Linkage and association of a functional DRD2 variant [Ser311Cys] and DRD2 markers to alcoholism,substance abuse and schizophrenia in Southwestern American Indians

Alcoholism is one of a group of common psychiatric diseases which are well-defined clinically and strongly influenced genetically, but which are likely to be highly heterogeneous in causation, genetically and otherwise. Dopamine is a key neurotransmitter in drug-mediated reinforcement. Based on association studies with the Taq1A downstream marker, the D2 dopamine receptor has been proposed to be the “Reward Deficiency Syndrome Gene.” Ser311Cys, a naturally occurring variant which largely inactivates transduction after D2 receptor activation, was abundant (0.16) in a Southwestern American Indian population we studied. Therefore, we were able to provide a critical test of the D2 hypothesis of vulnerability to alcoholism by evaluating Ser311Cys and also the intron-2 STR and Taq1A markers at this locus in a total of 459 subjects, including 373 sib pairs, from large families. The result is that neither alcoholism, substance use disorders nor schizophrenia show a relationship to Ser311Cys genotype, even when the 15 Cys311/Cys311 homozygous individuals are compared to others. Furthermore, sib pair analysis incorporating information across all three sib pair categories: concordant affected, discordant and concordant unaffected revealed no effect of DRD2 genotype or haplotype on alcoholism or substance use disorder. Am. J. Med. Genet. 74:386–394, 1997. © 1997 Wiley-Liss, Inc.     

When to conduct probabilistic linkage vs. deterministic linkage? A simulation study

IntroductionWhen unique identifiers are unavailable, successful record linkage depends greatly on data quality and types of variables available. While probabilistic linkage theoretically captures more true matches than deterministic linkage by allowing imperfection in identifiers, studies have shown inconclusive results likely due to variations in data quality, implementation of linkage methodology and validation method. The simulation study aimed to understand data characteristics that affect the performance of probabilistic vs. deterministic linkage.MethodsWe created ninety-six scenarios that represent real-life situations using non-unique identifiers. We systematically introduced a range of discriminative power, rate of missing and error, and file size to increase linkage patterns and difficulties. We assessed the performance difference of linkage methods using standard validity measures and computation time.ResultsAcross scenarios, deterministic linkage showed advantage in PPV while probabilistic linkage showed advantage in sensitivity. Probabilistic linkage uniformly outperformed deterministic linkage as the former generated linkages with better trade-off between sensitivity and PPV regardless of data quality. However, with low rate of missing and error in data, deterministic linkage performed not significantly worse. The implementation of deterministic linkage in SAS took less than 1 min, and probabilistic linkage took 2 min to 2 h depending on file size.DiscussionOur simulation study demonstrated that the intrinsic rate of missing and error of linkage variables was key to choosing between linkage methods. In general, probabilistic linkage was a better choice, but for exceptionally good quality data (<5% error), deterministic linkage was a more resource efficient choice.     

Assessing the contribution family data can make to case-control studies of rare variants

When pathogenic variants are rare then even among cases the proportion of subjects possessing a variant might be low, meaning that very large samples might be required to conclusively demonstrate evidence of an effect. Relatives of subjects within a case-control sample might provide useful additional information. The method of model-free linkage analysis implemented in MFLINK was adapted to incorporate linkage disequilibrium (LD) parameters in order to test for an effect of a putative pathogenic variant in complete LD with a disease locus. The effect of adding in to the analysis relatives of cases and controls found to carry the variant was investigated. When affected siblings or cousins of cases possessing the variant were incorporated they had a large effect on the results obtained. The evidence for involvement increased or reduced as expected, depending on whether or not the relatives themselves were found to possess the variant. The size of the effect was large relative to that expected from just increasing the size of a standard case-control sample. Affected relatives offer a valuable resource to assist the interpretation of case-control studies of rare variants. The method is capable of including other relative types and can deal with complex pedigrees.     

Design and Analysis of Genetic Association Studies to Finely Map a Locus Identified by Linkage Analysis: Assessment of the Extent to Which an Association Can Account for the Linkage

Association studies are often used to finely map quantitative trait loci identified by linkage analysis. Once a polymorphism associated with the trait has been identified, it may be useful to conduct linkage analyses which adjust for this polymorphism to determine the extent to which the association accounts for the linkage signal. However, methods for conducting statistical significance tests for an observed reduction in the linkage signal are not well developed. In the present study we develop methods for assessment of the statistical significance of an observed reduction in the variance due to the linked locus, with variance components or with Haseman-Elston linkage methods. Simulations indicate that these methods have appropriate levels of type I error and that, like other association statistics, their power depends on the magnitude of linkage disequilibrium between functional and marker alleles and on the extent of similarity between the frequency of the functional allele and the frequency of the associated marker allele. These methods can help determine which association results are likely due to strong linkage disequilibrium with functional alleles and, thus, can facilitate the selection of small chromosomal regions for more extensive study.     

Investigation of linkage and association/linkage disequilibrium of HLA A‐, DQA1‐, DQB1‐, and DRB1‐alleles in 69 sib‐pair‐ and 89 trio‐families with schizophrenia

The hypothesis that HLA antigens confer susceptibility to schizophrenic disorders has been tested by studying linkage and association in a family sample with 69 sib‐pair families. Suggestive evidence for linkage was obtained by nonparametric multipoint LOD score analysis with a maximum around DQB CAR (P = 0.0004), a microsatellite marker that is in linkage disequilibrium with the HLA antigen DQB1. Spurious evidence for negative association as calculated by the transmission disequilibrium test was found for HLA‐ DRB1*11 (chi‐square = 11.72, corrected P value = 0.03) and for the haplotype DQB1*301—DQA1*501—DRB1*11 (chi‐square = 11.3, corrected P value = 0.043). No evidence of association with these alleles was obtained in a sample of 89 trios with schizophrenic offspring and parents. Our results are not in favor of a direct involvement of the HLA system in development of schizophrenia, but are compatible with the possible existence of a susceptibility gene in the MHC region at chromosome 6p 21.31. © 2002 Wiley‐Liss, Inc.     

Detecting linkage disequilibrium in the presence of locus heterogeneity

Locus heterogeneity is a common phenomenon in complex diseases and is one of the most important factors that affect the power of either linkage or linkage disequilibrium (LD) analysis. In linkage analysis, the heterogeneity LOD score (HLOD) rather than LOD itself is often used. However, the existing methods for detecting linkage disequilibrium, such as the TDT and many of its variants, do not take into account locus heterogeneity. We propose two novel likelihood-based methods, an LD-Het likelihood and an LD-multinomial likelihood, to test linkage disequilibrium (LD) that explicitly incorporate locus heterogeneity in the analysis. The LD-Het is applicable to general nuclear family data but requires a working penetrance model. The LD-multinomial is only applicable to affected sib-pair data but does not require specification of a trait model. For affected sib-pair data, both methods have similar power to detect LD under the recessive model, but the LD-multinomial model has greater power when the underlying model is dominant or additive.     

A genetic epidemiologic investigation of breast cancer in families with bilateral breast cancer. II. Linkage analysis

We conducted genetic linkage analyses of breast cancer in 20 pedigrees, each having at least one case of bilateral breast cancer diagnosed before 50 years of age. We tested for linkage using inheritance models from previous segregation analyses, incorporating differences in risk based on menopausal status into the analyses. We tested for heterogeneity by predividing the data set based on the interval between diagnoses of the proband's two primaries (less than 1 year (synchronous) versus at least 2 years (asynchronous], and on the histological types of breast cancer in the pedigrees. Very tight linkage could be excluded between breast cancer and ABO, GC, GPT, MNS, and PGM1 for some of the different linkage analyses. A maximum lod score of +1.01 (at theta = 0.001) between ACP1 and a breast cancer susceptibility locus was seen in the asynchronous all-cases subsample.     

Unique PABP2 mutations in “Cajuns” suggest multiple founders of oculopharyngeal muscular dystrophy in populations with French ancestry

Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset autosomal dominant myopathy found world-wide, but with the highest incidence in French-Canadians. Short GCG expansions in the poly(A) binding protein 2 (PABP2) gene were identified recently as the molecular basis for OPMD in French-Canadians. All French-Canadian cases of OPMD have been traced to a single founder couple [Bouchard, 1997: Neuromuscul Disord 7(Suppl):S5–S11]. Cultural links between French-Canadians and Cajuns suggest that this same founder couple may have transmitted the OPMD mutation to Cajuns as well. To determine if OPMD patients from Louisiana share a founder effect with French-Canadian families, we collected blood samples and muscle biopsies from several Cajuns with OPMD for mutation and linkage studies. We found a unique ‘GCA GCG GCG’ insertion mutation in Cajuns. Consistent with these sequence data, we identified a disease haplotype in our Cajun families that is different from the ancestral haplotype defined in French-Canadians. These data prove that different founders introduced the PABP2 mutation to Cajuns and French-Canadians and lend support to emerging genealogical data suggesting that French-Canadians and Cajuns represent distinct immigrant groups from France. Am. J. Med. Genet. 86:477–481, 1999. © 1999 Wiley-Liss, Inc.     

An approach to investigating linkage for bipolar disorder using large Costa Rican pedigrees

Despite the evidence that major gene effects exist for bipolar disorder (BP), efforts to map BP loci have so far been unsuccessful. A strategy for mapping BP loci is described, focused on investigation of large pedigrees from a genetically homogenous population, that of Costa Rica. This approach is based on the use of a conservative definition of the BP phenotype in preparation for whole genome screening with polymorphic markers. Linkage simulation analyses are utilized to indicate the probability of detecting evidence suggestive of linkage, using these pedigrees. These analyses are performed under a series of single locus models, ranging from recessive to nearly dominant, utilizing both lod score and affected pedigree member analyses. Additional calculations demonstrate that with any of the models employed, most of the information for linkage derives from affected rather than unaffected individuals. © 1996 Wiley-Liss, Inc.     

Spondyloepiphyseal dysplasia in a cape town family: Linkage with the gene for type II collagen (COL2A1)

A moderately severe form of autosomal dominant (AD) spondyloepiphyseal dysplasia (SED) has been documented in 14 individuals in 3 generations of a family in Cape Town, South Africa. Affected persons had a short trunk; radiographic investigations indicated that skeletal involvement was worst in the hips and spine. Linkage studies with restriction fragment length polymorphisms (RFLPs) associated with the COL2A1 gene and the phenotype yielded a maximal LOD score of 4.51 at theta = 0.00. This result suggests that the structural locus for type II collagen is primarily involved in the pathogenesis of this form of SED. © 1992 Wiley-Liss, Inc.     

Linkage of familial alzheimer disease to chromosome 14 in two large early-onset pedigrees: Effects of marker allele frequencies on lod scores

Alzheimer disease (AD) is a devastating neurodegenerative disease leading to global dementia. In addition to sporadic forms of AD, familial forms (FAD) have been recognized. Mutations in the amyloid precursor protein (APP) gene on chromosome (CHR) 21 have been shown to cause early-onset AD in a small number of pedigrees. Recently, linkage to markers on CHR 14 has been established in several early-onset FAD pedigrees. We now report lod scores for CHR 14 markers in two large early-onset FAD pedigrees. Pairwise linkage analysis suggested that in these pedigrees the mutation is tightly linked to the loci D14S43 and D14S53. However, assumptions regarding marker allele frequencies had a major and often unpredictable effect on calculated lod scores. Therefore, caution needs to be exercised when single pedigrees are analyzed with marker allele frequencies determined from the literature or from a pool of spouses. © 1993 Wiley-Liss, Inc.     

A Robust Linkage Analysis Method Using Combined Allele Sharing and Transmission Disequilibrium Information from Case-Parent Tetrad Families

There are two types of linkage information, the allele sharing information and transmission disequilibrium information, that can be extracted from case-parent tetrad families for deriving statistics for test of linkage. By extracting allele sharing information the mean test can be derived. By extracting transmission disequilibrium information the transmission/disequilibrium test (TDT) can be derived. The power performances of the two tests are different with respect to the extent of linkage disequilibrium. The TDT is more powerful than the mean test when the extent of linkage disequilibrium is moderate to strong, but the mean test has better power performance than the TDT when linkage disequilibrium is weak. Some previous studies have proposed several post-combination analysis methods, which combine the two tests after they are derived using the two types of linkage information respectively, to yield robust test statistics against the interference of linkage disequilibrium. Instead of adopting the post-combination approach, in this paper we investigate the approach of using the pre-combination idea to yield robust statistics for test of linkage. The pre-combination methods combine the two types of linkage information first, and then use the combined information to construct robust test statistics. Simulation studies are conducted to compare the power performances of the proposed pre-combination tests with those of the existing post-combination methods.     

Serotonin transporter (5-HTT) gene and bipolar affective disorder

Interactions with antidepressants, as well as other biochemical evidence, implicate the serotonin transporter 5-HTT in the etiology of affective disorders. However, genetic studies have produced conflicting results concerning an association of 5-HTT with bipolar disorder. We examined a variable number tandem repeat in the regulatory region of this gene to investigate the possible contribution of 5-HTT to bipolar disorder susceptibility in a 22-pedigree series. By affected-sib-pair analysis and the transmission/disequilibrium test, we found no significant linkage or association of 5-HTT to bipolar disorder. During the course of this study, we adapted a PCR technique designed to amplify long templates to replicating long GC stretches with complex structure. We also refined the location of 5-HTT by radiation hybrid mapping, placing the locus between D17S1294 and SHGC-11022 on 17q11.2. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 81:37–40, 1998. © 1998 Wiley-Liss, Inc.     

X-linked myopia: Bornholm Eye Disease

Linkage analysis in a family with X-linked myopia gave a positive LOD score (z = 4.8 at theta = 0) for linkage to F8C. These results suggest a provisional assignment for the locus of this syndrome to the distal part of the X chromosome at Xq28. Based on the clinical and genetic evidence, a redefinition of this clinical syndrome, named Bornholm Eye Disease (BED), was made to include amblyopia, myopia, and deuteranopia. Facultative signs were optic nerve hypoplasia, reduced electroretinographic flicker function, and non-specific retinal pigment abnormalities.     

Gene homologies and linkage conservation

Rapid progress in the mapping of some mammalian genomes, especially those of man and the house mouse, has revealed the existence of chromosomal regions that have been conserved over long evolutionary periods. Different aspects of this subject have been treated in recent reviews (Renwick 1972, Ohno 1973, Bodmer 1975, Minna et al. 1976, Searle 1976, Finaz et al. 1977, Lalley et al. 1978 and Lundin 1979). Not only has it been possible to identify orthologous chromosomal regions in several mammalian species, but also quite extensive paralogous regions in man and the mouse have been suggested (Lundin 1979). For a definition of orthologous and paralogous genes see Lundin (1979).     

Comparison of human chromosome 19q13 and syntenic region on mouse chromosome 7 reveals absence,in man,of 11.6?Mb containing four mouse calcium-sensing receptor-related sequences: relevance to familial benign hypocalciuric hypercalcaemia type 3

Familial benign hypocalciuric hypercalcaemia (FBHH) is a genetically heterogeneous disorder that consists of three designated types, FBHH1, FBHH2 and FBHH3, whose chromosomal locations are 3q21.1, 19p and 19q13, respectively. FBHH1 is caused by mutations of a calcium-sensing receptor (CaSR), but the abnormalities underlying FBHH2 and FBHH3 are unknown. FBHH3, also referred to as the Oklahoma variant (FBHH_Ok), has been mapped to a 12cM interval, flanked by D19S908 and D19S866. To refine the location of FBHH3, we pursued linkage studies using 24 polymorphic loci. Our results establish a linkage between FBHH3 and 17 of these loci, and indicate that FBHH3 is located in a 4.1 Mb region flanked centromerically by D19S112 and telomerically by rs245111, which in the syntenic region on mouse chromosome 7 contains four Casr-related sequences (Gprc2a-rss). However, human homologues of these Gprc2a-rss were not found and a comparative analysis of the 22.0 Mb human and 39.3 Mb mouse syntenic regions showed evolutionary conservation of two segments that were inverted with loss from the human genome of 11.6 Mb that contained the four Gprc2a-rss. Thus, FBHH3 cannot be attributed to Gprc2a-rss abnormalities. DNA sequence analysis of 12 other genes from the interval that were expressed in the parathyroids and/or kidneys did not detect any abnormalities, thereby indicating that these genes are unlikely to be the cause of FBHH3. The results of this study have refined the map location of FBHH3, which will facilitate the identification of another CaSR or a mediator of calcium homeostasis.     

Instability of succinyl ester linkages in O2'-monosuccinyl cyclic AMP-protein conjugates at neutral pH

Chromatographic and immunological evidence is presented regarding the hydrolysis of the ester linkage of O2'-monosuccinyl cyclic AMP in neutral solutions. Such hydrolysis occurs whether the nucleotide derivative is present in free form in solution or conjugated through its succinyl carboxyl group via an amide bond to proteins. The latter process apparently occurs when succinyl cyclic AMP is conjugated to human serum albumin for use as an immunogen in the production of anti-cyclic AMP antibodies and when the derivative is coupled to the enzyme glucose-6-phosphate dehydrogenase (E.C. 1.1.1.49). The enzyme conjugate has been used in developing a homogeneous enzyme immunoassay for cyclic AMP. Inhibition of the catalytic activity of enzyme-cyclic AMP conjugates by anti-cyclic AMP antibody decreases with time, apparently due to the loss of cyclic AMP from enzyme-cyclic AMP conjugates stored in neutral solutions. In addition, the ability of free cyclic AMP to completely reverse the inhibition process decreases with time because of the presence of antibodies in the anti-cyclic AMP sera that apparently inhibit enzyme activity because of their binding specificity for the residual succinate-protein determinant sites of the enzyme conjugates. Lyophilization of the conjugates immediately after preparation helps to overcome the problem; however, in vivo hydrolysis of immunogens prepared with the succinyl cyclic AMP derivative may always occur. The consequence of this hydrolysis reaction and the subsequent formation of anti-succinyl-protein antibodies will be discussed with regard to existing RIAs for cyclic AMP and a new homogeneous enzyme immunoassay for the nucleotide.     

Estimating time‐varying RSA to examine psychophysiological linkage of marital dyads

One of the primary tenets of polyvagal theory dictates that parasympathetic influence on heart rate, often estimated by respiratory sinus arrhythmia (RSA), shifts rapidly in response to changing environmental demands. The current standard analytic approach of aggregating RSA estimates across time to arrive at one value fails to capture this dynamic property within individuals. By utilizing recent methodological developments that enable precise RSA estimates at smaller time intervals, we demonstrate the utility of computing time‐varying RSA for assessing psychophysiological linkage (or synchrony) in husband‐wife dyads using time‐locked data collected in a naturalistic setting.