Assessment of parent-of-origin effects in linkage analysis of quantitative traits

Methods are presented for incorporation of parent-of-origin effects into linkage analysis of quantitative traits. The estimated proportion of marker alleles shared identical by descent is first partitioned into a component derived from the mother and a component derived from the father. These parent-specific estimates of allele sharing are used in variance-components or Haseman-Elston methods of linkage analysis so that the effect of the quantitative-trait locus carried on the maternally derived chromosome is potentially different from the effect of the locus on the paternally derived chromosome. Statistics for linkage between trait and marker loci derived from either or both parents are then calculated, as are statistics for testing whether the effect of the maternally derived locus is equal to that of the paternally derived locus. Analyses of data simulated for 956 siblings from 263 nuclear families who had participated in a linkage study revealed that type I error rates for these statistics were generally similar to nominal values. Power to detect an imprinted locus was substantially increased when analyzed with a model allowing for parent-of-origin effects, compared with analyses that assumed equal effects; for example, for an imprinted locus accounting for 30% of the phenotypic variance, the expected LOD score was 4.5 when parent-of-origin effects were incorporated into the analysis, compared with 3.1 when these effects were ignored. The ability to include parent-of-origin effects within linkage analysis of quantitative traits will facilitate genetic dissection of complex traits.     

Race and the inheritance of low birth weight

This paper uses intergenerational data from the Panel Study of Income Dynamics (PSID) to address the black-white difference in propensities toward low birth weight (LBW). We determine that socioeconomic conditions account for some variation in low birth weight across race. Further, while race differences in the risk of low birth weight cannot be explained entirely, we find that the inheritance of parental birth weight status dramatically reduces the black-white gap in low birth weight. Intergenerational legacies of poor infant health explain the largest share of racial disparities in filial birth weight. We then try to assess whether this intergenerational transmission of low birth weight is indeed genetic by using grandparent-fixed effects models to factor out, to a great extent, family socioeconomic circumstances. We find that even within this framework, both father's and mother's birth weight status have an important impact on filial outcomes. However, the degree of inheritance is weaker for African Americans than for other races. Finally, we theorize that the importance of paternal birth weight status implies a genetic association that does not work through the uterine environment but rather through the fetus itself.     

Genome-wide linkage analysis of inherited hydrocephalus in the H-Tx rat

Inherited hydrocephalus in humans has received very little attention, most probably because known occurrences are sporadic and systematic investigation is difficult. The H-Tx rat, one of a number of rodent strains with inherited hydrocephalus, has a complex inheritance with more than one postulated susceptibility gene and 40% penetrance. The aim of this study was to perform a genome-wide scan on backcross progeny derived from H-Tx and Fisher F344 rats, to identify genomic regions associated with hydrocephalus. Penetrance of hydrocephalus in (H-Tx × F344) F₁× H-Tx was 12.3%. All severely hydrocephalic progeny (n = 185) and a subset of normal progeny (n = 128) were screened with 110 simple sequence length polymorphisms (SSLPs) with 83% coverage of the genome. A significant susceptibility locus was found on chromosome (Chr) 11 (LOD = 3.1). Three loci with suggestive linkage were found on Chr 17 (LOD = 2.4), on Chr 9 (LOD = 1.94), and on Chr 19 (LOD = 1.91). For the loci on Chr 11 and 19, hydrocephalus was associated with the heterozygous genotype, while the other two were recessive. Although none of the four loci was essential for the hydrocephalic phenotype, the additive effects of two, three, or four loci increased the penetrance in a linear fashion. Altogether these four loci accounted for 13.5% of the total variance. It is concluded that hydrocephalus in the H-Tx rat is associated with two, possibly four genetic loci, but that there may be additional undefined genetic and environmental influences. Received: 26 April 2000 / Accepted: 24 August 2000     

Detection of parent-of-origin effects in nuclear families using haplotype analysis

Despite the potential pitfalls of stratification, population-based association studies nowadays are being conducted more often than family-based association studies. However, the mechanism of genomic imprinting has lately been implicated in the etiology of genetic complex diseases and can be detected using statistics only in family-based designs. Powerful tests for association and imprinting have been proposed previously for case-parent trios and single markers. Since the power of association studies can be improved if multiple affected children and haplotypes are considered, we extended the parental asymmetry test (PAT) for imprinting to a test that is suited for both general nuclear families and haplotypes, called HAP-PAT. Significance of the HAP-PAT is determined via a Monte-Carlo simulation procedure. In addition to the HAP-PAT, we modified a haplotype-based association test, proposed by us before, in such a way that either only paternal or maternal transmissions contribute to the test statistic. The approaches were implemented in FAMHAP and we evaluated their performance under a variety of disease models. We were able to demonstrate the usefulness of our haplotype-based approaches to detect parent-of-origin effects. Furthermore, we showed that also in the presence of imprinting it is more reasonable to consider all affected children of a nuclear family, than to randomly select one affected child from each family and to conduct a trio study using the selected individuals.     

Rapid multipoint linkage analysis via inheritance vectors in the Elston-Stewart algorithm

The calculation of multipoint likelihoods of pedigree data is crucial for extracting the full available information needed for both parametric and nonparametric linkage analysis. Recent mathematical advances in both the Elston-Stewart and Lander-Green algorithms for computing exact multipoint likelihoods of pedigree data have enabled researchers to analyze data sets containing more markers and more individuals both faster and more efficiently. This paper presents novel algorithms that further extend the computational boundary of the Elston-Stewart algorithm. They have been implemented into the software package VITESSE v. 2 and are shown to be several orders of magnitude faster than the original implementation of the Elston-Stewart algorithm in VITESSE v. 1 on a variety of real pedigree data. VITESSE v. 2 was faster by a factor ranging from 168 to over 1,700 on these data sets, thus making a qualitative difference in the analysis. The main algorithm is based on the faster computation of the conditional probability of a component nuclear family within the pedigree by summing over the joint genotypes of the children instead of the parents as done in the VITESSE v. 1. This change in summation allows the parent-child transmission part of the calculation to be not only computed for each parent separately, but also for each locus separately by using inheritance vectors as is done in the Lander-Green algorithm. Computing both of these separately can lead to substantial computational savings. The use of inheritance vectors in the nuclear family calculation represents a partial synthesis of the techniques of the Lander-Green algorithm into the Elston-Stewart algorithm. In addition, the technique of local set recoding is introduced to further reduce the complexity of the nuclear family computation. These new algorithms, however, are not universally faster on all types of pedigree data compared to the method implemented in VITESSE v. 1 of summing over the parents. Therefore, a hybrid algorithm is introduced which combines the strength of both summation methods by using a numerical heuristic to decide which of the two to use for a given nuclear family within the pedigree and is shown to be faster than either method on its own. Finally, this paper discusses various complexity issues regarding both the Elston-Stewart and Lander-Green algorithms and possible future directions of further synthesis.     

Genome-wide linkage analysis of blood pressure under locus heterogeneity

We describe a method for mapping quantitative trait loci that allows for locus heterogeneity. A genome-wide linkage analysis of blood pressure was performed using sib-pair data from the Framingham Heart Study. Evidence of linkage was found on four markers (GATA89G08, GATA23D06, GATA14E09, and 049xd2) at a significance level of 0.01. Two of them (GATA14E09 and 049xd2) seem to overlap with linkage signals reported previously, while the other two are not linked to any known signals.     

Linkage analysis of adult height with parent-of-origin effects in the Framingham Heart Study

Current linkage analysis methods for quantitative traits do not usually incorporate imprinting effects. Here, we carried out genome-wide linkage analysis for loci influencing adult height in the Framingham Heart Study subjects using variance components while allowing for imprinting effects. We used a sex-averaged map for the 22 autosomes, while chromosomes 6, 14, 18, and 19 were also analyzed using sex-specific maps. We compared results from these four analyses: 1) non-imprinted with sex-averaged maps, 2) imprinted with sex-averaged maps, 3) non-imprinted with sex-specific maps, and 4) imprinted with sex-specific maps. We found four regions on three chromosomes (14q32, 18p11-q21, 18q21-22, and 19q13) with LOD scores above 2.0, with a maximum LOD score of 3.12, allowing for imprinting and sex-specific maps, at D18S1364 on 18q21. While we obtained significant evidence of imprinting effects in both the 18p11-q21 and 19q13 regions when using sex-averaged maps, there were no significant differences between the imprinted and non-imprinted LOD scores when we used sex-specific maps. Our results illustrate the importance of allowing for gender-specific effects in linkage analyses, whether these are in the form of gender-specific recombination frequencies, or in the form of imprinting effects.     

Efficient multipoint linkage analysis through reduction of inheritance space

Computational constraints currently limit exact multipoint linkage analysis to pedigrees of moderate size. We introduce new algorithms that allow analysis of larger pedigrees by reducing the time and memory requirements of the computation. We use the observed pedigree genotypes to reduce the number of inheritance patterns that need to be considered. The algorithms are implemented in a new version (version 2.1) of the software package GENEHUNTER. Performance gains depend on marker heterozygosity and on the number of pedigree members available for genotyping, but typically are 10-1,000-fold, compared with the performance of the previous release (version 2.0). As a result, families with up to 30 bits of inheritance information have been analyzed, and further increases in family size are feasible. In addition to computation of linkage statistics and haplotype determination, GENEHUNTER can also perform single-locus and multilocus transmission/disequilibrium tests. We describe and implement a set of permutation tests that allow determination of empirical significance levels in the presence of linkage disequilibrium among marker loci.     

Estimation of linkage in trisomic inheritance

 Based on F₂ families derived from selfed F₁ trisomic plants we have developed a genetic model to estimate linkage relationships between pairs of loci located on the extra chromosome. Genotypic frequencies of each class expected in a trisomic F₂ family have been calculated and the maximum-likelihood equations for recombination-fraction estimation have been derived for a variety of genetic situations. Morton’s test of homogeneity was used to compare recombination fractions estimated between loci exhibiting trisomic segregation to those obtained in families where the same loci showed Mendelian segregation. This method has been applied to an analysis of morphological, isozyme and RAPD data from faba bean (Vicia faba L.). Received: 11 October 1996 / Accepted: 21 March 1997     

Genome-wide linkage analysis of Arabidopsis genes required for leaf development

In most crop species, primary productivity depends mainly on the leaf. However, the genes that contribute to the making of plant leaves remain largely unknown. With a view to identifying the genes involved in leaf development in Arabidopsis thaliana, we previously isolated EMS-induced mutants with abnormally shaped leaves and demonstrated that they fall into 94 complementation groups. We present here the map positions of 76 of these genes, which have been obtained using a high-throughput genetic mapping method, based on the simultaneous coamplification by PCR of 21 polymorphic microsatellites and the semiautomated fluorescent detection of the products. The map positions and F2 mapping populations obtained in this work will be instrumental in the positional cloning of these genes, which are essential for leaf development.     

Genome-wide linkage analysis of malaria infection intensity and mild disease

Although balancing selection with the sickle-cell trait and other red blood cell disorders has emphasized the interaction between malaria and human genetics, no systematic approach has so far been undertaken towards a comprehensive search for human genome variants influencing malaria. By screening 2,551 families in rural Ghana, West Africa, 108 nuclear families were identified who were exposed to hyperendemic malaria transmission and were homozygous wild-type for the established malaria resistance factors of hemoglobin (Hb)S, HbC, alpha⁺ thalassemia, and glucose-6-phosphate-dehydrogenase deficiency. Of these families, 392 siblings aged 0.5–11 y were characterized for malaria susceptibility by closely monitoring parasite counts, malaria fever episodes, and anemia over 8 mo. An autosome-wide linkage analysis based on 10,000 single-nucleotide polymorphisms was conducted in 68 selected families including 241 siblings forming 330 sib pairs. Several regions were identified which showed evidence for linkage to the parasitological and clinical phenotypes studied, among them a prominent signal on Chromosome 10p15 obtained with malaria fever episodes (asymptotic z score = 4.37, empirical p-value = 4.0 × 10⁻⁵, locus-specific heritability of 37.7%; 95% confidence interval, 15.7%–59.7%). The identification of genetic variants underlying the linkage signals may reveal as yet unrecognized pathways influencing human resistance to malaria.     

Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat.

Bread wheat and durum wheat were examined for linkage disequilibrium (LD) using microsatellite markers distributed across the genome. The allele database consisted of 189 bread wheat accessions genotyped at 370 loci and 93 durum wheat accessions genotyped at 245 loci. A significance level of p < 0.001 was set for all comparisons. The bread and durum wheat collections showed that 47.9% and 14.0% of all locus pairs were in LD, respectively. LD was more prevalent between loci on the same chromosome compared with loci on independent chromosomes and was highest between adjacent loci. Only a small fraction (bread wheat, 0.9%; durum wheat, 3.2%) of the locus pairs in LD showed R2 values > 0.2. The LD between adjacent locus pairs extended (R2 > 0.2) approximately 2-3 cM, on average, but some regions of the bread and durum wheat genomes showed high levels of LD (R2 = 0.7 and 1.0, respectively) extending 41.2 and 25.5 cM, respectively. The wheat collections were clustered by similarity into subpopulations using unlinked microsatellite data and the software Structure. Analysis within subpopulations showed 14- to 16-fold fewer locus pairs in LD, higher R2 values for those pairs in LD, and LD extending further along the chromosome. The data suggest that LD mapping of wheat can be performed with simple sequence repeats to a resolution of <5 cM.     

RFLP inheritance and linkage in walnut

Thirty-two low-copy-number genomic DNA clones from a walnut (Juglans sp.) Pst I genomic library were used to establish a molecular-marker linkage map for walnut. The clones were hybridized to restriction-endonuclease-digested DNA from parent walnut trees involved in an interspecific backcross of (J. hindsii x J. regia) x J. regia in order to identify parental polymorphism. Sixty-three backcross progeny were analyzed to determine the inheritance and linkage of 48 RFLP loci. Sixty-six percent of the walnut cloned sequences detected duplicated, but unlinked, loci. Twelve linkage groups were identified by 42 of the RFLP loci. A Poisson probability method for estimating genome size was utilized to calculate the approximate walnut genome length as 1660 cM and to estimate that 138 markers would be needed to cover 95% of the walnut genome within 20 cM of each marker.     

Combination of linkage evidence in complex inheritance

The central problem of complex inheritance is to combine evidence from data that typically differ in markers, phenotypes, ascertainment, and other factors, without sacrificing the reliability that lods have given to linkage mapping for major loci. Here we evaluate 5 possible solutions on 200 replicates simulated in Genetic Analysis Workshop 10. Two methods differ from less efficient ones by distinguishing the tails of a normal distribution. Maximum likelihood scores (currently implemented only for the BETA model) and the approach of Self and Liang perform about as well as pooling samples, which is not feasible with heterogeneous data. With moderately heterogeneous data the Self and Liang method appears to be more efficient than maximum likelihood scores. Although improvements are being made in sample design and statistical analysis, the problem of combining linkage evidence from multiple data sets appears to have been solved. Allelic association presents different problems not yet addressed.     

Genome-wide SNP-based linkage analysis for ADNSHL families identifies novel susceptibility loci with positive evidence for linkage

The linkage search for susceptibility loci using SNP markers in hereditary hearing loss has proven challenging due to genetic heterogeneity. We conducted a genome-wide linkage analysis using high-density SNP markers in two Korean families (families coded SD-J and SR-167) with autosomal dominant non-syndromic hearing loss (ADNSHL). Evidence was found of linkage at 8q24.13~q24.3 and 10p11.21~q22.2 (LOD 3.01) in the SD-J family. In the case of family SR-167, which had the most affected members, the parametric LOD score was low owing to the lack of power for linkage analysis. However, using non-parametric linkage analysis, it was possible to obtain significant evidence for linkage at 10q22.1~q23.31 (LOD 1.79; NPL 6.47, P<0.00001). There is an overlapping region with a significant LOD score between the SD-J and SR-167 families, which encompasses 4 cM at 10q22.1~22.2. Interestingly, the characteristics of hearing loss in both families were similar, and the haplotype within overlapping region was shared in the affected individuals of the two families. We performed direct sequencing of the candidate genes that are thought to be causing the condition, but no disease-causing mutations were identified.     

Quantitative trait linkage analysis of longitudinal change in body weight

One of the great strengths of the Framingham Heart Study data, provided for the Genetic Analysis Workshop 13, is the long-term survey of phenotypic data. We used this unique data to create new phenotypes representing the pattern of longitudinal change of the provided phenotypes, especially systolic blood pressure and body weight. We performed a linear regression of body weight and systolic blood pressure on age and took the slopes as new phenotypes for quantitative trait linkage analysis using the SOLAR package. There was no evidence for heritability of systolic blood pressure change. Heritability was estimated as 0.15 for adult life "body weight change", measured as the regression slope, and "body weight gain" (including only individuals with a positive regression slope), and as 0.22 for body weight "change up to 50" (regression slope of weight on age up to an age of 50). With multipoint analysis, two regions on the long arm of chromosome 8 showed the highest LOD scores of 1.6 at 152 cM for "body weight change" and of >1.9 around location 102 cM for "body weight gain" and "change up to 50". The latter two LOD scores almost reach the threshold for suggestive linkage. We conclude that the chromosome 8 region may harbor a gene acting on long-term body weight regulation, thereby contributing to the development of the metabolic syndrome.     

Quantitative trait loci with parent-of-origin effects in chicken

We investigated potential effects of parent-of-origin specific quantitative trait loci (QTL) in chicken. Two divergent egg-layer lines differing in egg quality were reciprocally crossed to produce 305 F2 hens. Searching the genome using models with uni-parental expression, we identified four genome-wide significant QTL with parent-of-origin effects and three highly suggestive QTL affecting age at first egg, egg weight, number of eggs, body weight, feed intake, and egg white quality. None of these QTL had been detected previously using Mendelian models. Two genome-wide significant and one highly suggestive QTL show exclusive paternal expression while the others show exclusive maternal expression. Each of the parent-of-origin specific QTL explained 3-5 % of the total phenotypic variance, with the effects ranging from 0.18 to 0.4 phenotypic SD in the F2. Using simulations and further detailed analyses, it was shown that departure from fixation in the founder lines, grand-maternal effects (i.e. mitochondrial or W-linked) and Z-linked QTL were unlikely to give rise to any spurious parent-of-origin effects. The present results suggest that QTL with parent-of-origin specific expression are a plausible explanation for some reciprocal effects in poultry and deserve more attention. An intriguing hypothesis is whether these effects could be the result of genomic imprinting, which is often assumed to be unique to eutherian mammals.