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A Urquhart

Publications and source records attributed to A Urquhart.

At least 19 recordsLinked to original sources
PubMed2001

Sequence polymorphism in the human melanocortin 1 receptor gene as an indicator of the red hair phenotype.

We describe a minisequencing protocol for screening DNA samples for the presence of 12 mutations in the human melanocortin 1 receptor gene (MC1R), eight of which are associated with the red hair phenotype. A minisequencing profile which shows homozygosity for one of these mutations or the presence of two different mutations would strongly indicate that the sample donor is red haired. The absence of any red hair causing mutations would indicate that the sample donor does not have red hair. We report the frequencies of MC1R variants in the British red haired population.

Forensic Medicine↗
PubMed2001

Inferring ethnic origin by means of an STR profile.

We report the use of DNA profiles from six STR loci for inferring the ethnic origin of a crime stain and discuss how such inference may be used as intelligence information to reduce the expected number of interviews to resolve a case. To enable this work, databases have been created for five British ethnic groups (Caucasians, Afro-Caribbeans, Indian sub-continentals, Southeast Asians and Middle Easterners) that together comprise 99.7% of the UK population.

Asia, Southeastern↗
PubMed2001

Hodgkin's and non-Hodgkin's lymphoma of the head and neck.

OBJECTIVES/HYPOTHESIS: Lymphomas are a frequent cause of malignant lymphadenopathy in the head and neck. This study was performed to evaluate the head and neck manifestations of lymphomas and to emphasize the different presentations of Hodgkin's disease (HD) and non-Hodgkin's lymphoma (NHL). STUDY DESIGN: Retrospective review. METHODS: A retrospective review was made of all cases of lymphomas involving the head and neck at Marshfield Clinic (Marshfield, WI) between 1988 and 1996. Specifically, the clinical presentations, staging, and prognosis for HD and NHL with head and neck involvement were sought. RESULTS: Three hundred eleven patients were included in the study, 76 with HD and 235 with NHL. The median age at diagnosis for patients with HD was 27.7 years, and for patients with NHL, 67.2 years. This difference was highly significant (P <.001). No significant difference in gender was noted, with male patients occurring in 59% with HD and 49% with NHL (P=.135). Extranodal involvement including the oral cavity, oropharynx, nasopharynx, paranasal sinuses, and larynx occurred with HD in 3 patients (4%) and with NHL in 54 patients (23% P <.001). Cervical adenopathy consisted of a single node in 24% of patients with HD and 33% of those with NHL (no significant difference, P=.236). The difference in mediastinal nodal involvement was highly significant, occurring in 65% of patients with HD and 38% of patients with NHL(P <.001). Abdominal nodes occurred in 20% of cases of HD and 45% of cases of NHL (P<.001). A significant difference in constitutional symptoms was noted with 41% of cases in HD and 27% of cases in NHL (P=.020). For the percentage of patients with stage IV disease, there was a highly significant difference by diagnosis with 10% in HD and 36% in NHL (P <.001). The median follow-up time was 51 months, and 12% of patients with HD and 41% of patients with NHL died of their disease. Both the overall survival and survival from death attributable to disease were significantly better for HD(P<.001). CONCLUSIONS: Hodgkin's disease presents at a younger age and is less common than NHL. Cervical lymphadenopathy is the most common head and neck presentation for both diseases. Associated mediastinal adenopathy was more common with HD, and abdominal adenopathy with NHL. Constitutional symptoms were more common with HD. More advanced disease with a decreased overall survival was seen with NHL.

Adolescent↗
PubMed2001

Preoperative computed tomography scans for parotid tumor evaluation.

OBJECTIVE: We sought to determine whether an advantage is obtained in the routine use of computed tomography (CT) scans in preoperative assessments of parotid tumors. METHODS: A prospective study of 32 consecutive cases of patients who underwent evaluation for parotidectomies was performed. Twenty-nine received preoperative CT scans. The scans were systematically reviewed to see if they correlated with the clinical findings. Specifically, we compared clinical and CT assessments of tumor size, location, density, and malignancy. Further comparisons were performed based on postoperative tissue pathology. RESULTS: In our series of patients, routine preoperative CT scans resulted in the discovery of details not revealed on clinical examination: some masses were found to be extra-parotid rather than primary parotid tumors, some tumors deemed to be deep were superficial, tumor density was more clearly identified, and certain pathology correlates were clarified. Most importantly, there were instances of detection of additional tumors in the same lobe, and in one instance in the opposite lobe, that were not otherwise noticed. CONCLUSIONS: To reduce errors of omission in the treatment of suspected parotid tumors, it would seem appropriate to consider the inclusion of CT scans for the routine preoperative evaluation of all parotid masses.

Biopsy, Needle↗
PubMed1999

PEX13 is mutated in complementation group 13 of the peroxisome-biogenesis disorders.

The peroxisome-biogenesis disorders (PBDs) are a genetically and phenotypically diverse group of diseases caused by defects in peroxisome assembly. One of the milder clinical variants within the PBDs is neonatal adrenoleukodystrophy (NALD), a disease that is usually associated with partial defects in the import of peroxisomal matrix proteins that carry the type 1 or type 2 peroxisomal targeting signals. Here, we characterize the sole representative of complementation group 13 of the PBDs, a patient with NALD (patient PBD222). Skin fibroblasts from patient PBD222 display defects in the import of multiple peroxisomal matrix proteins. However, residual matrix-protein import can be detected in cells from patient PBD222, consistent with the relatively mild phenotypes of the patient. PEX13 encodes a peroxisomal membrane protein with a cytoplasmically exposed SH3 domain, and we find that expression of human PEX13 restores peroxisomal matrix-protein import in cells from patient PBD222. Furthermore, these cells are homozygous for a missense mutation at a conserved position in the PEX13 SH3 domain. This mutation attenuated the activity of human PEX13, and an analogous mutation in yeast PEX13 also reduced its activity. The mutation was absent in >100 control alleles, indicating that it is not a common polymorphism. Previous studies have demonstrated extragenic suppression in the PBDs, but the phenotypes of patient PBD222 cells could not be rescued by expression of any other human PEX genes. Taken together, these results provide strong evidence that mutations in PEX13 are responsible for disease in patient PBD222 and, by extension, in complementation group 13 of the PBDs.

Amino Acid Substitution↗
PubMed1996

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.

Buffers↗
PubMed1996

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.

Adult↗
PubMed1996

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.

Adult↗
PubMed1996

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.

Alleles↗
PubMed1995

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.

Alleles↗
PubMed1995

Variability in Cobb angle measurements in children with congenital scoliosis.

The variability in measurement of angles in congenital scoliosis is not known, but it is postulated that it is larger than that in adolescent idiopathic scoliosis due to skeletal immaturity, incomplete ossification, and anomalous development of the end-vertebrae. To determine this variability, we selected 54 radiographs of adequate quality showing 67 scoliotic curves from children with congenital scoliosis. The end-vertebrae were preselected. Each curve was measured by the Cobb method on two separate occasions by six different observers, using the same goniometer and marker. The intraobserver variability was +/- 9.6 degrees and the interobserver variability +/- 11.8 degrees. If 'significant progression' is to be used as a criterion for surgical fusion in congenital scoliosis, there should be at least a 23 degrees increase, the entire range of the interobserver variability, in the curvature to ensure that the perceived increase is not due to variability in measurement.

Analysis of Variance↗
PubMed1995

Simultaneous DNA 'fingerprinting', diagnosis of sex and single-gene defect status from single cells.

Sex and cystic fibrosis status have been previously diagnosed separately at the single cell level. We have developed a sensitive, reliable, accurate and rapid (within 5-6 h) system for the simultaneous diagnosis of sex, cystic fibrosis and a DNA 'fingerprint' within a single reaction from a variety of single cells. As contamination cannot be totally excluded, particularly at the single cell level, DNA 'fingerprinting' can be used to assess the risk of contamination. High sensitivity with single cells is combined with very high specificity (estimated matching probability of 10(-7)-10(-8)), allowing the source of the amplified cell to be identified with a very high degree of probability. Fluorescent primers were multiplexed for six tetranucleotide microsatellite sequences to determine the DNA fingerprint; the amelogenin gene was used to diagnose sex, and primers for the CFTR region were used to determine cystic fibrosis (CF) status. Analysis of the fluorescent product was undertaken using an automated DNA sequencer with Genescan software. This technique has many applications such as prenatal and preimplantation diagnosis, forensic identification of small or degraded samples, and detection of contamination sources. DNA fingerprints of single haploid spermatozoa and other cells can be assessed, so ensuring the detection of both diploid and haploid contamination during preimplantation diagnosis.

Cystic Fibrosis↗
PubMed1995

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.

Alleles↗
PubMed1994

Evaluation of an automated DNA profiling system employing multiplex amplification of four tetrameric STR loci.

We have examined the performance and reproducibility of an automated DNA profiling system which is based on the multiplex amplification of 4 tetrameric STR loci-HUMVWFA31/A. HUMTH01, HUMF13A1 and HUMFES/FPS. The system was able to type 100 pg of purified, undegraded, genomic DNA. At lower concentrations of DNA (below 100 pg), allelec drop-out occurred due to stochastic differences in allele copy number. Minor variation of individual PCR reagent concentrations or cycling temperatures did not result in a significant effect on the efficiency of amplification of any of the 4 loci in the quadruplex system. More substantial variation of reagent concentrations or cycling temperatures outside the optimum range of the system resulted in a reduction or complete loss of signal for one or more loci. This was also observed at high ionic strength or extreme pH. However, under all reagent concentrations and conditions studied, no artefact bands that could potentially result in the mistyping of a sample were apparent within the read region (130-240 bases) of the gel. Evaluation of both native and denaturing polyacrylamide gels revealed that, although native gels displayed faster run times, the sizing precision of such gels for certain STR loci was lower than that of denaturing gels. Also, artefact bands may be present within the read region of native gels. In conclusion the quadruplex amplification system described, coupled with automated fluorescence-based detection on denaturing polyacrylamide gels, appeared to be a robust and reliable system for individual identification.

Alleles↗
PubMed1994

Variation in short tandem repeat sequences--a survey of twelve microsatellite loci for use as forensic identification markers.

Alleles at 12 Short Tandem Repeat loci have been sequenced to investigate candidate loci for a multiplex Short Tandem Repeat system for forensic identification, and for single-locus amplification of Short Tandem Repeat loci. Variation from the consensus sequence was found at 6 loci, while one locus, D21S11, was found to be complex in sequence. The presence of non-consensus alleles does not rule out loci for inclusion as forensic identification markers, but size differences between alleles of 1 base pair require very precise sizing. We suggest criteria for the suitability of Short Tandem Repeat loci as forensic identification markers, and propose a universal allele nomenclature for simple and compound Short Tandem Repeats. The effect of the repeat unit sequence of the evolution of Short Tandem Repeats is discussed.

Alleles↗
PubMed1993

Sequence variability of the tetranucleotide repeat of the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus.

Sequence analysis of polymerase chain reaction (PCR) amplified products from the presumed tetranucleotide repeat at the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus shows far greater variability in both PCR product length and sequence than has been previously reported. Alleles differing in size by 1 bp exist, and accurate sizing is required if the locus is to be used to its full potential.

Actins↗
PubMed1993

The human D11S554 locus: four distinct families of repeat pattern alleles at one locus.

We have sequenced amplified products of 44 short tandem repeat alleles at the human D11S554 locus. The sequences revealed four distinct, but related, families of consensus repeat patterns. Six alleles deviated from the consensus patterns. Alleles differed in size by as little as one base pair, and precise sizing is required for analysis of alleles at this highly polymorphic locus. The evolution of alleles at the D11S554 locus and related short tandem repeat loci is discussed.

Alleles↗