Robustness and power of the unified model in the analysis of quantitative measurements

The resolution between skewness in the distribution of a quantitative trait and segregation of a major gene is a difficult issue in family studies. Quantitative data were simulated on six-member nuclear families in order to study the behavior of the unified model under these circumstances. Replicates of 100 nuclear families were generated assuming a multifactorial model with skewness. In the range where a major gene was falsely detected in 80%-100% of the simulations analyzed under the transmission probability or mixed models, use of the unified model reduces the frequency of false inference to between 10% and 40%. This protection against a false conclusion requires estimation of the three transmission probabilities and testing hypotheses of Mendelian transmission and equal transmission probabilities. Alternatively, it was shown that use of a transformation to remove skewness induced by a major gene leads to a decrease of power of approximately 55%. These results suggest that the unified model may obviate the need to compare analyses performed on transformed and untransformed data, particularly when skewness is low (less than 0.2) or high (greater than 0.4). For intermediate skewness (0.2-0.4), estimating segregation parameters under the mixed model simultaneously with a transformation to remove residual skewness can be considered as an alternative method.

Construction of human linkage maps: likelihood calculations for multilocus linkage analysis

Methods are given for efficient calculation of the likelihood for multilocus linkage in families comprised of grandparents, parents, and children. Such families are being used in large-scale cooperative efforts to build a detailed linkage map of the human genome. The methods are illustrated by an application to loci on chromosome 13.

A closely linked genetic marker for cystic fibrosis

Cystic fibrosis is a recessive genetic disorder, characterized clinically by chronic obstructive lung disease, pancreatic insufficiency and elevated sweat electrolytes; affected individuals rarely live past their early twenties. Cystic fibrosis is also one of the most common genetic diseases in the northern European population. The frequency of carriers of mutant alleles in some populations is estimated to be as high as 1 in 20, carrying a concomitant burden of about one affected child in 1,500 births. Because little is known of the essential biochemical defect caused by the mutant gene, a genetic linkage approach based on arbitrary genetic markers and family studies is indicated to determine the chromosomal location of the cystic fibrosis (CF) gene. We have now obtained evidence for tight linkage between the CF locus and a DNA sequence polymorphism at the met oncogene locus. This evidence, combined with the physical localization data for the met locus presented in the accompanying paper, places the CF locus in the middle third of the long arm of chromosome 7, probably between bands q21 and q31.

Genetic analysis of idiopathic hemochromatosis using both qualitative (disease status) and quantitative (serum iron) information

An ongoing family study of idiopathic hemochromatosis in Brittany, France, allowed us to investigate the segregation of this trait and its linkage and association to the HLA-A locus in 147 pedigrees, comprising 1,408 individuals with over 900 characterized for relevant biological parameters and typed for HLA. The joint consideration of affection status and serum iron concentration reveals no dominance effect on the latter trait and documents the increased information afforded by the consideration of a biological correlate of liability to affection for disease exhibiting incomplete penetrance. Our overall results are in general agreement with published results on a Utah family study.

Multilocus linkage analysis in humans: detection of linkage and estimation of recombination

Multilocus linkage analysis is investigated from the viewpoint of the efficiency of recombination estimates under different strategies for detecting linkage and determining gene order within a linkage group. We consider the appropriateness of assuming no interference with data available in human genetic studies. Examples are given to show the significance of multilocus analysis in humans. A computer program package, LINKAGE, for multilocus linkage analysis is described.

Demonstration of a common major gene with pleiotropic effects on immunoglobulin E levels and allergy

Atopic disease is generally recognized to be familial, although specific genetic components have yet to be identified. High levels of a unique class of immunoglobulins, immunoglobulin E (IgE), have been shown to be associated with allergies. Several investigators have reported evidence indicating a recessive regulatory locus where an individual with the homozygous recessive genotype has persistently elevated levels of IgE. Willcox and Marsh [1978] have proposed a hypothesis relating IgE production and liability to become allergic. A test of this hypothesis was carried out in the present study. Bivariate segregation analysis of IgE levels and allergy was performed on 173 nuclear families, and the results indicate that an IgE regulatory locus contributes to the familial transmission of allergy. The results are further discussed in the context of the Willcox and Marsh hypothesis.

Clusters of HLA class II beta restriction fragments describe allelic series

Eighty-eight HLA haplotypes have been investigated for the presence or absence of 52 restriction fragments generated by four restriction enzymes (EcoRI, EcoRV, HindIII, BamHI), and detected by a DQ beta cDNA probe. Correlation analysis showed several sets of positively associated fragments forming 11 clusters. They constitute three different allelic series. The first coincides with DR alleles, the second with DQ alleles, and within the third, one cluster coincides with DRw53 (MT). As shown by comparative hybridization, most fragments belonging to the DR- as well as the DQ-related series correspond to DQ beta genes. In contrast, the MT-related series corresponds to DR beta genes. The evolutionary significance of these restriction fragment clusters is discussed.

Strategies for multilocus linkage analysis in humans

The increasing number of DNA polymorphisms characterized in humans will soon allow the construction of fine genetic maps of human chromosomes. This advance calls for a reexamination of current methodologies for linkage analysis by the family method. We have investigated the relative efficiency of two-point and three-point linkage tests for the detection of linkage and the estimation of recombination in a variety of situations. This led us to develop the computer program LINKAGE to perform multilocus linkage analysis. The investigation also enables us to propose a method of location scores for the efficient detection of linkage between a disease locus, or a new genetic marker, and a linkage group previously established from a reference panel of families. The method is illustrated by an application to simulated pedigree data in a situation akin to Duchenne muscular dystrophy. These results show that considerable economy and efficiency can be brought to the mapping endeavor by resorting to appropriate strategies of detecting linkage and by constructing the human genetic map on a common reference panel of families.

Easy calculations of lod scores and genetic risks on small computers

A computer program that calculates lod scores and genetic risks for a wide variety of both qualitative and quantitative genetic traits is discussed. An illustration is given of the joint use of a genetic marker, affection status, and quantitative information in counseling situations regarding Duchenne muscular dystrophy.

Specific immune responses after booster immunization with tetanus toxoid in man: study of kinetics, family segregation, and linkage to HLA of in vitro lymphocyte proliferative responses and serum-antibody responses

Kinetics and family transmission of antigen-specific in vitro cell-mediated responses were investigated in 68, and serum-antibody responses to tetanus toxoid (TT) in 73 individuals from a total of 12 families. Proliferative responses to highly purified TT monomer were studied in 6- to 7-day lymphocyte cultures. The effect of booster immunization was detectable 7 (D7) and 30 (D30), but not 120 days (D120) later. The sex of donors was not found to have any influence. A significant influence of the time interval since the last immunization was found for the responses at D7 and D30. Data were correspondingly adjusted for segregation and linkage analyses. Several transmission hypotheses for the data obtained at D7 and D30 were evaluated by likelihood ratio tests. Observations at D30 were compatible with the hypothesis of a control by a dominant genetic determinant for high responses closely linked to the major histocompatibility complex region. No such evidence could be found for D7. After booster immunization, mean antibody levels determined on D7, D30 (peak of response), and D120 were found to be higher than those prior to immunization (D0). The sex of the donors was found to have no influence on antibody responses. The time interval since the last immunization and the age of donors both had a slight influence, and data were correspondingly adjusted for segregation and linkage analyses, which showed no evidence of genetic control of the antibody responses or of linkage to HLA.

A unified model for complex segregation analysis

Various methods have been proposed for statistical inference of major genes by segregation analysis of human familial data. An attempt is made to resolve some divergences that have occurred in this context by the consideration of a unified model, with some practical applications.

Genetic regulation of plasma and red blood cell magnesium concentration in man. II. Segregation analysis

A previous paper in this series reported that genetic factors play a major role in the familial transmission of plasma (P) and red blood cell (RBC) magnesium (Mg) concentrations. We report here the results of commingling analysis based on a random sample of unrelated individuals, and complex segregation analysis of a random sample of nuclear families. For RBC Mg, there is evidence for a mixture of two distributions, but not for three. For P Mg, there is no evidence for commingling. Complex segregation analysis under a mixed model yielded significant support for a major gene effect on RBC Mg, but not on P Mg. Parameter estimates indicated that the data are compatible with a rather common major gene (q = .23) for elevated RBC Mg, roughly 5% of the population being homozygotes for this gene, that the nonfamilial factors account for a small fraction of the total variance, and that the overlap of distributions of homozygotes is not large.

A genetic study of hyper-alpha-lipoproteinemia

Because of its association with longevity and reduced incidence of coronary heart disease, it becomes important to find out how elevated HDL-cholesterol levels are determined. Analyses of family data from Cincinnati initially suggested environmental factors common to sibs; however, some form of dominant inheritance could not be ruled out. Reanalysis of the Cincinnati data by Iselius and Lalouel concluded against a major locus, but did identify three families as possibly segregating for a major locus. Analysis of an additional 26 kindreds from the same population in Cincinnati by Siervogel and associates concluded that a major gene could be causing familial aggregation of high density lipoprotein in white kindreds. In this analysis, we pooled all the white Cincinnati kindreds (n = 31), and investigated the familial transmission using complex segregation analysis. We failed to obtain clear evidence for major locus determination. Under the parsimonious hypothesis of no major locus, the polygenic heritability and common sibling environmental correlation were estimated as 0.531 and 0.263, respectively, consistent with other evidence.

Lambda Ig constant region genes are translocated to chromosome 8 in Burkitt's lymphoma with t(8;22)

By in situ hybridization of normal human chromosomes with a cloned genomic probe specific for the constant region of the lambda immunoglobulin genes, band 22q11 was preferentially labelled. In two cell lines with t(8;22) derived from Burkitt's lymphoma a strong signal was noted on the 8q+ chromosome derivative, indicating that the constant region of the lambda Ig gene cluster was translocated from chromosome 22 to chromosome 8. In addition, the signal observed on the 22q- derivative chromosome was stronger than the background in one of the two cell lines tested, but not in the other. The implications are that the break point in chromosome 22 in some cases lies within the Ig gene itself or between clusters of such genes, and that different cases have different break points.

[Genetic effect on specific human immune responses to tetanus anatoxin]

Kinetics and family transmission of antigen specific immune responses were investigated before and 7, 30 and 120 days after booster immunization with tetanus toxoid (TT) in 73 individuals from 12 families. The study of TT specific in vitro lymphocyte proliferative response and of TT antibody levels by radioimmunoassay were performed in parallel; the effect of booster immunization was detectable 7 and 30 days later and still 120 days later for antibody response. No influence of the sex of donors was found. Because of the significant influence on the level of responses of the time interval since last immunization, data were correspondingly adjusted for segregation and linkage analysis. Observations at day 30 were compatible with the hypothesis of control by a dominant genetic determinant for high proliferative responses closely linked to the major histocompatibility complex region.

A genetic study of red blood cell zinc concentration in man

Red blood cell zinc levels vary linearly with age within each sex. Age- and sex-adjusted zinc levels generated 6 familial correlations in nuclear families and twins. A simple additive polygenic model, with genetic heritability of zinc (h2) as the only unknown parameter, gave an excellent fit (X2(5) = 0.97, p greater than 0.96), with the corresponding estimate of h2 = 0.790 +/- 0.032. Commingling analysis supported the hypothesis that the logarithmic zinc values are approximately distributed according to a mixture of three normal distributions. Some support was found for a major gene hypothesis by complex segregation analysis under the mixed model. However, all the evidence came just from one family in which one of the 3 children's zinc value was over 3 standard deviations above the mean. When that family was excluded, there was no more evidence for a major gene. Under the most parsimonious mutlifactorial model that assumes equal heritabilities in children and adults, the heritability was estimated as 0.748 +/- 0.079, in good agreement with the outcome of path analysis. Biological interpretations are put forward and discussed.

Genetic regulation of plasma and red blood cell magnesium concentrations in man. I. Univariate and bivariate path analyses

This paper concerns an analysis of family resemblance for magnesium concentrations, based on data from nuclear families and twins. Neither red blood cell magnesium nor plasma magnesium varies with age in children (under 20 years of age). Whereas adult plasma magnesium varies linearly with age, the red cell magnesium clearly showed a nonlinear trend: quadratic for males and a fifth-degree polynomial for females. Transformed magnesium concentrations generated six correlations in nuclear families and twins for each of the two traits. Separate univariate analyses, using a simple linear model with four parameters, strongly suggested that genetic factors are primarily responsible for the observed family resemblance. Both traits were then analyzed simultaneously using a simple bivariate model. We found that one common genetic factor alone could not explain all the 24 correlations generated for the bivariate analysis. The most parsimonious model involved only three parameters: genetic heritability for red blood cell magnesium (.922 +/- .014), genetic heritability for plasma magnesium (.721 +/- .040), and the genetic correlation between the two traits (.233 +/- .040).

Detection of carriers for Duchenne muscular dystrophy. Quality control of creatine kinase assay

A report by Bullock and coworkers has emphasized the need for standardization of the CK assay in carrier detection for DMD. A collaborative study, according to a well-specified design and involving two laboratories in Paris and Lyon, indicates that the reliability of this assay can be improved provided that special attention is paid to information about participating subjects, laboratory protocol, and repeated sampling. On a random sample of young women, mean and variance of ln(CK) are 1.66 and 0.015 respectively. Within and between variance components are in a 3:4 ratio, homogeneous between populations. Additional use of a common test serum should insure good reliability of this assay among laboratories.

Path analysis under generalized assortative mating. II. American I.Q

Rice, Cloninger & Reich (1980) showed that correlational data on American I.Q. is consistent with a rather low genetic heritability. Here we confirm their general results with a more parsimonious model. From phenotypic data alone, the estimates of genetic and cultural heritability are 0·31 and 0·42, respectively. Using environmental indices, the parsimonious estimates become 0·34 and 0·26, respectively.

Complex segregation analysis with pointers

Complex segregation analysis has been extended to apply to nuclear families and relatives outside the nuclear family that have led to its ascertainment. These individuals are referred to as pointers. The mixed model of Morton and MacLean has been modified to allow for a sex-linked major gene, mutation, and generational differences in multifactorial transmission for adults and children, respectively. The model and methods used in implementing it are described, as well as the rationale underlying this approach to analysis of pedigree data.

Resolution of linkage for irregular phenotype systems

A method is given to resolve pleiotropy from linkage; to detect and estimate recombination free of incomplete penetrance, etiological heterogeneity, and other phenomena; and to estimate gametic frequencies for the main and test loci jointly. Large pedigrees, a liability indicator specifying risk groups (based on age, sex, or other factors), gametic disequilibrium, different recombination values in the two sexes, multiple alleles at the test locus, and a mixture of linked and unlinked marker loci are provided for. Parametrization of the marker locus is the same as for segregation analysis with pointers. The output includes standard errors, likelihood ratio tests of hypotheses, and a standard lod table for each sex separately. A model of closely linked complementing factors which can simulate recombination is also considered.

Immunogenetics of response to a purified antigen from group A streptococci. II. Linkage of response to HLA

Employing an in vitro blastogenesis model, evidence has been set forth for a major gene locus which controls response to a purified, extracellular antigen from group A streptococci. Response to this antigen is inherited in an autosomal dominant manner. Analysis of the data for linkage to HLA was done with the computer program LINKAS which can resolve pleiotropy from linkage and can detect and estimate recombination in the presence of etiological heterogeneity. Maximum likelihood estimation and likelihood ratio tests were used to assess the relative support for competing hypotheses. The results of this analysis indicate that at least two loci are involved in one of two ways: one locus that is closely linked to HLA and one locus that is unlinked; or a two-locus system of complementary alleles which are both tightly linked to HLA.

Immunogenetics of response to a purified antigen from group A streptococci. I. Complex segregation analysis

A purified, extracellular protein, M. W. 17500, from group A streptococci was used in an in vitro model to study genetic aspects of immune responsiveness. Peripheral blood lymphocytes from members of eight nuclear families and one kindred of three generations were isolated and purified by F-icoll-Isopaque flotation and cultured together with varying concentrations of antigen. A summary measure of the antigen response data (measured as CPM) was constructed through a weighted regression analysis of response on dose. Commingling analysis of the standardized regression coefficients provided evidence for the existence of two underlaying distributions. Segregation analysis confirmed that response to this antigen is controlled by a major gene and is inherited in an autosomal dominant manner.

Probability calculations in pedigrees under complex modes of inheritance

It is shown that the method of Heuch and Li for recursive calculation of conditional genotype probabilities in pedigrees also applies to joint phenotype probability calculations. This procedure was applied to complex modes of inheritance, with possible applications to both genetic analysis and genetic counseling.

Linkage studies in spinocerebellar ataxia (SCA)

Data are now available on 9 pedigrees in detail and 4 pedigrees as lod scores only. Linkage to HLA is significant (Z = 5.53 at recombination rates of 0.223 in males and 0.327 in females). Tight linkage is excluded. Nine pedigrees which appear to be typical olivopontocerebellar atrophy (OPCA I) have recombination rates of 0.150 in males and 0.300 in females. The remaining 4 pedigrees are clinically atypical or include discrepant data and give no evidence for linkage. The symbol SCA1 is proposed for a locus on chromosome 6 (loosely linked to HLA), at which at least one allele produces OPCA I (Menzel type). It is not yet clear whether other clinical types are determined by alleles at different loci, although this is suggested by several pedigrees, including a Danish pedigree of OPCA with dementia. Linkage evidence will be decisive in delineating the ataxias.

Frequencies of Gm and Km allotypes in the population of Singapore, Sri Lanka and Punjabis in North India

Serum samples from Sinhalese subjects, from Punjab and from Singapore have been studied. The Gm phenotypes found are very numerous and we can observe some similarities concerning the Gm gene frequencies between the Singapore Indians with the Indians of North India, and with the Sinhalese. In contrast, Gm gene frequencies found among Chinese and Malays from Singapore are quite different from those found among Indians of Singapore. Our results here are very similar to those obtained in Malaya studies.

A maximum likelihood map of chromosome 1

Thirteen loci are mapped on chromosome 1 from genetic evidence. The maximum likelihood map presented permits confirmation that Scianna (SC) and a fourteenth locus, phenylketonuria (PKU), are on chromosome 1, although the location of the latter on the PGM1-AMY segment is uncertain. Eight other controversial genetic assignments are rejected, providing a practical demonstration of the resolution which maximum likelihood theory brings to mapping.

Neural tube malformations: complex segregation analysis and calculation of recurrence risks

Familial data on neural tube malformations in Great Britain were submitted to segregation analysis under the mixed model. Maternal and fetal factors cannot be discriminated in the absence of substantial bodies of data on spina bifida survivors who reproduce or on half-sibs. Early abortion studies would allow differential mortality in utero to be taken into account. After fitting the mixed and generalised single locus models, it is concluded that the multifactorial model can provisionally be used for calculation of recurrence risks. Pathogenic hypotheses implicating twinning seem to rest on little evidence.

Complex segregation analysis of diabetes mellitus

Complex segregation analysis was applied to a sample of 12,293 nuclear families each with at least 1 diabetic patient. The families were divided into two groups depending on the proband's treatment: insulin-dependent (IDG) and insulin-independent (IIG). Heterogeneity analysis has revealed a highly significant difference in the IIG group when families were divided into different mating types. The higher recurrence risk was found in the group with affected mothers. Also evidence for a major recessive gene was found in the IGG group, while it was not possible to distinguish between the hypothesis for absence of a major locus and absence of polygenic inheritance in the IDG group. Risks to develop the disease were calculated for a few typical situations.

Common and uncommon immunoglobulin haplotypes among Lebanese communities

Allotypes of IgG1, IgG2, IgG3, and IgA2 subclasses were investigated in seven Lebanese communities (three Moslem and four Christian). The Gm-Am haplotypes found were mainly those prevalent in Caucasians with a low frequency of haplotypes usually observed in Africans and Orientals. The difference between highlanders and lowlanders as expressed by G2m(23) was highly significant and suggested a possible adaptation to selective pressure related to the gamma2 genes, possibly due to endemic malaria in the past. Exceptional Gm-Am haplotypes were unambiguously determined by family studies. Some were characterized either by a deletion or a repression or, in contrast, by a partial or total duplication of gamma genes. Two others had uncommon combinations of allotypes: Gm17;23;5,10,11,13,14 A2m1, where G1m (17) was present without G1m (1); and Gm3;23;5,14 A2m1, where the CH3 allotypes G3m (10,11,13) were lacking.

Recurrence risks in complex inheritance with special regard to pyloric stenosis

A large body of data on segregating families is used to generate specific recurrence risks conditional on sex and birth order for the best-fitting model of polygenes plus maternal effect. The method is general for diseases of complex inheritance, and lies within the competence of any serious genetic clinic. The question of whether consultees demand as much specificity should be subordinate to the question of whether counsellors are justified in providing less.

Linkage mapping from pair-wise recombination data

The problem of obtaining a genetic map of a linkage group from pair-wise recombination data is considered. A non-parametric approach is proposed, that does not require the definition of a mapping function, computation of coefficients of coincidence, nor knowledge of map length or sex differences in recombination. An application to Bridges and Morgan's (1923) data on chromosome 3 of Drosophila melanogaster is presented.