Concordance Study Between the AmpFℓSTR® MiniFilerTM PCR Amplification Kit and Conventional STR Typing Kits*
Authors: Hill Carolyn R. , Kline Margaret C. , Mulero Julio J. , Lagacé Robert E. , Chang Chien‐Wei , Hennessy Lori K. , Butler John M. 
Published: June 2007

Abstract:  The AmpFℓSTR® MiniFilerTM polymerase chain reaction amplification kit developed by Applied Biosystems enables size reduction on eight of the larger STR loci amplified in the Identifiler® kit, which will aid recovery of information from highly degraded DNA samples. The MiniFilerTM Kit amplifies CSF1PO, FGA, D2S1338, D7S820, D13S317, D16S539, D18S51, and D21S11 as well as the sex‐typing locus amelogenin. A total of 1308 samples were evaluated with both the MiniFilerTM and Identifiler® STR kits: 449 African American, 445 Caucasian, 207 Hispanic, and 207 Asian individuals. Full concordance between Identifiler and MiniFiler Kits was observed in 99.7% (10,437 out of 10,464) STR allele calls compared. The 27 differences seen are listed in Table 1 and encompass the loci D13S317 (n = 14) and D16S539 (n = 10) as well as D18S51 (n = 1), D7S820 (n = 1), and CSF1PO (n = 1). Genotyping discrepancies between the Identifiler and MiniFiler kits were confirmed by reamplification of the samples and further testing using the PowerPlex® 16 kit in many cases. DNA sequence analysis was also performed in order to understand the nature of the genetic variations causing the allele dropout or apparent repeat unit shift.

Summary of 27 discordant STR profiling results observed in this study between the Identifiler® and MiniFiler™ kits for 449 different AA, 445 C, 207 H, and 207 A samples.

Locus
Ethnicity
Source
MiniFiler
Identifiler
PP16
Genetic Variation

1
CSF1PO
H
IBB
11,11
11, “11.1”
11,11
One base insertion in Identifiler amplicon outside of MiniFiler and PP16 primers

2
D7S820
AA
IBB
8,11
8,”9.3”
8,11
5 base deletion in Identifiler amplicon outside of MiniFiler and PP16 primers

3
D13S317
H
IBB
11,11
9,11
9,11
4 base deletion in the reverse MiniFiler primer binding region

4
D13S317
H
IBB
13,13
9,13
9,13
(same as sample no. 3)

5
D13S317
H
IBB
14,14
9,14
9,14
(same as sample no. 3)

6
D13S317
AA
IBB
11,11
9,11
9,11
(same as sample no. 3)

7
D13S317
AA
IBB
12,12
8,12
8,12
(same as sample no. 3)

8
D13S317
AA
IBB
11,11
8,11
8,11
(same as sample no. 3)

9
D13S317
AA
IBB
13,13
10,13
10,13
(same as sample no. 3)

10
D13S317
AA
IBB
11,11
9,11
9,11
(same as sample no. 3)

11
D13S317
AA
IBB
12,12
9,12
9,12
(same as sample no. 3)

12
D13S317
AA
DDC
10,10
9,10
 

13
D13S317
C
IBB
12,12
9,12
9,12
(same as sample no. 3)

14
D13S317
C
DDC
11,11
10,11
 

15
D13S317
C
DDC
8,8
8,10
 

16
D13S317
A
DDC
12,12
10,12
 

17
D16S539
AA
DDC
9,9
9,11
 

18
D16S539
AA
IBB
12,12
11,12
11,12
A/G SNP in MiniFiler primer binding site

19
D16S539
AA
MLN
11,11
9,11
9,11
(same as sample no. 18)

20
D16S539
AA
DDC
14,14
11,14
11,14
(same as sample no. 18)

21
D16S539
AA
DDC
9,9
9,11
9,11
(same as sample no. 18)

22
D16S539
AA
DDC
13,13
11,13
 

23
D16S539
AA
DDC
12,12
11,12
 

24
D16S539
AA
DDC
12,12
11,12
 

25
D16S539
AA
DDC
9,9
9,12
 

26
D16S539
A
ABI
11,11
10,11
 
G/A SNP in MiniFiler primer binding site

27
D18S51
H
IBB
13,15
15,15
13,15
Allele 13 C/T SNP in Identifiler primer binding site

Sample sources include IBB, MLN, DDC, and ABI. With only three exceptions (see samples no. 1, 2, 27), PowerPlex® 16 (PP16) results agree with the Identifiler® results for these samples. DNA sequencing was performed to ascertain the genetic variation responsible for the discordance of the impacted allele (shown in bold font). Note that sample no. 15 is the child of sample no. 14, sample no. 20 is the child of sample no. 21, and sample no. 22 is the child of sample no. 23.

AA, African American; C, Caucasian; H, Hispanic; A, Asian; MLN, Millennium; IBB, Interstate Blood Bank; DDC, DNA Diagnostic Center; ABI, Applied Biosystems.