Single Large Pedigree Research Articles

Clinical and molecular heterogeneity in the Brugada syndrome: a novel gene locus on chromosome 3.

Brugada syndrome is a form of idiopathic ventricular fibrillation characterized by a right bundle-branch block pattern and ST elevation (STE) in the right precordial leads of the ECG. Sodium channel blockers increase STE. Mutations of the cardiac sodium channel SCN5A cause the disorder, and an implantable cardioverter-defibrillator is often recommended for affected individuals. Mutations in other genes have not been identified, and it is not known if the efficacy of drug testing or the malignancy of arrhythmias correlates to the gene defect. We performed histories, physical examinations, ECGs, and drug testing on a large multigenerational family with Brugada syndrome. DNA isolated from blood samples, polymorphic genomic markers, and polymorphisms within candidate sodium channels were used for a genome-wide screen, fine mapping, and linkage analysis. We identified 12 affected individuals (right bundle-branch block, > or =1-mm STE) with an autosomal dominant inheritance pattern characterized by incomplete penetrance that appeared to be dependent on age and sex. Four affected individuals had syncope and 2 had documented ventricular arrhythmias, but there was minimal family history of sudden death. Procainamide infusions did not identify additional affected individuals. Linkage was present to an approximately equal 15-cM region on chromosome 3p22-25 (maximum LOD score=4.00). The sodium channel genes SCN5A, SCN10A, and SCN12A on chromosome 3 were excluded as candidates (LOD scores < or =-2). A Brugada syndrome locus distinct from SCN5A is associated with progressive conduction disease, a low sensitivity to procainamide testing, and a relatively good prognosis in a single large pedigree.

A follow-up linkage study supports evidence for a bipolar affective disorder locus on chromosome 21q22.

Evidence for linkage between bipolar affective disorder (BP) and 21q22 was first reported by our group in a single large pedigree with a lod score of 3.41 with the PFKL locus. In a subsequent study, with denser marker coverage in 40 multiplex BP pedigrees, we reported supporting evidence with a two-point lod score of 2.76 at the D21S1260 locus, about 6 cM proximal to PFKL. For cost-efficiency, the individuals genotyped in that study comprised a subset of our large pedigree sample. To augment our previous analysis, we now report a follow-up study including a larger sample set with an additional 331 typed individuals from the original 40 families, improved marker coverage, and an additional 16 pedigrees. The analysis of all 56 pedigrees (a total of 862 genotyped individuals vs. the 372 genotyped previously), the largest multigenerational BP pedigree sample reportedly analyzed to date, supports our previous results, with a two-point lod score of 3.56 with D21S1260. The 16 new pedigrees analyzed separately gave a maximum two-point lod score of 1.89 at D21S266, less than 1 cM proximal to D21S1260. Our results are consistent with a putative BP locus on 21q22.

Use of Closely Related Affected Individuals for the Genetic Study of Complex Diseases in Founder Populations

We propose a method, the maximum identity length contrast (MILC) statistic, to locate genetic risk factors for complex diseases in founder populations. The MILC approach compares the identity length of parental haplotypes that are transmitted to affected offspring with the identity length of those that are not transmitted to affected offspring. Initially, the statistical properties of the method were assessed using randomly selected affected individuals with unknown relationship. Because both nuclear families with multiple affected sibs and large pedigrees are often available in founder populations, we performed simulations to investigate the properties of the MILC statistic in the presence of closely related affected individuals. The simulation showed that the use of closely related affected individuals greatly enhances the power of the statistic. For a given sample size and type I error, the use of affected sib pairs, instead of affected individuals randomly selected from the population, could increase the power by a factor of two. This increase was related to an increase of kinship-coefficient contrast between haplotype groups when closely related individuals were considered. The MILC approach allows the simultaneous use of affected individuals from a founder population and affected individuals with any kind of relationship, close or remote. We used the MILC approach to analyze the role of HLA in celiac disease and showed that the effect of HLA may be detected with the MILC approach by typing only 11 affected individuals, who were part of a single large Finnish pedigree.

Interrelationships between low density lipoprotein receptor defect, serum fatty acid composition, and serum cholesterol concentration

It is known that, in the general human population, serum fatty acid composition is correlated with serum triacylglycerol and cholesterol concentrations. The goal of the present study was to analyze whether the same is true of individuals who have a low density lipoprotein receptor (LDL-R) defect. Concentrations of 16 different fatty acids, cholesterol, triacylglycerol, and major lipoproteins in serum were determined in eight individuals who had (FH-North Karelia), the most common LDL-R defect in Finland, which causes familial hypercholesterolemia, and in their 30 relatives belonging to a single large pedigree as controls. The average number of double bonds (i.e., degree of desaturation) in serum fatty acids correlated negatively with the concentrations of serum total cholesterol ( r = 0.27, P < 0.05) and total triacylglycerol ( r = −0.71, P < 0.001) and positively with the number of fish meals per week ( r = 0.50, P < 0.01), which was analyzed in all pedigree members jointly. These effects were similar in individuals having LDL-R defect, in which group the correlation coefficients were −0.31 ( P = NS), −0.99 ( P < 0.001), and 0.79 ( P = NS) for serum total cholesterol, triacylglycerol, and weekly fish meals, respectively. Thus, LDL-R defect does not impair the correlation between serum fatty acid composition and serum triacylglycerol concentration. This result is in agreement with dietary studies that have shown that familial hypercholesterolemia patients respond very favorably to dietary therapy.

An Unknown Genetic Defect Increases Venous Thrombosis Risk, through Interaction with Protein C Deficiency

We used two-locus segregation analysis to test whether an unknown genetic defect interacts with protein C deficiency to increase susceptibility to venous thromboembolic disease in a single large pedigree. Sixty-seven pedigree members carry a His107Pro mutation in the protein C gene, which reduces protein C levels to a mean of 46% of normal. Twenty-one carriers of the mutation and five other pedigree members had verified thromboembolic disease. We inferred the presence in this pedigree of a thrombosis-susceptibility gene interacting with protein C deficiency, by rejecting the hypothesis that the cases of thromboembolic disease resulted from protein C deficiency alone and by not rejecting Mendelian transmission of the interacting gene. When coinherited with protein C deficiency, the interacting gene conferred a probability of a thrombotic episode of approximately 79% for men and approximately 99% for women, before age 60 years.

A long-range restriction map across 3 Mb of the chromosome 11 breakpoint region of a translocation linked to schizophrenia: localization of the breakpoint and the search for neighbouring genes.

A balanced t(1;11)(q42.1;q14.3) translocation segregates with schizophrenia and related mental illness in a single large Scottish pedigree. We have constructed a long-range restriction map covering at least 3 Mb of the chromosome 11 breakpoint region and conducted searches for genes whose expression could be altered by the translocation, resulting in schizophrenia. Novel transcribed sequences of unknown function clustered around putative CpG islands, located approximately 500 kb and 700 kb above the breakpoint, represent the only evidence to date for expressed genes within the mapped region.

Detection of Gene-Environment Interactions in Joint Segregation and Linkage Analysis

We compare approaches for analysis of gene-environment (G x E) interaction, using segregation and joint segregation and linkage analyses of a quantitative trait. Analyses of triglyceride levels in a single large pedigree demonstrate the two methods and show evidence for a significant interaction (P=.015 when segregation analysis is used; P=.006 when joint analysis is used) between a codominant major gene and body-mass index. Genotype-specific correlation coefficients, between triglyceride levels and body-mass index, estimated from the joint model are rAA=.72, rAa=.49, and raa=. 20. Several simulation studies indicate that joint segregation and linkage analysis leads to less-biased and more-efficient estimates of a G x E-interaction effect, compared with segregation analysis alone. Depending on the heterozygosity of the marker locus and its proximity to the trait locus, we found joint analysis to be as much as 70% more efficient than segregation analysis, for estimation of a G x E-interaction effect. Over a variety of parameter combinations, joint analysis also led to moderate (5%-10%) increases in power to detect the interaction. On the basis of these results, we suggest the use of combined segregation and linkage analysis for improved estimation of G x E-interaction effects when the underlying trait gene is unmeasured.

Discordant segregation of Xq28 markers and a mutation in the L1 gene in a family with X linked hydrocephalus.

X linked recessive hydrocephalus is the most common hereditary form of hydrocephalus. Genetic analysis indicates that the majority of cases are caused by mutations in a single gene in Xq28, recently identified as the gene for neural cell adhesion molecule L1. Genetic heterogeneity for this disorder was suggested following the description of a single large pedigree where X linked hydrocephalus showed lack of linkage to Xq28 markers flanking the L1 gene. Mutation analysis in this family shows a single base pair deletion within the coding sequence of the L1 gene that would result in truncation of the mature protein. The nature of the mutation and its segregation with the disease through the pedigree indicate that it is the cause of X linked hydrocephalus in this family. These results are at odds with data obtained through segregation of alleles for markers flanking the L1 gene. Somatic and germline mosaicism is the most plausible explanation for these data, which also provide further evidence for genetic homogeneity of X linked hydrocephalus.

Linkage of the gene that encodes the alpha 1 chain of type V collagen (COL5A1) to type II Ehlers-Danlos syndrome (EDS II).

Ehlers-Danlos syndrome (EDS) is a group of heritable disorders of connective tissue with skin, ligaments and blood vessels being the main sites affected. The commonest variant (EDS II) exhibits an autosomal dominant mode of inheritance and is characterized by joint hypermobility, cigarette paper scars, lax skin and excessive bruising. As yet no gene has been linked to EDS II, nor has linkage been established to a specific region of the genome. However, several candidate genes encoding proteins of the extracellular matrix have been excluded. Using an intragenic simple sequence repeat polymorphism, we report linkage of the COL5A1 gene, which encodes the alpha 1(V) chain of type V collagen, to EDS II. A maximum LOD score (Zmax) for linkage of 8.3 at theta = 0.00 was generated for a single large pedigree.

Genetic analysis of glucokinase and the chromosome 20 diabetes susceptibility locus in families with type 2 diabetes.

Mutations of the glucokinase gene (chromosome 7p) have been shown to cause some cases of familial maturity onset diabetes of youth (MODY) but few, if any, cases of late onset familial Type 2 diabetes. A further single large pedigree with MODY has shown linkage to a marker for the adenosine deaminase gene (ADA, chromosome 20q), although the diabetes susceptibility gene at this locus has not been identified. We have studied members of 19 families with familial Type 2 diabetes (including 10 European families, 6 families from the Indian subcontinent, and 3 families of Afro-Caribbean origin), 2 of which were of MODY type (and both European), with a glucokinase marker and a marker linked to ADA, to examine whether glucokinase, or the unknown defect on chromosome 20, are implicated in diabetes in our pedigrees. Several models were constructed for standard two-point linkage analysis. Glucokinase is not the cause of diabetes in all of these families but was excluded in only one MODY family. It was possible to exclude both loci in the second MODY pedigree. No evidence was found of linkage to either marker in this multi-ethnic population under the models used. At least one further locus is involved in determining susceptibility to MODY.

Development of a microsatellite genetic map spanning 5q31–q33 and subsequent placement of the LGMD1A locus between D5S178 and IL9

Limb-girdle muscular dystrophy (LGMD) is a genetically and clinically heterogeneous group of disorders. We previously localized an autosomal dominant form of the disorder (LGMD1A) to chromosome 5q22–31 by linkage analysis in a single large pedigree. After developing a microsatellite genetic map incorporating six loci in q31–33 of chromosome 5 and spanning 35 cM, we have refined the original localization. Using multipoint analysis, LGMD1A is localised to a 7 cM region between the markers IL9 and D5S178 with odds > 1000 : 1.

Identification of a sixth locus for autosomal dominant retinitis pigmentosa on chromosome 19.

We report the mapping of a sixth locus for autosomal dominant retinitis pigmentosa (adRP) to 19q13.4. After a total genome linkage search using over 300 markers in a single large pedigree, marker loci on the long arm of chromosome 19 showed significant linkage with the disease locus. Since the mapping information for the marker loci used in this study was derived from two different genome maps, we established genetic distances between relevant marker loci so that linkage information could be combined from both maps. A conventional three point analysis between the adRP phenotype and markers D19S180 and D19S214 gave a maximum lod score of 4.87. Combining data from these and other markers, we used the recently described multiple two point programme FASTMAP to simulate a multipoint analysis of the full data set. This gave a lod score of 5.34 in the interval between markers D19S180 and D19S214. Recently this laboratory has also reported the linkage of another form of retinal degeneration known as cone-rod dystrophy (CRD) to a genetically different set of markers from 19q. Linkage data presented here clearly supports the existence of two separate retinal genes in this part of the genome.

A Gibbs sampling approach to linkage analysis.

We present a Monte Carlo approach to estimation of the recombination fraction theta and the profile likelihood for a dichotomous trait and a single marker gene with 2 alleles. The method is an application of a technique known as 'Gibbs sampling', in which random samples of each of the unknowns (here genotypes, theta and nuisance parameters, including the allele frequencies and the penetrances) are drawn from their posterior distributions, given the data and the current values of all the other unknowns. Upon convergence, the resulting samples derive from the marginal distribution of all the unknowns, given only the data, so that the uncertainty in the specification of the nuisance parameters is reflected in the variance of the posterior distribution of theta. Prior knowledge about the distribution of theta and the nuisance parameters can be incorporated using a Bayesian approach, but adoption of a flat prior for theta and point priors for the nuisance parameters would correspond to the standard likelihood approach. The method is easy to program, runs quickly on a microcomputer, and could be generalized to multiple alleles, multipoint linkage, continuous phenotypes and more complex models of disease etiology. The basic approach is illustrated by application to data on cholesterol levels and an a low-density lipoprotein receptor gene in a single large pedigree.

Maternally inherited myopathy and cardiomyopathy: association with mutation in mitochondrial DNA tRNA Leu(UUR)

Different point mutations of the mitochondrial genome, which all affect the ability of mitochondria to translate their own genes and lead to partial defects of mtDNA-dependent respiratory complexes, are related to distinct clinical mitochondrial disorders. A new maternally inherited disorder, characterised by a combination of adult-onset myopathy and cardiomyopathy, with no clinical involvement of the nervous system, was found in members of a single large pedigree. A heteroplasmic new mutation was identified in the mtDNA gene specifying tRNA Leu (UUR). This mutation segregated specifically with the disorder, and there were significant correlations between the proportion of the mtDNA that was of the mutant form and the activities (normalised for citrate synthase activity) of the two mtDNA-dependent respiratory enzymes (complex I, r=-0·71, p<0·005: complex IV r=-0·77, p<0·005) and the maximum oxygen consumption (r=-0·82, p<0·005), a physiological index of aerobic metabolism. These findings strongly suggest that the tRNA Leu (UUR) mutation is the genetic cause of this disorder, and that lesions of mtDNA should be considered in the differential diagnosis of the hereditary cardiomyopathies.

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)

Linkage analysis of multiple endocrine neoplasia type 1 with INT2 and other markers on chromosome 11

We evaluated linkage between the locus for multiple endocrine neoplasia type 1 (MEN1) and several polymorphic DNA markers on chromosome 11 in a single large pedigree. On the basis of the finding of a basic fibroblast growth factor (bFGF)-like substance circulating in plasma of MEN1 patients, we chose a bFGF-related gene known to be localized to 11q13 as one of the markers. This gene locus, INT2, was found to be closely linked to the MEN1 gene. Pairwise and multipoint analyses with INT2 confirm the recent finding by C. Larsson et al. (1988, Nature (London) 332: 85–87) of MEN1 linkage to another marker, skeletal muscle glycogen phosphorylase, at 11q13.

New Strategies in Linkage Research in Psychiatry

Pedigree sampling, marker choice strategies, and technologies for polymorphism detection are current issues in psychiatric genetics linkage research. In order to find a causative gene there are advantages in studying a series of medium size pedigree versus a single large pedigree. This strategy study can resolve the issue of heterogenity in a population, is less vulnerable to persons marrying in to a pedigree with illness genes, and additionally, associations valid in several pedigrees may help to identify a disease gene. Presently, the heterozygosity information content of the majority of RFLP systems is suboptimal, making less efficient the construction of precise genetic maps. “Qualitative” electrophoretic separations rely on DNA composition upon the conformation of DNA. These methods, such as denaturing gradient gel electrophoresis, do not rely only on polymorphisms located in restriction enzyme sites, but detect compositional differences which are reflected in electrophoretic separations. These new t...

Linkage and segregation analyses of apolipoproteins A1 and B, and lipoprotein cholesterol levels in a large pedigree with excess coronary heart disease: the Bogalusa Heart Study.

Robust methods were employed, using data from a single large pedigree, to screen serum apolipoprotein A1 and B levels, serum lipoprotein cholesterol levels, and ratios of serum lipoprotein cholesterol fractions to apolipoprotein A1 and B levels for genetic linkage to 31 polymorphic markers. Segregation analyses were performed for each of the apolipoprotein and lipoprotein cholesterol fractions to obtain estimates for use in applying likelihood methods of linkage analysis. Trait-marker combinations for which linkages were suggested from the robust methods were then reexamined for linkage using the likelihood (lod score) method. Results from the segregation analyses were consistent with major gene determination of apo B and HDL-C levels, the HDL-C to apo A1 ratio, the LDL-C to apo B ratio, and a measure of relative content of cholesterol in HDL-C and LDL-C. Linkage between haptoglobin and the HDL-C/apo A1 ratio was suggested, with a lod score of 1.72 at theta = 0.05.

Exclusion of linkage of loci on chromosome 19 with multiple endocrine neoplasia, type 2.

Linkage between seven loci on chromosome 19 and multiple endocrine neoplasia type 2a (MEN2A) was examined in a single large Swedish pedigree. A total of 50 cM was excluded from the male genetic map by pairwise analysis and an estimated 63 cM by multipoint analysis. Using existing data on the likelihood of different marker-marker distances and taking into account current exclusions on other chromosomes, the probability that the gene for MEN2A segregating in this pedigree could still be located on chromosome 19 is approximately 0.28%.

Tracking of high- and low- density-lipoprotein cholesterol from childhood to young adulthood in a single large kindred with familial hypercholesterolemia

Tracking of high- and low-density-lipoprotein cholesterol (HDLC, LDLC) from childhood to young adulthood was assessed in 77 children and in 53 adults from a single large pedigree with familial hypercholesterolemia who were respectively ≤19 and ≥20 years old when first studied in 1973, with reassessment in 1984. No children and only five of the adults had received LDLC lowering therapy from 1973 to 1984. The rank correlations between the 1973 and 1984 measurements for LDLC were 0.73, 0.74 and 0.87; and for HDLC were 0.55, 0.73 and 0.65 ( P < 0.0001 for all correlations), respectively for relatives who were ≤12, 13 to 19, and ≥20 years old in 1973. The 1973:1984 LDLC and HDLC correlations, categorized by relationships to the proband, were as follows: (1) unrelated, LDLC = 0.16, HDLC = 0.56 ∗ ∗ P < 0.05. ; (2) first-degree relatives, LDLC = 0.90, † † P < 0.0001. HDLC = 0.30; (3) second-degree relatives, LDLC = 0.79, † HDLC = 0.39; and (4) other relatives, LDLC = 0.62, † HDLC = 0.64. † All nine of the probands' first-degree relatives who were above the age-sex specific LDLC 95th percentile in 1973 were also greater than the 95th percentile for LDLC in 1984. Similarly, seven of eight second-degree relatives with LDLC greater than the 95th percentile in 1973 were greater than the 95th percentile in 1984, as were ten of 15 other relatives. LDLC levels in childhood in this extended kindred were highly predictive of adult values. HDLC levels in childhood in this kindred were also highly predictive of adult levels. Despite the selection biases of relationship and familial hypercholesterolemia, tracking of total and LDL cholesterol, combining all relatives in this extended kindred, was similar to that previously reported in free-living subjects. High level tracking of LDLC and HDLC from childhood to adulthood emphasis the importance of childhood measurements of LDLC and HDLC, particularly in familial hypercholesterolemic kindreds at high risk for premature coronary heart disease.