Programs for determining parameters in complex genetic models for linkage analysis: GEN-PAR and EPI-PAR.
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Epidemiologic Methods↗
Biomedical subjects
R Plaetke
Publications and source records attributed to R Plaetke.
Codistribution of a sensory gating deficit and schizophrenia in multi-affected families.
Because the clinical diagnosis of schizophrenia has not generally been an adequate phenotypic marker to detect the genes that convey risk for schizophrenia, efforts have been directed toward the identification of more elementary neuronal dysfunctions in schizophrenic patients and their families. Psychophysiological studies of sensory gating and selective attention suggest that defects in these brain functions are present in schizophrenic patients and some of their relatives. This study examines one of these defects in sensory gating, failure to suppress the P50 evoked response to repeated auditory stimuli. Six pedigrees, chosen because of the presence of large sibships containing several cases of schizophrenia, were studied. A mathematical model was developed to assess the familial association of the P50 defect with schizophrenia. The model preserves the quantitative nature of the data and is suitable for use in a sample with small numbers of pedigrees comprising many individuals. It is thus suitable for the evaluation of putative phenotypes in families to be studied by linkage analysis with polymorphic genetic markers. The results suggest that the P50 defect is familially associated with schizophrenia.
Adult↗
Linkage disequilibrium between DNA markers at the low-density lipoprotein receptor gene.
We determined pairwise linkage disequilibria between 12 restriction fragment length polymorphism (RFLP) markers at or near the low-density lipoprotein receptor (LDLR) locus on chromosome 19p13.2-13.1 in 92 unrelated individuals. Of these 12 RFLPs, two were newly identified under a cosmid-based strategy designed to screen for RFLPs. We estimated linkage disequilibrium by determining three different measurements: D (the maximum likelihood estimate of linkage disequilibrium), D' (Lewontin's normalized estimate of D), and r (an index of gametic correlation). When r was used as the estimate of linkage disequilibrium, five of the 66 comparisons were significant according to a level of significance adjusted by the Bonferroni-Holm correction. Only four pairs of RFLPs within a 100 kb region that included the LDLR gene itself were in significant linkage disequilibrium. Although we were able to detect strong linkage disequilibrium between some pairs of RFLPs in this sample, most RFLPs at the LDLR locus were not in strong linkage disequilibrium despite their physical proximity.
Alleles↗
Diagnosis of neurofibromatosis I by using tightly linked, flanking DNA markers.
We tested 132 individuals from 21 families segregating an allele for neurofibromatosis type 1 (NF-1), by using nine RFLPs tightly linked to the NF-1 locus. Family members had requested DNA testing either to determine whether "at risk" children were carrying the NF-1 allele or to determine whether their respective families would be informative for prenatal testing. Predictions about whether a child carries the NF-1 mutation were possible for all 32 at-risk offspring (greater than 98% accuracy based on the recombination estimates currently available for these DNA markers). At least one informative probe was available for all 23 matings in these 21 families; flanking markers were informative for 10 matings. Pairwise analysis showed that several of the polymorphisms were in tight linkage disequilibrium; few recombination events were observed with these markers in the families under study. We conclude that the DNA probes used in this study perform well for diagnostic testing of NF-1 in familial cases. A subset of five probe-enzyme systems (pHHH202/RsaI, p11-3C4.2/MspI, pTH17.19/Bg/II, p11-2C11.7/BamHI, and p11-2F9.8/TaqI) provide reliable linkage information for both clinical testing and prenatal diagnosis.
Alleles↗
Unequal crossingover between homologous chromosomes is not the major mechanism involved in the generation of new alleles at VNTR loci.
To investigate the hypothesis that unequal exchange between homologous chromosomes is involved when new alleles are generated at VNTR loci, we used genetic linkage maps to identify flanking markers surrounding a VNTR marker locus. The minisatellite probe lambda MS1 was selected, as the hypervariable locus it detects undergoes spontaneous generation of new alleles in the germline at a rate of approximately 5%. Multipoint linkage analysis placed lambda MS1 within a cluster of polymorphic marker loci on chromosome 1p. Using the two closest flanking markers, CMM8 and YNZ2, we were able to characterize 12 new-allele events in terms of crossingover between the flanking markers. Statistical analysis of these data has allowed us to reject the model that assumes that events generating new alleles always involve unequal exchange between homologous chromosomes at meiosis.
Alleles↗
Characterization of eight VNTR loci by agarose gel electrophoresis.
Allelic frequencies and their confidence intervals were obtained for eight independent VNTR loci from a sample of more than 75 Utah Caucasians. Using high-resolution agarose gel electrophoresis, we were able to resolve alleles at the D17S5 locus that differed by only one repeating unit; it was therefore possible to name the alleles according to the number of repeating units each contained. Two a priori probabilities were calculated for each VNTR locus separately and for all eight loci jointly: (i) the "power of exclusion" for an alleged father/mother/child trio and for an alleged parent/child duo, and (ii) the "probability of matching" when two unrelated individuals or two siblings are genotyped.
Alleles↗
Selection on recombination in subdivided populations with stabilizing selection.
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Computer Simulation↗
Linkage analysis of schizophrenia: the D1 dopamine receptor gene and several flanking DNA markers.
Alterations in dopaminergic activity may play an important role in the pathogenesis of schizophrenia. The central effects of dopamine are mediated by at least five G protein-coupled receptors, D1, D2, D3, D4 and D5. The D1 receptor maps to 5q35.1 and it identifies an Eco RI as well as a Taq I RFLP. In the present study we undertook a linkage analysis between the D1 receptor RFLPs and schizophrenia in 9 multigenerational families in which segregation of disease was consistent with autosomal dominant inheritance and reduced penetrance. Several flanking DNA markers were also analyzed as the D1 receptor RFLPs were relatively uninformative in our families. Pairwise analyses of schizophrenia and several flanking markers indicate that inheritability of this region is unlikely to be involved in the pathogenesis of schizophrenia in the 9 families studied.
Chromosome Mapping↗
Effects of three genetic loci in a pedigree with multiple lipoprotein phenotypes.
In the course of familial investigations of coronary artery disease, we identified an extended kinship in which several members were affected with type IIa hyperlipoproteinemia (HLPIIa), type III dyslipoproteinemia (DLPIII), or hypobetalipoproteinemia (HBLP). To study the genetic defects responsible for plasma lipoprotein abnormalities in this pedigree and to investigate the phenotypic effect of different genotypic combinations, we used molecular markers for apolipoprotein (apo) B, apo E, and the low density lipoprotein (LDL) receptor to characterize segregation at each locus. Linkage analysis showed that elevated LDL cholesterol levels and the HBLP phenotype were due to defects at the LDL receptor and the apo B loci, respectively. One pedigree member, who inherited both an LDL receptor allele linked with elevated LDL cholesterol levels and an apo B allele linked with HBLP, had a normal lipoprotein phenotype. Seven patients who simultaneously inherited the defective LDL receptor allele and one or two apo E2 alleles manifested DLPIII. The E2 alleles in this pedigree were shown by DNA sequence analysis to be the common E2 158 (arginine----cysteine) allele. These findings suggested a possible interaction between the abnormal LDL receptor and apo E2 alleles, resulting in the expression of DLPIII in the presence of a single copy of ago E2.
Adolescent↗
HLA-antigens in a Tunisian familial chondrocalcinosis.
Thirty members of a Tunisian family with hereditary chondrocalcinosis were typed for HLA-A, B, and DR antigens: 7 affected and 23 unaffected subjects in three consecutive generations. The haplotype A1 B12 DR3 was found in all affected subjects and in 8 unaffected members. Chondrocalcinosis in this family may be associated with the haplotype A1 B12 DR3. The mode of transmission was autosomal dominant with incomplete penetrance.
Chondrocalcinosis↗