Model-based linkage analysis with imprinting for quantitative traits: ignoring imprinting effects can severely jeopardize detection of linkage

Genes with imprinting (parent-of-origin) effects express differently when inheriting from the mother or from the father. Some genes for development and behavior in mammals are known to be imprinted. We developed parametric linkage analysis that accounts for imprinting effects for continuous traits, implementing it in MORGAN. To study misspecification of imprinting on linkage analysis, we simulated eight markers over a 35 cM region with phenotypes where imprinting contributes 0, 25, 50, and 75% of the variance of a quantitative trait locus (QTL) effect and analyzed them under all four models. Multipoint lod scores were computed and maximized over the same 35 cM region. Our most important finding is the dramatic lod score improvement under the correct imprinting model over the no-imprinting model. For data with minor QTL allele frequency 0.05, the correct model provided the highest lod scores with maximum expected lod scores over 4 in all settings. Ignoring imprinting provided the lowest lod scores with maximum expected lod scores between -9.9 and 2.4. In the extreme scenario, cases with max lod > or =3 from the correct imprinting model and max lod < or =-2 from the no-imprinting model occurred in 86% of replications. Models with misspecified imprinting produced lod scores intermediate between those with correct imprinting and with no imprinting. The effects of model misspecification were less pronounced for singlepoint analysis. Our multipoint results illustrate that ignoring true imprinting severely impairs detection of linkage and erroneously excludes genomic regions (with max lod <-2), whereas accounting for it can substantially improve linkage detection.     

Evaluation of replication studies, combined data analysis, and analytical methods in complex diseases

Due to genetic heterogeneity, phenocopies, incomplete penetrance, misdiagnosis, and unknown mode of inheritance, linkage studies of most complex diseases are unlikely to provide conclusive findings with unambiguously high lod scores. Typically, several marginally significant lod scores or elevated lod scores are observed in a genome-wide screen. However, it is usually difficult to differentiate these findings from false positives (type I errors). Two approaches are commonly used to guard against false positives: replication studies in independent samples and combined data analysis. In the current paper, we evaluated these two common approaches using simulated data where data from multiple groups were available and locations of disease genes were known. We found replication studies and combined data analysis performed similarly in terms of their ability to identify true and false positive linkages. Both approaches confirmed two true linkages and did not confirm any false positive linkages. The results also indicated that it is not appropriate to apply the criteria proposed for confirming significant evidence for linkage to confirm regions with only suggestive evidence for linkage. The current results support previous findings that parametric analysis using an incorrect genetic model can still identify a true linkage.     

数据格式化技术在护理电子文书程序开发中的应用

目的：根据用户需求,实现护理电子文书程序的文本编辑与格式化打印功能。方法：在用户编辑时,通过格式化程序实现对编辑字段用户录入的内容格式化处理并存入数据库,打印时,通过对数据库保存的数据进行提取并调用格式化代码将数据填充至目标表格指定区域实现输出格式化。结果：该数据格式化技术使护理电子文书程序具有高效的编辑与智能排版输出的功能。结论：数据格式化技术的应用不依赖第三方软件的控件,具有用户易操作、程序集成度高、执行速度快、消耗系统资源少、代码可复用等优点,值得推广应用。     

Outpatient consultations from a family practice residency program: nine years' experience

Previous reports of consultation rates from family practice physicians have included small sample sizes and have suggested higher rates in residency training programs. This report summarizes 9 years of data involving 161 family practice physicians in a residency training program and shows an overall rate of 1.4 percent for outpatient consultations. Otolaryngology, orthopedics, obstetrics/gynecology, and general surgery were the most frequent disciplines consulted. These data are helpful in designing health care systems that include family practice residency programs.     

Genetic analysis workshop III: Use of multidimensional scaling in chromosome mapping

Two-point methods were used throughout. Male and female lod scores were calculated using LIPED. Edwards' programs, ZLODS and OBM, were used for joint analysis of the lod scores. ZLODS estimates recombination fractions. OBM calculates the likelihood and estimates the map distances for a given ordering of loci. Since OBM will only analyze a specified ordering, multidimensional scaling was used as a general method for establishing linkage groups and likely orderings within them.     

Exploring linkage of chromosome 18 markers and bipolar disease

The linkage reports of bipolar disease and chromosome 18 markers are controversial. We used the GAW10 data sets to further explore several observations: 1) a possible parent-of-origin effect with only “paternal” pedigrees showing linkage; 2) the preponderance of women affected with bipolar disease, and 3) the possible existence of phenocopies in the bipolar data sets. We performed linkage analysis allowing for independent male/female recombination fractions. Our hypothesis was that if there is linkage only in “paternal” pedigrees, then the lod score would maximize at low male and high female recombination fractions. We did not find such an effect in the combined data set. There was no consistent effect on the difference of male and female recombination fractions, suggesting that an effect is not detectable in this data set with this method. In addition, there is interesting evidence for a recessively inherited, highly penetrant gene in a subset of families. Allowing for higher penetrances for bipolar disease in women than in men had no effect on the lod scores. There was also not much difference in the lod scores calculated under the assumption of a phenocopy rate versus no phenocopies. From simulation studies, we would have expected some effect if there were linkage and phenocopies were present. © 1997 Wiley-Liss, Inc.     

Linkage between the APOB gene and serum apoB levels in a large pedigree from the Bogalusa heart study

Maximum likelihood linkage analyses were performed to test for linkage between serum apoB levels and several candidate gene markers including apolipoprotein B, lipoprotein lipase, hepatic lipase, cholesterol ester transfer protein, and apolipoprotein AI in a large pedigree. Parameters of general Mendelian inheritance derived from maximum likelihood segregation analysis of the serum apoB levels were used in the linkage analysis. The highest two-point lod score between the quantitative trait and a marker defined by a single restriction digest was 1.86 at recombination fraction (θ) = 0. This was observed for linkage between serum apoB levels and the presence or absence of a PvuII digestion site in the apoB gene. Linkage between serum apoB levels and polymorphisms of the apoB gene defined by the two restriction digests EcoR1 and PvuII was supported by a lod score of 3.30, while inclusion of VNTR typings led to a lod score of 2.33. None of the other candidate genes gave positive evidence of linkage. © 1994 Wiley-Liss, Inc.

1 This article is a US government work and, as such, is in the public domain in the United States of America.

     

An evaluation of affected-sib-pair methods and transmission/disequilibrium tests for detecting genes underlying a complex trait

For the analysis of complex traits, it is of interest to compare a few nonparametric methods such as affected-sib-pair (ASP) analyses and transmission/disequilibrium tests (TDT). The affected-sib-pair approaches we have examined here are ASP and ALL-SP which are implemented in SIBPAIR program. We also applied the BETA program which has not so far been extensively compared with other methods. The study indicates that the ASP program and the BETA program give concordant results although BETA tends to give higher lod scores. However, when all sibs were included in the analysis (ALL-SP), linkage signals became weaker, compared with ASP and BETA. The TDT detected 66 positive signals at a significance level of 0.05 and identified a true locus. Overall, our results suggest that affected-sib-pair analysis has reasonable power (p < 0.0001) to detect linkage given the disease model and the family structure specified in the GAW11 Problem 2 data set.     

Distribution of lod Scores in Oligogenic Linkage Analysis

In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the i^th quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oli‐gogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood‐ratio statistic. © 2001 Wiley‐Liss, Inc.     

The effect of misspecifying allele frequencies in incompletely typed families

To examine the effect of a misspecified marker allele frequency, the segregation of a marker unlinked to Alzheimer's disease was simulated for the typed members of the GAW8-FAD4 pedigree. Lod scores were calculated for different assumed marker allele frequencies. The results show that a misspecification of marker frequency can lead to spuriously high lod scores. The affecteds-only method for linkage analysis is even more sensitive in regard to marker frequency misspecification. Therefore, we recommend estimation of marker allele frequencies from the actual family data. The simple estimator we considered in this paper seems to be sufficient. © 1993 Wiley-Liss, Inc.     

Adaptations of Linkage and Association Methods for the Study of Asthma,A Complex Trait

Early studies that found significant linkage between markers on 5q and asthma and IgE have not been reproduced. In an attempt to improve the power of these studies we performed a variance components linkage analysis and transmission‐disequilibrium tests (TDT) with haplotypes using markers on 5q, using the Southampton and Perth data sets supplied by GAW. The linkage analysis with covariates revealed a maximum lod of 1.57 in the Perth families. The addition of age and RAST significantly improved the fit of the null models but did not improve the lod scores. The TDT tests showed a marginally significant association with D5S393 and D5S399 and with three markers together (IL9, IL4, D5S393). We conclude that further studies are needed to delineate the environmental contribution to this disease so that the genetic factors can be more easily identified. In addition, haplotype analysis may help to identify specific genetic effects. © 2001 Wiley‐Liss, Inc.     

Comparison of evidence supporting a chromosome 6 alcoholism gene

A whole genome scan has been conducted on 105 families ascertained for probands with a diagnosis of alcoholism by the Collaborative Study on the Genetics of Alcoholism (COGA). To identify chromosomal regions likely to contain genes contributing to the development of this disorder, data from 296 highly polymorphic markers have been analyzed using the MAPMAKER/SIBS [Kruglyak and Lander, 1995] and GENEHUNTER-PLUS [Kruglyak et al., 1996; Kong and Cox, 1997] multipoint linkage programs. Chromosome 6 exhibited lod scores greater than 3.0 and was further tested by two-point linkage analyses at each marker along the chromosome to assess the consistency of results from these allele sharing linkage programs. Two-point linkage was assessed with MAPMAKER/SIBS, GENEHUNTER-PLUS and the SIBPAL subprogram of the SAGE package of genetic epidemiology programs [Elston, 1997].     

Distribution and magnitude of type I error of model-based multipoint lod scores: implications for multipoint mod scores

The multipoint lod score and mod score methods have been advocated for their superior power in detecting linkage. However, little has been done to determine the distribution of multipoint lod scores or to examine the properties of mod scores. In this paper we study the distribution of multipoint lod scores both analytically and by simulation. We also study by simulation the distribution of maximum multipoint lod scores when maximized over different penetrance models. The multipoint lod score is approximately normally distributed with mean and variance that depend on marker informativity, marker density, specified genetic model, number of pedigrees, pedigree structure, and pattern of affection status. When the multipoint lod scores are maximized over a set of assumed penetrances models, an excess of false positive indications of linkage appear under dominant analysis models with low penetrances and under recessive analysis models with high penetrances. Therefore, caution should be taken in interpreting results when employing multipoint lod score and mod score approaches, in particular when inferring the level of linkage significance and the mode of inheritance of a trait.     

Nonparametric linkage analysis using person-specific covariates

Linkage analysis provides an important tool for mapping genes for complex disease. However its usefulness has been limited by inadequate marker density, inadequate sample sizes and the possibility that different genes account for different subtypes of the disease (phenotypic heterogeneity). The first two limitations can be addressed by high-density single nucleotide polymorphism (SNP) genotyping and the pooling of large sets of multiple-case families. Phenotypic heterogeneity can be addressed by analyses that weigh the contributions of affected family members according to characteristics of their disease phenotypes. Here we introduce a method for including such person-specific weights in nonparametric linkage analysis. We show with simulations that such weighting can provide stronger linkage signals when a causal polymorphism affects some manifestations of the disease more than others. We applied the method to prostate cancer linkage data in a region on chromosome 19p, and obtained higher lod scores by assigning weights of one to men with early-onset aggressive cancers, weights of zero to those with late-onset nonaggressive cancers, and intermediate weights to all other affected men. We have developed a modified version of GENEHUNTER that allows inclusion of person-specific weights in the nonparametric analyses. This program is freely available at http://med.stanford.edu/epidemiology/statisticalSoftware/weightedKAC.     

Somatic allele loss in genetic linkage analysis of cancer

The ability to detect or reject genetic linkage in studies of human cancer is often diminished because multiple affected relatives in a pedigree are unavailable for analysis. The observation of somatic allele loss in tumors can provide knowledge about gametic phase. Therefore, consideration of tumor genotype data could be used to obtain knowledge about gametic phase ordinarily gained from a larger sample of individuals in cancer families. The objective of the present study is to describe a method for improving the power to detect or reject genetic linkage by using knowledge about somatic genetic changes in tumor tissue. A modification to the lod score method of linkage analysis is proposed in which knowledge of gametic phase in the linkage likelihood is inferred from observations of loss of constitutional heterozygosity (LoH) in tumor tissue. This methodology was evaluated using a double backcross nuclear family with a pair of offspring. The expected lod score improved substantially when tumor genotype data were included in the analysis. For example, when the haplotype remaining in tumor tissue was identical to the inherited haplotype in constitutional tissue 99% of the time, linkage analyses without tumor genotype data would require a 2–5 times larger sample of offspring pairs to conclude linkage with an expected lod score value of 3 or greater, compared to analyses incorporating tumor genotype data. These results suggest that consideration of tumor genotype data using the proposed method can substantially improve the power of linkage analyses in cancer families. © 1994 Wiley-Liss, Inc.     

Modeling the phenotype in parametric linkage analysis of bipolar disorder

The definition of phenotype is a major problem in genetic studies of psychiatric disorders. Most linkage studies in bipolar disorder have defined the phenotype as a dichotomous trait and have usually employed different hierarchical classifications in order to overcome uncertainty resulting from phenotypic variability. In this study we explored the advantages of maximizing the evidence for linkage over different phenotypic definitions when conducting parametric linkage analysis of a complex trait. The GAW10 Problem 1 was used, focusing on chromosome 18 data sets. Three major phenotypic models were analyzed: quasi-quantitative, liability-based and affection-status models. Overall, no single phenotypic model performed consistently better than the others (i.e., lod scores greater than 1.0). Each model yielded higher lod scores than the others in particular instances, suggesting that it might be useful in exploratory data analysis, where the phenotype is variable, to maximize evidence for linkage over different phenotypic models. © 1997 Wiley-Liss, Inc.     

Linkage analysis of 150 high-risk prostate cancer families at 1q24-25

Confirmation of linkage and estimation of the proportion of families who are linked in large independent datasets is essential to understanding the significance of cancer susceptibility genes. We report here on an analysis of 150 high-risk prostate cancer families (2,176 individuals) for potential linkage to the HPC1 prostate cancer susceptibility locus at 1q24-25. This dataset includes 640 affected men with an average age at prostate cancer diagnosis of 66. 8 years (range, 39-94), representing the largest collection of high-risk families analyzed for linkage in this region to date. Linkage to multiple 1q24-25 markers was strongly rejected for the sample as a whole (lod scores at theta = 0 ranged from -30.83 to -18. 42). Assuming heterogeneity, the estimated proportion of families linked (alpha) at HPC1 in the entire dataset was 2.6%, using multipoint analysis. Because locus heterogeneity may lead to false rejection of linkage, data were stratified based on homogeneous subsets. When restricted to 21 Caucasian families with five or more affected family members and mean age at diagnosis < = 65 years, the lod scores at theta = 0 remained less than -4.0. These results indicate that the overall portion of hereditary prostate cancer families whose disease is due to inherited variation in HPC1 may be less than originally estimated.     

Family density of alcoholism and linkage information in the analysis of the COGA data

In this study of GAW11 Problem 1, we analyzed the genome scan data in families weighted according to the density of alcoholism among the probands' siblings. We hypothesized that certain disease-predisposing alleles may be common in the general population, rendering high-density sibships less informative for linkage. Three types of families were found in the data, with the prevalence of alcoholism of 1.0, 0.78, and 0.24 in the probands' sibships. The linkage results showed several peak lod scores on chromosomes 1, 2, 4, 8, 11, 19, and 21, the majority of which originated in only one or two types of families. However, for almost all markers, the maximum lod scores observed without the weights were equal to or exceeded the values obtained for any single type of family. These results indicate that although the stratification of families may be theoretically justified, in practice the best strategy is to use all available information.     

Computationally efficient multipoint linkage analysis on extended pedigrees for trait models with two contributing major Loci

We have developed a computationally efficient method for multipoint linkage analysis on extended pedigrees for trait models having a two-locus quantitative trait loci (QTL) effect. The method has been implemented in the program, hg_lod, which uses the Markov chain Monte Carlo (MCMC) method to sample realizations of descent patterns conditional on marker data, then calculates the trait likelihood for each realization by efficient exact computation. Given its computational efficiency, hg_lod can handle data on large pedigrees with a lot of unobserved individuals, and can compute accurate estimates of logarithm of odds (lod) scores at a much larger number of hypothesized locations than can any existing method. We have compared hg_lod to lm_twoqtl, the first publically available linkage program for trait models with two major loci, using simulated data. Results show that our method is orders of magnitude faster while the accuracy of QTL localization is retained. The efficiency of our method also facilitates analyses with multiple trait models, for example, sensitivity analysis. Additionally, since the MCMC sampling conditions only on the marker data, there is no need to resample the descent patterns to compute likelihoods under alternative trait models. This achieves additional computational efficiency.     

Bias in multipoint linkage analysis arising from map misspecification

Multipoint linkage analysis methods are often used in human genetic studies. Although multipoint methods increase power for a linkage analysis and will become essential if use of diallelic markers becomes widespread, the methods in use assume an accurate meiotic marker map. Unfortunately, uncertainties in estimates of between-marker meiotic distances are large. Also, sex-averaged maps are generally used, but recombination rates differ in males and females. Both these types of map misspecification can lead to lod score bias, but such bias has not previously been systematically quantified. We examine multipoint lod score bias arising from these map misspecifications, in both the presence and absence of actual linkage. We define bias as the expected difference between the lod score computed under the misspecified map and that computed under the true map. With actual linkage, any map misspecification causes negative bias in lod scores, resulting in loss of power to detect linkage. In most cases, bias is modest, only reaching clearly detectable levels when both types of misspecification are substantial. In the absence of linkage, map misspecification can cause positive or negative bias: falsely assuming a 1:1 female:male ratio always causes positive bias; using too large a distance gives a positive bias; using too small a distance gives a negative bias. This bias can inflate the false-positive rate, especially when the sample size is modest. We conclude that although current sex-averaged maps are suitable for a first-pass multipoint screen, the potential for bias from map misspecification should be evaluated in following up results from such an analysis.