A novel quantitative trait locus on chromosome 1 with pleiotropic effects on HDL-cholesterol and LDL particle size in hypertensive sibships

BACKGROUND: High-density lipoprotein (HDL)-cholesterol, triglycerides, and LDL particle size are correlated lipid traits. Abnormal levels of these traits are frequent in hypertensive individuals and contribute to increased risk of coronary heart disease (CHD). We performed univariate and bivariate linkage analyses to identify genomic regions that influence levels of these traits and exert pleiotropic effects on the traits in hypertensive sibships. METHODS: Subjects included 691 non-Hispanic white individuals (mean age 63.1+/-8.5 years, 57% women, 78% hypertensive) ascertained through sibships with two or more individuals diagnosed with hypertension before age 60 years. The LDL particle size was measured by polyacrylamide gel electrophoresis and triglycerides were log-transformed to reduce skewness. Genotypes were measured at 366 microsatellite marker loci distributed across the 22 autosomes. Univariate and bivariate linkage analyses were performed using a variance components approach. RESULTS: Significant (P < .001) genetic correlations were confirmed for all pairwise combinations of the traits. Univariate linkage analyses demonstrated evidence of linkage (defined as multipoint LOD scores > or =1.3) for HDL-cholesterol on chromosomes 1p, 3p, 9q, and 18q; for log triglycerides on chromosome 10q; and for LDL particle size on chromosomes 2p and 8p. Pairwise bivariate linkage analyses of the three traits revealed a region with pleiotropic effects on HDL-cholesterol and LDL particle size on chromosome 1p (LOD score 4.48). CONCLUSIONS: These findings indicate the presence of a quantitative trait locus on chromosome 1 that has pleiotropic effects on HDL-cholesterol and LDL particle size and may therefore influence CHD susceptibility in hypertensive sibships.     

A unified framework for linkage and association analysis of quantitative traits

We give a unified treatment of the statistical foundations of population based association mapping and of family based linkage mapping of quantitative traits in humans. A central ingredient in the unification involves the efficient score statistic. The discussion focuses on generalized linear models with an additional illustration of the Cox (proportional hazards) model for age of onset data. We give analytic expressions for noncentrality parameters and show how they give qualitative insight into the loss of power that occurs if the scientist's assumed genetic model differs from nature's "true" genetic model. Issues to be studied in detail in the future development of this approach are discussed.     

Targeted gene duplication and disruption for analyzing quantitative genetic traits in mice.

Experimental analysis of complex quantitative genetic traits, such as essential hypertension, should be greatly facilitated by being able to manipulate the expression of a gene in living animals without altering the nucleotide sequence, chromosomal location, or regulatory elements of the gene. To explore this possibility, we have used targeted gene disruption and duplication to generate mice that are genetically identical [(129 x C57BL6)F1] except for having one, two, or three functional copies of the gene coding for angiotensinogen. The two-copy animals have two normal copies of the angiotensinogen gene; the one-copy and three-copy animals have one normal copy with the other either disrupted or duplicated by gene targeting. The duplicated pair of genes was generated by a special form of gap-repair gene targeting that tandemly duplicates the whole of a gene together with 5' and 3' flanking regions. We find progressively and significantly higher levels of the gene product in the animals having increasing numbers of gene copies: the one-copy animals have steady-state plasma angiotensinogen levels approximately 35% of normal (P < 0.0001), and the three-copy animals have levels approximately 124% of normal (P < 0.004). Detailed information about regulatory sequences is not required for this type of experiment; nor is it necessary to have DNA clones or targeting constructs that cover the whole of the target gene. Varying gene copy numbers by targeting consequently offers a promising approach to quantitative genetics.     

Tendency to serious sequelae of infection with the human immunodeficiency virus in sibships with hemophilia

Cofactors for the clinical expression of infection due to the human immunodeficiency virus (HIV) are not well understood. We asked if there was a familial tendency to the development of complications of HIV infection. We examined 35 hemophilic sibships in which at least two brothers with classic hemophilia (factor VIII deficiency) were infected with HIV. Twenty-four (34%) of the 70 patients had serious sequelae of infection, and 46 (66%) were asymptomatic or had only lymph node enlargement. Using Fisher's exact test, we found the concordance among siblings for serious sequelae of HIV infection was greater than would be expected by chance. When analysis was restricted to include only siblings known to be infected for more than two years, this concordance was still present. In the study population, birth order and mean yearly usage of factor VIII concentrate were unrelated to the outcome of HIV infection. The data indicate a familial tendency to serious complications of HIV infection. The factor(s) responsible for this familial tendency are currently under investigation.     

Rates of change in quantitative traits from fixation of new mutations.

Expressions are derived for the response to directional selection for a quantitative trait that comes from fixation of new mutations in a finite population. For additive genes with a distribution of mutant gene effects symmetric about zero, the response from fixing mutations occurring in a single generation is 2 Ni sigma 2M/sigma, in which N is the effective population size, i is the selection intensity, sigma is the phenotypic standard deviation, and sigma 2M is the increment in variance in the generation immediately after occurrence of the mutations. This response is 2N times that immediately after occurrence of the mutations. With continuous mutation each generation, the asymptotic rate of response is also 2Ni sigma 2M/sigma and the asymptotic variance is independent of i. For completely dominant mutations with symmetric effects, the rates are Ni sigma 2M/sigma; and for recessive mutations the rates are proportional to (Ni)1/2. If the distribution of mutant gene effects, a, is not symmetric about zero, responses depend on the mean square of effects of mutations with positive effect, rather than on the variance of their effects. Rates of change in fitness and of traits correlated with fitness are also analyzed. It is argued that new mutations have contributed substantially to long-term responses in many laboratory selection experiments.     

Dissecting the heterogeneity of rheumatoid arthritis through linkage analysis of quantitative traits

OBJECTIVE: To dissect the heterogeneity of rheumatoid arthritis (RA) through linkage analysis of quantitative traits, specifically, IgM rheumatoid factor (IgM-RF) and anti-cyclic citrullinated peptide (anti-CCP) autoantibody titers. METHODS: Subjects, 1,002 RA patients from 491 multiplex families recruited by the North American RA Consortium, were typed for 379 microsatellite markers. Anti-CCP titers were determined based on a second-generation enzyme-linked immunosorbent assay, and IgM-RF levels were quantified by immunonephelometry. We used the Merlin statistical package to perform nonparametric quantitative trait linkage analysis. RESULTS: For each of the quantitative traits, evidence of linkage, with logarithm of odds (LOD) scores of >1.0, was found in 9 regions. For both traits, the strongest evidence of linkage was for marker D6S1629 on chromosome 6p (LOD 14.02 for anti-CCP and LOD 12.09 for RF). Six other regions with LOD scores of >1.0 overlapped between the 2 traits, on chromosomes 1p21.1, 5q15, 8p23.1, 16p12.1, 16q23.1, and 18q21.31. Evidence of linkage to anti-CCP titer but not to RF titer was found in 2 regions (chromosomes 9p21.3 and 10q21.1), and evidence of linkage to RF titer but not to anti-CCP titer was found in 2 regions (chromosomes 5p15.2 and 1q42.3). Several covariates were significantly associated with 1 or both traits, and linkage analysis exploring the covariate effects revealed striking effects of sex in modulating linkage signals for several chromosomal regions. For example, sex had a striking impact on the linkage results for both quantitative traits on chromosome 6p (P = 0.0007 for anti-CCP titer and P = 0.0012 for RF titer), suggesting a sex-HLA region interaction. CONCLUSION: Analysis of quantitative components of RA is a promising approach for dissecting the genetic heterogeneity of this complex disorder. These results highlight the potential importance of sex or other covariates that may modulate some of the genetic effects that influence the risk of specific disease manifestations.     

HSP90 affects the expression of genetic variation and developmental stability in quantitative traits

Modulation of the activity of the molecular chaperone HSP90 has been extensively discussed as a means to alter phenotype in many traits and organisms. Such changes can be due to the exposure of cryptic genetic variation, which in some instances may also be accomplished by mild environmental alteration. Should such polymorphisms be widespread, natural selection may be more effective at producing phenotypic change in suboptimal environments. However, the frequency and identity of buffered polymorphisms in natural populations are unknown. Here, we employ quantitative genetic dissection of an Arabidopsis thaliana developmental response, hypocotyl elongation in the dark, to detail the underpinnings of genetic variation responsive to HSP90 modulation. We demonstrate that HSP90-dependent alleles occur in continuously distributed, environmentally responsive traits and are amenable to quantitative genetic mapping techniques. Furthermore, such alleles are frequent in natural populations and can have significant effects on natural phenotypic variation. We also find that HSP90 modulation has both general and allele-specific effects on developmental stability; that is, developmental stability is a phenotypic trait that can be affected by natural variation. However, effects of revealed variation on trait means outweigh effects of decreased developmental stability, and the HSP90-dependent trait alterations could be acted on by natural selection. Thus, HSP90 may centrally influence canalization, assimilation, and the rapid evolutionary alteration of phenotype through the concealment and exposure of cryptic genetic variation.     

Heritability and familiality of type 2 diabetes and related quantitative traits in the Botnia Study

Aims/hypothesis  

To study the heritability and familiality of type 2 diabetes and related quantitative traits in families from the Botnia Study in Finland.     

Heritability of quantitative traits associated with type 2 diabetes mellitus in large multiplex families from South India

India is a major contributor to the global public health burden of diabetes. We have undertaken a family study of large multiplex families from Chennai, South India, and report on the familial aggregation of quantitative traits associated with type 2 diabetes mellitus in these pedigrees. Five hundred twenty-four individuals older than 19 years from 26 large multiplex pedigrees were ascertained. Detailed questionnaires and phenotype data were obtained on all participating individuals including fasting blood glucose, fasting insulin, lipid profiles, height, weight, and other anthropometric and clinical measures. Heritability estimates were calculated for all quantitative traits at the univariate level, and bivariate analyses were done to determine the correlation in genetic and environmental control across these quantitative traits. Heritability estimates ranged from 0.21 to 0.72. The heritability estimates for traits most directly related to type 2 diabetes mellitus were 0.24 ± 0.08 for fasting blood glucose and 0.41 ± 0.09 for fasting insulin. In addition, there was evidence for common genetic control for many pairs of these traits. These bivariate analyses suggested common genes for fasting insulin and central obesity measures (body mass index, waist, and hip), with complete genetic correlation between fasting insulin and waist. Quantitative traits associated with type 2 diabetes mellitus have heritabilities suggestive of some familial or genetic effect. The evidence for pleiotropic control of insulin and central obesity-related traits supports the presence of an insulin resistance syndrome in South Asians with a tendency for central obesity.     

Asymptomatic adults and older siblings with biotinidase deficiency ascertained by family studies of index cases

Summary We report 32 biotinidase-deficient patients detected by family studies in the index cases. The study group consisted of 10 mothers, 4 fathers and 18 siblings. There were 17 individuals (3 mothers, 4 fathers and 10 siblings) with profound biotinidase deficiency (BD) (< 10% of mean normal activity) and 15 (7 mothers and 8 siblings) with partial BD (10–30% of mean normal activity). In the profound BD group, only three siblings were symptomatic. Dermatitis, microcephaly, developmental delay and convulsions were observed. The patients with partial BD did not have any clinical symptoms except one sibling with borderline IQ score. None of the parents was symptomatic. Family investigation of patients with BD is very important for the detection of asymptomatic patients who are at risk of exhibiting symptoms at any age. Careful evaluation of these untreated individuals with BD is important to obtain additional information about the natural history of this disorder and may provide clues to phenotype–genotype relationships and treatment regimes.     

Linkage analysis of 2q14-q23 and 5q32 with blood pressure quantitative traits in Chinese sib pairs

OBJECTIVES: Several genome-wide scans recently accomplished in the ethnic Chinese revealed a number of candidate loci possibly contributing to essential hypertension, and some appeared to be replicable in 2q14-q23 and 5q32. The current study aimed to examine the linkage of qualitative and blood pressure quantitative traits in essential hypertension with these genomic regions in a large sample of Chinese hypertensive families. METHODS: We performed a genetic analysis on 148 randomly ascertained families containing 328 affected sib pairs, grouped into two geographically distinct subsets. Five highly informative microsatellite markers (D2S151, D2S142, D5S2090, D5S413 and D5S2013) were genotyped, and linkage analyses were performed with different genetic models. RESULTS: We did not observe consistent evidence for excess allele sharing identity by descent in either of the qualitative or the quantitative test. However, higher LOD scores were found at D5S2013 in North Group subset with Haseman-Elston and maximum likelihood (ML) variance (no dominance variance, NDV) algorithms. With the ML (NDV) algorithm, the LOD was 1.410 for diastolic blood pressure at this locus, although this was not statistically significant. CONCLUSIONS: These findings provide no evidence to support a significant linkage of 2q14-q23 or 5q32 with essential hypertension or blood pressure quantitative traits in the ethnic Chinese, and indicate the aetiologic diversity and complexity of hypertension. Previous reports implied 2q14-q23 or beta 2- adrenergic receptor gene potentially linked to essential hypertension in the ethnic Chinese. To replicate these results and perform quantitative linkage analysis, we genotyped members of 148 hypertensive families with five highly informative microsatellite markers. We observed no evidence of excess allele sharing identity by descent in sib pairs, revealing a lack of linkage between 2q14-q23 or 5q32 (chromosome region harboring the gene encoding beta 2 adrenergic receptor) and hypertension in our study sample.     

Age- and gender-dependent heterogeneous proportion of variation explained by SNPs in quantitative traits reflecting human health

Age-related effects are often included as covariates in the analytical model for genome-wide association analysis of quantitative traits reflecting human health. Nevertheless, previous studies have hardly examined the effects of age on the proportion of variation explained by single nucleotide polymorphisms (PVSNP) in these traits. In this study, the PVSNP estimates of body mass index (BMI), waist-to-hip ratio, pulse pressure, high-density lipoprotein cholesterol level, triglyceride level (TG), low-density lipoprotein cholesterol level, and glucose level were obtained from Korean consortium metadata partitioned by gender or by age. Restricted maximum likelihood estimates of the PVSNP were obtained in a mixed model framework. Previous studies using pedigree data suggested possible differential heritability of certain traits with regard to gender, which we observed in our current study (BMI and TG; P < 0.05). However, the PVSNP analysis based on age revealed that, with respect to every trait tested, individuals aged 40 to 49 exhibited significantly lower PVSNP estimates than individuals aged 50 to 59 or 60 to 69 (P < 0.05). The consistent heterogeneous PVSNP with respect to age may be due to degenerated genetic functions in individuals between the ages of 50 and 69. Our results suggest the genetic mechanism of age- and gender-dependent PVSNP of quantitative traits related to human health should be further examined.     

Low-density lipoprotein particle size and coronary atherosclerosis in subjects belonging to hypertensive sibships

BACKGROUND: Dyslipidemia in hypertensive sibships may be characterized by atherogenic small low-density lipoprotein (LDL) particles. Whether LDL particle size is associated with the extent of coronary atherosclerosis in hypertensive sibships is unknown. METHODS: Subjects (n = 792, mean age 62 years, 60% women) were ascertained through sibships containing at least two individuals with essential hypertension diagnosed before age 60 years. The LDL particle size was measured by polyacrylamide gel electrophoresis. Coronary artery calcium (CAC) was measured noninvasively by electron beam computed tomography, and CAC score was calculated using the method of Agatston et al. Sex-specific multiple regression models were used to assess independent predictors of LDL particle size and the association of LDL particle size with CAC. RESULTS: In all, 76% of women and 77% of men were hypertensive. In each sex, independent predictors of smaller LDL particle size were total cholesterol, triglycerides, and lower HDL cholesterol. In women, greater age was an additional predictor of smaller LDL particle size. After adjustment for age and statin use, LDL particle size was significantly associated with the amount of CAC in women but not in men. After further adjustment for HDL cholesterol, triglycerides, diabetes, smoking, and hypertension, LDL particle size was not independently associated with CAC in either sex. CONCLUSIONS: After adjustment for age and statin use, LDL particle size was found to be significantly related to CAC quantity in women but not in men belonging to hypertensive sibships. In women, LDL particle size may mediate some of the atherogenic effects of low-HDL cholesterol-high-triglyceride dyslipidemia, but does not appear to be independently associated with the extent of coronary atherosclerosis in either sex.     

Mapping of quantitative trait loci underlying ethanol metabolism in BXD recombinant inbred mouse strains

BACKGROUND: Genetic factors are well known to play an important role in determining individual differences in the metabolism of ethanol (EtOH), and several specific polymorphic loci have been identified that significantly contribute to the variability of EtOH metabolism in humans. However, these variant genes are either alcohol or aldehyde dehydrogenases, and the identification of new gene products that contribute to variation in alcohol metabolism would be useful. METHODS: To identify quantitative trait loci (QTLs), we correlated variation in polymorphic markers with blood EtOH concentration and the rate of EtOH metabolism (beta) in C57BL/6J and DBA/2J strains and in 25 of their recombinant inbred strains after 2 and 3 g/kg of EtOH intraperitoneally. RESULTS: A QTL associated with beta values for both doses was definitively mapped to the proximal region of chromosome 17, syntenic with human chromosome 6q25-27. Seven to 12 chromosomal regions were provisionally identified for each phenotype; several were associated with 2 or more phenotypes. Each QTL suggests the location of a gene or genes affecting EtOH pharmacokinetics. Candidate genes suggested by these analyses included several whose gene products are known to be induced by EtOH (e.g., superoxide dismutase, glutathione transferase, and cytochrome P450 2E1), as well as several whose gene products have signaling functions likely to contribute to this induction. CONCLUSIONS: These studies provide evidence for the existence of genes affecting EtOH metabolism in multiple chromosomal regions. Future studies will be required to identify the chromosome 17 gene product. Use of other genetic populations, such as B6D2F2 crosses, will be required to determine which of the provisional loci represent true and which represent false-positive associations.     

Mucin gene expression in gallbladder epithelium with black pigment stone ascertained by in situ hybridization

Black pigment stones are usually found in patients with liver cirrhosis or hemolytic disease. Mucoglycoproteins are present in a significant amount in black pigment stones and contribute to the matrix of gallstones. Epithelium of stone-containing gallbladders contains much more mucin than those without stones. In this study, we try to determine by in situ hybridization the mucin gene expression in black stone-containing gallbladders and try to find the diversity of mucin gene expression in gallbladders containing black pigment stones and those without stones. In situ hybridization with DIG-tailed oligonucleotides was performed on sections of paraffin-embedded tissues of gallbladders with black pigment stones (n = 10) and those without stones (n = 6) to identify the expression of MUC1, MUC2, MUC3, MUC4, MUC5B and MUC6 in gallbladder epithelium. The findings showed that (1) mRNA expression of MUC1, MUC3, MUC5B and MUC6 were found in all gallbladders with black pigment stones, while they were expressed in 33.3%, 83.3%, 83.3% and 66.7% respectively in those without stones. They were expressed more strongly and extensively in gallbladders with stones when compared to those without stones. (2) MUC2 and MUC4 labeling were absent in gallbladders without stones, while they were present in 20% and 60% of gallbladders with black pigment stones, respectively. We conclude that MUC3, MUC5B and MUC6 were the main mucin gene expression in either gallbladder with or without stones. Altered mucin gene expression occurred in gallbladders with black pigment stones, such as the presence of MUC2 and MUC4 and increased expression of MUC1, MUC3, MUC5B and MUC6 in black stone-containing gallbladders. The higher incidence and stronger labeling intensity of mucin gene expression of MUC2, MUC3, MUC5B and MUC6 in black stone-containing gallbladder may reflect abundant mucin content in these gallbladders. Increased expression of MUC2 and MUC4 in black stone-containing gallbladder epithelium indicated that intestinal metaplasia and altered mucin genes could occur in diseased gallbladders.