Frequency of GCH1 deletions in Dopa-responsive dystonia

We performed a systematic study on the frequency of point mutations and deletions of the gene GCH1 in dopa-responsive dystonia (DRD). A total of 136 dystonia patients were studied. Fifty of these had a sustained response to oral L-Dopa therapy (group 1: definite diagnosis of DRD), whereas the response to L-Dopa was incomplete or not tested in 86 patients (group 2: possible diagnosis of DRD). We found a GCH1 point mutation in 27 patients of group 1 (54%) and in four patients of group 2 (5%). Of these, nine single and one double mutation have not been described before. GCH1 deletions were detected in four patients of group 1 (8%) and in one patient of group 2 (1%). Among GCH1 point-mutation-negative patients with a definite diagnosis of DRD (group 1), the frequency of GCH1 deletions was 17% (4/23). We conclude that GCH1 deletion analysis should be incorporated into the routine molecular diagnosis of all patients with DRD with a sustained response to L-Dopa.

Distribution of two Asian-related coding SNPs in the MC1R and OCA2 genes

Very little is known about the genes and mechanisms affecting skin lightening in Asian populations. In this study, two coding SNPs, c.G1129A (R163Q) at the MC1R (melanocortin 1 receptor) gene and c.A1962G (H615R) at the OCA2 (oculocutaneous albinism type II) gene, were investigated in a total of 1,809 individuals in 16 populations from various areas. The Q163 and R615 alleles prevailed almost exclusively in East and Southeast Asian populations. Wright's F (ST) was 0.445 for R163Q and 0.385 for H615R among the 16 populations. The frequency of the Q163 allele was higher in Northeast Asians than in Southeast Asians. The frequency of the R615 allele was highest in South China and unlikely to be associated with levels of ultraviolet radiation. This allele may be a good marker to study the genetic affinity among East Asians because of its restricted distribution and marked difference in allele frequency.

Distribution of the F374 Allele of the SLC45A2 (MATP) Gene and Founder-Haplotype Analysis

The membrane-associated transporter protein (MATP) plays an important role in melanin synthesis. The L374F mutation in the SLC45A2 gene encoding MATP has been suggested to be associated with skin colour in major human populations. In this study more detailed distribution of the F374 allele was investigated in 1649 unrelated subjects from 13 Eurasian populations and one African population. The highest allele frequency was observed in Germans (0.965); French and Italians showed somewhat lower frequencies; and Turks had an intermediate value (0.615). Indians and Bangladeshis from South Asia were characterized by low frequencies (0.147 and 0.059, respectively). We also found the F374 allele in some East and Southeast Asian populations, and explained this by admixture. Haplotype analysis revealed that the haplotype diversity was much lower in Germans than in Japanese, and suggest that the L374F mutation occurred only once in the ancestry of Caucasians. The large differences in distribution of the F374 allele and its haplotypes suggest that this allele may be an important factor in hypopigmentation in Caucasian populations.

Characterization of genomic rearrangements of the alpha1-acid glycoprotein/orosomucoid gene in Ghanaians

In this study, the structure of the alpha1-acid glycoprotein (AGP), or orosomucoid (ORM), gene was investigated in a Ghanaian mother and her child, who shared an unusual variant, ORM1 S2(C), found by isoelectric focusing. Three remarkable changes of nucleotide sequence were observed: (1) The two ORM1 alleles, ORMI*S and ORMI*S2(C), had the AGP2 gene-specific sequence at one and three regions, respectively, in exon 5 to intron 5. The variant allele originating from ORMi*S was characterized by a G-to-A transition, resulting in an amino acid change from valine to methionine, which is also detected in ORM1 F2, a form that is common in Europeans. (2) The AGP2 gene of the child, inherited from the father, was duplicated, as revealed by long-range polymerase chain reaction. (3) Three new mutations were observed in two exons of the AGP2 genes of the mother and child. All of these novel genomic rearrangements, which were not observed in Japanese subjects, may have arisen through point mutation, gene conversion, and unequal crossover events. It is likely that the rearrangement of the AGP gene has often occurred in Africans.

Application of Y-chromosomal STR haplotypes to forensic genetics

This paper delivers population genetic data on Y-chromosomal short tandem repeat (STR) polymorphisms along with reports of unusual observations and casework. Population studies were carried out on the Y-specific STR polymorphisms DYS19, DYS385 I+II, DYS389 I+II, DYS390, DYS391, DYS392, and DYS393 in population samples from North India, Turkey, and Germany. In all three populations the vast majority of haplotypes was observed only once, especially in the Turkish group. Highly unusual cases are reported. In a German individual, we observed the variant allele DYS392*11.1, whereas a Turkish haplotype revealed a duplication at locus DYS19. Application of Y-chromosomal STR markers to forensic genetics was demonstrated in two cases: 1) a deficient paternity case, and 2) a father/son pair, where the Amelogenin primers failed to amplify the Y-homolog. In forensic genetics, Y-chromosomal STR polymorphisms are highly welcomed as an additional tool.

Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes

The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.

Molecular analysis of the human orosomucoid gene ORM1*Q0köln responsible for incompatibility in a German paternity case

In a German paternity test, an alleged father was excluded only by reverse homozygosity of ORM1 phenotypes (mother ORM1 S, child ORM1 S and alleged father ORM1 F1) out of the 28 classical and DNA markers investigated. Without the ORM1 system the biostatistical probability of paternity was calculated to exceed 99.999%. The intensity of the immunoprinted bands of the ORM1 protein for the child and alleged father after isoelectric focusing appeared to be reduced to about half. To identify a possible null allele, gene-specific amplification followed by single-strand conformation polymorphism and sequencing analyses were carried out. Deletion of one of the two copies of a 4 bp direct repeat sequence (GTCT) in exon 4 of the consensus sequence of ORM1*F1 was observed in the child and alleged father. Thus, the sharing of a rare mutant gene, ORM1*Q0köln, increased the probability of paternity.

Sequence analysis and population data on the 'new' short tandem repeat locus D5S2360

We have studied the sequence structure and population genetics of a 'new' short tandem repeat polymorphism at locus D5S2360 in German Caucasians. Sequencing at this locus revealed a considerable variation, which is characterized by a tetranucleotide (AGAT)(n) repeat pattern with (GAT), (AGATT), and (AG) repeats dispersed throughout the alleles. These microvariations do not necessarily alter the size of the alleles. They may vary by one or two pairs or they may remain unchanged in size. At locus D5S2360 we observed 33 allelic lengths comprising at least 36 different alleles. Population data revealed a high polymorphism with a heterozygosity rate of approximately 92.5%.

A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males

A 9-locus microsatellite framework (minimal haplotype), previously developed for forensic purposes so as to facilitate stain analysis, personal identification and kinship testing, has been adopted for the establishment of a large reference database of male European Y-chromosomal haplotypes. The extent of population stratification pertaining to this database, an issue crucial for its practical forensic application, was assessed through analysis of molecular variance (AMOVA) of the 20 regional samples included. Despite the notion of some significant haplotype frequency differences, which were found to correlate with known demographic and historic features of Europeans, AMOVA generally revealed a high level of genetic homogeneity among the populations analyzed. Owing to their high diversity, however, accurate frequency estimation is difficult for Y-STR haplotypes when realistic (i.e. moderately sized) datasets are being used. As expected, strong pair-wise and higher order allelic associations were found to exist between all markers studied, implying that haplotype frequencies cannot be estimated as products of allele frequencies. A new extrapolation method was therefore developed which treats haplotype frequencies as random variables and generates estimates of the underlying distribution functions on the basis of closely related haplotypes. This approach, termed frequency 'surveying', is based upon standard population genetics theory and can in principle be applied to any combination of markers located on the Y-chromosome or in the mitochondrial genome. Application of the method to the quality assured reference Y-STR haplotype database described herein will prove very useful for the evaluation of positive trace-donor matches in forensic casework.

Human autosomal short tandem repeat types in Jat Sikhs from North India

This study provides Jat Sikhs population data in North India for nine short tandem repeat (STR) loci.

Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs

A number of applications of analysis of human Y-chromosome microsatellite loci to human evolution and forensic science require reliable estimates of the mutation rate and knowledge of the mutational mechanism. We therefore screened a total of 4,999 meioses from father/son pairs with confirmed paternity (probability >/=99. 9%) at 15 Y-chromosomal microsatellite loci and identified 14 mutations. The locus-specific mutation-rate estimates were 0-8. 58x10-3, and the average mutation rate estimates were 3.17x10-3 (95% confidence interval [CI] 1.89-4.94x10-3) across 8 tetranucleotide microsatellites and 2.80x10-3 (95% CI 1.72-4.27x10-3) across all 15 Y-chromosomal microsatellites studied. Our data show a mutational bias toward length increase, on the basis of observation of more repeat gains than losses (10:4). The data are in almost complete agreement with the stepwise-mutation model, with 13 single-repeat changes and 1 double-repeat change. Sequence analysis revealed that all mutations occurred in uninterrupted homogenous arrays of >/=11 repeats. We conclude that mutation rates and characteristics of human Y-chromosomal microsatellites are consistent with those of autosomal microsatellites. This indicates that the general mutational mechanism of microsatellites is independent of recombination.

Usefulness of conventional blood groups, DNA-minisatellites, and short tandem repeat polymorphisms in paternity testing: a comparison

A total of 215 paternity cases were analysed after testing 24 marker systems. Despite technical advantages of polymerase chain reaction related polymorphisms (automatisation, employment of robots, lesser requirements concerning of quality and quantity of DNA) it could be shown that the exclusive employment of a parentage testing kit is compromised by an increased risk of erroneous conclusions. It is estimated that in about 3-4% of the cases ambiguous situations have to be expected which are caused by the occurrence of single or double exclusions. In these cases it is impossible to decide whether the exclusions indicate either true nonpaternity or a de novo mutation. The situation might become even more complicated if an involvement of a close relative of the alleged father cannot be ruled out. We cautiously advance the hypothesis that in parentage testing DNA minisatellite polymorphisms from an optimal set of tools.

Human orosomucoid (ORM1) subtyping: further population genetic data and reports on the feasibility to type aged blood samples and stains

Genetic polymorphism of serum orosomucoid (ORM1) was investigated in 1072 unrelated German Caucasians using isoelectric focusing followed by Western blotting and EIA. The estimated allele frequencies were ORM1 *F1 = 0.5690, ORM1 *S = 0.3927, ORM1 *F2 = 0.0368, ORM1 *F2S = 0.0009 and ORM1 *F5 = 0.0005. The method was successfully applied to determine ORM1 phenotypes in aged blood samples and blood stains. The results indicated that the ORM protein is a informative and remarkably robust blood group system.

Specificity of head-up tilt testing in adolescents: effect of various degrees of tilt challenge in normal control subjects

OBJECTIVES

This study sought to determine the specificity of commonly used tilt protocols in children.

BACKGROUND

Tilt table testing is commonly utilized in the evaluation of children and adolescents with syncope despite a lack of uniformity in tilt protocols and a lack of studies of specificity in normal control subjects.

METHODS

Sixty-nine normal control volunteers (12 to 18 years old, 38 male, 31 female) with no previous history of syncope, presyncope or arrhythmia underwent tilting to 80 degrees, 70 degrees or 60 degrees for a maximum of 30 min on a motorized table with a footboard support. Autonomic maneuvers, including deep breathing, carotid massage, Valsalva maneuver and diving reflex, were performed before tilt testing to determine whether the response to these maneuvers could identify subjects prone to fainting during tilt testing.

RESULTS

Symptoms of presyncope and frank syncope were elicited in 24 of 69 subjects (13 male, 11 female): 6 (60%) of 10 were tilted at 80 degrees, 9 (29%) of 31 at 70 degrees and 9 (32%) of 28 at 60 degrees. Tilt testing at 80 degrees was terminated after the tenth subject by the institutional review board. The mean time to a positive test response was 10.5 min at 80 degrees, 14.2 min at 70 degrees and 13.2 min at 60 degrees. In the 80 degrees tilt, 4 of 10 subjects had a positive response within 10 minutes, whereas only 3 of 31 and 2 of 28 had a positive response within < 10 min at 70 degrees and 60 degrees tilt angles, respectively. Subjects with and without a positive response to tilt testing were similar with respect to age; gender; PR, QRS and QT intervals; and baseline heart rate and blood pressure. Likewise, responses to other autonomic function tests performed were similar in tilt-positive and tilt-negative patients. The power for detecting a significant difference between patients tilted at 80 degrees versus 60 degrees and 70 degrees was 0.45 and for detecting differences in autonomic tone between tilt-positive (n = 24) and tilt-negative (n = 45) subjects was 0.8.

CONCLUSIONS

Children appear to be more susceptible to orthostatic stress than adults. Therefore, tilt protocols commonly used in adults lack specificity in teenage patients. A specificity > 85% may be obtained by performing the tilt test at 60 degrees or 70 degrees for no longer than 10 min.

Population genetic and family data for the human minisatellite locus D16S309 (MS205) in Germans

The distribution of restriction fragments at the DNA minisatellite locus D16S309 was estimated by investigating blood samples from 2617 unrelated West German Caucasians and 1269 offspring. Furthermore segregation of fragments was studied in a large family and in trios. Altogether 2296 meioses were studied, revealing 7 paternal and 3 maternal mutations. Inspection of "phenotypes" did not reveal any remarkable deviation from Hardy-Weinberg equilibrium.

Novel polymorphisms and haplotypes in the human coagulation factor XIII A-subunit gene

Novel polymorphic sites within the coding region of the human coagulation factor XIII A-subunit (F13A) gene and their haplotypic combinations with the other polymorphic sites thus far reported are presented. Polymorphic bands were detected in exons 2, 5, 8, 12 and 14 by using single strand conformational polymorphism analysis and antithetic forms of the polymorphic exons were linked with each other, cosegregating as distinct sequence haplotypes. In Finnish, German, and Russian populations a total of 18 haplotypes were observed of possible 72 haplotypic combinations of the 5 exons. Ten of the haplotypes detected were found to have no novel mutations but to be only combinations of preexisting mutations. No tightly associated combinations in pairwise comparisons between antithetic forms of the polymorphic exons were observed, indicating that there may be recombinational hotspots within the F13A gene region.

Recent observations in human DNA-minisatellite mutations

We report maternal and paternal mutation rates at loci D1S7 (MS1), D7S21 (MS31), D12S11 (MS43A), and D7S22 (G3). The respective mutation rates were as follows: [table: see text] At loci D7S21, D12S11, and D7S22 statistically significant differences in mutation rates exist between the sexes. No such difference was observed at locus D1S7. However inspection of the latter data reveals that by mutation at spermiogenesis approximately two-thirds of the fragments showed an addition of repetitive units, while a 50: 50 ratio was encountered in the series of maternal mutations. We also report the observation of naturally occurring 3-fragment patterns.

GEDNAP IV and V. The 4th and 5th Stain Blind Trials using DNA technology

In the collaborative exercise GEDNAP IV one EDTA blood sample (2 ml) and 5 bloodstains (0.5 ml on cotton) were investigated and in GEDNAP V, a total of 8 bloodstains (0.5 ml on cotton), including 2 mixed bloodstains. DNA typing was carried out using the RFLP systems YNH24/Hinf I and MS43a/Hinf I and the PCR systems HLA DQ alpha, D1S80, ApoB and YNZ22. In both exercises approximately 20 laboratories obtained results using the RFLP systems. Of the PCR systems, D1S80 was the most commonly used (14 labs in GEDNAP IV; 18 labs in GEDNAP V). The interlaboratory standard deviation for YNH24 in both exercises was approx. 0.6%, for MS43a 0.7-2.2% (GEDNAP IV) and 0.4-1.4% (GEDNAP V), depending on the fragment size. The fragment size calculation performed in each laboratory yielded a standard deviation twice that obtained when the fragment size calculation was performed centrally (IfR, Münster). In GEDNAP III, a system-specific corridor was developed to define the limits of deviation; this was modified for the present study by combining the fragment size ranges of YNH24 and MS43a. In both studies a subgroup of laboratories was involved in preliminary exercises using three PCR VNTRs and the system HLA DQ alpha. Owing to the substantial variation in experience of the participating laboratories with PCR typing the results obtained in these two studies do not fulfil the basic quality criteria of the GEDNAP studies.

DNA-minisatellite mutations: recent investigations concerning distribution and impact on parentage testing

At least 815 meioses were studied in the HinfI polymorphisms of DNA minisatellite loci D1S7, D2S44, D7S21, D7S22, and D12S11 in order to collect data on respective mutation rates. At locus D7S21 (probe MS31) a striking difference between the paternal and maternal mutation rate was observed (1.5% versus 0.2%). This study also describes, how to deal biostatistically with paternal mutations in parentage testing. Possible implications of mutations are illustrated by the description of 2 cases. Case 1 reports an "exclusion" of mother and father with probe MS1. Case 2 describes 2 paternal "exclusions" with probes MS31 and G3. The statistical likelihood for a paternal "exclusion" with 2 of the 5 probes is 0.13%. By omitting probe MS1, this frequency can be reduced to 0.02%. Nevertheless, the second case clearly shows, that informative blood group markers cannot be replaced by DNA polymorphisms.

Pathologic explanation for hypoechoic halo seen on sonograms of malignant liver tumors: an in vitro correlative study

OBJECTIVE

The purpose of this study was to evaluate the morphologic substrate of the hypoechoic halo seen on sonograms of malignant liver tumors.

MATERIALS AND METHODS

We used sonograms and pathologic examinations to evaluate 17 cadaveric livers with macroscopic tumors (three primary liver tumors, 14 metastases). During sonography (3.5 and 5.0 MHz), a representative section plane was marked, and the same section was examined histologically. Emphasis was placed on the architecture of the tumor and the morphology of the periphery of the tumor that could account for the hypoechoic halo seen on sonograms.

RESULTS

In 13 of 17 hepatic tumors, a hypoechoic halo was detected on sonograms. Histopathologic examination showed an intratumoral rim consisting of proliferating tumor cells in 12 cases and an extratumoral rim of compressed liver parenchyma in all 13 cases. A detailed comparison of sonographic and histopathologic findings showed that the hypoechoic halo corresponded to a greater concentration of tumor cells and areas of less marked fibrosis and necrosis in the periphery of the tumors. This occurred in 11 cases. In one case, histologic studies showed that the hypoechoic rim was caused by compressed liver parenchyma. In another case, the hypoechoic halo was caused by intratumoral (cellular peripheral zone of tumor) and extratumoral (compressed liver parenchyma) components. All four tumors without a halo at sonography were uniform histologically.

CONCLUSION

The sonographic halo seen on sonograms of malignant liver tumors seems to be caused predominantly by a zone of proliferating tumor in the periphery of the lesion.

Biostatistical basis of individualization and segregation analysis using the multilocus DNA probe MZ 1.3: results of a collaborative study

A collaborative study using the multilocus minisatellite DNA probe MZ 1.3 was carried out to investigate segregation information, mutation rate, DNA fragment frequencies as well as band sharing characteristics. The fingerprint patterns of 393 children as well as 694 unrelated individuals were analysed after digestion of DNA with the restriction enzyme HinfI. A mutation rate of 1% per meiosis or 0.04% per band was found with a mean number of 26 bands/individual. It was shown that maternal and paternal fragments are inherited in equal proportions. Population frequencies of restriction fragments demonstrated a distribution with increasing frequencies in the small fragment size range below 10 kb as well as the absence of very common or very rare fragments. Our data can be used to calculate simple exclusion probabilities based on the number of non-maternal bands in the child.

Size calculation of restriction enzyme HaeIII-generated fragments detected by probe YNH24 by comparison of data from two laboratories: the generation of fragment-size frequencies

Restriction fragment-length polymorphism of locus D2S44 detected by the highly polymorphic probe YNH24 and restriction endonuclease HaeIII can be used to improve parentage testing when representative fragment-size frequencies can be obtained. By joining the results of different laboratories, it is possible to set up a meaningful databank. Therefore, the same randomly chosen samples were tested for the HaeIII RFLP detected by probe YNH24 in Düsseldorf (DUS) and Amsterdam (AMS). The results of the different fragment-size calculations obtained by using internal markers and a computerized system (DUS-cad and AMS-cad), and by using external markers and manual calculations (DUS-man), were analyzed. Comparing these results, no statistically significant differences were seen. The results obtained with probe YNH24 and enzyme HaeIII in Düsseldorf and Amsterdam can be used to attain a sufficient number of samples to generate relevant fragment-size frequencies.

Population genetic data determined for five different single locus minisatellite probes

We report on the population genetic data (frequencies of restriction fragments, heterozygosity rates, and mutation rates) obtained by analysis of approximately 1100 Hinfl-digested DNAs from West Germans. Probe G3 detects a common 1.7 kb DNA fragment showing a population frequency of about 13%. All the other fragments detected with probes MS1, MS31, MS43, G3 and YNH24 show frequencies of less than 8%. These data suggest that single locus DNA probes can provide valuable information for parentage evaluation and individualization.

BamHI polymorphism of locus D2S44 in a West German population as revealed by VNTR probe YNH24

BamHI polymorphism at the VNTR locus D2S44 was investigated, concentrating on band frequencies, mutation rate and confirmation of Mendelian inheritance. In this series 39 restriction fragments showing frequencies less than 10% could clearly be distinguished. No mutations could be observed and the Mendelian character of inheritance is beyond reasonable doubt.

Gm and Km frequencies in West Germans: usefulness of typing Gm(1,2,3,10,21) and Km(1,3) in paternity cases

The immunoglobulin allotypes G1m(1,2,3) and G3m(10,21) were typed in 2855 unrelated West German adult individuals. 1455 individuals were typed for the factors Km(1,3). Phenotype and haplotype frequencies are reported. The usefulness of this routine typing programme in paternity tests is demonstrated in three case reports.

Comparison of different X-ray films for 32P-autoradiography using various intensifying screens at -20 degrees C and -70 degrees C

The amplifier effect of different intensifying screens on commercially available X-ray films was tested in autoradiography with 32P at -20 degrees C and -70 degrees C. For the films X-Omat AR, RX and HR-G in combination with the screens G 12 and Lgy-S 600, there was no significant enhancement of blackening at -70 degrees C compared with -20 degrees C. Therefore exposure at -20 degrees C is generally feasible, if an appropriate film-screen combination is used.

Photodestruction of acetylcholinesterase

Ultraviolet irradiation of 11S acetylcholinesterase (acetylcholine acetylhydrolase, EC 3.1.1.7) produces a loss of tryptophan fluorescence which is best described as the sum of two separable first-order processes, one much more rapid than the other. In addition, the enzyme undergoes an all-or-none inactivation that is monotonically first order. Simultaneous with activity loss, photoscission takes place and results in a molecular weight drop of 1 x 10(5); this decrease is first order with a rate constant identical to that for enzymatic inactivation. These processes are accompanied by apparent conformational changes, as shown by circular dichroic and difference absorption spectra. The relative photochemical inactivation efficiency of incident light is unity when corrected for the wavelength dependence of fluorescence excitation, which is consistent with an efficient Förster resonance transfer of energy among the aromatic chromophores. The extreme sensitivity of acetylcholinesterase to photodestruction upon photon absorption and the several events that follow it not only suggest that these findings might be a basis for a useful molecular probe of the structure of this enzyme, but also indicate that additional care should be taken when conducting spectroscopic studies in the UV region.