

Nelson et al. (2002)

D16S659

PP16  vs COfiler

Loss of allele 12 with PP16; fine with COfiler

1/1537

Budowle et al. (2001)

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)

D18S51

MiniFiler vs ID vs PP16

MF: 13,15 and ID: 15,15

caused by SNP in the Identifiler primer binding site

1/1308

Hill et al. (2007)

D18S51

 

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)

D21S11

PP16  vs ProPlus

Loss of allele 32.2 with PP16; fine with ProPlus

1/1537

Budowle et al. (2001)

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
         

***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

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
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

 

 

 

 

 

 

 

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.

Variant Alleles

Tri-Allelic Patterns

Information on Variant STR Alleles Sequenced at NIST

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.

 

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Last Updated: 08/04/2016