Concordance study between the AmpFlSTR((R)) MiniFiler (TM) PCR amplification kit and conventional STR typing kits
ABSTRACT The AmpFlSTR MiniFiler 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 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 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.
Full-textDOI: · Available from: Julio J Mulero, Apr 07, 2014
- SourceAvailable from: Franz Neuhuber
[Show abstract] [Hide abstract]
- "The same applies to primer binding site mutations, which can result in a loss of amplification of a parentally inherited allele. These mutations are usually older and can be resolved after amplification with alternative primers   . "
ABSTRACT: Well defined estimates of mutation rates are a prerequisite for the use of short tandem repeat (STR-) loci in relationship testing. We investigated 65 isolated genetic inconsistencies, which were observed within 50,796 allelic transfers at 23 STR-loci (ACTBP2 (SE33), CD4, CSF1PO, F13A1, F13B, FES, FGA, vWA, TH01, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1132, D8S1179, D12S391, D13S317, D16S539, D17S976, D18S51, D19S433, D21S11) in Caucasoid families residing in Austria and Switzerland. Sequencing data of repeat and flanking regions and the median of all theoretically possible mutational steps showed valuable information to characterise the mutational events with regard to parental origin, change of repeat number (mutational step size) and direction of mutation (losses and gains of repeats). Apart from predominant single-step mutations including one case with a double genetic inconsistency, two double-step and two apparent four-step mutations could be identified. More losses than gains of repeats and more mutations originating from the paternal than the maternal lineage were observed (31 losses, 22 gains, 12 losses or gains and 47 paternal, 11 maternal mutations and 7 unclear of parental origin). The mutation in the paternal germline was 3.3 times higher than in the maternal germline. The results of our study show, that apart from the vast majority of single-step mutations rare multi-step mutations can be observed. Therefore, the interpretation of mutational events should not rigidly be restricted to the shortest possible mutational step, because rare but true multi-step mutations can easily be overlooked, if haplotype analysis is not possible.Forensic Science International: Genetics 08/2011; 6(3):381-6. DOI:10.1016/j.fsigen.2011.07.015 · 4.60 Impact Factor
Forensic Science International: Genetics 06/2011; 6(2):e78-9. DOI:10.1016/j.fsigen.2011.05.010 · 4.60 Impact Factor
- "Usually, concordance studies are required in order to detect allelic dropout or null alleles in a sample set when different kits are used for the same markers but which have different PCR primers  . In our study, after comparing almost 27,500 alleles using the Identifiler–NGM (the Identifiler and the NGM kits have the same primers in the common markers), the PowerPlex ESX17 and the Investigator ESS systems (3 kits Â 15 loci Â 2 alleles/ locus Â 284 samples), concordance in the genotyping results of all, three kits was observed in 99.99% (25,557 out of 25,560) STR allele calls compared. "
Forensic Science International: Genetics 06/2011; 5(3):e79-80. DOI:10.1016/j.fsigen.2010.07.002 · 4.60 Impact Factor
- "Minimum allele frequencies (MAF) for PCRbased loci, based on statistical and population genetics theory  were determined. Concordance studies are important to determine the possibility of any allelic dropout or null alleles present in a data set   resulting in an incorrect exclusion of two samples that come from a common source if different PCR primers are used. In our study, from almost 4500 alleles compared between the Identifiler and the PowerPlex ESX17 systems (2 kits Â 11 loci Â 2 alleles/locus Â 104 samples), full concordance between the typing results for the two kits was observed in 99.96% (4574 out of 4576) STR allele calls compared. "