Evolution of the HOXB6 intergenic region: motif conservation at the lateral plate mesoderm (LPM) enhancer element.

This study reports the results of a comparative sequencing study in higher primates, focusing on the intergenic region located between HOXB6 and HOXB7. We have examined an 832 bp. region, encompassing a putative Lateral Plate Mesoderm (LPM) enhancer element in a variety of anthropoid apes. The interspecific comparisons reveal extensive substitutions occurring within this region, with a marked bias in favor of C-->T transitions within the enhancer element. The pattern of these substitutions suggests that the LPM enhancer region is subject to specific sequence and compositional constraints that are only revealed through comparative sequencing. These constraints produce an enhancer signature, the CpG microisland, which may be useful in identifying additional regulatory elements located within the HOX complexes. J. Exp. Zool. (Mol. Dev. Evol.) 285:170-176, 1999.

A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus.

A four-site haplotype system at the dopamine D2 receptor locus (DRD2) has been studied in a global sample of 28 distinct populations. The haplotype system spans about 25 kb, encompassing the coding region of the gene. The four individual markers include three TaqI restriction site polymorphisms (RSPs) -- TaqI "A", "B", and "D" sites -- and one dinucleotide short tandem repeat polymorphism (STRP). All four of the marker systems are polymorphic in all regions of the world and in most individual populations. The haplotype system shows the highest average heterozygosity in Africa, a slightly lower average heterozygosity in Europe, and the lowest average heterozygosities in East Asia and the Americas. Across all populations, 20 of the 48 possible haplotypes reached a frequency of at least 5% in at least one population sample. However, no single population had more than six haplotypes reaching that frequency. In general, African populations had more haplotypes present in each population and more haplotypes occurring at a frequency of at least 5% in that population. Permutation tests for significance of overall disequilibrium (all sites considered simultaneously) were highly significant (P<0.001) in all 28 populations. Except for three African samples, the pairwise disequilibrium between the outermost RSP markers, TaqI "B" and "A", was highly significant with D' values greater than 0.8; in two of those exceptions the RSP marker was not polymorphic. Except for those same two African populations, the 16-repeat allele at the STRP also showed highly significant disequilibrium with the TaqI "B" site in all populations, with D' values usually greater than 0.7. Only four haplotypes account for more than 70% of all chromosomes in virtually all non-African populations, and two of those haplotypes account for more than 70% of all chromosomes in most East Asian and Amerindian populations. A new measure of the amount of overall disequilibrium shows least disequilibrium in African populations, somewhat more in European populations, and the greatest amount in East Asian and Amerindian populations. This pattern seems best explained by random genetic drift with low levels of recombination, a low mutation rate at the STRP, and essentially no recurrent mutation at the RSP sites, all in conjunction with an "Out of Africa" model for recent human evolution.

Analyses of cross species polymerase chain reaction products to infer the ancestral state of human polymorphisms.

In numerous population genetic and disease association studies decisions about the ancestry of polymorphic alleles are often made based on the relative frequency of the alleles in the extant populations with the most frequent allele being deemed as ancestral. However, the frequency of an allele in a population is generally not a perfect indicator of its ancestral status. A more accurate method to assess ancestral/derived status of polymorphic alleles involves identification of shared alleles between species. We used this strategy to examine genomic regions homologous to several human polymorphisms in four species of non-human primates. Cross species polymerase chain reaction (CS-PCR), with primers designed from human sequence, was used to investigate regions of interest. Nineteen polymorphisms at six loci (DRD2, HOXB@, PAH, D4S10, RBP3, and RET) were examined either by restriction fragment length analysis of PCR products (PCR-RFLP) or by direct sequencing. At seventeen of the eighteen PCR-RFLPs, non-human primates were monomorphic and identical to each other for either lack of restriction enzyme site or presence of the site. Thus, at these seventeen polymorphic sites the shared alleles are most likely to be the ancestral ones in humans. In several cases we have used sequence data to further demonstrate that the nucleotide at the site of the polymorphism is conserved between species confirming the hypothesis of a single ancestral allele. However, not all human alleles can be simply resolved into ancestral and derived; sequence data from one PCR-RFLP (in an intron of the PAH locus) and a single strand conformational polymorphism (SSCP) in the 3' untranslated region (UTR) of the DRD2 gene illustrate this point.

DRD2 haplotypes containing the TaqI A1 allele: implications for alcoholism research.

In recent years, a possible role of the dopamine D2 receptor (DRD2) locus in the etiology of alcoholism has been the focus of considerable attention. The literature now contains a mix of association studies with positive and negative conclusions. Various methodological flaws undermine the claims in many of the studies that conclude a positive association exists between alcoholism and the DRD2*A1 allele at the Taql "A" site. Although the studies with negative findings have more often come from studies using better analytic methodology, satisfactory resolution of whether or not genetic variation at the DRD2 locus plays some role in the etiology of alcoholism is unlikely to come from additional studies of the kind conducted thus far; an approach enlightened by a more thorough understanding of the population genetics of DRD2 and the phylogenetic origins of the DRD2 alleles is one alternative. If genetic variation at the DRD2 locus affects susceptibility to alcoholism, then such variation has a mutational and evolutionary history that can be traced with the aid of the various genetic polymorphisms that have been identified at the DRD2 locus. In this study, a third Taql restriction fragment-length polymorphism at DRD2, the Taql "D" site, has been converted to polymerase chain reaction-based typing and its frequencies determined in 22 populations from around the world. Haplotypes defined by the polymorphisms at the Taql "B" and "A" sites, and the short tandem repeat polymorphism in intron 2 have been constructed and the diversity of haplotypes containing the DRD2*A1 allele examined for all 22 populations. The ancestral origins of the three Taql polymorphisms have also been determined by sequencing the homologous regions in other higher primates. Because A1-containing haplotypes in populations of European, Middle Eastern, and African origin show considerable diversity within and among populations, properly designed association studies in populations descended from those areas of the world need to use haplotypes, not a single allelic system, and need to use appropriate methods to compensate for the near impossibility of genetically matching unrelated control samples.

No association between alcoholism and multiple polymorphisms at the dopamine D2 receptor gene (DRD2) in three distinct Taiwanese populations.

This study examined whether there is evidence for an association between alcoholism and the alleles of the TaqI A, TaqI B, and short tandem repeat polymorphisms (STRP), both individually and as haplotypes, at the dopamine D2 receptor gene (DRD2) in males of three populations from Taiwan. We studied 46 Chinese Han (21 alcoholics and 25 nonalcoholics), 42 Atayal (21 alcoholics and 21 nonalcoholics), and 40 Ami (20 alcoholics and 20 nonalcoholics). Alcoholism was diagnosed according to DSM-III-R criteria and all individuals in the alcoholic groups were severely affected. Significant linkage disequilibrium occurs for the three polymorphic sites in all three populations. No significant association was observed between any of the three polymorphisms at the DRD2 locus, tested individually and as haplotypes, and alcoholism in the three subject groups. We conclude that no association exists between genetic variation at the DRD2 locus and alcoholism in Chinese Han, Atayal, and Ami males.

DNA workbench: a database package to manage regional physical mapping.

DNA Workbench (DW) is a client-server database to manage physical mapping data that will form the basis for sequencing and efforts in biologically interesting regions of a chromosome. DW draws maps at different levels of resolution in either of two modes: proportional, when the sizes of objects and the physical distances between them are known accurately or approximately, and nonproportional, when most physical distance information in a region is not available, but order information is. DW interacts with the user primarily through the map graphic. Selection of individual objects on the graphic lets the user inspect and modify the underlying data. DW also manages dependency tracking between map objects and has a rudimentary form of version control. It is currently used to manage information on the DRD2 region on chromosome 11, and on the HOX region of chromosome 17.

Evolution of haplotypes at the DRD2 locus.

We present here the first evolutionary perspective on haplotypes at DRD2, the locus for the dopamine D2 receptor. The dopamine D2 receptor plays a critical role in the functioning of many neural circuits in the human brain. If functionally relevant variation at the DRD2 locus exists, understanding the evolution of haplotypes on the basis of polymorphic sites encompassing the gene should provide a powerful framework for identifying that variation. Three DRD2 polymorphisms (TaqI "A" and "B" RFLPs and the (CA)n short tandem repeat polymorphic in all the populations studied, and they display strong and significant linkage disequilibria with each other. The common haplotypes for the two TaqI RFLPs are separately derived from the ancestral haplotype but predate the spread of modern humans around the world. The knowledge of how the various haplotypes have evolved, the allele frequencies of the haplotypes in human populations, and the physical relationships of the polymorphisms to each other and to the functional parts of the gene should now allow proper design and interpretation of association studies.

Craniomaxillofacial trauma in the elderly.

PURPOSE: Limited data are currently available regarding the nature of craniomaxillofacial fractures in the geriatric population. This retrospective study reviews 109 hospital records dating from 1981 to mid-1993. The goal of this study was to provide details relevant to these types of injuries. RESULTS: Most patients were injured in motor vehicle accidents (MVA) or fall-related episodes. Females sustained 43.9% of the fractures while males sustained 56.1%. In females, falls were the most common cause of fractures, while in males MVAs caused the majority of fractures (P < .01). Most fractures were found in the upper midface region (60.3%) and the mandible (27.5%). MVAs and falls were responsible for 82.7% of all mandibular fractures. The majority of fractures were treated nonsurgically (49.5%); however, 37.6% were treated with open reduction and internal fixation. The in-hospital mortality rate was 11.1%, and there were three postoperative complications. CONCLUSION: The geriatric craniomaxillofacial trauma patient is readily treatable with both aggressive surgical measures and more conservative approaches. Elderly patients often have an underlying medical condition that may subsequently alter the patient's treatment. The findings of this study also suggest that more preventive measures and methods of minimizing mortality and morbidity need to be implemented.

Wound complications in patients receiving adjuvant chemotherapy after mastectomy and immediate breast reconstruction for breast cancer.

A retrospective study was done to evaluate the frequency and severity of wound complications in 112 patients with breast cancer who received adjuvant chemotherapy following mastectomy with immediate breast reconstruction. Data on wound complications were available for 120 mastectomies. The rate of complications in 36 mastectomies treated with chemotherapy after mastectomy and immediate reconstruction was compared to that in 84 mastectomies not receiving adjuvant therapy. There were 25 wound complications (20.8%) in the entire group. The rate of wound complications was 27.8% (10 of 36 mastectomies) in the group treated with adjuvant chemotherapy and 17.9% (15 of 84 mastectomies) in the group that did not receive adjuvant therapy (P = 0.13). No patient had a delay in the initiation of adjuvant therapy because of wound complications secondary to immediate reconstruction. Logistic regression analysis found no correlation between age, type of operation, tumor pathology, stage, number of lymph nodes harvested, type of prosthesis or chemotherapy, and wound complications in patients undergoing immediate breast reconstruction after mastectomy. The frequency of wound complications was not increased in patients receiving adjuvant chemotherapy after mastectomy and immediate breast reconstruction. The administration of adjuvant chemotherapy does not need to be delayed in patients who have had immediate breast reconstruction following mastectomy for breast cancer.

Linkage study of a susceptibility locus for schizophrenia in the pseudoautosomal region.

Several lines of evidence suggest that the sex chromosomes have a role in the expression of schizophrenia. Gender differences in response to treatment, age at onset of illness, and prognosis indicate an influence of sex in differential expression of schizophrenia. On the basis of a higher-than-expected concordance for sex among siblings with schizophrenia, as well as the findings of cytogenetic abnormalities of the sex chromosomes in some schizophrenia patients, a pseudoautosomal location for a schizophrenia susceptibility locus has been proposed. To test this hypothesis, we investigated genetic linkage of the pseudoautosomal region to schizophrenia in a large Swedish kindred. Using pairwise analyses we tested eight markers spanning the most telomeric region to the boundary of the sex-specific region. In addition, we used multi-point analysis with five markers spanning the region to test for the presence of a schizophrenia susceptibility locus in the pseudoautosomal region. No evidence was found for linkage to schizophrenia under the given genetic model: "autosomal" dominant, f (penetrance) = 0.72, q (gene frequency) = 0.02, phenocopies = 0.001.

The double-reversing Z-plasty in primary palatoplasty: operative experience and early results.

The double-reversing Z-plasty of Furlow for closure of the soft palate was used in 34 children with various types of cleft palate. Mean age at repair was 12.8 months. Intraoperative experience was favorable, with acceptable operating time and blood loss. Length of hospitalization averaged 1.9 days. Postoperatively, two children experienced temporary stridor, which resolved within 24 to 48 hours. One child had dehiscence of the hard palate (Von Lagenbeck repair) 4 weeks postoperatively, and three children developed small oronasal fistulae. Early speech evaluation demonstrated adequate soft palate mobility in 33 of 34 patients, with observable velopharyngeal function. Twelve children had mild velar compromise, with eight exhibiting slight nasal air escape.

An objective assessment of treatment for orbital hypertelorism.

A retrospective statistical analysis of orbital hypertelorism correction was performed by comparing the preoperative and postoperative intercanthal distances of these patients with published age-matched normal values. Forty-five patients who had undergone surgery over a 15-year period with an average follow-up of 5 years (6 months to 14 years) were evaluated. Comparison of age-normalized preoperative and postoperative intercanthal distances revealed a significant difference for orbital hypertelorism patients as a group (p < 0.0001), patients with clefts (p < 0.0001), patients with nasoencephalocele (p < 0.01), and patients with frontonasal dysplasia (p < 0.05), but not for those patients with craniofacial dysostosis (p < 0.20). Multiple analyses of variance revealed a significant interaction existing between the extent of preoperative deformity and the cause of hypertelorism for both the postoperative deformity and the total amount of correction achieved, but not for the type of surgery or for the age at which the surgery was performed.

Status of the search for a major genetic locus for affective disorder in the Old Order Amish.

We have resumed the search for an autosomal linkage with affective disorder in the Old Order Amish and report the pairwise linkage results after screening 185 marked loci. No positive evidence of genetic linkage was found, and we estimate that roughly 23% of the autosomal genome has been excluded from linkage.

Rearrangement of the retinoic acid receptor gene in acute promyelocytic leukemia.

The retinoic acid receptor-alpha (RAR-alpha) gene was previously localized to chromosome 17q21, a region close to the t(15;17) (q22;q21) abnormality in acute promyelocytic leukemia (APL). We used the RAR-alpha gene as a probe and found that eight of nine APL patient samples with t(15;17) (q22;q21) showed rearranged bands. A tenth APL patient was diploid and demonstrated no rearrangement. One patient who had rearrangement as an acute leukemia did not have rearrangement in remission. The results obtained from intron/exon mapping of the RAR-alpha gene demonstrated that breakpoints of seven of the eight patients occurred within intron 1. Northern blot analysis of leukemic samples indicated the expression of two RAR-alpha mRNA of 2.7 and 3.7 kb. However, two additional mRNA of 4.1 and 3.2 kb were found in an APL patient. We conclude that the RAR-alpha gene is directly involved in the t(15;17) translocation in APL and may transcribe aberrant messages.

Progress in the search for genetic linkage with Tourette syndrome: an exclusion map covering more than 50% of the autosomal genome.

Gilles de la Tourette syndrome is a neuropsychiatric disorder with an autosomal dominant mode of inheritance and reduced penetrance at a single genetic locus. Several research groups have genetic linkage studies underway to detect the chromosomal location of the gene that predisposes for this disorder. Strong and clear evidence of linkage has not yet been produced for Tourette syndrome. This paper presents an overview of the methods and progress of the groups centered at Yale University and Erasmus University in excluding linkage from a large portion of the genome. Our labs have screened 228 genetic marker loci for linkage with a gene for this disorder in a series of affected families in the United States, Canada, The Netherlands, and Norway. More than 50% (and perhaps as much as 66%) of the autosomal genome has now been excluded on the assumption that genetic heterogeneity is not an important factor in the Tourette syndrome pedigrees pooled for this summary.

A refined linkage map for DNA markers around the pericentromeric region of chromosome 10.

A refined genetic linkage map for the pericentromeric region of human chromosome 10 has been constructed from data on 12 distinct polymorphic DNA loci as well as the locus for multiple endocrine neoplasia type 2A (MEN 2A), a dominantly inherited cancer syndrome. The map extends from D10S24 (at 10p13-p12.2) to D10S3 (at 10q21-q23) and is about 70 cM long. Overall, higher female than male recombination frequencies were observed for this region, with the most remarkable female excess in the immediate vicinity of the centromere, as previously reported. Most of the DNA markers in this map are highly informative for linkage and the majority of the interlocus intervals are no more than 6 cM apart. Thus this map should provide a fine framework for future efforts in more detailed mapping studies around the centromeric area. A set of ordered cross-overs identified in this work is a valuable resource for rapidly and accurately localizing new DNA clones isolated from the pericentromeric region.

Linkage relationships of human arginine vasopressin-neurophysin-II and oxytocin-neurophysin-I to prodynorphin and other loci on chromosome 20.

The structural genes for human prepro-arginine-vasopressin-neurophysin II (prepro-AVP-NPII; ARVP) locus and prepro-oxytocin-neurophysin-I (prepro-OT-NPI; OT) locus are closely linked separated by only 12 kilobasepairs of DNA. These two loci have been assigned to chromosome 20 by previous studies of somatic cell hybrids. We used Southern blots to analyze a restriction fragment length polymorphism detected by a probe for prepro-OT-NPI to determine the linkage relationships for the ARVP/OT loci using samples from the Centre d'Etude du Polymorphisme Humain (Paris, France) collection of families. The ARVP/OT loci demonstrated extremely close linkage with the prodynorphin (PDYN) locus, with no recombinants (theta of 0) and a log10 odds score of 5.2. Previous observations have shown the ARVP and PDYN peptides to be coexcreted in the same neurosecretory granules of some pituitary axons and that increased transcription of both genes occurs with osmotic stimulation. The combined ARVP/PT/PDYN group was also found to demonstrate linkage with other anonymous DNA segments on chromosome 20, including D20S4, D20S5, and D20S6. Using multilocus linkage analysis, the ARVP/OT loci map to the distal short arm of chromosome 20 about 15 centimorgans toward the telomere from the D20S5 locus, which is located near the middle of the short arm at 20p 12.21. These linkage relationships establish that the secretory and transcriptional associations of ARVP and PDYN extend to a close physical relationship in the human genome. Furthermore, the restriction fragment length polymorphism detected by these loci can serve as accurate markers in segregation studies of putative defects involving the OT, ARVP, or PDYN loci as well as provide a tool for studying the location of other genes, such as GH-releasing hormone.