A simple method to detect linkage for rare recessive diseases: An application to juvenile diabetes

A simple procedure designed specifically to detect linkage for rare recessive diseases is described. The method uses information on identity by descent scores for a pair of sibs at a marker locus conditioned on the number of affected sibs in the pair. A procedure for estimating the recombination fraction is described, and a table facilitating the likelihood ratio test of linkage is provided. The method, when applied to a collection of multiplex families segregating for juvenile diabetes mellitus, suggests the possibility that this disease is linked to the HLA complex. The method is found to compare favorably to the maximum likelihood approach, for which the computer program LIPED gives a maximum lod score of 2.48 at a male and female recombination fraction of theta = 0.20.     

Identification of regions of positive selection using Shared Genomic Segment analysis

We applied a shared genomic segment (SGS) analysis, incorporating an error model, to identify complete, or near complete, selective sweeps in the HapMap phase II data sets. This method is based on detecting heterozygous sharing across all individuals within a population, to identify regions of sharing with at least one allele in common. We identified multiple interesting regions, many of which are concordant with positive selection regions detected by previous population genetic tests. Others are suggested to be novel regions. Our finding illustrates the utility of SGS as a method for identifying regions of selection, and some of these regions have been proposed to be candidate regions for harboring disease genes.     

Inference in linkage analysis of multifactorial traits using recombinant inbred strains of mice

Recombinant inbred strains have been shown to be important tools for segregation and linkage analysis of multifactorial traits. Tests of association have been used as robust methods of linkage detection, however, guidelines for forming inferences from significance levels have not been generally available. In this paper, lessons learned from a Bayesian statistical approach to linkage analysis of Mendelian traits have been applied to studies of multifactorial traits. Criteria for detection of linkage based on Bonferroni's correction for multiple testing are also discussed.     

Bivariate genome-wide linkage analysis for traits BMD and AAM: Effect of menopause on linkage signals

Osteoporosis is an age-related systemic skeletal disease, characterized by low bone mineral density (BMD). Low BMD is closely associated with late age at menarche (AAM). Our previous bivariate genome-wide linkage analyses (GWLAs) between BMD and AAM identified two shared genomic regions in 2584 Caucasian females including both pre- and post-menopausal females. However, menopause often causes dramatic bone loss in post-menopausal females; this may introduce some confounding effects on the bivariate GWLA for BMD and AAM.     

小儿常染色体隐性遗传多囊肾病临床分析

目的探讨小儿常染色体隐性遗传多囊肾病（autosomal recessive polycystic kidney disease，ARPKD）的临床特点。方法回顾我院1995年1月～2006年12月收治的16例小儿ARPKD的临床资料。结果16例ARPKD中，男11例，女5例，影像学诊断14例，病理学诊断2例，肾脏影像学显示囊肿广泛分布于皮质和髓质。起病时以泌尿系症状就诊仅7例（43．75％），以肾脏外症状就诊3例（18．75％），其他就诊原因包括早产1例，出生时重度窒息1例，血尿素氮-肌酐（Bun—Cr）升高2例，贫血1例，外伤后肾囊肿破裂性腹痛1例。确诊时有12例（75％）肾衰竭，8例（50％）生长迟缓，10例（62．5％）合并肾脏外病变。随诊8例，4例死亡（分别死于先天性肺发育不良、重度窒息后多器官功能衰竭、进行性肾衰竭以及终末期肾病合并胆管细胞癌肾脏转移），1例透析，1例肾移植，1例肾功能正常，1例肝硬化。结论ARPKD为先天遗传性、进行性的肾脏和肝脏损害，小儿期临床表现形式多样，产前诊断对减少ARPKD畸形儿的出生有重要意义。     

An improved multipoint sib-pair analysis of quantitative traits

Kruglyak and Lander (1995) recently published a multipoint sib-pair procedure based on the expected distribution of zero, one and two marker alleles shared identical by descent (ibd) and the method of maximum-likelihood (ML). Their approach uses phenotypic sib-pair differences, which ignores the bivariate structure of sib-pair data. Their simulations suggested that their method was more powerful than the regression method of Haseman and Elston (1972). We show through computation and simulation that their approach can be made more powerful still if the bivariate nature of sib-pair data is acknowledged. In addition, methods based on the average number of shared alleles that also employ bivariate ML procedures (Nance and Neale, 1989; Xu and Atchley, 1995) are more powerful than the approach they recommend and very similar to true ML using the distribution of ibd. The simple ML approach using the average number of shared alleles that we recommend seems to offer both optimal power and flexibility.     

Automated linkage analysis in psychiatric disorders

A genome-wide search for linkage of micro-satellite markers to chromosomal loci containing genes responsible for the major psychoses is a laborious task which can be carried out with greater speed and economy by introducing automation to several steps in the procedure. We describe the use of the Automated Linkage Preprocessor (ALP) program for the computer analysis of the waveform generated by fluorescein-labelled markers after electrophoretic separation. (To obtain a copy send a request to A.F. Brown at the below MRC address or use Anonymous FTP to ftp.hgu.mrc.ac.uk . Software is in directory pub/ALP.) The program runs on a PC in the Microsoft Windows environment, and is used in conjunction with an automated laser fluorescence (ALF) sequencer (Pharmacia) and its Fragment Manager? software to detect and size the PCR products, filter out peaks of fluorescence due to nonallele fragments, and generate genotypes in a format suitable for direct input to standard linkage analysis programs. The method should offer the advantages of speed, accuracy, and reduced cost. Its use in linkage studies in a large family with manic-depressive illness is discussed. © 1995 Wiley-Liss, Inc.     

New options for prenatal diagnosis in autosomal recessive polycystic kidney disease by mutation analysis of the PKHD1 gene

Due to the poor prognosis of severe autosomal recessive polycystic kidney disease (ARPKD), there is a strong demand for prenatal diagnosis (PD). Reliable PD testing is possible by molecular genetic analysis only. Although haplotype-based analysis is feasible in most cases, it is associated with a risk of misdiagnosis in families without pathoanatomically proven diagnosis. Linkage analysis is impossible in families where DNA of the index patient is not available. Direct mutation analysis of the recently identified polycystic kidney and hepatic disease 1 gene opens new options in families to whom a reliable PD cannot be offered on the basis of linkage analysis. We for the first time report two cases with PD based on mutation detection, illustrating the new options for PD in ARPKD.     

Shared Genomic Segment Analysis. Mapping Disease Predisposition Genes in Extended Pedigrees Using SNP Genotype Assays

We examine the utility of high density genotype assays for predisposition gene localization using extended pedigrees. Results for the distribution of the number and length of genomic segments shared identical by descent among relatives previously derived in the context of genomic mismatch scanning are reviewed in the context of dense single nucleotide polymorphism maps. We use long runs of loci at which cases share a common allele identically by state to localize hypothesized predisposition genes. The distribution of such runs under the hypothesis of no genetic effect is evaluated by simulation. Methods are illustrated by analysis of an extended prostate cancer pedigree previously reported to show significant linkage to chromosome 1p23. Our analysis establishes that runs of simple single locus statistics can be powerful, tractable and robust for finding DNA shared between relatives, and that extended pedigrees offer powerful designs for gene detection based on these statistics.     

Mapping the gene for juvenile onset neuronal ceroid lipofuscinosis to chromosome 16 by linkage analysis

The ceroid-lipofuscinoses are a group of inherited neurodegenerative disorders characterised by the accumulation of autofluorescent lipopigment in neurones and other cell types. The underlying biochemical defect is unknown. Juvenile onset neuronal ceroidlipofuscinosis (Batten disease; Spielmeyer-Vogt disease) is an autosomal recessive trait. Linkage studies were undertaken to determine the location of the Batten disease (CLN3) mutation. Studies were carried out on 205 members of 42 families in which there were 76 affected individuals. Families originated from 7 North European countries and Canada. Serum samples from 23 families, including a total of 48 affected children, were tested for a set of “classical markers.” A positive lod score was found with the haptoglobin (Hp) system. The combined male and female maximum lod score was 3.00 at θ = 0.00 and θ = 0.26, respectively. This provided an indication of localisation to the long arm of chromosome 16. Linkage analysis was then carried out in 42 families using DNA markers for loci on human chromosome 16. The maximal lod score between Batten disease and the locus D16S148 calculated for combined sexes was 6.05. No recombinants were observed. Multilocus analysis using 5 loci indicated the most likely order to be HP–D16S151–D16S150–CLN3–D16S148–D16S147. Work is in progress to refine the genetic and physical localisation of the Batten disease gene using additional markers in this region and a panel of somatic cell hybrids. Methods are now available which should allow the gene to be isolated and characterised.     

Genomic mismatch scanning in pedigrees

The new method of genomic mismatch scanning allows the high-resolutionmapping of identity by descent on the chromosomes of two relatedindividuals. Modelling recombinant events as a continuous Markovprocess, the authors design experiments and statistical testsfor the use of this technique on sets of affected individualsin pedigrees in order to determine candidate regions for genescontributing to the disease.     

Exact Trait-Model-Free Tests for Linkage Detection in Pedigrees

A number of trait-model-free tests have been proposed for linkage detection between a genomic region and a trait. These tests involve testing the dependence in segregation between a trait and marker alleles by assigning a score to every possible identity-by-descent configuration of the pedigree members without modeling the trait, and then averaging the scores over all such configurations compatible with the observed marker genotypes and genealogical relationship of the pedigree members. In this paper we propose a permutation test as an alternative to the existing exact trait-model-free tests for linkage detection. The proposed test is computationally efficient and is applicable on complex multigeneration pedigree structures. In this paper, we have compared the performance of the permutation test with two other exact trait-model-free tests for linkage detection on simulated datasets. We have demonstrated that the proposed permutation test is fully robust against mispecification of marker allele frequencies and has very good power for linkage detection. The permutation test is implemented in the program lm_ibdtests within the framework of MORGAN 2.8 ( http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml ).     

Autosomal recessive inheritance of Charcot-Marie-Tooth disease associated with sensorineural deafness

Three siblings with a combination of sensorineural deafness and the Charcot-Marie-Tooth syndrome have been investigated in a consanguineous Indian kindred. This syndrome, which to the best of our knowledge has not previously been reported, is probably inherited as an autosomal recessive trait.     

Theory of genetic counseling for rare recessive traits with consanguinity

The theory of assessing genetic risk for rare autosomal recessive traits in the face of extensive consanguinity is explored. A general lemma is proved that justifies the partition of posterior probability and recursive incorporation of it, as a means of reducing the logic of analysis to steps of manageable complexity: the conditions are that either the components should be independent or that each component, as it is added, is conditioned on the occurrence of all earlier components. An example is given of a pedigree in which the tracing of a gene by the method of expected proportions is misleading, and another that points up the importance of the posterior information. Four classes of patterns are identified and appropriate methods devised for handling them: the single consanguineous loop, multiple mutually-external loops, nested loops, and multiple closures. The latter problem may be treated in general by the use of truncated generating functions, with or without the use of matrix methods.     

Estimating time‐varying RSA to examine psychophysiological linkage of marital dyads

One of the primary tenets of polyvagal theory dictates that parasympathetic influence on heart rate, often estimated by respiratory sinus arrhythmia (RSA), shifts rapidly in response to changing environmental demands. The current standard analytic approach of aggregating RSA estimates across time to arrive at one value fails to capture this dynamic property within individuals. By utilizing recent methodological developments that enable precise RSA estimates at smaller time intervals, we demonstrate the utility of computing time‐varying RSA for assessing psychophysiological linkage (or synchrony) in husband‐wife dyads using time‐locked data collected in a naturalistic setting.     

Genome-wide linkage analysis in a Dutch multigenerational family with attention deficit hyperactivity disorder

Attention deficit hyperactivity disorder (ADHD) is a common neuropsychiatric disorder. Genetics has an important role in the aetiology of this disease. In this study, we describe the clinical findings in a Dutch family with eight patients suffering from ADHD, in whom five had at least one other psychiatric disorder. We performed a genome-wide (parametric and nonparametric) affected-only linkage analysis. Two genomic regions on chromosomes 7 and 14 showed an excess of allele sharing among the definitely affected members of the family with suggestive LOD scores (2.1 and 2.08). Nonparametric linkage analyses (NPL) yielded a maxNPL of 2.92 (P=0.001) for marker D7S502 and a maxNPL score of 2.56 (P=0.003) for marker D14S275. We confirmed that all patients share the same haplotype in each region of 7p15.1–q31.33 and 14q11.2–q22.3. Interestingly, both loci have been reported before in Dutch (affected sib pairs) and German (extended families) ADHD linkage studies. Hopefully, the genome-wide association studies in ADHD will help to highlight specific polymorphisms and genes within the broad areas detected by our, as well as other, linkage studies.     

Autosomal recessive retinitis pigmentosa locus maps on chromosome 1q in a large consanguineous family from Pakistan

A large Pakistani family with several consanguineous marriages is described, in which autosomal recessive retinitis pigmentosa is segregating. Linkage studies revealed close linkage between the disease locus and six loci on chromosome 1q (D1S158, F13B, D1S422, D1S412, D1S413, and D1S53) with maximum lod scores ranging from 0.988-4.657 at Θ=0.065-0.235. However, the analysis of individual nuclear families showed very close linkage without recombination in three branches and several recombinants and negative lod scores throughout in the fourth branch. These results strongly suggest that mutations of two different genes are responsible for the disease in the 'linked' and 'unlinked' branches. Parallel to the linkage heterogeneity, clear phenotypic differences have been observed among the 'linked' and 'unlinked' parts. Our findings demonstrate that in case of recessive disorders the possibility of non-allelic genetic heterogeneity should always be considered, even within the same kindred and in genetic isolates if a largely extended pedigree is analysed.     

Genome-wide linkage analysis of allergic rhinoconjunctivitis in a Swedish population

BACKGROUND: Allergic rhinoconjunctivitis is a common complex disorder characterized by itching and irritation in the nose, bouts of sneezing, watery rhinorrhoea, nasal congestion and itchy eyes with tears and swelling. Like other atopic disorders such as allergic asthma and atopic dermatitis, the development involves complex interactions of genes and environmental factors. OBJECTIVE: The purpose of this study was to identify susceptibility loci for allergic rhinoconjunctivitis. METHODS: We conducted a genome-wide linkage analysis using a non-parametric, affected-relative-pair method. The 250 families used were collected originally for an atopic dermatitis linkage study. RESULTS: Three regions showed favour in evidence of linkage to allergic rhinoconjunctivitis: 3q13 (D3S1278: logarithm of odds ratio (LOD)=1.64, P<0.003), 4q34-35 (D4S1652: LOD=1.49, P<0.005) and 18q12 (D18S535: LOD=1.94, P<0.002). In addition, four regions showed weaker evidence in favour of linkage: 6p22-24 (D6S1959: LOD=1.39, P<0.006), 9p11-q12 (D9S1118: LOD=1.15, P<0.02), 9q33.2-34.3 (D9S915: LOD=1.29, P<0.01) and 17q11.2 (D17S1294: LOD=1.13, P<0.02). In single-point analysis, one locus on chromosome 3 close to marker D3S1278 reaches the suggestive level (LOD=2.28, P<6 x 10(-4)) while one on chromosome 17 close to marker D17S921 almost reaches this level (LOD=2.17, P<8 x 10(-4), Table 3). CONCLUSION: Our results support the linkage to allergic rhinoconjunctivitis on 3q13, 6p23-p24 and 9q34.3 shown in previous investigations.