Non-uniform phenotyping of D12S391 resolved by second generation sequencing

Abstract

Non-uniform phenotyping of five case work samples were observed in the D12S391 locus. The samples were typed at least twice with the AmpFℓSTR NGM SElect PCR Amplification Kit and different alleles were called with GeneMapper ID-X in the different experiments. Detailed analyses of the electropherograms suggested that the individuals were heterozygous with two alleles that differed in size by one nucleotide. This was confirmed by amplifying the samples with the PowerPlex ESX 17 system. D12S391 is a complex STR with variable numbers of AGAT and AGAC repeats. Second generation sequencing revealed that separation of two alleles differing by one nucleotide in length was poor if the number of AGAT repeats in the short allele was higher than in the long allele. A total of 45 individuals with microvariants or off-ladder alleles in D12S391 were sequenced. Thirty different alleles were detected and sixteen of these were not previously reported.

Forensic and population genetic analyses of Danes, Greenlanders and Somalis typed with the Yfiler ® Plus PCR amplification kit

“…All samples were investigated with Yfiler 1 Plus according to the manufacturer's protocol with modifications in the reaction volume (12.5 ml), the volume of input DNA (0.5 ml) and the number of PCRcycles (25)(26)(27)(28)(29). Prior to electrophoresis, 1 ml of the amplified products and 0.5 ml of GeneScan TM 600 LIZ 1 Size Standard v. 2.0 were added to 9.5 ml of deionized Hi-Di TM formamide and denatured for 3 min at 95 C. The samples were electrophoresed on an Applied Biosystems 1 3500 Â L Genetic Analyzer (Thermo Fisher Scientific, Waltham, MA, USA) according to the recommendations of the manufacturer except for a slight modification of the injection time (12 s).…”

Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples

“…However, as predicted nearly five years ago [10], massively parallel sequencing technologies (MPS) are now finding their way into the forensic arena [8,[11][12][13][14][15][16][17][18][19][20]. These technologies largely remove the greatest existing technical and cost barriers to mtGenome sequencing of low DNA quality and quantity specimens.…”

Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing

“…They provide the possibility to (1) obtain detailed sequence information on the traditional forensic genetic markers, (2) type combinations of markers that cannot be typed in the same assay with the currently used methods, and (3) collect massive amounts of data from either one individual or large amount of data from many individuals simultaneously. SGS of STRs [1][2][3][4][5][6] and mtDNA [7,8] Life Technologies TM developed a SNP typing assay for human identification named the Ion Torrent TM HID SNP panel. An early version of this panel (v0.1) was recently tested by Budowle and co-workers [9].…”