Monte Carlo estimation of variance component models for large complex pedigrees.

Variance component models are widely used in animal and plant breeding. In human genetics, they can be used to identify, among other traits associated with the definition of disease, those that have a significant genetic component in their aetiology. In addition, they can be used in genetic counselling. Most of the methods currently proposed for estimating variance component models often involve repeated inversion of large matrices, resulting in intensive computations, large storage requirements, and numerical instability. Consequently, these methods are restricted to data on nuclear families, to small pedigrees, or to designed pedigrees of simple form. In this paper, the authors propose a method for estimating variance component models for large complex pedigrees using jointly the EM algorithm and the Gibbs sampler. The method can handle variance component models with multiple variance components, without the need for repeated inversion of large matrices even on large complex pedigrees. The method is conceptually simple, numerically stable, and easy to implement.     

The genetics of systemic lupus erythematosus stratified by renal disease: linkage at 10q22.3 (SLEN1), 2q34-35 (SLEN2), and 11p15.6 (SLEN3)

Renal disease occurs in 40-75% of systemic lupus erythematosus (SLE) patients and significantly contributes to morbidity and mortality. We used two pedigree stratification strategies to explore the impact of the ACR renal criterion for SLE classification upon genetic linkage with SLE. In both we used SLE as the phenotype. First, we evaluated genome scan data from >300 microsatellite markers in the 75 pedigrees that had at least one SLE affected with the SLE renal criterion. A maximum-likelihood parametric model approach produced a maximum screening LOD score of 3.16 at 10q22.3 in the European-American (EA) pedigrees. The African-American (AA) pedigrees obtained a maximum screening LOD score of 2.58 at 11p15.6. A multipoint sib-pair regression analysis produced P = 0.0000008 in EA at 10q22.3 (SLEN1) and P = 0.000001 in AA at 2q34-35 (SLEN2). A second stratification strategy explored the renal criterion in 35 pedigrees with two or more SLE patients with renal disease and produced a LOD score of 3.34 at 11p15.6 in AA (SLEN3). Sib-pair analysis in these 35 pedigrees revealed P = 0.00003 at 4q13.1 in EA, P = 0.00003 at 11p13 and 0.00007 at 3q23 in AA. Thus, multiple genetic linkages are related to the renal criterion in SLE. Of the significant genetic linkages with SLE described herein, those at 10q22.3 in the EA pedigrees (SLEN1) and at 2q34-35 in the AA pedigrees (SLEN2) have not been previously described.     

Problem of sex ratio in cases of type I syndactyly.

Fifty pedigrees of type I syndactyly were analysed for sex ratio and segreation pattern. Thirty-four of the pedigrees were from the published reports; 16 were collected in the State of Utah. Pedigrees with affected individuals showing webbing between the second and third toes are characterized by a sex ratio of affected individuals favouring males and a highly significant excess of affected sons of heterozygous fathers. A similar distorted segregation pattern is present in those pedigrees when the webbing involves the second and third toes and/or the third and fourth fingers, but not in those pedigrees when the webbing involves other digits. The reason for the distorted segregation pattern is unknown. Hypothesis include abnormal chromosome segregation and gametic selection.     

Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering

Whole genome sequence data for small pedigrees has been shown to provide sufficient information to resolve detailed haplotypes in small pedigrees. Using such information, recombinations can be mapped onto chromosomes, compared with the segregation of a disease of interest and used to filter genome sequence variants. We now show that relatively inexpensive SNP array data from small pedigrees can be used in a similar manner to provide a means of identifying regions of interest in exome sequencing projects. We demonstrate that in those situations where one can assume complete penetrance and parental DNA is available, SNP recombination mapping using Boolean logic identifies chromosomal regions identical to those detected by multipoint linkage using microsatellites but with much less computation. We further show that this approach is successful because the probability of a double crossover between informative SNP loci is negligible. Our observations provide a rationale for using SNP arrays and recombination mapping as a rapid and cost-effective means of incorporating chromosome segregation information into exome sequencing projects intended for disease-gene identification.     

Confirmation of linkage of Sj?gren-Larsson syndrome to chromosome 17 in families of different ethnic origins.

Linkage analysis in two consanguineous pedigrees of Pakistani and English origin and one further Indian family in which affected subjects have Sjögren-Larsson syndrome (SLS) showed linkage to chromosome 17. Linkage of SLS to D17S783 and D17S805 has been reported in Swedish pedigrees, but since those data were generated from a single ethnic group originating from a common ancestor, there remained the question of whether this disease is genetically heterogeneous. This report confirms the linkage in non-Swedish pedigrees and, therefore, provides evidence to support a single locus for SLS.     

The unique characteristics of Thai Leber hereditary optic neuropathy: analysis of 30 G11778A pedigrees

Leber hereditary optic neuropathy (LHON) is characterized by acute or subacute bilateral visual loss, and affects mostly young males. The most common mitochondrial DNA mutation responsible for LHON worldwide is G11778A. Despite different genetic backgrounds, which are believed to influence the disease expression, most features of LHON are quite common in different populations. However, there seem to be a few ethnic-specific differences. Analyses of our 30 G11778A LHON pedigrees in Thailand showed some characteristics different from those of Caucasians and Japanese. In particular, our pedigrees showed a lower male to female ratio of affected persons (2.6:1) and much higher prevalence of G11778A blood heteroplasmy (37% of the pedigrees contained at least one heteroplasmic G11778A individual). Heteroplasmicity seemed to influence disease manifestation in our patients but did not appear to alter the onset of the disease. The estimated overall penetrance of our G11778A LHON population was 37% for males and 13% for females. When each of our large pedigrees were considered separately, disease penetration varied from 9 to 45% between the pedigrees, and also varied between different branches of the same large pedigree. Survival analysis showed that the secondary LHON mutations G3316A and C3497T had a synergistic deleterious effect with the G11778A mutation, accelerating the onset of the disease in our patients.     

Discriminating among single locus models using small pedigrees

Simulated small pedigrees (2 parents, 4 offspring) were used to illustrate the applications and limitations of a “model choice” approach designed to detect genetic heterogeneity in familial diseases. While it is possible to identify groups of pedigrees which have different genetic causes for quantitative phenotypic trait(s), theoretical limitations on discriminating between 4 single locus models exist for certain pedigree structures. These limitations originate from the overlapping phenotypic predictions of the various genetic models. Such limitations must be carefully considered in the design of genetic studies. Studies aimed at detecting genetic heterogeneity in familial diseases should limit the different genetic models being considered and tailor the sampling strategy to avoid collecting pedigrees which are non-informative for certain comparisons.     

2型糖尿病家系与尾加压素2基因多态性

目的探讨我国常州地区汉族家系2型糖尿病与尾加压素2(urotensinⅡ,UT-Ⅱ)基因rs228648多态性位点的关系。方法采用家系内外对照的病例对照研究,并设置无家族史的普通病例组,应用聚合酶链反应-限制性片段长度多态性技术,对rs228648(G/A)多态性进行基因分型。结果家系中携带AG和AA基因型者患病风险分别为GG型的1.98(95%可信区间=1.19～3.29)和2.46(95%可信区间=1.39～4.34)倍,家系病例组A等位基因频率高于内对照组及普通病例组(P=0.01)。内对照组A等位基因频率高于外对照组(P=0.001)。内对照组携带AG基因型者的胰岛素抵抗指数、胰岛素敏感指数以及胰岛初期分泌功能指数均高于GG基因型者(P<0.05)。结论rs228648多态性位点变异可能是2型糖尿病的危险因素之一,家系人群该基因变异与其胰岛功能间存在关联。     

An integrated microcomputer system to maintain a genetic register for Huntington disease

A microcomputer program has been designed to maintain a large data base for Huntington disease. This program facilitates such data manipulation as adding, altering, retrieving, deleting, and printing pedigrees. The program is self-contained and has a risk-calculating routine built in which automatically provides both the Mendelian and age-modified risks. This package is capable of printing the pedigrees on a simple printer or, alternatively, creates an output-file which can be used with a dedicated plotting program for drawing the pedigrees and their data on a plotter. The program has a routine which can provide a series of statistical data from the register including age-of-onset, diagnosis, death, and other useful information.     

Ophthalmic genetics: a genealogical guide to sources in England and Wales.

Large pedigrees are fundamental to seeking new genes; they can be constructed on the basis of a family history but can frequently be enlarged considerably from public records. Genealogical sources in England and Wales consist of public records such as civil registration of births, marriages, and deaths, census returns, wills, and church records. Details are given as to their use and where they are to be found. In addition, examples are given of how archival material and pathology reports may be used to compile extensive pedigrees which can span 10 generations.     

Problems in detecting etiological heterogeneity in genetic disease illustrated with retinitis pigmentosa

Simulated data were generated under four etiologic mechanisms for each of 20 different pedigree structures drawn from a study of families ascertained through a proband with retinitis pigmentosa. These simulated data were then used to identify subgroups of pedigrees which best supported each of three genetic mechanisms (autosomal dominant, autosomal recessive, X-linked recessive with 10% penetrance of disease in heterozygous females) and a non-genetic, sporadic mechanism. Results of these studies show that pedigrees identified as supporting one genetic model in a 'model choice' approach tend to be etiologically homogeneous, but are not truly representative of all the phenotypic combinations possible under that mechanism. The problem of etiologic heterogeneity is most acute when dealing with pedigrees less than size 10. Pedigrees lumped under a non-genetic, sporadic mechanism are extremely heterogeneous and studies of the natural history of diseases where both genetic and non-genetic mechanisms may be operating (such as with retinitis pigmentosa) should avoid using this group of largely simplex pedigrees.     

Utilising Family‐Based Designs for Detecting Rare Variant Disease Associations

Rare genetic variants are thought to be important components in the causality of many diseases but discovering these associations is challenging. We demonstrate how best to use family‐based designs to improve the power to detect rare variant disease associations. We show that using genetic data from enriched families (those pedigrees with greater than one affected member) increases the power and sensitivity of existing case–control rare variant tests. However, we show that transmission‐ (or within‐family‐) based tests do not benefit from this enrichment. This means that, in studies where a limited amount of genotyping is available, choosing a single case from each of many pedigrees has greater power than selecting multiple cases from fewer pedigrees. Finally, we show how a pseudo‐case–control design allows a greater range of statistical tests to be applied to family data.     

偏执型与未分化型精神分裂症家系两个靶染色体易感位点的连锁分析

目的 探讨中国人群中精神分裂症亚型与1号染色体长臂1q21-25和6号染色体短臂6p21-25易感基因位点的相关性.方法 在染色体1q21-25区域中选择5个微卫星标记和6p21-25区域中选择8个微卫星标记对36个来自中国河南省的精神分裂症家系(19个偏执型和17个未分化型)中的242个个体进行基因分型及参数和非参数连锁分析.结果 36个精神分裂症家系的1号染色体参数分析时,在显性遗传模式下,D1S484得到多点异质性对数优势记分法(heterogeneity Log of odds score method,HLOD)值为1.33 (α=0.38).非参数分析时,在D1S484得到多点非参数连锁(nonparametric linkage,NPL)值为1.89(P=0.0188);D1S2878单点NPL值为2.11(P=0.0111),多点NPL值为2.41(P=0.0053);D1S196多点NPL值为1.59(P=0.0383).提示以上3个位点存在连锁.在17个未分化型家系中,D1S484多点NPL值为1.60(P=0.0367);D1S2878单点 NPL值为1.95(P=0.0145),多点NPL值为2.39(P=0.0041); D1S196多点NPL值为 1.74(P=0.0255).这与以上36个家系提示连锁的位点相同.在19个偏执型家系中,5个微卫星标记位点均未提示连锁.36个精神分裂症家系的6号染色体分析发现,除19个偏执型精神分裂症家系参数连锁分析在隐性模式下D6S289位点单点HLOD值为1.26(α=0.40),多点HLOD值为1.12(α=0.38)和非参数连锁分析在D6S289位点单点NPL值为1.52(P=0.0402),多点NPL值为1.92(P=0.0206)之外,36个精神分裂症家系总体分析和其中17个未分化型家系分型分析的结果显示8个微卫星标记位点均未提示有连锁.结论 在染色体1q23.3 和1q24.2区域可能存在与中国河南省未分化型精神分裂症相关的易感基因;在6p23区域可能存在与偏执型精神分裂症相关的易感基因.

Abstract：

Objective To investigate the relationship of susceptibility loci in chromosomes 1q21-25 and 6p21-25 and schizophrenia subtypes in Chinese population. Methods A genomic scan and parametric and non-parametric analyses were performed on 242 individuals from 36 schizophrenia pedigrees, including 19 paranoid schizophrenia and 17 undifferentiated schizophrenia pedigrees, from Henan province of China using 5 microsatellite markers in the chromosome region 1q21-25 and 8 microsatellite markers in the chromosome region 6p21-25, which were the candidates of previous studies. All affected subjects were diagnosed and typed according to the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revised (DSM-Ⅳ-TR; American Psychiatric Association, 2000). All subjects signed informed consent. Results In chromosome 1, parametric analysis under the dominant inheritance mode of all 36 pedigrees showed that the maximum multi-point heterogeneity Log of odds score method (HLOD) score was 1.33 (α=0.38). The non-parametric analysis and the single point and multi-point nonparametric linkage (NPL) scores suggested linkage at D1S484, D1S2878, and D1S196. In the 19 paranoid schizophrenias pedigrees, linkage was not observed for any of the 5 markers. In the 17 undifferentiated schizophrenia pedigrees, the multi-point NPL score was 1.60 (P=0.0367) at D1S484. The single point NPL score was 1.95 (P=0.0145) and the multi-point NPL score was 2.39 (P=0.0041) at D1S2878. Additionally, the multi-point NPL score was 1.74 (P=0.0255) at D1S196. These same three loci showed suggestive linkage during the integrative analysis of all 36 pedigrees. In chromosome 6, parametric linkage analysis under the dominant and recessive inheritance and the non-parametric linkage analysis of all 36 pedigrees and the 17 undifferentiated schizophrenia pedigrees, linkage was not observed for any of the 8 markers. In the 19 paranoid schizophrenias pedigrees, parametric analysis showed that under recessive inheritance mode the maximum single-point HLOD score was 1.26 (α=0.40) and the multi-point HLOD was 1.12 (α=0.38) at D6S289 in the chromosome 6p23. In nonparametric analysis, the single-point NPL score was 1.52 (P=0.0402) and the multi-point NPL score was 1.92 (P=0.0206) at D6S289. Conclusion Susceptibility genes correlated with undifferentiated schizophrenia pedigrees from D1S484, D1S2878, D1S196 loci, and those correlated with paranoid schizophrenia pedigrees from D6S289 locus are likely present in chromosome regions 1q23.3 and 1q24.2, and chromosome region 6p23, respectively.     

Ancestral inference: I. The problem and the method

A method for inferring the ancestral genotypes for the founders of a population is developed. This method uses the algorithms for the computation of probabilities on pedigrees of arbitrary complexity, developed by Cannings et at. (1978) and implemented by Thompson (19773). When characteristics are simply determined by underlying genotypes the inference problem is simplified, and larger and more complex pedigrees may therefore be analysed. The problem of estimating the allele frequencies to be used in computing prior genotype probabilities for those founders on whom a likelihood function is not required is discussed. The same method allows us to compute extinction probabilities for any combination of original founder genes; these probabilities are interesting parameters of pedigree structure, which, since they relate to the actual genes present in a population, help to provide a clearer understanding of observed distributions of autosomal traits. I am grateful to Dr A. W. F. Edwards and T. Beaty for comments on an earlier draft.     

Age of onset in familial early onset Alzheimer's disease correlates with genetic aetiology

Age of onset is the most robust clinical feature demarcating aetiologic subtypes of familial Alzheimer's disease. It has previously been noted that early onset disease (arbitarily below the age of 65 years) conforms to an autosomal dominant pattern of transmission. Late onset disease is generally thought to have a more complex aetiology. We present data here suggesting that early onset disease can be subdivided by genetic aetiology with which age of onset correlates. In general, those pedigrees showing linkage to the chromosome 14 locus have a mean age of onset in the forties whereas those pedigrees with an APP mutation have an age of onset in the fifties. © 1993 Wiley-Liss, Inc.     

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 (? = 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.     

Genetic Covariation Underlying Reading,Language and Related Measures in a Sample Selected for Specific Language Impairment

Specific language impairment is a developmental language disorder characterized by failure to develop language normally in the absence of a specific cause. Previous twin studies have documented the heritability of reading and language measures as well as the genetic correlation between those measures. This paper presents results from an alternative to the classical twin designs by estimating heritability from extended pedigrees. These pedigrees were previously studied as part of series of molecular genetic studies of specific language impairment where the strongest genetic findings were with reading phenotypes rather than language despite selecting pedigrees based on language impairments. To explore the relationship between reading and language in these pedigrees, variance components estimates of heritability of reading and language measures were conducted showing general agreement with the twin literature, as were genetics correlations between reading and language. Phonological short-term memory, phonological awareness and auditory processing were evaluated as candidate mediators of the reading-language genetic correlations. Only phonological awareness showed significant genetic correlations with all reading measures and several language measures while phonological short-term memory and auditory processing did not.     

The AD1 locus in familial Alzheimer disease

The AD1 locus on chromosome 21 (MIM 104300) maps to the β-amyloid precursor locus (APP) at approximately 27·7 Mb from pter (10·9 cM in males and 33·9 cM in females), flanked proximally by D21S8 and distally by D21S111, with D21S124 and D21S210 close but of uncertain order. AD1 accounts for 63±11 % of multiplex Alzheimer pedigrees for which lod scores have been reported. Since a much smaller proportion of pedigrees have mutations in the cDNA for β-amyloid (APP exons 16 and 17), it is likely that the AD1 locus spans controlling elements near those exons. There is no evidence for a second locus on chromosome 21. The remaining pedigrees may include sporadic cases as well as mutations at an AD2 locus on another chromosome.     

Genome scan stratified by the presence of anti-double-stranded DNA (dsDNA) autoantibody in pedigrees multiplex for systemic lupus erythematosus (SLE) establishes linkages at 19p13.2 (SLED1) and 18q21.1 (SLED2)

Anti-double-stranded DNA (anti-dsDNA) is arguably one of the most specific autoantibodies in systemic lupus erythematosus (SLE). This antibody is associated with more severe SLE and with glomerulonephritis. From 196 pedigrees multiplex for SLE, we selected those that had any SLE affected positive for anti-dsDNA by the Crithidia luciliae kinetoplast imunofluorescence assay. This stratification strategy tested the hypothesis that anti-dsDNA would identify a more genetically homogeneous group of pedigrees, in which previously undetected linkage effects could be established. A genome screen data for linkage to SLE was available at 307 microsatellite markers for this selected group of 71 pedigrees: 37 European-American, 29 African-American, and five others. The most significant results were obtained at 19p13.2 (LOD(max) = 4.93), named SLED1, in the 37 European-American pedigrees using a dominant model with mixed penetrances (92% for females and 49% for males) at 100% homogeneity (theta = 0). A second linkage effect, SLED2, was established in the 29 African-American pedigrees at 18q21.1 (LOD(max) = 3.40) using a recessive model with 100% penetrance (theta = 0.1). Parametric and non-parametric multipoint analyses were performed, which provided further evidence and support of susceptibility genes residing in these regions. In conclusion, two powerful linkages have been detected with SLE based on the presence of anti-dsDNA. These findings show SLE to be a richly complicated disease phenotype that is now ripe for important new discovery through a genetic approach.     

亚甲基四氢叶酸还原酶基因C677T突变与冠心病的连锁分析

目的探讨亚甲基四氢叶酸还原酶(methylenetetrahydrofolate reductase, MTHFR)基因C677T突变是否与冠心病连锁。方法应用传递不平衡检验(transmission/disequilibrium test, TDT)分析了先证者一级亲属中至少有1例冠心病患者的冠心病家系45个,调查了212人。其中完整核心家系、父母一方、双方基因型缺失家系分别为21、2和22个。PCR-RFLP鉴定MTHFR基因C677T位点基因型。结果 23个核心家系经经典TDT分析,杂合子父母传递给患病子女的T等位基因频率未显著偏离50%(P＞0.05);对40个符号要求的同胞组资料的同胞传递不平衡检验(sib transmission/desequilibrium test, STDT)和同胞组不平衡检验(sibship disequilibruium test, SDT)检验均未发现受累子代与非受累子代T等位基因分布差异有显著性(P＞0.05)。结论 MTHFR基因C677T突变与冠心病不连锁,提示该位点可能不是中国人冠心病的遗传易患因子之一。