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Concordance Study Between the AmpFℓSTR ® MiniFiler TM PCR Amplification Kit and Conventional STR Typing Kits *
Author(s) -
Hill Carolyn R.,
Kline Margaret C.,
Mulero Julio J.,
Lagacé Robert E.,
Chang ChienWei,
Hennessy Lori K.,
Butler John M.
Publication year - 2007
Publication title -
journal of forensic sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.715
H-Index - 96
eISSN - 1556-4029
pISSN - 0022-1198
DOI - 10.1111/j.1556-4029.2007.00491.x
Subject(s) - concordance , genotyping , typing , polymerase chain reaction , locus (genetics) , biology , microsatellite , genetics , microbiology and biotechnology , allele , genotype , gene
Abstract: The AmpFℓSTR ® MiniFiler TM 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 MiniFiler TM 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 MiniFiler TM 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. 1— 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 Variation1 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 siteSample 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.