Statistical analysis of data for three British ethnic groups from a new STR multiplex.

Data have been collected from 602 Caucasians, 190 Afro-Caribbeans and 257 Asians of Indo/Pakistani descent who have been profiled using a new six locus short tandem repeat (STR) multiplex. The data have been analysed by conventional significance testing methods: the exact test, homozygosity, and conventional goodness of fit to Hardy-Weinberg proportions. Frequency tables are given and the expected performance in British forensic casework is discussed.

Statistical analysis of data for three British ethnic groups from a new STR multiplex

Data have been collected from 602 Caucasians, 190 Afro-Caribbeans and 257 Asians of Indo/Pakistani descent who have been profiled using a new six locus short tandem repeat (STR) multiplex. The data have been analysed by conventional significance testing methods: the exact test, homozygosity, and conventional goodness of fit to Hardy-Weinberg proportions. Frequency tables are given and the expected performance in British forensic casework is discussed.(AU)

Validation of the Applied Biosystems Prism 377 automated sequencer for the forensic short tandem repeat analysis.

The Applied Biosystems (ABI) Prism 377 DNA sequencer has been evaluated in an attempt to increase the throughput of samples for short tandem repeat (STR) analysis, in both forensic casework and the UK National Criminal Intelligence DNA Database. The gel system assessed consisted of 0.2 mm, 4% acrylamide 6 M urea gels, with a well-to-read distance of 36 cm. Gels were run at a constant voltage of 3 kV and constant temperature of 51 degrees C. The run time of our second generation multiplex (SGM) STR system was achieved in less than 2 h. Rigorous validation has been performed on the instrument hardware and software. Complete resolution of 1 base differences was obtained, up to and beyond 350 bases; sizing precision across gels was more than 2-fold higher than the 373A and the sensitivity was increased by one third.

Validation of highly discriminating multiplex short tandem repeat amplification systems for individual identification.

Short tandem repeat (STR) loci are routinely employed for individual identification. WE have examined the performance and reproducibility of a highly informative co-amplification system containing the tetranucleotide STR loci: HUMVWFA31/A, HUMTH01, D20S85, D8S1179, HUMFIBRA, D21S11, and D18S51, in conjunction with the amelogenin sex test, in addition to a modified system omitting the locus D20S85. Polymerase chain reaction (PCR) products were fluorescently detected on an automated sequencer and automatically sized against an internal size standard by Genescan software. Both systems were routinely able to type 500 pg of undegraded DNA. At DNA concentrations between 50-500 pg, partial profiles were produced, but no allelic drop-out was observed. Balanced amplification of all loci occurred over a wide range of DNA concentrations from 50 pg to 10 ng. Alteration of reagent concentrations and cycling parameters from optimal resulted in variation in the efficiency of individual locus amplification relative to the other loci within the system. This was also observed at high ionic strength or extreme pH. However, at all reagent concentrations and conditions, allelic drop-out was not observed. These multiplex systems have potential in both routine forensic and intelligence database applications.

A new method of STR interpretation using inferential logic--development of a criminal intelligence database.

A short tandem repeat (STR) system consisting of seven multiplexed loci has recently been introduced in the UK to support a National strategy to create large DNA databases for criminal intelligence purposes. The process uses automated sequencers, employing dye-labelled primers. Identification of tetrameric loci such as HUMTH01 are straightforward. Sizing windows are estimated by running a series of control allelic ladders on several gels and 'unknown' samples are designated if they fall within a defined window. However, utilisation of complex STRs (eg. D21S11) characteristically have common variants which differ by just 2 bp. In addition, rare alleles are encountered which may differ by just 1 bp from a common variant. To assist with the identification of alleles, we have introduced a series of allelic ladders, so that direct comparisons with 'unknown' samples can be made on the same gel. To designate an allele, it should be within 0.5 bp of an allelic ladder marker. Not all alleles (in particular rare alleles) can be included within an allelic ladder, however their expected positions can be easily calculated by reference to existing alleles in the ladder. Measurement of band shift is also a useful diagnostic tool. A series of guidelines are described to enable reliable allelic identification. These guidelines can be converted into computer programmes which form the basis of an expert system.

The validation of a 7-locus multiplex STR test for use in forensic casework. (II), Artefacts, casework studies and success rates.

PCR-based DNA typing of biological evidence is now widely used in forensic analyses due to the obvious advantages of enhanced sensitivity, the ability to distinguish discrete alleles and efficacy with degraded samples. A multiplex short tandem repeat (STR) system has been previously developed which successfully co-amplifies six STR loci HUMTH01, D21S11, D18S51, D8S1179, HUMVWF31/A and HUMFIBRA (FGA) in conjunction with the X-Y homologous gene Amelogenin. This is known as the second generation multiplex system (SGM). Detection of the PCR products is undertaken on ABD 373A or 377 automated sequencers using denaturing polyacrylamide gels coupled with fluorescent-based technology. We have evaluated this system for routine forensic use and demonstrated that the technique is robust and reproducible under conditions consistent with those encountered in a forensic environment. A total of 132 stains from simulated and actual casework were analysed, together with relevant control areas and reference samples. The success rate was high with 76% of stains giving full profiles; we were also able to successfully detect and interpret mixtures. No mistyping was observed. A detailed examination of each of these profiles has assisted in the development of guidelines for casework interpretation. Although artefacts, stutter peaks and undenatured DNA were occasionally observed, these did not interfere with the accuracy of interpretation. In addition 38 samples, previously examined using the quadruplex system, were analysed with the SGM to enable a direct comparison to be made between the systems. The performance of the system with poor quality samples demonstrated its use as a rapid and powerful technique for individual identification.

The validation of a 7-locus multiplex STR test for use in forensic casework. (I). Mixtures, ageing, degradation and species studies.

We have evaluated a multiplex STR system for routine forensic use, which co-amplifies six short tandem repeat (STR) loci; HUMTH01, D21S11, D18S51, D8S1179, HUMVWF31/A and HUMFIBRA (FGA), in conjunction with the X-Y homologous gene Amelogenin. Analysis of PCR products employs denaturing polyacrylamide gels coupled with fluorescent labelled primers and detection is undertaken on ABD 373A automated sequencers. The technique was shown to be robust and reproducible when samples were analysed under conditions consistent with those encountered in a forensic environment. The system was demonstrated to be human specific and is suitable for use with both aged and degraded material. Somatic stability was proven with a wide range of tissue types and we were able to detect mixtures at ratios between 1:10 and 10:1. During this study no incidence of sample mis-typing due to allelic or locus drop-out was observed. Furthermore, although additional artefact bands were occasionally encountered these did not interfere with the interpretation of results. The performance of the system with poor quality samples demonstrated its suitability as a powerful tool in forensic investigation.

Automated short tandem repeat (STR) analysis in forensic casework--a strategy for the future.

Short tandem repeat (STR) loci are routinely analysed for forensic purposes in the UK. Because small regions of DNa are amplified, successful results are more likely to be obtained from highly degraded material where the DNA fragment length may be < 500 bp. The method is superceeding conventional analysis with single locus probes (SLPs). Dimeric STR loci display stutter artefacts, hence STRs used in casework are restricted to tri or tetrameric loci. Some STRs are complex repeats and have more alleles than simple repeats - for example the locus D21S11 has 21 alleles which differ in size by 2 bp because of the presence/absence of a hexanucleotide within the block of tetrameric repeats. These loci are of great potential interest because they combine increased discriminating power with reduced potential to stutter. Multiplexing 4 different loci with different dye labelled primers (i.e. carrying out polymerase chain reaction of 4 loci simultaneously) using the ABD 373A automated sequencer enables a large numbers of samples to be processed. In addition data aquisition and manipulation is automated so that minimum postelectrophoresis operator input is required. It is our aim to develop a system equivalent in power to that of 4 single locus probes. To achieve this we have developed an octoplex system consisting of 7 loci and a sex test (amelogenin locus) which has a probability of chance of association of 10(-9); the power of this system is equivalent to that achieved by 4 conventional SLPs.

A highly discriminating octoplex short tandem repeat polymerase chain reaction system suitable for human individual identification.

Through the use of fluorescence-based polymerase chain reaction systems, a highly discriminating multiplex with the potential for individual identification has been developed. The use of multiple dye technology enabling loci with overlapping size ranges to be co-amplified has enabled us to successfully amplify seven tetranucleotide short tandem repeat loci within a single reaction resulting in a discriminating power in the region of 1 x 10(9). Three out of the seven loci employed exhibit alleles differing in size by only 2 bp as opposed to the conventional 4 bp, which results in such loci being more powerful in terms of distinguishing between samples, particularly when co-amplified in this manner. The size ranges of the loci contained within the system are such that windows still exist for the inclusion of additional loci at a later stage, which could increase the discriminating power of the system still further. In addition, further weight and utility is lent to the system through the incorporation of a simple and reliable sex test involving the amplification of a segment of the X-Y homologous gene Amelogenin.

Highly discriminating heptaplex short tandem repeat PCR system for forensic identification.

We describe a highly discriminating multiplex short tandem repeat PCR human identification system that gives a matching probability for Caucasians of European ancestry of 2.94 x 10(-8) or 5.66 x 10(-10) when used in combination with a previously described system. The system produces discrimination equal to or greater than four single locus probes (restriction fragment length polymorphism [RFLP] typing of variable nucleotide tandem repeat [VNTR] loci). The test is robust and reproducible and works with 1-10 ng of template DNA, using fluorescent detection of PCR products from either 4 or 6 short tandem repeat loci and the X-Y homologous gene amelogenin, giving simultaneous sex diagnosis.

Methionine hydroxy analog (free acid) reduces avian kidney damage and urolithiasis induced by excess dietary calcium.

Urinary acidification previously was shown to be an effective treatment for calcium-induced urolithiasis in domestic fowl, but diuresis caused by the acidifying agent (ammonium chloride) was an undesirable side effect. Because supplemental dietary methionine reportedly acidifies mammalian urine, an experiment was conducted to evaluate the efficacy of the free acid form of methionine hydroxy analog (MHA) as an acidifying agent for treating avian urolithiasis. From 5 to 17 wk of age, immature Single Comb White Leghorns were fed diets containing normal calcium (1%) or high calcium (3.5%). Diets were supplemented with 0, 0.3 or 0.6% MHA. Relative to birds fed the normal calcium diets, birds fed the high calcium diet without added MHA were in a state of metabolic alkalosis and excreted more alkaline urine containing high levels of calcium. Birds fed the high calcium diet without MHA also had significantly higher kidney asymmetry ratios, a higher incidence of gross kidney damage, and a higher incidence of urolith formation when compared with birds fed normal calcium diets. When compared with the high calcium diet without MHA, the high calcium diet supplemented with 0.6% MHA significantly acidified the urine without causing detectable metabolic acidosis, significantly reduced kidney asymmetry and gross kidney damage, and reduced the incidence of urolith formation without increasing water consumption or urine flow. These data demonstrate that MHA effectively prevents calcium-induced kidney damage in domestic fowl without causing undesirable side effects. MHA did increase both fractional and absolute calcium excretion during calcium loading.

Calcium oxalate crystals in the thyroid. Their identification, prevalence, origin, and possible significance.

Calcium oxalate crystals are not encountered in normal animal tissues, except for the human thyroid, where they were found in 79 of 100 routine consecutive autopsies. They appear during childhood, and numbers of crystals increase with age. In diffuse hyperplasia, prevalence was higher, but crystals were fewer than expected. In adenomas and carcinomas, crystals were decreased except for three cases with a striking focal increase. None was found in 22 adult primate thyroids. After Clorox digestion of human thyroids, calcium oxalate dihydrate was identified by x-ray diffraction and infrared spectroscopy. Origin, tissue and species localization are discussed in relation to ascorbate metabolism, thyroperoxidase, and calcitonin. Possible metabolic roles are suggested. Calcium oxalate crystals injected in animals and humans initiate a foreign body reaction with giant cells. In Hashimoto's thyroiditis, crystals disappear but occasionally remain with giant cell reaction. In subacute thyroiditis, granulomas are related more to colloid than to crystals.

Characterization and composition of uroliths from domestic fowl.

Urolithiasis (kidney stone formation) is an acquired degenerative kidney lesion affecting sexually mature and immature domestic fowl. For the present study, uroliths were collected from three commercial flocks during outbreaks of urolithiasis. Uroliths also were collected from a research flock in which urolithiasis was induced by feeding immature chickens a diet formulated to contain excess calcium (3.25% Ca) and .4% available phosphorus. All uroliths were tested by x-ray diffractometry, infrared spectrophotometry, and emission spectrography. With one exception, the stones were composed of compact masses of microcrystalline to fine pleomorphic crystals of calcium sodium urate, with random substitution of magnesium for calcium, and potassium for sodium. No initiating nidus was evident. One of four stones from one laying hen flock was positively identified as an ammonium acid (hydrogen) urate. The unique calcium-sodium-urate stone composition in all but one of the stones tested suggests that similar processes were involved in stone formation in the four different flocks.

Etiopathogenesis of uncommon canine uroliths. Xanthine, carbonate, drugs, and drug metabolites.

Metabolic disorders, medication, and diagnostic agents may be associated with urolithiasis in dogs. Examples of uroliths that have been uncommonly encountered in dogs include xanthine, dolomite, tetracycline, and sulfonamides. Detection of these and other apparently uncommon uroliths requires a high index of suspicion and proper methods of analysis.

Limitations of the rat remnant kidney model of chronic renal failure: absence of calcium oxalate tissue injury.

We have studied the rat remnant kidney model as a tool to assess the impact of secondary oxalosis on renal failure. Although the plasma of uremic rats demonstrated increased levels of oxalic acid, deposits of oxalate crystals in tissue were not observed. The absence of such deposits in the remnant kidney, as well as other tissues, may be due to a lesser degree of hyperoxalemia observed in the rat compared to man or may reflect that uremic deaths among the experimental animals occurred prior to formation of detectable calcium oxalate deposition. We conclude that the rat remnant kidney is not a suitable model to study the impact of uremic oxalosis in man.

Triamterene stone: advantage of crystallographic analysis.

Microscopic crystallographic analysis of renal calculi provides clinically useful information concerning the pathogenesis of stone disease and is, therefore, superior to conventional chemical analysis of stones. The advantages of crystallography, performed at a centralized, experienced stone-analysis center, are highlighted by the recent discovery of triamterene deposits in kidney stones. Deposits of other medications and their metabolites have also been uncovered. Two case reports are presented, the clinical implications of these and related findings are discussed.

Triamterene nephrolithiasis.

We identified triamterence in 181 renal calculi (o.4% of 50.000 calculi submitted for analysis). Triamterene formed the nucleus of the stone or was deposited with calcium oxalate or uric acid. One third of these stones were mainly or entirely triamterene, though a similar proportion had only minor amounts. A recommended dose of triamterene-hydrochlorothiazide sufficed to produce triamterene deposition in renal calculi. We estimate the annual incidence of the complication to be one per 1,500 users of triamterene-hydrochlorothiazide. Triamterene lithiasis develops particularly in persons who have had a renal stone, and they should not receive this drug.