AmpFlSTR Profiler Plus and AmpFlSTR COfiler analysis of tissues stored in GenoFix, a new tissue preservation solution for mass disaster DNA identification.

A preliminary study was conducted to assess the capability of a new alcohol-based tissue fixative, GenoFix, to preserve DNA from biopsy tissues stored at room temperature and/or -20 degrees C in a freezer, for subsequent short tandem repeat (STR) DNA typing analysis. Fresh human smooth muscle samples were stored at room temperature in GenoFix for one month and up to one year and seven months before being processed using the megaplex STR systems, AmpFlSTR Profiler Plus and AmpFlSTR COfiler. Alternatively, muscle tissues in GenoFix were placed at -20 degrees C in a freezer for up to 3 1/2 years following two to three months in the fixative at room temperature. DNA analysis was also carried out on tissues stored in GenoFix for one month at room temperature and subsequently paraffin-embedded and stored at room temperature for four years. The AmpFlSTR Profiler Plus and AmpFlSTR COfiler STR profiles produced, using DNA extracted from all fixed tissue samples, were of very good quality. The fluorescent signals were well balanced across the nine STR loci or six loci comprised in the megaplexes surveyed and profiles showed no differences with those observed for the control blood of the respective donor patients. Continuous exposure to GenoFix at room temperature (up to one year and seven months) did not compromise the STR typing analysis of the fixed tissues. No adverse effects were noted on the STR typeability of tissues fixed with GenoFix and stored at -20 degrees C in a freezer for up to 3 1/2 years. STR profiles generated from the paraffin-embedded tissues fixed in GenoFix were of excellent quality. This preliminary study suggests that GenoFix can be used to store tissue samples at room temperature for up to one year and seven months or at -20 degrees C in a freezer for longer storage (up to 3 1/2 years). This new and odorless tissue fixative promotes tissue and DNA preservation in a very effective manner and as such may prove useful in criminal investigations or mass disaster identifications carried out in remote locations and in which a small or large number of tissue samples are collected for further analyses.

Fingerprint enhancement revisited and the effects of blood enhancement chemicals on subsequent profiler Plus fluorescent short tandem repeat DNA analysis of fresh and aged bloody fingerprints.

This study was aimed at determining the effect of seven blood enhancement reagents on the subsequent Profiler Plus fluorescent STR DNA analysis of fresh or aged bloody fingerprints deposited on various porous and nonporous surfaces. Amido Black, Crowle's Double Stain. 1,8-diazafluoren-9-one (DFO), Hungarian Red, leucomalachite green, luminol and ninhydrin were tested on linoleum, glass, metal, wood (pine, painted white), clothing (85% polyester/15% cotton, 65% polyester/35% cotton, and blue denim) and paper (Scott 2-ply and Xerox-grade). Preliminary experiments were designed to determine the optimal blood dilutions to use to ensure a DNA typing result following chemical enhancement. A 1:200 blood dilution deposited on linoleum and enhanced with Crowle's Double Stain generated enough DNA for one to two rounds of Profiler Plus PCR amplification. A comparative study of the DNA yields before and after treatment indicated that the quantity of DNA recovered from bloody fingerprints following enhancement was reduced by a factor of 2 to 12. Such a reduction in the DNA yields could potentially compromise DNA typing analysis in the case of small stains. The blood enhancement chemicals selected were also evaluated for their capability to reveal bloodmarks on the various porous and nonporous surfaces chosen in this study. Luminol. Amido Black and Crowle's Double Stain showed the highest sensitivity of all seven chemicals tested and revealed highly diluted (1:200) bloody fingerprints. Both luminol and Amido Black produced excellent results on both porous and nonporous surfaces, but Crowle's Double Stain failed to produce any results on porous substrates. Hungarian Red, DFO, leucomalachite green and ninhydrin showed lower sensitivities. Enhancement of bloodmarks using any of the chemicals selected, and short-term exposure to these same chemicals (i.e., less than 54 days), had no adverse effects on the PCR amplification of the nine STR systems surveyed (D3S 1358, HumvWA, HumFGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) or of the gender determination marker Amelogenin. The intensity of the fluorescent signals was very similar and the allele size measurements remained constant and identical to those of untreated bloody fingerprints. No additional background fluorescence was noted. Continuous exposure (for 54 days) to two of the seven enhancement chemicals selected (i.e., Crowle's Double Stain and Hungarian Red) slightly reduced the amplification efficiency of the longer STR loci in profiles of fresh and 7 to 14-day-old bloodprints. This suggests that long-term exposure to these chemicals possibly affects the integrity of the DNA molecules. This study indicates that significant evidence can be obtained from fresh or aged bloody fingerprints applied to a variety of absorbent and nonabsorbent surfaces which are exposed to different enhancement chemicals for short or long periods of time. It also reaffirms that PCR STR DNA typing procedures are robust and provide excellent results when used in concert with fluorescence-based detection assays after fingerprint identification has taken place.

Validation of highly polymorphic fluorescent multiplex short tandem repeat systems using two generations of DNA sequencers.

Validation studies are a crucial requirement before implementation of new genetic typing systems for clinical diagnostics or forensic identity. Two different fluorescence-based multiplex DNA profiling systems composed of amelogenin, HumD21S11 and HumFGA (referred to as multiplex 1A), and HumD3S1358, HumD21S11 and HumFGA (multiplex 1B) have been evaluated for use in forensic identification using the Applied Biosystems Model 373A and Prism 377 DNA Sequencers, respectively. Experiments were aimed at defining the limit of target DNA required for reliable profiling, the level of degradation that would still permit amplification of the short tandem repeat (STR) loci examined, and the robustness of each locus in the multiplexes after samples were exposed to environmental insults. In addition, the specificity of the multiplexes was demonstrated using nonhuman DNAs. Forensically relevant samples such as cigarette butts, chewing gum, fingernails and envelope flaps were processed using both an organic extraction procedure and a QIAamp protocol. DNAs and resultant multiplex STR profiles were compared. The validation of the triplex STR systems was extended to include over 140 nonprobative casework specimens and was followed with a close monitoring of initial casework (over 300 exhibits). Our results document the robustness of these multiplex STR profiling systems which, when combined with other multiplex systems, could provide a power of discrimination of approximately 0.9999.

Population genetic characteristics of the STR Loci D21S11 and FGA in eight diverse human populations.

A highly polymorphic multiplex short tandem repeat (STR) system composed of D21S11, FGA, and the sex-typing system amelogenin (AMG) has been used to investigate allele frequency distributions in two Canadian Caucasian samples (British Columbia and Alberta), three Canadian aboriginal populations (Coastal Salishans from British Columbia, Ojibwa from northern Ontario, and Cree from Saskatchewan), and three ethnic groups from Singapore (Chinese, Malays, and Asian Indians). Using the automated fluorescence detection approach on an ABD 373A DNA Sequencer, we distinguished 20 D21S11 and 22 FGA alleles with a nearly equal representation of two- and four-base variants. An overlap in allele sizes for both STR loci across populations was observed, but frequency differences were noted. Statistical analysis revealed that (1) both D21S11 and FGA loci conform to Hardy-Weinberg equilibrium in all eight surveyed populations based on five different tests and (2) both STR loci are in linkage equilibrium. Results from the 2 x N contingency table exact tests for population differentiation demonstrated that the Canadian samples from two different provinces were not distinguishable from one another at either STR locus and therefore could be combined to form one Caucasian group. Likewise, Chinese and Malays from Singapore did not show significant differences at either STR locus. In contrast, all other examined populations exhibited differences deemed statistically significant. As a complement to our study, we compared D21S11 allele frequency distributions in 21 worldwide populations and FGA allele frequency distributions in 14 populations. Many alleles never previously reported in worldwide populations were identified in Canadian aboriginal and Asian samples from this study. Twenty-four D21S11 and 29 FGA alleles were distinguished in worldwide groups. Interesting similarities in allele frequency distribution patterns across populations suggest that the STR polymorphism at these loci predates the geographic dispersal of ancestral human populations. This study further demonstrates the utility of highly informative STR loci such as D21S11 and FGA in human population evolutionary history and in forensic medicine.

Characterization of human lymphoid cell lines GM9947 and GM9948 as intra- and interlaboratory reference standards for DNA typing.

The incorporation of reference DNA is crucial to the validation of any DNA typing protocol. Currently, reference DNA standards are restricted to molecular size DNA ladders and/or tumor cell line DNA. Either of these, however, presents some limitations. We have rigorously characterized two Epstein-Barr virus (EBV)-immortalized human lymphoid cell lines--GM9947 (female) and GM9948 (male)--to determine their suitability as alternative in-line standards for three widely employed allele profiling strategies. Twenty-one highly polymorphic VNTR-based allelic systems (7 RFLPs, 2 AmpFLPs, and 12 STRs) distributed over 12 chromosomes were scrutinized along with 3 gender-based discriminatory systems. The genetic stability of each locus was confirmed over a period of 225 in vitro population doublings. Allele size estimates and degree of informativeness for each of the 21 VNTR systems were compiled. The reproducibility of allele scoring by traditional RFLP analyses, using both cell lines as reference standards, was also verified by an interlaboratory validation study involving 13 analysts from two geographically distinct forensic laboratories. Taken together, our data indicate that GM9947 and GM9948 genomic DNAs could be adopted as reliable reference standards for DNA typing.

DNA typing for bone marrow engraftment follow-up after allogeneic transplant: a comparative study of current technologies.

DNA typing is widely used to document engraftment after allogeneic bone marrow transplantation (BMT). Most DNA typing procedures discriminate allogeneic engraftment on the basis of DNA length polymorphisms or sequence variations found in variable number of tandem repeat (VNTR) loci, or the presence of Y chromosome-specific DNA We have compared 3 types of VNTR analysis, their respective mode of allele detection and Y chromosome DNA detection in order to assess the strengths and limitations of each approach. Chimerism was assessed in 8 recipients after allogeneic BMT. Samples were subjected to 6 restriction fragment length polymorphism (RFLP) loci-analysis using radioactivity, 2 amplified fragment length polymorphism (AmpFLP) loci-analysis using a silver-stain mode of detection, 12 short tandem repeat (STR) loci-analysis using fluorescence detection and Y chromosome analysis. We evaluated each procedure for its ability to (1) discriminate sibling donor-recipient pairs in our samples; (2) generate a concordant chimerism diagnosis; and (3) detect and assess the contribution of minority components in mixed-chimera situations. In sex-mismatched BMTs with a female graft donor, Y chromosome probing has proven most efficient. In all other cases, AmpFLPs proved to be a rapid and efficient procedure with sufficient discriminating capability and sensitivity to warrant their use in clinical settings. STRs are rapid as well but require a larger loci complement to discriminate efficiently and they do not currently detect, under our conditions, all mixed chimeras. RFLPs are clearly superior at discriminating siblings but are time-consuming and serve best in cases where AmpFLP and STR analyses fail.

DNA typing with fluorescently tagged short tandem repeats: a sensitive and accurate approach to human identification.

Human identification through DNA analysis has faced tremendous changes in the past seven years. The advent of the polymerase chain reaction (PCR) technology coupled with the discovery of amplifiable minisatellites and microsatellites known as amplified fragment length polymorphisms and short tandem repeats (STRs), respectively, allow allelic profiles to be obtained with minute amounts of target DNA even in a degraded state. Very recently, a new dimension in DNA typing analysis was opened with the development of instruments for automated real-time analysis of fluorescent amplification products. In order to derive an automated approach to DNA typing, STR systems were evaluated for sensitivity and accuracy using the Gene Scanner and compared to other DNA typing methods currently in use. Eight different STR systems (encompassing tri-, tetra- and pentanucleotide repeats) were investigated, and conditions for their amplification with fluorescence-tagged primers, resolution on polyacrylamide gels and analysis on a fluorescent DNA fragment analyzer were optimized. Using these conditions, discrete allelic profiles were obtained following amplification of DNA extracted from various cell lines, liquid blood, dry bloodstains and hair samples. Amplification from serial dilutions of template DNA indicated that the minimal amount of target DNA required to detect a fluorescent signal on the Gene Scanner for any of the eight STR systems examined is approximately 100 picograms. The level of precision obtained for real-time allele size determination was observed to be +/- 0.2 to 0.5 base pair (intragel) and +/- 0.5 to 1.5 base pairs (intergel). Consequently, PCR-based DNA typing with fluorescent STR primers and automated analysis provides the enhanced level of precision, accuracy and sensitivity required for forensic casework analysis. Moreover, this approach offers significant advantages for the routine processing of large numbers of DNA samples, greatly facilitates and expedites the generation of allelic profile databases and enables investigators to perform the simultaneous survey of several different loci from single individuals and/or forensic samples.

Two cytotoxic cell proteinase genes are differentially sensitive to sodium butyrate.

The 5'-flanking regions of two cytotoxic cell protease genes, CCP1 and 2, are sufficient to confer cytotoxic T lymphocyte-specific expression when fused to a reporter gene. The two regulatory regions are, however, differentially sensitive to treatment of the recipient cell, MTL 2.8.2, with sodium butyrate. With CCP1 a six-fold increase in cat expression was observed, whereas CCP2 was insensitive to the butyrate treatment. One major butyrate-sensitive regions was defined in the CCP1 5'-flanking sequence between -243 to -112 and another less effective one between-682 to -427. These fragments of DNA were also able to confer responsiveness to butyrate when ligated to a heterologous fos promoter. These sequences within the 5' flank of CCP1 share homology with other elements that have been defined as butyrate-responsive. We believe that our results argue against a pleiotropic affect of butyrate such as histone acetylation. More likely sodium butyrate is mediating a specific stimulation of transcription through modification of the activities of selected transcriptional regulatory proteins that in turn affect their interactions with proteins bound to the promoter.

Transcription of two cytotoxic cell protease genes is under the control of different regulatory elements.

Precursor cytotoxic T lymphocytes are activated upon interaction with antigen and interleukin 2. The development of the mature killer cell phenotype is achieved by the transcription of a number of function related genes including those encoding a family of cytotoxic cell proteases (CCP). Two of these proteases, CCP1 and CCP2 encoded by C11 and B10, are shown in this report to contain cell-specific transcriptional regulatory elements within their 5'-flanking regions. Two positive regulatory sequences were mapped for C11 (-682 to -427 and -243 to -112) and one for B10 (-279 to -189). In addition each flanking region contains a region of DNA (B10 -1617 to -1049 and C11 -427 to -243) that has a negative influence on transcription. The positive regions do not appear to correspond to any previously characterized regulatory elements but do map to the same region as DNase I hypersensitive sites. When ligated to heterologous promoters these elements can still stimulate transcription but cell-specificity of expression is lost. In addition the conbination of positive regulatory region and promoter is important for the stimulatory effect. The ability of these regulatory sequences to function and to determine cell-specific transcription does not appear to be an intrinsic property but also depends upon the context.

Factors influencing transient expression in cytotoxic T cells following DEAE dextran-mediated gene transfer.

A number of transfection protocols have been tested for the introduction of exogenous DNA into cytotoxic T cells. These included electroporation, lipofection, calcium phosphate coprecipitation, polybrene-assisted gene transfer, and DEAE dextran-mediated transfer. Only the latter gave significant and reproducible transfection efficiencies coupled with low toxicity. The DEAE dextran protocol was optimized for the transfection of a transcription reporter construct pRSVcat into a cloned cytotoxic cell line. Among the parameters investigated were cell density, amount of input DNA, concentration of DEAE dextran, DNA adsorption time, temperature, use of permeabilization and expression facilitators, and recovery time. The optimized protocol was then used to demonstrate the presence of cis-acting regulatory regions in the 5'-flanking sequences of two cytotoxic cell-specific serine protease genes and, in addition, was shown to be applicable to other cloned T-cell lines.

Synthesis and processing of small B2 transcripts in mouse embryonal carcinoma cells.

B2 genes are short repeated sequences which are transcribed by RNA polymerase III. Abundant transcripts accumulate in embryonic and transformed cells, but transcripts are rare or absent from normal differentiated cell types. During retinoic acid-induced differentiation of P19 embryonal carcinoma cells, an early transient increase in B2 RNA levels is followed by a rapid drop in expression. The marked changes in B2 RNA levels are most likely due to transcriptional modulation since B2 RNA stabilities are unaffected by differentiation. At least four short-lived B2 RNAs with apparent lengths of 150, 180, 240, and 500 nucleotides were characterized. The two larger RNAs are polyadenylated and are more stable in cells. A cDNA of a B2 gene was isolated which was over 99% identical to the consensus sequence. This B2 cDNA can be transcribed in human cells and yields at least two distinct transcripts. We propose a model for B2 RNA metabolism which describes transcription, posttranscriptional modification and processing, and nucleocytoplasmic transport.

Cloning of a gene that encodes a new member of the human cytotoxic cell protease family.

A family of unusual serine proteases that are believed to be involved in the effector mechanism of cell-mediated cytotoxicity have previously been described in the mouse. However, in the human only one gene encoding a member has been isolated. By use of a mixture of murine cDNAs as probes, a second human gene has now been isolated. The primary structures of the gene and the predicted protein are very similar to those of the mouse. In addition, in keeping with the postulated involvement in cytolysis, transcripts were detected only in cytotoxic cells. The organization of the coding and noncoding regions of the gene, the clustering of family members, and the chromosomal location, close to the alpha chain of the T cell antigen receptor, are all conserved between human and mouse.