Multiplex amplification of STR loci with gender alleles using infrared fluorescence detection

Infrared fluorescent automated detection of thirteen short tandem repeat polymorphisms and one gender-determining system of the CODIS core system

We used an infrared (IR) automated fluorescence monolaser sequencer for the analysis of 13 autosomal short tandem repeat (STR) systems (TPOX, D3S1358, FGA, CSF1PO, D5S818, D7S820, D8S1179, TH01, vWA, D13S317, D16S359, D18S51, D21S11) and the X-Y homologous gene amelogenin system. These two systems represent the core of the combined DNA index systems (CODIS). Four independent multiplex reactions, based on the polymerase chain reaction (PCR) technique and on the direct labeling of the forward primer of every primer pair, with a new molecule (IRDye800), were set up, permitting the exact characterization of the alleles by comparison with ladders of specific sequenced alleles. This is the first report of the whole analysis of the STRs of the CODIS core using an IR automated DNA sequencer. The protocol was used to solve paternity/maternity tests and for population studies. The electrophoretic system also proved useful for the correct typing of those loci differing in size by only 2 bp. A sensibility study demonstrated that the test can detect an average of 10 pg of undegraded human DNA. We also performed a preliminary study analyzing some forensic samples and mixed stains, which suggested the usefulness of using this analytical system for human identification as well as for forensic purposes.

Evaluation of an automated technique for assessment of marrow engraftment after allogeneic bone marrow transplantation using a commercially available kit

Several methods have been used to evaluate engraftment after allogeneic bone marrow transplantation (BMT). We assessed the usefulness of a multiple short tandem repeat (STR) amplification kit combined with a capillary electrophoresis unit for DNA identity analysis in the evaluation of engraftment after BMT. For 17 of 18 patients, at least 1 locus showed unique alleles for the donor and the recipient. In all cases, at least 1 locus was informative for the presence of small amounts of recipient DNA. The results from STR analysis were the same as Southern blot analysis in 14 of 17 cases. Differences included mixed chimerism detected only with STR analysis, informative loci present only with STR analysis, and informative loci present only with Southern blot analysis (1 case each). By using mock mixed chimeras, minor populations of 5% were detected routinely in all loci using the kit manufacturer's default protocol. By increasing the amount of amplified DNA, minor populations of 1% were detected in all cases but not in all loci. This single reaction technique provides for faster results, reduced workforce needs, and greater sensitivity than traditional Southern blot.

Infrared fluorescent detection of D1S80 alleles

A genetic locus D1S80 containing a variable number of tandem repeats (VNTR) has been used extensively in forensic analysis and paternity testing. In the current research, the D1S80 locus was amplified using polymerase chain reaction (PCR) technology and the alleles detected using a high sensitivity infrared (IR) fluorescence automated DNA sequencer. IR-labeled amplification products were generated using oligonucleotide primers which were covalently linked to an infrared fluorescent dye (IRD41) at the 5'-end. Human genomic DNA (1.0 ng or less) isolated from blood and various simulated forensic samples was successfully amplified using this technology. Allelic bands were detected by incorporation of the IR fluorescent dye into PCR products. Both Long Ranger and polyacrylamide denaturing gels permitted clear resolution of individual alleles that differ by only one repeat unit. In the smaller gels a separation distance of only 15 cm allowed separation of the alleles in less than 2 h from sample loading to visualization. This system combines IR fluorescence chemistry and laser technology thus eliminating the need for post-electrophoretic gel handling for the detection of D1S80 alleles. Real-time detection is valuable for immediate visualization of the data and the alleles are displayed as familiar autoradiogram-like images which can also be analyzed by computer. By loading a 64-lane gel twice it is possible to type at least 120 samples in 1 day using a single gel.