Complex Segregation Analysis on Multi-Modal Distributions

By using sib-pairs and parent-pairs data, Tai and Gross (1988) proposed a method to test the existence of a 2-allele major locus for a quantitative trait. This method is extended to include three alleles at a major locus in this paper. One may perform this extension in a feasible and practical manner. To show the advantage of this extension, a simulated data set of nuclear families from a 3-allele ordered dominant (i.e., A > B, A > W and B > W in our notation) major locus model for a quantitative trait is analyzed by a 2-allele codominant major locus mixed model and a 3-allele ordered dominant major locus mixed model. The result shows that our method can distinguish between ambiguous trimodal distributions.     

A score test for the linkage analysis of qualitative and quantitative traits based on identity by descent data from sib-pairs

We propose a general likelihood-based approach to the linkage analysis of qualitative and quantitative traits using identity by descent (IBD) data from sib-pairs. We consider the likelihood of IBD data conditional on phenotypes and test the null hypothesis of no linkage between a marker locus and a gene influencing the trait using a score test in the recombination fraction theta between the two loci. This method unifies the linkage analysis of qualitative and quantitative traits into a single inferential framework, yielding a simple and intuitive test statistic. Conditioning on phenotypes avoids unrealistic random sampling assumptions and allows sib-pairs from differing ascertainment mechanisms to be incorporated into a single likelihood analysis. In particular, it allows the selection of sib-pairs based on their trait values and the analysis of only those pairs having the most informative phenotypes. The score test is based on the full likelihood, i.e. the likelihood based on all phenotype data rather than just differences of sib-pair phenotypes. Considering only phenotype differences, as in Haseman and Elston (1972) and Kruglyak and Lander (1995), may result in important losses in power. The linkage score test is derived under general genetic models for the trait, which may include multiple unlinked genes. Population genetic assumptions, such as random mating or linkage equilibrium at the trait loci, are not required. This score test is thus particularly promising for the analysis of complex human traits. The score statistic readily extends to accommodate incomplete IBD data at the test locus, by using the hidden Markov model implemented in the programs MAPMAKER/SIBS and GENEHUNTER (Kruglyak and Lander, 1995; Kruglyak et al., 1996). Preliminary simulation studies indicate that the linkage score test generally matches or outperforms the Haseman-Elston test, the largest gains in power being for selected samples of sib-pairs with extreme phenotypes.     

A sib-pair strategy for the use of restriction fragment length polymorphisms to study the mode of transmission of type II diabetes.

Three models for explaining the joint distribution of DNA insertional elements and type II diabetes in sibships are given as potential candidates for resolving the mode of transmission for this common non-Mendelian disorder. While the distributions predicted from all models are subject to the same rigid marginal constraints, only two models can be considered genetic (a combined major locus multifactorial background model and a two-locus model). A sequential probability ratio test is proposed to distinguish between these two models. Once the probands have been ascertained and using realistic parameter estimates, it is shown that, on the average, fewer than 100 affected sib-pairs are required to reach a decision at the 1% significance level with 99% power.     

Parental assignment in fish using microsatellite genetic markers with finite numbers of parents and offspring

Deterministic predictions for the proportion of offspring assigned to different numbers of parent-pairs are developed in order to investigate the power of microsatellite loci for parental assignment in fish species. Comparisons with stochastic simulation results show that predictions based on exclusion probabilities are accurate, provided that the number of parents involved in the crosses is large. Accounting for sampling of parents gave very accurate predictions for a small number of parents and a single biallelic locus. For large numbers of loci or large numbers of alleles per locus stochastic simulations are, however, the only available method to predict the power of assignment of a particular set of loci when the number of parents is small. Nine 5-allele loci or six 10-allele loci with equifrequent alleles, are sufficient for assigning, with certainty, parents to 99% of the fish resulting from either 100 or 400 crosses. Results simulating a set of highly polymorphic microsatellites developed for Atlantic salmon show that the four most informative loci are sufficient to assign at least 99% of the offspring to the correct pair with 100 crosses involving 100 males and 100 females. An additional locus is required for correctly assigning 99% of the offspring when the 100 crosses are produced with 10 males and 10 females.     

Maximum likelihood estimation of genetic parameters of HLA-linked diseases using data from families of various sizes

This paper is concerned with estimating parameters associated with HLA-linked diseases. We consider a single disease locus closely linked to HLA, allowing a disease and a normal allele. The parameters to be estimated are the penetrances of the genotypes at the disease locus, the population frequency of the disease allele, and the distance of the disease locus from HLA. The presently used method of estimation uses HLA-sharing information from affected sib-pairs. The method proposed here generalizes the previous approach, using data from all sibs (affected or unaffected) in a family of any size. It allows immediate generalizations to the use of information on parental affectedness status and population prevalence.     

Dissecting the correlation structure of a bivariate phenotype: Common genes or shared environment?

High correlations between two quantitative traits may be either due to common genetic factors or common environmental factors or a combination of both. In this study, we develop statistical methods to extract the genetic contribution to the total correlation between the components of a bivariate phenotype. Using data on bivariate phenotypes and marker genotypes for sib-pairs, we propose a test for linkage between a common QTL and a marker locus based on the conditional cross-sib trait correlations (trait 1 of sib 1—trait 2 of sib 2 and conversely) given the identity-by-descent (i.b.d.) sharing at the marker locus. We use Monte-Carlo simulations to evaluate the performance of the proposed test under different trait parameters and quantitative trait distributions. An application of the method is illustrated using data on two alcohol-related phenotypes from a project on the collaborative study on the genetics of alcoholism.     

HLA-dependent GM effects in insulin-dependent diabetes: evidence from pairs of affected siblings.

In a recent study of GM allotype frequencies in HLA-defined subsets of patients with insulin-dependent diabetes mellitus (IDDM) and similarly defined healthy sibling controls, we found evidence for an HLA-dependent GM effect on IDDM susceptibility. To circumvent problems inherent in such patient-control studies of complex diseases, we have now examined sharing of genes in the HLA and GM regions in 26 informative pairs of siblings who were both affected with IDDM. We found that: (1) in the total sample of affected sib-pairs, sharing of two HLA haplotypes was increased compared to Mendelian expectations, in agreement with many previous studies; (2) in the total sample, sharing of GM region genes (as measured by GM phenotype concordance) was not different from Mendelian expectations, given the distribution of parental mating types; and (3) affected sib-pairs who shared two HLA haplotypes showed significantly increased sharing of GM region genes compared to affected sib-pairs who shared one or zero HLA haplotypes (P = .018). These results provide new evidence for HLA-dependent effects of a locus at or near GM on susceptibility to IDDM.     

HLA-associated diseases: a new method for performing linkage analysis with other markers than HLA.

It has been shown that genetic factors within the HLA region are involved in the etiology of several diseases. For some of these, the existence of another genetic factor has been suggested, although not proven. A possible way to give evidence for another locus (G) is to show that the disease and an unlinked HLA-marker locus (M) do not segregate independently. The usual lod-score method, which assumes monogenic inheritance, is inappropriate for this test. We propose a correction of this method for performing a linkage analysis between the G and M loci, taking into account the role of HLA. A very simple way of using the HLA information is by modifying, for each individual of a pedigree, the penetrance values at the G locus according to the number of HLA haplotypes shared with the index case. These penetrance values are inferred from the observed IBD (identity-by-descent) distribution of HLA haplotypes in a sample of affected sib-pairs. The advantage of using this empirical distribution is that it is not based on any assumptions concerning the mode of inheritance at the HLA-linked locus. This correction method was established using a two-locus model with restrictive assumptions. Its value is discussed for various sets of parameters in more general and realistic two-locus models using simulations.     

Inheritance of Adrenal Phenylethanolamine N-Methyltransferase Activity in the Rat

Phenylethanolamine N-methyltransferase (PNMT) is the enzyme that catalyzes the S-adenosyl-L-methionine-dependent methylation of (-)norepinephrine to (-)epinephrine in the adrenal medulla. Adrenal PNMT activity is markedly different in two highly inbred rat strains; enzyme activity in the F344 strain is more than fivefold greater than that in the Buf strain. Initial characterization of the enzyme in the two inbred strains reveals evidence for catalytic and structural differences, as reflected in dissimilar Km values for the cosubstrate (S-adenosyl-L-methionine) and prominent differences in thermal inactivation curves. To assess adrenal PNMT activity in an F344 X Buf pedigree, we employed a statistical procedure to test for one- and two-locus hypotheses in the presence of within-class correlations due to cage or litter effects. The PNMT data in the pedigree are best accounted for by segregation at a simple major locus superimposed upon a polygenic background; data obtained from the biochemical studies suggest that the major locus is a structural gene locus.     

Non-Locus-Specific Polygenes Giving Responses to Selection for Gene Conversion Frequencies in Ascobolus Immersus

Selection for higher and lower meiotic conversion frequencies was investigated in the fungus Ascobolus immersus. Strains carrying the same known gene conversion control factors, which have major effects on conversion frequencies at their specific target locus, sometimes gave significant differences in conversion frequency. Selection for high or low conversion frequencies at the w1-78 site was practiced for five generations, giving significant responses in both directions. These responses were due to polygenes, or genes of minor effect, not to new conversion control factors of major effect. Crosses of selected strains to strains with other mutations showed that the genes' effects were not specific to w1-78, but could affect conversion frequencies of another mutation, w1-3C1, at that locus and of two other loci, w-BHj and w9, which are unlinked to w1 or to each other. The proportional changes in gene conversion frequency due to selection varied according to the locus and site involved and according to the conversion control factor alleles present. There were differences of >/=277% in conversion frequency between ``high' and ``low' strains. Selection for conversion frequency had little effect on other features of conversion, such as the frequency of postmeiotic segregation or the relative frequencies of conversion to mutant or wild type.     

An ancient retrovirus-like element contains hot spots for SINE insertion

Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. Mys elements are a type of LTR-containing retrotransposon present in Sigmodontine rodents. In this study we have shown that one particular insert, mys-9, is an extremely old insert present in multiple species of the genus Peromyscus. We have found that different copies of this insert show a surprising range of sizes, due primarily to a continuing series of SINE (short interspersed element) insertions into this locus. We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers.     

Genetic determinants of human health span and life span: progress and new opportunities

We review three approaches to the genetic analysis of the biology and pathobiology of human aging. The first and so far the best-developed is the search for the biochemical genetic basis of varying susceptibilities to major geriatric disorders. These include a range of progeroid syndromes. Collectively, they tell us much about the genetics of health span. Given that the major risk factor for virtually all geriatric disorders is biological aging, they may also serve as markers for the study of intrinsic biological aging. The second approach seeks to identify allelic contributions to exceptionally long life spans. While linkage to a locus on Chromosome 4 has not been confirmed, association studies have revealed a number of significant polymorphisms that impact upon late-life diseases and life span. The third approach remains theoretical. It would require longitudinal studies of large numbers of middle-aged sib-pairs who are extremely discordant or concordant for their rates of decline in various physiological functions. We can conclude that there are great opportunities for research on the genetics of human aging, particularly given the huge fund of information on human biology and pathobiology, and the rapidly developing knowledge of the human genome.     

The loss of statistical power to distinguish populations when certain samples are ambiguous

Case-control studies are used to map loci associated with a genetic disease. The usual case-control study tests for significant differences in frequencies of alleles at marker loci. In this paper, we consider the problem of comparing two or more marker loci simultaneously and testing for significant differences in haplotype rather than allele frequencies. We consider two situations. In the first, genotypes at marker loci are resolved into haplotypes by making use of biochemical methods or by genotyping family members. In the second, genotypes at marker loci are not resolved into haplotypes, but, by assuming random mating, haplotypes can be inferred using a likelihood method such as the expectation-maximization (EM) algorithm. We assume that a causative locus has two alleles with a multiplicative effect on the penetrance of a disease, with one allele increasing the penetrance by a factor pi. We find, for small values of pi-1 and large sample sizes, asymptotic results that predict the statistical power of a test for significant differences in haplotype frequencies between cases and a random sample of the population, both when haplotypes can be resolved and when haplotypes have to be inferred. The increase in power when haplotypes can be resolved can be expressed as a ratio R, which is the increase in sample size needed to achieve the same power when haplotypes are resolved over when they are not resolved. In general, R depends on the pattern of linkage disequilibrium between the causative allele and the marker haplotypes but is independent of the frequency of the causative allele and, to a first approximation, is independent of pi. For the special situation of two di-allelic marker loci, we obtain a simple expression for R and its upper bound.     

Genomic analysis I: inheritance units and genetic selection in the rapid discovery of locus linked DNA markers.

We propose, and test using a Monte-Carlo analysis (a computer-based numerical analysis using a random number generator), a novel and efficient method to obtain sets of DNA markers linked to any inherited genetic locus. The method consists of a targeted search that is based on the common inheritance among members of an outbred pedigree, of discrete chromosome lengths, which we call inheritance units, to obtain DNA markers linked to the locus. In cases where two individuals inherit the same trait through two different lines of descent from a common ancestor, the set of inheritance units in each of the two genomes includes an inheritance unit that is identical in both individuals for a substantial distance on both sides of the DNA sequence which confers the trait. The power of the technique derives from the genetic selection that reduces the size and number of the inheritance units as the generational distance between the two individuals being compared increases.     

Unbiased application of the transmission/disequilibrium test to multilocus haplotypes

When the transmission/disequilibrium test (TDT) is applied to multilocus haplotypes, a bias may be introduced in some families for which both parents have the same heterozygous genotype at some locus. The bias occurs because haplotypes can only be deduced from certain offspring, with the result that the transmissions of the two parental haplotypes are not independent. We obtain an unbiased TDT for individual haplotypes by calculating the correct variance for the transmission count within a family, using information from multiple siblings if they are available. An existing correction for dependence between siblings in the presence of linkage is retained. To obtain an unbiased multihaplotype TDT, we must either count transmissions from one randomly chosen parent or count all transmissions and estimate the significance level empirically. Alternatively, we may use missing-data techniques to estimate uncertain haplotypes, but these methods are not robust to population stratification. An illustration using data from the insulin-gene region in type 1 diabetes shows that the validity and power of the TDT may vary by an order of magnitude, depending on the method of analysis.     

Affected sib-pair analysis of the GLUT1 glucose transporter gene locus in non-insulin-dependent diabetes mellitus (NIDDM): evidence for no linkage

Despite the strong evidence for a major role played by genetic factors in the aetiology of non-insulin-dependent diabetes mellitus (NIDDM), the genes involved are still unknown. Association studies of candidate genes for the inheritance of NIDDM have so far yielded inconclusive results. Some evidence exists for an association between NIDDM and the glucose transporter gene GLUT1, involved in basal glucose transport, although this has not been confirmed. In the present study we have tested the hypothesis of linkage between NIDDM and the GLUT1 gene, using affected sib-pairs. With this method the concordance observed for a given gene marker is compared with that expected under the assumption of no linkage between that marker and the disease. Fifty-four pedigrees (22 Italians and 32 British), for a total of 82 sibpairs were studied by the affected sib-pair method proposed by Weeks and Lange, using two restriction fragment length polymorphisms (RFLPs) at the GLUT1 locus, the MspI RFLP, at an estimated 0.171 recombination frequency from the GLUT1 gene, and the XbaI RFLP, located within the GLUT1 gene and previously shown to be associated with the disease. Results showed that the MspI marker and NIDDM segregate independently; for the XbaI RFLP, linkage could be shown only if the results were weighted by the allele frequency [f(p) = 1/p], and only in the Italian and the combined (Italian and British) sib-pair groups. Multilocus analysis with both markers was also negative. We conclude that the GLUT1 gene is very unlikely to play a major role in the aetiology of NIDDM, although an accessory role cannot be excluded, and studies of the gene sequence should help to clarify this question.     

Family study and segregation analysis of Tourette syndrome: evidence for a mixed model of inheritance.

To investigate the transmission of Tourette syndrome (TS) and associated disorders within families, complex segregation analysis was performed on family study data obtained from 53 independently ascertained children and adolescents with TS and their 154 first-degree relatives. The results suggest that the susceptibility for TS is conveyed by a major locus in combination with a multifactorial background. Other models of inheritance were definitively rejected, including strictly polygenic models, all single major locus models, and mixed models with dominant and recessive major loci. The frequency of the TS susceptibility allele was estimated to be .01. The major locus accounts for over half of the phenotypic variance for TS, whereas the multifactorial background accounts for approximately 40% of phenotypic variance. Penetrance estimates suggest that all individuals homozygous for the susceptibility allele at the major locus are affected, whereas only 2.2% of males and 0.3% of females heterozygous at the major locus are affected. Of individuals affected with TS, approximately 62% are heterozygous and approximately 38% are homozygous at the major locus. While none of the families had two parents affected with TS, 19% of families had two parents affected with the broader, phenotype, which includes TS, chronic tic disorder, or obsessive-compulsive disorder.     

The potential for sexually antagonistic polymorphism in different genome regions

Sex differences in the fitness effects of alleles at a single locus (intralocus sexual antagonism, or SA) have several evolutionary consequences. Among the consequences of SA, polymorphisms at genes partially linked to the sex-determining region of the sex chromosome pair potentially drive the evolution of suppressed recombination between the sex chromosomes. Understanding the conditions under which SA polymorphism can exist at such pseudo-autosomal (or PAR) loci should increase understanding of the evolution of recombination between sex chromosome pairs, and can help predict when we may expect potentially empirically detectable allele frequency differences between the sexes. Models so far published have concluded that PAR genes can maintain SA polymorphisms over a wider range of selection coefficients than autosomal ones, but have used restrictive assumptions. We expand the modeling of SA alleles at a single locus with the full range of degrees of linkage to the male-specific region, to include strong or weak selection and the possibility of different dominance coefficients in the two sexes. We confirm the previous major conclusion that SA polymorphisms are generally maintained in a larger region of parameter space if the locus is in the PAR than if it is autosomal.     

Novel susceptibility locus at 22q11 for diabetic nephropathy in type 1 diabetes

Background

Diabetic nephropathy (DN) affects about 30% of patients with type 1 diabetes (T1D) and contributes to serious morbidity and mortality. So far only the 3q21–q25 region has repeatedly been indicated as a susceptibility region for DN. The aim of this study was to search for new DN susceptibility loci in Finnish, Danish and French T1D families.

Methods and Results

We performed a genome-wide linkage study using 384 microsatellite markers. A total of 175 T1D families were studied, of which 94 originated from Finland, 46 from Denmark and 35 from France. The whole sample set consisted of 556 individuals including 42 sib-pairs concordant and 84 sib-pairs discordant for DN. Two-point and multi-point non-parametric linkage analyses were performed using the Analyze package and the MERLIN software. A novel DN locus on 22q11 was identified in the joint analysis of the Finnish, Danish and French families by genome-wide multipoint non-parametric linkage analysis using the Kong and Cox linear model (NPL_pairs LOD score 3.58). Nominal or suggestive evidence of linkage to this locus was also detected when the three populations were analyzed separately. Suggestive evidence of linkage was found to six additional loci in the Finnish and French sample sets.

Conclusions

This study identified a novel DN locus at chromosome 22q11 with significant evidence of linkage to DN. Our results suggest that this locus may be of importance in European populations. In addition, this study supports previously indicated DN loci on 3q21–q25 and 19q13.