Analysis of the HUMTH01 allele frequencies in the Spanish population

Genetic marker typing based on DNA amplification by the polymerase chain reaction (PCR) increasingly is being employed in forensic casework and for paternity testing. The allele frequencies were determined using PCR for 120 unrelated Spanish Caucasians for the locus HUMTHOH1. Six alleles were observed, with frequencies ranging from 0.013 (allele 11) to 0.254 (allele 10). The observed heterozygosity was 75.8%, and the power of discrimination is 0.92. The genotype distribution meets Hardy-Weinberg expectations.

Quantitation of polymerase chain reaction products by capillary electrophoresis using laser fluorescence

In samples where the amount of DNA is limited, the polymerase chain reaction (PCR) can amplify specific regions of the DNA. A quantitative analysis of the PCR product would be desirable to ensure sufficient DNA is available for analysis. In this study, we examine the use of capillary electrophoresis (CE) with laser fluorescence detection for quantitation of PCR products. A coated open tubular capillary was used with a non-gel sieving buffer and a fluorescent intercalating dye to obtain results within 20 minutes. Using an internal standard, peak migration time was below 0.1% relative standard deviation (R.S.D.) with a peak area precision of 3% R.S.D. In comparison to quantitation by hybridization, (i.e., slot blot) and spectrophotometric analysis, capillary electrophoresis shows distinct advantages due to its ability to separate unincorporated primers and PCR byproducts from the targeted PCR product. The results demonstrate that CE can be used to monitor the quality and quantity of the PCR product.

Swiss population data on the loci HLA-DQ alpha, LDLR, GYPA, HBGG, D7S8, Gc and D1S80

Allele and genotype frequencies for seven polymerase chain reaction-based DNA genetic markers were determined in a Swiss sample population. The loci are D1S80, HLA-DQ alpha, low density lipoprotein receptor, glycophorin A, hemoglobin G gammaglobin, D7S8, and group-specific component. All loci meet Hardy-Weinberg expectations. In addition, there is no detectable association of alleles between loci. The frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a DNA profile in the Swiss population.

Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA

We provide experimental evidence showing that, during the restriction-enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragments are small enough to prevent their reliable sizing on a Southern gel. As a result of such nondetectability of DNA fragments, individuals who show a single-band DNA profile at a VNTR locus may not necessarily be true homozygotes. In a population database, when the presence of such nondetectable alleles is ignored, we show that a pseudodependence of alleles within as well as across loci may occur. Using a known statistical method, under the hypothesis of independence of alleles within loci, we derive an efficient estimate of null allele frequency, which may be subsequently used for testing allelic independence within and across loci. The estimates of null allele frequencies, thus derived, are shown to agree with direct experimental data on the frequencies of HaeIII-null alleles. Incorporation of null alleles into the analysis of the forensic VNTR database suggests that the assumptions of allelic independence within and between loci are appropriate. In contrast, a failure to incorporate the occurrence of null alleles would provide a wrong inference regarding the independence of alleles within and between loci.

Greater differences in forensic DNA profile frequencies estimated from racial groups than from ethnic subgroups

A National Research Council (NRC) report asserted that genetic diversity between subgroups within a race is greater than between races. While this is counterintuitive to the basic tenets of human population genetics, the forensic application of statistical estimates of DNA profile frequencies has been questioned. The general approach used for estimating DNA profile frequencies by the majority of North American forensic laboratories is the use of the product rule on fixed bin allele frequencies derived from general population group databases. An informal analysis of the differences in frequency estimates within Hinf I-generated RFLP data determined in three ethnically distinct population groups--Norwegians, Spanish, and Turks--and in Caucasians and Blacks from the United States is presented. The VNTR loci analyzed are D2S44, D7S21, and D12S11. The data demonstrate that the assertion by the NRC is unfounded and that major population group databases, in lieu of subpopulation databases, can be used to provide estimates of DNA profile frequencies without consequences of wrongful bias.

Evaluation of Hinf I-generated VNTR profile frequencies determined using various ethnic databases

Concerns have been raised about hypothetical problems arising from the use of statistics for determining the likelihood of occurrence of DNA profiles for forensic purposes. A major contention is that reference databases based on subgroups of a major population category rather than on general (or major) population groups, might yield large differences in the estimated likelihood of occurrence of DNA profiles. This hypothetical issue is based on the assertion by some people that the differences among subgroups within a race would be greater than between races (at least for forensic purposes). To evaluate the effects of the above concern the likelihood of occurrence of 615 Hinf I-generated target DNA profiles was estimated using fixed bin frequencies from various ethnic databases and the multiplication rule. Based on the data in this study, differences in allele frequencies at a particular locus do not have substantial effects on VNTR profile frequency estimates when subgroup reference databases from within a major population group are compared. In contrast, the greatest variation in statistical estimates occurs across-major population groups. Therefore, the assertion, by some critics that the differences among subgroups within a race would be greater than between races (at least for forensic purposes), is unfounded. The data in the study support that comparisons across major population groups provide valid estimates of DNA profile frequencies without forensically significant consequences. The data do not support the need for alternate procedures, such as the ceiling principle approach, for deriving statistical estimates of DNA profile frequencies.

Analysis of short tandem repeat (STR) HUMVWA in the Spanish population

Amplification by polymerase chain reaction (PCR) of variable number of tandem repeat (VNTR) loci and subsequent typing by electrophoresis and silver staining has become a useful tool for identity testing. One viable group of genetic markers amenable to amplification by PCR is the short tandem repeat (STR) loci. A horizontal discontinuous polyacrylamide gel electrophoresis (PAGE) method was used to type the amplified products of the STR HUMVWA. Typing for VWA of 120 unrelated Spanish Caucasians was done. Six alleles were observed with frequencies in the range 0.096-0.242. The genotype distribution meets Hardy-Weinberg expectations (0.25 < P < 0.50). The heterozygosity was 73.3% and the discrimination power (DP) 0.94. Simultaneously, in a small sample of families (n = 24) no new mutations could be found.

D1S80 allele frequencies in a Chinese population

Allele frequencies for the VNTR locus D1S80 were determined in a Chinese population sample using the polymerase chain reaction and subsequent analysis of the amplified products by polyacrylamide gel electrophoresis and silver staining. A total of 18 nominal D1S80 alleles were observed in 105 unrelated Chinese. The data demonstrate that D1S80 is highly polymorphic in Chinese with a heterozygosity of 90.5%. The D1S80 frequency distribution meets Hardy-Weinberg expectations. This D1S80 data can be used in forensic analyses and paternity tests to estimate the frequency of a DNA profile in a Chinese population.

Sequential multiplex amplification (SMA) of genetic loci: a method for recovering template DNA for subsequent analyses of additional loci

A method called Sequential Multiplex Amplification (SMA) has been developed whereby a limited amount of DNA extracted from a sample can be reutilized for several single polymerase chain reaction (PCR) amplifications. The method involves recovery of genomic template DNA by microfiltration of PCR-amplified samples. Up to 5 different loci have been typed, each in a single system PCR-based assay, beginning with a test quantity of 5 ng template DNA. Genotypes of the DNA donors were compared with those obtained from individual amplifications and shown to be identical. This could be a useful technique for typing a number of loci from a limited amount of DNa and to recover template DNA from samples previously subjected to PCR. Obviously, when small quantities of template DNA are available, this technique can prove quite useful.

The assessment of frequency estimates of Hae III-generated VNTR profiles in various reference databases

The likelihood of occurrence of 1964 Hae III-generated target DNA profiles was estimated using fixed bin frequencies from various regional and ethnic databases and the multiplication rule. The databases generally were from the following major categories: Black, Caucasian, Hispanic, Oriental, and American Indian. It was found that subdivision, either by ethnic group or by U.S. geographic region, within a major population group did not substantially affect forensic estimates of the likelihood of occurrence of a DNA profile. As expected, the greatest variation in estimates for within-group estimates was among American Indian databases. Because the greatest variation in statistical estimates occurs across-major population groups, in most cases, there will be no unfair bias applying general population database estimates. Therefore, based on empirical data, there is no demonstrable need for using alternate approaches, such as the ceiling approach, to derive statistical estimates. The current practice of using general population databases and the multiplication rule provides valid estimates of the likelihood of occurrence of a DNA profile.

Horizontal polyacrylamide gel electrophoresis for the separation of DNA fragments

A discontinuous borate/formate buffer system is presented for horizontal polyacrylamide gel electrophoresis of DNA fragments. The resolution potential of the system could be altered by changing the total monomer concentration (5-9%T), the concentration of the crosslinker piperazine diacrylamide (2-5%CPDA), as well as the concentration of formate in the gel (40-120 mM), the leading ion of the buffer system. The separation of DNA fragments would be improved by increasing the migration distance from 22 to 28 cm. This discontinuous polyacrylamide gel electrophoresis system proved highly reproducible.

Swiss population data on three tetrameric short tandem repeat loci--VWA, HUMTHO1, and F13A1--derived using multiplex PCR and laser fluorescence detection

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci VWA, HUMTHO1, and F13A1 were determined in a Swiss population sample using multiplex PCR and subsequent electrophoresis in DNA sequencing gels processed by automated laser fluorescence detection. The technique allows single base pair resolution and rapid typing, with a concomitant reduction in the potential for human transcriptional typing errors. All loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the 3 loci. The allelic frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a multiple STR locus DNA profile in the Swiss population.

Forensic validation of the STR systems SE 33 and TC 11

Population studies on Caucasians from northwest Germany were carried out using the short tandem repeat (STR) systems SE 33 (Locus: ACTBP2) and TC 11 (Locus: 11p15.5). After electrophoresis in PAG 26 alleles could be identified for SE 33 in a sample size of 180 unrelated individuals and 6 alleles were found for TC 11 in 110 individuals. The combined mean exclusion chance for both systems was 0.96 and the discrimination index 0.999. No significant deviations from Hardy-Weinberg equilibrium could be demonstrated. In a small sample of families (SE 33 - n = 21; TC 11 - n = 30) no new mutations could be found. Positive and reproducible results for both STRs could be obtained from 50 pg template DNA.

Multigenerational amplification of a reference ladder for alleles at locus D1S80

The interlaboratory typing of DNA specimens that have been amplified at the D1S80 locus necessitates the use of a standard allelic reference ladder. This communication describes a technique in which individual, amplified alleles are isolated, combined, and amplified by PCR to produce a functional reference ladder composed of many of the alleles that occur at this locus. The amplified ladder can serve directly as a template source for production of the next generation of reference ladder. This process, in which each amplified ladder serves as the template for the next has been carried through multiple generations.

A comparison of the fixed bin method with the floating bin and direct count methods: effect of VNTR profile frequency estimation and reference population

When the results of a forensic comparison of highly polymorphic variable number tandem repeat (VNTR) loci fail to exclude a suspect as a possible contributor of biological evidence, it is desirable to convey to the trier of fact the significance of the match. Furthermore, in a forensic context, it is desirable that the estimated frequency of occurrence be conservative, that is, that any uncertainty in the estimate will favor the accused. Using an empirical approach with a data base of 2046 individuals belonging to one of four population groups, this study examined the effect of the method used to estimate frequency of occurrence of a VNTR profile from a reference data base, and the consequences of using a data base that may not represent the circumstances of the crime. The fixed bin method was at least as conservative as the floating bin and genotype counting (direct counting) methods. Secondly, for forensic purposes, profile frequency estimates from different reference populations do not deviate greatly. VNTR profiles are rare in any of the data bases.

PCR-amplification and detection of the human D1S80 VNTR locus. Amplification conditions, population genetics and application in forensic analysis

A series of experiments has been performed to evaluate amplification and typing of the D1S80 VNTR locus. The validation study that has been carried out showed that correct D1S80 typing results can be obtained when a defined amplification protocol and a high-resolution polyacrylamide gel electrophoresis method are used. The use of the Chelex extraction protocol has substantially reduced the processing time. DNA-extraction, amplification and subsequent typing can be performed in one day. The discrimination power of this locus is 0.94 in a Dutch Caucasian population sample. The system is extremely sensitive: 0.1 ng of genomic DNA gave a correct typing result. The test could also detect the correct genotypes in mixed samples containing DNA from different individuals. Even if the major type was in a 20-fold excess, the minority type could still be amplified and typed correctly. We have found no deviation from Hardy-Weinberg equilibrium in a Dutch Caucasian population sample. Evidence for the somatic stability of this locus was obtained from a set of experiments where we compared DNA-profiles from corresponding blood, semen and saliva samples. The results of this study suggest that in the near future analysis of the D1S80 locus by DNA-amplification can be applied in actual forensic case work.

Population data of the HLA DQ alpha locus in Dutch Caucasians. Comparison with other population studies

The HLA DQ alpha amplification and typing kit has been designed to be used by the forensic community for purposes of identity testing. The introduction of any new DNA marker in forensic identity testing requires the establishment of a population database for the relevant population(s). To this end allele and genotype frequencies for the HLA DQ alpha locus were determined in a Dutch Caucasian population sample and compared with 7 other population genetic studies. In our population sample the HLA DQ alpha genotype frequencies did not deviate from Hardy-Weinberg expectations and for this locus the power of discrimination is 0.94. A test for homogeneity of the HLA DQ alpha population data based on the allele frequency counts for 8 Caucasian population samples was performed and significant differences were found (P = 0.007). The differences in the frequency of the HLA DQ alpha 2 and 3 alleles are the major cause of this deviation. No deviation from population homogeneity was observed when we compared the genotype frequency distributions among the 8 Caucasian population samples. Combined with the extensive validation studies from Comey and Budowle and Helmuth et al. this population genetic study will allow HLA DQ alpha typing to be used in forensic identity testing in the Netherlands.

On allele frequency computation from DNA typing data

Forensic applications of DNA typing data require the estimation of the frequencies of all observed alleles, which is currently done by a fixed set of groupings (binning) of alleles in a database. Recently it's validity has been questioned on the ground that when a DNA fragment size is close to a bin boundary, the frequencies of all adjacent bins should be added. On the contrary, the current forensic database indicates that when the match window of a DNA fragment overlaps 2 bins, it is enough to consider the bin with the larger frequency, and this never underestimates the frequency within the match interval with the current choice of fixed-bin widths. On average, the current fixed-bin procedure yields an allele frequency at least 2-fold higher than that of a floating-bin.

Composite PAGE: an alternate method for increased separation of amplified short tandem repeat alleles

Genetic typing of short tandem repeat (STR) loci may require electrophoretic separation techniques which, depending on the locus, can resolve alleles differing in size by only 2, 3 or 4 base pairs (bps). Many such loci can be separated by horizontal, discontinuous polyacrylamide gel electrophoresis (hd-PAGE). However, some loci present particular separation challenges. A composite (or step) gel system consisting of 2 zones, anodal and cathodal, which differ by pore size and ionic strength, has been developed to augment resolution of DNA fragments without a need for additional electrophoretic equipment. Depending on pore size, as well as ionic strength, initial migration can be increased or decreased to effect resolution. When compared with hd-PAGE, this composite gel electrophoretic system can result in enhanced resolution of PCR amplified STR alleles.

PCR amplification and typing of the HLA DQ alpha gene in forensic samples

The polymerase chain reaction (PCR) was used to amplify the HLA DQ alpha gene using DNA recovered from evidentiary samples. Amplified HLA DQ alpha DNA was then typed using sequence-specific oligonucleotide probes. Slight modifications of previously published DNA extraction methods improved typing success of bloodstains and semen-containing material. Evidentiary samples, consisting of 206 known bloodstains, 26 questioned bloodstains, and 123 questioned semen-containing evidentiary materials were analyzed from 96 cases previously analyzed by restriction fragment length polymorphism (RFLP) typing in the FBI Laboratory. Of the known bloodstains, 98.5% yielded DQ alpha typing results. Of the questioned samples, 102 of 149 (24/26 bloodstains and 78/123 semen-containing materials), or 68%, produced typing results. Of the 78 cases that were RFLP inclusions, 59 yielded interpretable DQ alpha results and these were all inclusions. The remaining 19 cases could not be interpreted for DQ alpha. Of the 18 RFLP exclusions, eleven were DQ alpha exclusions, four were DQ alpha inclusions, and three could not be interpreted for DQ alpha. It is expected that because of the difference in discrimination potential of the two methods, some RFLP exclusions would be DQ alpha inclusions. Some samples that failed to produce typing results may have had insufficient DNA for analysis. Employment of a human DNA quantification method in DQ alpha casework would allow the user to more consistently use sufficient quantities of DNA for amplification. It also could provide a guide for determining if an inhibitor of PCR is present, thus suggesting the use of a procedure to improve amplification. This study provides support that the HLA DQ alpha typing procedure is valid for typing forensic samples.

Effects of nonoxinol-9 on the ability to obtain DNA profiles from postcoital vaginal swabs

Nonoxinol-9, the active ingredient of many spermicide foams and creams, has been shown to inactivate effectively high titres of HIV in vitro. Therefore the early administration of nonoxinol-9, perhaps by a rape victim herself, has been suggested as a potential prophylactic therapy for prevention of a possible HIV infection. For forensic DNA identity testing, it becomes pertinent to determine whether nonoxinol-9 could have an adverse effect on the recovery of high molecular weight DNA from postcoital vaginal swabs and thereby have an impact on restriction fragment length polymorphism (RFLP) analysis. If high molecular weight DNA can not be recovered, it may still be possible to proceed with analyses using PCR-based tests. In order to investigate the potential effects of nonoxinol-9, inserts, gels, or sponges containing nonoxinol-9 were applied either 15 min pre- or 15 to 60 min post coitus. Postcoital vaginal swabs were taken one and six h after sexual intercourse, the DNA was isolated and DNA identity typing was performed. The results demonstrate that nonoxinol-9 has no negative effect on the ability to obtain DNA profiles, either RFLP or PCR-based, from postcoital vaginal swabs. The quantity of extractable high molecular weight DNA obtained (as determined by slot-blot analysis) was comparable with that from uncontaminated postcoital vaginal swabs. RFLP patterns and PCR-based typing results at the HLA-DQ alpha and D1S80 loci from the nonoxinol-9 treated swabs were consistent with the uncontaminated control swabs and the corresponding whole blood samples of the donors. Therefore an early prophylactic administration of the topical anti-HIV agent nonoxinol-9 is not an impedient for obtaining DNA profiles from evidentiary material.

The forensic significance of various reference population databases for estimating the rarity of variable number of tandem repeat (VNTR) loci profiles

The likelihood of occurrence of 1,964-HaeIII-generated target DNA profiles was estimated using fixed bin VNTR frequencies from various Caucasian, Black, and Hispanic databases and the product rule. The data in this study demonstrate that for forensic purposes there are smaller differences in statistical estimates of DNA profile frequencies among subgroup databases than among estimates across major population databases. This observation does not support the premise asserted by the NCR Report (1992) that the differences among subgroups within a race would be greater than between races (at least for forensic purposes). Therefore, the data do not support the need for alternative procedures, such as the ceiling principle approach (NRC Reports, 1992), for deriving statistical estimates of DNA profile frequencies. Comparisons across major population groups provide reasonable, reliable, and meaningful estimates of DNA profile frequencies without forensically significant consequences.

Population genetics and forensic efficiency data of 4 AMPFLP's

Family studies were carried out in a population sample from north west Germany using 4 amplifiable VNTR polymorphic systems D1S80 (MCT118), ApoB, D17S30 (YNZ22) and COL2A1. Separation was carried out in polyacrylamide gels and visualised using silver staining. In family studies (n = 30) no evidence of new mutations was found. The population study of unrelated individuals (mothers and putative fathers) showed that all 4 systems were highly polymorphic and similar to other population studies. The combined exclusion chance was calculated to be approximately 99% and the combined discrimination index 1.5.10(-4). The Hardy-Weinberg equilibrium was checked by forming groups of alleles and no significant deviations could be found in all systems.