Hereditary evaluation of multiple developmental abnormalities in the Havanese dog breed

The Havanese is a toy breed that presents with a wide range of developmental abnormalities. Skeletal defects, particularly osteochondrodysplasia (OCD), are the most frequently observed anomalies. Cataracts, liver shunts, heart murmurs, and missing incisors are also common in this breed. Estimates of heritability and complex segregation analyses were carried out to evaluate modes of transmission for these abnormalities. A moderate heritability was identified and evidence for a single major locus was found. Novel statistical analysis methods were used to identify four traits that co-segregate: cataracts, hepatic abnormalities, OCD, and cardiac abnormalities. A canine-specific microarray was used to identify changes in gene expression in the liver that accompany the aforementioned developmental problems. One hundred and thirteen genes were found to be differentially regulated in the Havanese.     

家族高发性2型糖尿病的遗传模式研究

对1999～2000年门诊及住院的家族高发性2型糖尿病患者为先证者的136个大家系进行研究,以探讨该病的遗传模式。对家系人群采用Falconer 法估算遗传率,用Penrose法进行多基因分析,并用S.A.G.E-REGD软件拟合A型回归Logistic模型进行复合分离分析的方法,对家族高发性2型糖尿病家系进行研究。结果表明,136个大家系的2型糖尿病遗传率为94.07%±5.84%,提示在这些家系中可能有显性主基因存在。多基因分析研究表明,在该人群中,2型糖尿病因性别不同而存在两种遗传模式。复合分离分析拒绝单纯环境模型、非传递模型、共显性模型,接受隐性模型和显性模型,但隐性模型为最佳遗传模式。因此,2型糖尿病具有高度的遗传性和遗传异质性,总体表现为多因子遗传,在部分遗传背景较一致的家系人群中可能存在由主要基因决定的常染色体显性遗传。 Abstract:This study is to explore the genetic model of type 2 diabetes mellitus (type 2 DM) among the hereditary family.One hundred and thirty-six pedigrees of familial type 2 DM were studied.The heritability of type 2 DM was estimated according to Falconer's method and the multi-factorial inheritance analyzed according to Penrose's method.Complex segregation analysis was performed using S.A.G.E-REGD.The heritability of familial type 2 DM was 9407%±5.84%.Dominant major gene might influence the genesis of type 2 DM.Analysis of multi-factorial inheritance indicated that there be two genetic patterns respectively in male and female populations.By complex segregation analysis,environment,non-transmitted and co-dominant inheritance were rejected.Autosomal dominant (AD) inheritance and autosomal recessive (AR) inheritance was accepted but AR inheritance was the best pattern.This study suggested that type 2 DM had significant heritability and genetic heterogeneity,which appeared to be a disease of multi-factorial inheritance generally and autosomal dominant (AD) inheritance in part of pedigrees.     

Complex segregation analysis of nonsyndromic cleft lip and palate.

This study was undertaken to examine the inheritance pattern of nonsyndromic cleft lip with or without cleft palate (CL/P). Complex segregation analysis using the unified model as in POINTER and the regressive model as in REGD programs were applied to analyze a midwestern U.S. Caucasian population of 79 families ascertained through a proband with CL/F. In REGD, the dominant or codominant Mendelian major locus models of inheritance were the most parsimonious fit. In POINTER, besides the Mendelian major locus model, the multifactorial threshold (MF/T) model and the mixed model were also consistent with the observed data. However, the high heritability parameter of .93 (SD .063) in the MF/T model suggests that any random exogenous factors are unlikely to be the underlying mechanisms, and the mixed model indicates that this high heritability is accounted for by a major dominant locus component. These findings indicate that the best explanation for the etiology of CL/P in this study population is a putative major locus associated with markedly decreased penetrance. Molecular studies may provide further insight into the genetic mechanism underlying CL/P.     

Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information

MOTIVATION: It is important to predict the outcome of patients with diffuse large-B-cell lymphoma after chemotherapy, since the survival rate after treatment of this common lymphoma disease is <50%. Both clinically based outcome predictors and the gene expression-based molecular factors have been proposed independently in disease prognosis. However combining the high-dimensional genomic data and the clinically relevant information to predict disease outcome is challenging. RESULTS: We describe an integrated clinicogenomic modeling approach that combines gene expression profiles and the clinically based International Prognostic Index (IPI) for personalized prediction in disease outcome. Dimension reduction methods are proposed to produce linear combinations of gene expressions, while taking into account clinical IPI information. The extracted summary measures capture all the regression information of the censored survival phenotype given both genomic and clinical data, and are employed as covariates in the subsequent survival model formulation. A case study of diffuse large-B-cell lymphoma data, as well as Monte Carlo simulations, both demonstrate that the proposed integrative modeling improves the prediction accuracy, delivering predictions more accurate than those achieved by using either clinical data or molecular predictors alone.     

Segregation analysis of schizophrenia and related disorders

Segregation analysis was applied to 79 nuclear families ascertained through chronic schizophrenic probands. Analysis was performed on the diagnosis of schizophrenia alone and on schizophrenia and schizotypal personality disorder (milder phenotype) combined. The models used were the transmission probability model and the mixed model. Because the disease is associated with reduced fertility, all likelihoods were calculated conditional on parental phenotypes. However, compatibility of the mating-type distribution predicted by each model with the observed was also examined. In all analyses, results suggested consistency with genetic transmission. In the analysis of schizophrenia alone, discrimination among models was difficult. In the analysis including the milder phenotypes, all single-locus models without polygenic background were excluded, while pure polygenic inheritance could not be eliminated. The polygenic model also gave good agreement with supplementary observations (lifetime disease incidences, mating-type distribution, and monozygotic twin concordance). The estimated components of variance for the polygenic model were: polygenes (H) 81.9%; common sib environment (B) 6.9%; random environment (R) 11.2%. Although the polygenic model was parsimonious, segregation analysis and the supplementary observations were also consistent with a mixed model, with a single major locus making a large contribution to genetic liability. Such a locus is more likely to be recessive than dominant, with a high gene frequency and low penetrance. The most likely recessive mixed model gave the following partition of liability variance: major locus, 62.9%; polygenes, 19.5%; common sib environment, 6.6%; and random environment, 11.0%.     

Segregation analysis reveals evidence of a major gene for Alzheimer disease.

In an attempt to resolve the relative influences of major genes, multifactorial heritability, and cohort effects on the susceptibility to Alzheimer disease (AD), complex segregation analysis was performed on 232 nuclear families. All families were consecutively ascertained through a single proband who was referred for diagnostic evaluation of a memory disorder. The results suggest that susceptibility to AD is determined, in part, by a major autosomal dominant allele with an additional multifactorial component. Single-locus, polygenic, sporadic, and no-transmission models, as well as recessive inheritance of the major effect, were significantly rejected. Excess transmission from the heterozygote was marginally significant and probably reflects the presence of phenocopies or perhaps the existence of two or more major loci for AD. The frequency of the AD susceptibility allele was estimated to be .038, but the major locus accounts for only 24% of the transmission variance, indicating a substantial role for other genetic and nongenetic mechanisms in the causation of AD.     

Complex segregation analysis of non-myoclonic idiopathic generalized epilepsy in families ascertained from probands affected with idiopathic epilepsy with tonic-clonic seizures in Antioquia,Colombia

In an attempt to identify the possible role of major genes, multifactorial inheritance, and cohort effects in the susceptibility to idiopathic epilepsy with generalized tonic-clonic seizures of the awakening type (GTCS), complex segregation analysis was performed in 196 nuclear families ascertained through affected probands with idiopathic epilepsy with GTCS belonging to the Paisa community of Antioquia (Colombia). Models postulating no transmission, single major locus (dominant and recessive) only, and multifactorial component only, were rejected. Since the codominant single major locus model could not be rejected and models that assign no major locus to transmission, no polygenic component to transmission, and no transmission of the major effect were rejected, complex segregation analysis suggested that a major autosomal codominant allele together with a multifactorial component (mixed model) best explained clustering of idiopathic epilepsy with GTCS in families of the Paisa community. The deficit of transmission of heterozygotes (0.17) is compatible with the existence of epistasis acting on a major gene whose frequency was estimated to be 0.0211. Its transmission variance accounts for 81% of the susceptibility to idiopathic epilepsy with GTCS. The complementary variance (19%) is due to the polygenic component. Received: 19 January 1996 / Revised: 11 March 1996     

The gene for dominant white color in the pig is closely linked to ALB and PDGRFRA on chromosome 8.

White is a widespread coat color among domestic pig breeds and is controlled by an autosomal dominant gene I. The segregation of this gene was analyzed in a reference pedigree for gene mapping developed by crossing the European wild pig and a Large White domestic breed. The gene for dominant white color was shown to be closely linked to the genes for albumin (ALB) and platelet-derived growth factor receptor alpha (PDGFRA) on chromosome 8. An unexpected phenotype with patches of colored and white coat was observed among the F1 and F2 animals. The segregation data indicated that the phenotype was controlled by a third allele, denoted patch (Ip), most likely transmitted by one of the Large White founder animals. It is shown that the ALB, PDGFRA, I linkage group shares homologies with parts of mouse chromosome 5, human chromosome 4, and horse linkage group II, all of which contain dominant genes for white or white spotting. Candidate genes for the dominant white and patch mutations in the pig are proposed on the basis on these linkage homologies and the recent molecular definition of the dominant white spotting (W) and patch (Ph) mutations in the mouse.     

An exact form of the breeder's equation for the evolution of a quantitative trait under natural selection

Starting with the Price equation, I show that the total evolutionary change in mean phenotype that occurs in the presence of fitness variation can be partitioned exactly into five components representing logically distinct processes. One component is the linear response to selection, as represented by the breeder's equation of quantitative genetics, but with heritability defined as the linear regression coefficient of mean offspring phenotype on parent phenotype. The other components are identified as constitutive transmission bias, two types of induced transmission bias, and a spurious response to selection caused by a covariance between parental fitness and offspring phenotype that cannot be predicted from parental phenotypes. The partitioning can be accomplished in two ways, one with heritability measured before (in the absence of) selection, and the other with heritability measured after (in the presence of) selection. Measuring heritability after selection, though unconventional, yields a representation for the linear response to selection that is most consistent with Darwinian evolution by natural selection because the response to selection is determined by the reproductive features of the selected group, not of the parent population as a whole. The analysis of an explicitly Mendelian model shows that the relative contributions of the five terms to the total evolutionary change depends on the level of organization (gene, individual, or mated pair) at which the parent population is divided into phenotypes, with each frame of reference providing unique insight. It is shown that all five components of phenotypic evolution will generally have nonzero values as a result of various combinations of the normal features of Mendelian populations, including biparental sex, allelic dominance, inbreeding, epistasis, linkage disequilibrium, and environmental covariances between traits. Additive genetic variance can be a poor predictor of the adaptive response to selection in these models. The narrow-sense heritability sigma2A/sigma2P should be viewed as an approximation to the offspring-parent linear regression rather than the other way around.     

Evidence of a rare gene for low systolic blood pressure in the Framingham Heart Study

A major risk factor for coronary heart disease in both men and women is elevated systolic blood pressure (SBP). We performed segregation analysis on age, sex-adjusted, and transformed systolic blood pressure data on 1,141 families from the Framingham cohort-offspring study using the segregation analysis program POINTER. The results of hypothesis testing revealed: (1) these data are consistent with familial transmission; (2) there is evidence for the transmission of a rare, major gene for low SBP with a gene frequency of q = 0.02; and (3) most of the transmissible component to SBP can be attributed to the polygenic background with H = 0.31.     

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B

Background

Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible.

Results

Through genome-wide association analyses in three breeds (greyhounds, Rottweilers, and Irish wolfhounds), we identify 33 inherited risk loci explaining 55% to 85% of phenotype variance in each breed. The greyhound locus exhibiting the strongest association, located 150 kilobases upstream of the genes CDKN2A/B, is also the most rearranged locus in canine osteosarcoma tumors. The top germline candidate variant is found at a >90% frequency in Rottweilers and Irish wolfhounds, and alters an evolutionarily constrained element that we show has strong enhancer activity in human osteosarcoma cells. In all three breeds, osteosarcoma-associated loci and regions of reduced heterozygosity are enriched for genes in pathways connected to bone differentiation and growth. Several pathways, including one of genes regulated by miR124, are also enriched for somatic copy-number changes in tumors.

Conclusions

Mapping a complex cancer in multiple dog breeds reveals a polygenic spectrum of germline risk factors pointing to specific pathways as drivers of disease.     

Estimation of segregation and linkage parameters in simulated data. I. Segregation analyses with different ascertainment schemes.

We report the results of a simulation study designed to assess the capability of segregation analysis to detect Mendelian transmission and to estimate genetic model parameters for complex qualitative traits, characterized by heritability in the range 0.20-0.45 and low heterozygote penetrance. The pedigree analysis package, PAP, was used to perform the analyses. For all data sets, models of no transmission could be rejected. In most cases, models of Mendelian transmission could not be rejected; however, several samples approached significance levels. When Mendelian transmission was assumed, reasonably good parameter estimates were obtained, although heterozygote penetrances were often overestimated. Different sampling schemes were imposed on the simulated data in order to examine the extent of information loss with the reduction in sample size. One of these strategies (a sequential sampling scheme) appears to have resulted in critical loss of information in some cases.     

SNP-based heritability and genetic architecture of cranial cruciate ligament rupture in Labrador Retrievers

Cranial cruciate ligament rupture (CCLR) is one of the leading causes of pelvic limb lameness in dogs. About 6% of Labrador Retrievers suffer from this orthopedic problem. The aim of this study was to determine the heritability of CCLR in this breed using SNP array genotyping data. DNA samples were collected from CCLR-affected dogs (n = 190) and unaffected dogs over the age of 8 years (n = 143). All 333 dogs were genotyped directly or imputed up to approximately 710k SNPs on the Affymetrix Axiom CanineHD SNP array. Heritability of CCLR was calculated using multiple methodologies, including linear mixed models, Bayesian models and a model that incorporates LD. The covariates of sex and sterilization status were added to each analysis to assess their impact. Across the algorithms of these models, heritability ranged from 0.550 to 0.886, depending on covariate inclusion. The relatively high heritability for this disease indicates that a substantial genetic component contributes to CCLR in the Labrador Retriever.     

Conclusions of segregation analysis for family data generated under two-locus models.

Susceptibility to a disease may involve the interactive effect of two genes. What conclusions will be drawn by segregation analysis in such a case? To answer this question, we considered a set of two-locus models and the corresponding exact distribution for 300 families. We investigated the conclusions and parameter estimations obtained for this sample, by comparing the likelihood expectations of the unified model and of more restricted models. In many cases, segregation analysis leads to the conclusion of a major gene effect, with or without a polygenic component--usually without a polygenic component in multiplicative models (i.e., where two genes have a multiplicative effect) and with such a component in nonmultiplicative models. For all the models considered, existence of a major gene effect is supported by transmission probability tests; there is evidence for transmission and agreement with the hypothesis of Mendelian transmission. Accordingly, there is no means of detecting that the effect of a major gene, with or without a polygenic component, does not correspond to the correct model. In addition, the parameter estimates for the major gene do not correspond to the characteristics of either of the two genes of the true model. This may substantially affect further linkage analysis.     

Natural selection. VI. Partitioning the information in fitness and characters by path analysis

Three steps aid in the analysis of selection. First, describe phenotypes by their component causes. Components include genes, maternal effects, symbionts and any other predictors of phenotype that are of interest. Second, describe fitness by its component causes, such as an individual's phenotype, its neighbours’ phenotypes, resource availability and so on. Third, put the predictors of phenotype and fitness into an exact equation for evolutionary change, providing a complete expression of selection and other evolutionary processes. The complete expression separates the distinct causal roles of the various hypothesized components of phenotypes and fitness. Traditionally, those components are given by the covariance, variance and regression terms of evolutionary models. I show how to interpret those statistical expressions with respect to information theory. The resulting interpretation allows one to read the fundamental equations of selection and evolution as sentences that express how various causes lead to the accumulation of information by selection and the decay of information by other evolutionary processes. The interpretation in terms of information leads to a deeper understanding of selection and heritability, and a clearer sense of how to formulate causal hypotheses about evolutionary process. Kin selection appears as a particular type of causal analysis that partitions social effects into meaningful components.     

Comparison of Family History and SNPs for Predicting Risk of Complex Disease

The clinical utility of family history and genetic tests is generally well understood for simple Mendelian disorders and rare subforms of complex diseases that are directly attributable to highly penetrant genetic variants. However, little is presently known regarding the performance of these methods in situations where disease susceptibility depends on the cumulative contribution of multiple genetic factors of moderate or low penetrance. Using quantitative genetic theory, we develop a model for studying the predictive ability of family history and single nucleotide polymorphism (SNP)–based methods for assessing risk of polygenic disorders. We show that family history is most useful for highly common, heritable conditions (e.g., coronary artery disease), where it explains roughly 20%–30% of disease heritability, on par with the most successful SNP models based on associations discovered to date. In contrast, we find that for diseases of moderate or low frequency (e.g., Crohn disease) family history accounts for less than 4% of disease heritability, substantially lagging behind SNPs in almost all cases. These results indicate that, for a broad range of diseases, already identified SNP associations may be better predictors of risk than their family history–based counterparts, despite the large fraction of missing heritability that remains to be explained. Our model illustrates the difficulty of using either family history or SNPs for standalone disease prediction. On the other hand, we show that, unlike family history, SNP–based tests can reveal extreme likelihood ratios for a relatively large percentage of individuals, thus providing potentially valuable adjunctive evidence in a differential diagnosis.     

Evidence for a major gene influence on persistent developmental stuttering

Stuttering is a complex developmental speech disorder of unknown etiology. There is a substantial aggregation of stuttering in families, suggesting a genetic component to the disorder. However, the exact mode of transmission is still unknown. An earlier study of 56 multigenerational pedigrees ascertained through single adult probands (38 males and 18 females) found that biological relatives of persistent developmental stutterers have an approximately 10-fold higher risk than in the general population; risk is higher for male relatives, and proband's sex does not affect recurrence and relative risks. In the present paper we conduct a complex segregation analysis of the same data, using the logistic regression model of the SAGE software. Based on the comparisons of model likelihoods, the Mendelian model was selected over all other nongenetic models and the general transmission model. This model was further refined into the most parsimonious model, which shows an autosomal dominant major gene effect influenced by two covariates: sex and affection status of parents. With this model applied to 47 informative multiplex pedigrees, a power calculation based on linkage simulation produced an average lod score of 6.8 for 10-cM density genome scan markers. These results give impetus for a genomewide linkage analysis of susceptibility to persistent developmental stuttering.     

Evidence for a major gene influence on tumor necrosis factor-alpha expression in tuberculosis: path and segregation analysis

OBJECTIVE: Tuberculosis (TB) is a growing global public health problem. Several studies suggest a role for host genetics in disease susceptibility, but studies to date have been inconsistent and a comprehensive genetic model has not emerged. A limitation of previous genetic studies is that they only analyzed the binary trait TB, which does not reflect disease heterogeneity. Furthermore, these studies have not accounted for the influence of shared environment within households on TB risk, which may spuriously inflate estimates of heritability. METHODS: We conducted a household contact study in a TB-endemic community in Uganda. Antigen-induced tumor necrosis factor-alpha (TNFalpha) expression, a key component of the underlying immune response to TB, was used as an endophenotype for TB. RESULTS: Path analysis, conducted to assess the effect of shared environment, suggested that TNFalpha is heritable (narrow sense heritability = 34-66%); the effect of shared environment is minimal (1-14%), but gene-environment interaction may be involved. Segregation analysis of TNFalpha suggested a major gene model that explained one-third of the phenotypic variance, and provided putative evidence of natural selection acting on this phenotype. CONCLUSION: Our data further support TNFalpha as an endophenotype for TB, as it may increase power to detect disease-predisposing loci.     

Investigation of inheritance of chronic inflammatory bowel diseases by complex segregation analysis.

OBJECTIVE--To investigate the mode of inheritance of ulcerative colitis and Crohn''s disease by complex segregation analysis. DESIGN--Cross sectional population based survey of familial occurrence of chronic inflammatory bowel disease. SETTING--Population of the Copenhagen county in 1987. SUBJECTS--662 patients in whom inflammatory bowel disease had been diagnosed before 1979, of whom 637 (96%) provided adequate information. Of 504 patients with ulcerative colitis, 54 had 77 relatives with ulcerative colitis and of 133 patients with Crohn''s disease, five had seven relatives with Crohn''s disease. MAIN OUTCOME MEASURES--Patterns of segregation of either disease as assessed by complex segregation analysis performed with the computer program POINTER. RESULTS--The analysis suggested that a major dominant gene with a penetrance of 0.20-0.26 is present in 9-13% of adult patients with ulcerative colitis. The analysis did not allow for other components in the familial aggregation. For Crohn''s disease the best fitting model included a major recessive gene with complete penetrance, for which 7% of the patients are homozygous. However, this model was not significantly different from a multifactorial model. CONCLUSIONS--The segregation pattern indicates that a major dominant gene has a role in ulcerative colitis, and suggests that a major recessive gene has a role in Crohn''s disease.