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Chromosomes 8 and 10 workshop.

The chromosomes 8 and 10 workshop took place at the Sixth World Congress on Psychiatric Genetics from October 6th-10th, 1998 in Bonn, Germany. Aim of the workshop was to discuss and summarize reports on potential susceptibility genes for psychiatric disorders. Linkage-findings on chromosome 8 concentrate on 8p22-p21 and include mainly schizophrenic disorders. Two areas on chromosome 10 were reported to contain potential susceptibility genes for schizophrenic as well as for affective disorders. The strongest findings were reported for 10p14-p11, while other groups communicated also linkage data for the telomeric part of the long arm to the workshop.

Bipolar Disorder↗

Genetic loci ordering instability: an example.

In attempting to establish the order of genetic loci by constructing a map from pairwise linkage data, one assumes that the loci satisfy a linear-order relation. If the data utilized in the construction are not consistent with the linear-order assumption, then a very small change in the data may lead to a large qualitative change in the map. An example of such an instability is presented in this paper.

Chromosome Mapping↗

Home injuries and built form--methodological issues and developments in database linkage.

BACKGROUND: The aim of this body of research is to determine whether injuries in the home are more common in particular types of housing. Previous home injuries research has tended to focus on behaviours or the provision of safety equipment to families with young children. There has been little consideration of the physical environment. This study reports methodological developments in database linkage and analysis to improve researchers abilities to utilise large administrative and clinical databases to carry out health and health services research. METHODS: The study involved linking a database of home injuries obtained from an emergency department surveillance system with an external survey of all homes in an area and population denominators for home types derived from a health service administrative database. Analysis of injury incidence by housing type was adjusted for potential biases due to deprivation and distance to hospital. For non-injured individuals data confidentiality considerations required the deprivation and distance measures be imputed. The process of randomly imputing these variables and the testing of the validity of this approach is detailed. RESULTS: There were 14,081 first injuries in 112,248 residents living in 54,081 homes over a two-year period. The imputation method worked well with imputed and observed measures in the injured group being very similar. Re-randomisation and a repeated analysis gave identical results to the first analysis. One particular housing type had a substantially elevated odds ratio for injury occurrence, OR = 2.07 (95% CI: 1.87 to 2.30). CONCLUSIONS: The method of data linkage, imputation and statistical analysis used provides a basis for improved analysis of database linkage studies.

Accidents, Home↗

DNA linkage analysis of X-linked retinoschisis.

Four families with juvenile retionoschisis (RS) have been studied by linkage analysis utilizing eleven polymorphic X-chromosomal markers. The results suggest a close linkage between DXS43, DXS41, and DXS208 and the RS locus at Xp22. The RS locus is distal to the OTC locus, DXS84, and the DMD locus but proximal to DXS85. No recombination events were observed between the RS locus and DXS43 and DXS41. The maximum likelihood estimate of the recombination fraction (theta) was thus zero and the peak lod scores (z) were 4.98 (DXS43) and 4.09 (DXS41). The linkage data suggest that the gene order on Xp is DXS85-(DXS43, RS, DXS41)-DMD-DXS84-OTC.

Chromosome Mapping↗

Functional implications of the spectrum of mutations found in 234 cases with X-linked juvenile retinoschisis. The Retinoschisis Consortium.

X-linked retinoschisis (XLRS) is the most common cause of juvenile macular degeneration in males, resulting in vision loss early in life. The gene involved in XLRS was identified recently. It encodes a protein with a disoidin domain, suggested to be involved in cell-cell interactions. We have screened the gene for mutations in 234 familial and sporadic retinoschisis cases and identified 82 different mutations in 214 (91%). Thirty one mutations were found more than once, i.e. 2-10 times, with the exception of the 214G-->A mutation which was found in 34 apparently unrelated cases. The origin of the patients, the linkage data and the site of the mutations (mainly CG dinucleotides) indicate that most recurrent mutations had independent origins and thus suggest the existence of a significant new mutation rate in XLRS1. The mutations identified cover the entire spectrum, from small intra-genic deletions (7%), to nonsense (6%), missense (75%), small frameshifting insertions/deletions (6%) and splice site mutations (6%). Since, regardless of the mutation type, no females with a typical RS phenotype were identified, RS seems to be caused by loss-of-function mutations only. Mutations occurred non-randomly, with hotspots at several CG dinucleotides and a C6stretch. Exons 1-3 contained few, mainly translation-truncating mutations, arguing against an important functional role for this segment of the protein. Exons 4-6, encoding the discoidin domain, contained most, mainly missense mutations. An alignment of 32 discoidin domain proteins was constructed to reveal the consensus sequence and to deduce the functional importance of the missense mutations identified. The mutation analysis revealed a high preponderance of mutations involving or creating cysteine residues, pointing to sites important for the tertiary folding and/or protein function, and highlights several amino acids which may be involved in XLRS1-specific protein-protein interactions. Despite the enormous mutation heterogeneity, patients have relatively uniform clinical manifestations although with great intra-familial variation in age at onset and progression.

Adolescent↗

Genetic heterogeneity of familial hemiplegic migraine.

Familial hemiplegic migraine (FHM) is an autosomal dominant variety of migraine with aura. We previously mapped a gene responsible for this disorder to the short arm of chromosome 19, within a 30-cM interval bracketed by D19S216 and D19S215. Linkage analysis conducted on two large pedigrees did not show any evidence of heterogeneity, despite their clinical differences due to the presence, in one family, of cerebellar ataxia and nystagmus. Herein we report linkage data on seven additional FHM families including another one with cerebellar ataxia. Analysis was conducted with a set of seven markers spanning the D19S216-D19S215 interval. Two-point and multipoint lod score analyses as well as HOMOG testing provided strong evidence for genetic heterogeneity. Strong evidence of linkage was obtained in two families and of absence of linkage in four families. The posterior probability of being of the linked type was > .95 in the first two families and < .01 in four other ones. It was not possible to draw any firm conclusion for the last family. Thus, within the nine families so far tested, four were linked, including those with associated cerebellar ataxia. We could not find any clinical difference between the pure FHM families regardless of whether they were linked. In addition to the demonstration of genetic heterogeneity of FHM, this study also allowed us to establish that the most likely location of the gene was within an interval of 12 cM between D19S413 and D19S226.

Ataxia↗

The role of T cell receptor beta chain genes in susceptibility to rheumatoid arthritis.

OBJECTIVE: To evaluate the role of the T cell receptor beta chain locus (TCRB) in genetic susceptibility to rheumatoid arthritis (RA). METHODS: Twenty-eight multiplex RA families were recruited from 3 rheumatology outpatient departments. All members were genotyped for a highly informative microsatellite (V beta 6.7), a V beta 12.2 SSCP marker, and a biallelic C beta restriction fragment length polymorphism. Data were analyzed by the SIBPAL program to assess identity-by-descent in affected sib-pairs. RESULTS: Using the V beta 12.2 marker, there was suggestive evidence of increased sib-pair sharing (P = 0.005) in affected offspring (a P value of 0.001 is generally taken to establish linkage). Data for V beta 6.7 and C beta yielded significance levels of 0.06 and 0.19, respectively. CONCLUSION: These data suggest that a gene in or linked to the TCRB complex may confer genetic susceptibility to RA in these families. Confirmation in a larger panel of families is required.

Adolescent↗

New X-linked syndrome of mental retardation, gynecomastia, and obesity is linked to DXS255.

We describe 14 males from 3 successive generations in a family who have X-linked mental retardation (XLMR), obesity, gynecomastia, speech difficulties, emotional lability, tapering fingers, and small feet. Linkage analysis using markers spread along the X chromosome demonstrated a gene localisation close to the centromere. Maximum lod scores for markers near the centromere, all at theta = 0.00, were 1.36 for DXS72, and 1.46 for DXYS1. The closest flanking markers which showed recombination were DXS84 and DXS94, defining the physical localisation within Xp21.1-q22. DXS255 was fully informative with lod-1 confidence interval for theta of 0.00-0.12. Clinical findings and linkage data in this family distinguish it from the Börjeson-Forssman-Lehmann syndrome and other previously described XLMR syndromes.

Adolescent↗

Narrowing down the region of the Vf locus for scab resistance in apple using AFLP-derived SCARs.

A narrow-down strategy to restrict the Vf region, which controls resistance to the fungal disease apple scab in apple, to a genetic distance of 0.4 cM is presented. Using 11 AFLP-derived SCARs and three RAPD-derived SCARs, all linked to the Vf gene, we subjected 1,412 scab-resistant individuals from 16 mapping populations to genotype analysis. Eleven recombinant individuals were identified within a genetic distance of 0.9 cM around the Vf gene. Using these 11 recombinants, we achieved fine-resolution of several AFLP-derived SCAR markers surrounding the Vf gene, resulting in the following genetic linkage map: ACS-6 and ACS are located left of the Vf gene at genetic distances of 0.2 cM and 0.1 cM, respectively; ACS-7 and ACS-9 are inseparable from the Vf gene; ACS-8, ACS-10, and ACS-4 are located to the right of the Vf gene at genetic distances of 0.1 cM, 0.4 cM, and 0.5 cM, respectively; the remaining five SCARs-ACS-11, ACS-5, ACS-2, ACS-1, and AL07-are inseparable and are located right of the Vf gene at a genetic distance of 0.7 cM. By integrating this linkage data with our previous physical map, we generated a revised map of the narrowed-down region of Vf.

Ascomycota↗

Genetic polymorphism of human C4-binding protein.

Two different forms of human C4-bp, C4-bp A and C4-bp B, have been identified by isoelectric focusing (IEF) of neuraminidase-treated EDTA-plasma samples. Family studies demonstrate Mendelian segregation of these forms, indicating that they are under gentic control. This conclusion is supported by IEF analysis of the two variants purified by affinity chromatography. Under completely denaturing conditions, C4-bp B was found to be composed of two subunits that focused at different pH, whereas C4-bp A contains only the more basic one. These results suggest that a single autosomal locus with at least two codominant alleles coding for the subunits controls the IEF variation of C4-bp in humans. The allele designated C4BP*1 codes for a subunit that, after neuraminidase treatment, focuses at pH = 6.65. The allele C4BP*2 codes for a different subunit that focuses at pH = 6.60. The C4-bp A phenotype corresponds to the genotype C4BP*1,C4BP*1 and the phenotype C4-bp B to the genotype C4BP*1,C4BP*2. The phenotype corresponding to the C4BP*2,C4BP*2 homozygous genotype has not been encountered thus far. Initial linkage data indicate that the C4BP locus is not closely linked to either the HLA or to the C3 loci.

Animals↗

Candidate genes, pathways and mechanisms for bipolar (manic-depressive) and related disorders: an expanded convergent functional genomics approach.

Identifying genes for bipolar mood disorders through classic genetics has proven difficult. Here, we present a comprehensive convergent approach that translationally integrates brain gene expression data from a relevant pharmacogenomic mouse model (involving treatments with a stimulant--methamphetamine, and a mood stabilizer--valproate), with human data (linkage loci from human genetic studies, changes in postmortem brains from patients), as a bayesian strategy of crossvalidating findings. Topping the list of candidate genes, we have DARPP-32 (dopamine- and cAMP-regulated phosphoprotein of 32 kDa) located at 17q12, PENK (preproenkephalin) located at 8q12.1, and TAC1 (tachykinin 1, substance P) located at 7q21.3. These data suggest that more primitive molecular mechanisms involved in pleasure and pain may have been recruited by evolution to play a role in higher mental functions such as mood. The analysis also revealed other high-probability candidates genes (neurogenesis, neurotrophic, neurotransmitter, signal transduction, circadian, synaptic, and myelin related), pathways and mechanisms of likely importance in pathophysiology.

Animals↗

Fine mapping of X-linked clasped thumb and mental retardation (MASA syndrome) in Xq28.

The MASA syndrome is an X-linked disorder with mental retardation, spastic paraparesis, and adducted thumbs as the most characteristic features. We performed linkage analysis, using Xq28 markers, on a large MASA syndrome family. The maximum lodscore was 6.37 at 0 recombination for DXS52 and 5.99 at 0 recombination for DXS305. Crossovers were demonstrated between the disorder and DXS455. Clinical and linkage data from this family further support the hypothesis that the MASA syndrome and X-linked hydrocephalus are allelic disorders.

Chromosome Mapping↗

The human chromosome 19 linkage group FUT1 (H), FUT2 (SE), LE, LU, PEPD, C3, APOC2, D19S7 and D19S9.

Families segregating for deficiency of the H alpha-2-L-fucosyltransferase, FUT1, have been investigated for linkage between FUT1 and other markers on chromosome 19. The results provide evidence for close linkage between FUT1 and FUT2 and for looser linkage between FUT1 and APOC2 and between FUT1 and D19S7. Pairwise linkage data are also reported between other markers investigated.

Blood Grouping and Crossmatching↗

Close linkage between X-linked ectodermal dysplasia and a cloned DNA sequence detecting a two allele restriction fragment length polymorphism in the region Xp11-q12.

EDA (ectodermal dysplasia, anhidrotic) is an X-linked recessive disorder characterized by hypohidrosis, hypoor anodontia, and hypotrichosis. A possible linkage between the gene for EDA and a number of restriction fragment length polymorphisms (RFLPs) spread over the X chromosome was investigated in two Danish families segregating EDA. No recombination between the gene for EDA and our probe pTAK8, which detects a two allele polymorphism in the region Xp11-q12, was found in nine informative meiotic events (seven of which are phase known), giving a maximal lod score of 2.41 at a recombination fraction of 0.00. This juxtacentromeric location of the gene for EDA agrees well with the linkage data obtained with the other markers used in this study.

Adolescent↗

Using overall allele-sharing to detect the presence of large-scale data errors and parameter misspecification in sib-pair linkage studies.

Data errors and marker allele frequency misspecification can lead to incorrect inference in linkage analysis. Here we demonstrate the effect of each on an allele-sharing statistic in a sample of sib pairs. In the context of relationship testing, we propose a new test that compares the sample genome-wide sib-pair allele sharing to its expectation and show that this test can detect the presence of large-scale data and model errors.

Alleles↗

Health and environment analysis for decision making.

This article gives a overview of the HEADLAMP project and its background. The project aims at bringing valid and useful information on the local and national health impacts of environmental hazards to those responsible for environmental health protection. Its main tools are health and environment data linkage methods, environmental health indicators used to quantify and monitor the local situation, and the interpretation and decision-making process. The project has 3 main characteristics which differentiate it from ad hoc epidemiological studies: (i) it is based on scientifically established relationships between environmental exposures and health effects; (ii) it uses routinely-collected data, or where necessary, new data collected using low-cost techniques; and (iii) it aims at providing information on which to base preventive action against environmental health problems. Based on these characteristics, a framework is proposed for the application of HEADLAMP for managing specific environmental health problems.

Environmental Exposure↗

Exclusion mapping of 12 X-linked disease loci and 10 DNA probes from the long arm of the X-chromosome.

Specific chromosome rearrangements associated with disease entities are invaluable resources for physical mapping. A deletion on the X chromosome of a male leads to the nullisomy for X-linked genes, resulting in the onset of genetic diseases and/or the absence of the DNA probe detectable sequences. This permits the localization of these loci within the deleted area. On the other hand, the region for some other X-linked loci can be excluded from the deleted area according to the absence of the characteristic symptoms of the disease and/or the presence of the hybridization signals. An interstitial deletion on the long arm of the X chromosome of a male has been characterized by high resolution banding. The karyotype of the proband is 46,Y,del(X)(pter----q21.1::q21.33----qter). The regions for 12 X-linked disease loci as well as 10 DNA probes are excluded from the deleted area, and localized either proximally or distally to the deletion. The results also reveal a controversy in the present linkage data concerning the assignment of these loci.

Abnormalities, Multiple↗

Gene mapping and other tools for discovery.

Genetic mapping provides a means of understanding the molecular basis of inherited diseases whose biochemistry is unknown. Adequate pedigrees, informative genetic markers, and accurate identification of the disease phenotype are necessary. For dominant inheritance, mapping studies can be done in a single large pedigree; the larger the number of affected individuals sampled the better the estimate of recombination between the gene causing the disease and one or more nearby genetic markers. For recessive inheritance, nuclear families with more than one affected sibling provide the best information. The development of many polymorphic DNA markers on the human genome has contributed to the success of mapping unknown genes because, as the genome is now densely covered with markers, the probability is good that at least one marker will be linked to the disease locus in a family that is segregating a disease allele. Most genetic markers now in use depend upon restriction fragment length polymorphisms (RFLPs), which are either the result of single-base-pair substitution or the presence of a variable number of tandemly repeated oligonucleotide units at a locus (VNTRs). RFLPs can be recognized by digesting DNA with restriction enzymes and separating the fragments by size on an electrophoretic gel. VNTRs can vary widely among individuals, and they provide more linkage information than single-site polymorphic markers because family members are more likely to be heterozygous. Genetic maps of each chromosome, constructed from linkage data relating marker loci to one another in normal reference families, permit rational choices of markers for disease-mapping studies.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosome Mapping↗