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Schizophrenia spectrum disorders: an autosomal-wide scan in multiplex pedigrees.

Genome-wide linkage studies, examining the relationship between the schizophrenia syndrome(s) and possible susceptibility regions within the human genome have identified multiple regions within which linkage to the syndrome may be explored. No regions have been found to provide supportive evidence for linkage in all cohorts. These findings are consistent with the schizophrenia syndrome being genetically heterogeneous, with genetic susceptibility arising from multiple sites which are differentially distributed in from pedigree to pedigree. The authors present data from an autosomal-wide scan of 30 multiplex pedigrees, each with a mean of 4.1 members affected with a schizophrenia spectrum disorder with respect to regions of interest for linkage with the schizophrenia spectrum disease(s). Partial, though not significant replications of susceptibility sites at D1S518 (P=0.029) described by Shaw et al. (1998: Shaw, S.H., Kelly, M., Smith, A.B., Shields, G., Hopkins, P.J., Loftus, J., Laval, S.H., Vita, A., DeHert, M., Cardon, L.R., Crow, T.J., Sherrington, R., DeLisi, L.E., 1998. A Genome-wide search for schizophrenia susceptibility genes. Am. J. Med. Genet. (Neuropsychiatric Genet.) 81, 364-376.), and at D5S426 (P=0.015) described by : Silverman, J.M., Greenberg, D.A., Altstiel, L.D., Siever, L.J., Mohs, R.C., Smith, C.J., Zhou, G., Hollander, T.Y., Yang, X.-P., Kedache, M., Li, G., Zaccario, M.L., Davis, K.L., 1996. Evidence of a locus for schizophrenia and related disorders on the short arm of chromosome 5 in a large pedigree. Am. J. Med. Genet. 67, 162-171.) were documented using multipoint non-parametric (NPL) statistics. Two additional novel regions worthy of further investigation were identified at D1S1150 (P=0.004) and at D20S171 (P=0.009). Previously reported genomic regions of interest for the schizophrenias are reviewed in the context of the same/flanking markers utilized with the present cohort of pedigrees. The data further suggests that only a fraction of pedigrees multiplex for schizophrenia link at any single susceptibility region.

Chromosomes, Human↗

Ethical issues in bipolar disorders pedigree research: privacy concerns, informed consent, and grounds for waiver.

Focusing on bipolar disorders research, this article considers ethical issues of informed consent and privacy arising in genetic pedigree research at two stages: the construction of tentative pedigrees to determine family eligibility for study and, subsequently, the enrollment of subjects in and conduct of the family study. Increasing concern to protect the privacy of family members of primary subjects or probands, following ethical controversy over a survey study at Virginia Commonwealth University, has led some researchers and Institutional Review Boards (IRBs) to apply informed consent requirements to those represented on a tentative pedigree at the initial stage of research. This article analyzes the possible benefits, risks, and burdens to prospective subjects of seeking prospective consent for pedigree construction at this initial stage. It argues that the likely risk-benefit ratio favors granting a waiver of consent requirements for this stage of pedigree research and presents grounds for IRBs to grant such a waiver. The article closes by considering particular ethical concerns that should be addressed in the informed consent discussion when enrolling subjects in pedigree studies of bipolar disorder, including concerns about subjects' competence to consent, management of interim and incidental findings, and issues particular to psychiatric research.

Bipolar Disorder↗

A schizophrenia-susceptibility locus at 6q25, in one of the world's largest reported pedigrees.

We have completed a genome scan of a 12-generation, 3,400-member pedigree with schizophrenia. Samples from 210 individuals were collected from the pedigree. We performed an "affecteds-only" genome-scan analysis using 43 members of the pedigree. The affected individuals included 29 patients with schizophrenia, 10 with schizoaffective disorders, and 4 with psychosis not otherwise specified. Two sets of white-European allele frequencies were used-one from a Swedish control population (46 unrelated individuals) and one from the pedigree (210 individuals). All analyses pointed to the same region: D6S264, located at 6q25.2, showed a maximum LOD score of 3.45 when allele frequencies in the Swedish control population were used, compared with a maximum LOD score of 2.59 when the pedigree's allele frequencies were used. We analyzed additional markers in the 6q25 region and found a maximum LOD score of 6.6 with marker D6S253, as well as a 6-cM haplotype (markers D6S253-D6S264) that segregated, after 12 generations, with the majority of the affected individuals. Multipoint analysis was performed with the markers in the 6q25 region, and a maximum LOD score of 7.7 was obtained. To evaluate the significance of the genome scan, we simulated the complete analysis under the assumption of no linkage. The results showed that a LOD score >2.2 should be considered as suggestive of linkage, whereas a LOD score >3.7 should be considered as significant. These results suggest that a common ancestral region was inherited by the affected individuals in this large pedigree.

Adult↗

Monte Carlo pedigree disequilibrium test for markers on the X chromosome.

Because of the need for fine mapping of disease loci and the availability of dense single-nucleotide-polymorphism markers, many forms of association tests have been developed. Most of them are applicable only to triads, whereas some are amenable to nuclear families (sibships). Although there are a number of methods that can deal with extended families (e.g., the pedigree disequilibrium test [PDT]), most of them cannot accommodate incomplete data. Furthermore, despite a large body of literature on association mapping, only a very limited number of publications are applicable to X-chromosomal markers. In this report, we first extend the PDT to markers on the X chromosome for testing linkage disequilibrium in the presence of linkage. This method is applicable to any pedigree structure and is termed "X-chromosomal pedigree disequilibrium test" (XPDT). We then further extend the XPDT to accommodate pedigrees with missing genotypes in some of the individuals, especially founders. Monte Carlo (MC) samples of the missing genotypes are generated and used to calculate the XMCPDT (X-chromosomal MC PDT) statistic, which is defined as the conditional expectation of the XPDT statistic given the incomplete (observed) data. This MC version of the XPDT remains a valid test for association under linkage with the assumption that the pedigrees and their associated affection patterns are drawn randomly from a population of pedigrees with at least one affected offspring. This set of methods was compared with existing approaches through simulation, and substantial power gains were observed in all settings considered, with type I error rates closely tracking their nominal values.

Chromosomes, Human, X↗

Multipoint linkage analysis with many multiallelic or dense diallelic markers: Markov chain-Monte Carlo provides practical approaches for genome scans on general pedigrees.

Computations for genome scans need to adapt to the increasing use of dense diallelic markers as well as of full-chromosome multipoint linkage analysis with either diallelic or multiallelic markers. Whereas suitable exact-computation tools are available for use with small pedigrees, equivalent exact computation for larger pedigrees remains infeasible. Markov chain-Monte Carlo (MCMC)-based methods currently provide the only computationally practical option. To date, no systematic comparison of the performance of MCMC-based programs is available, nor have these programs been systematically evaluated for use with dense diallelic markers. Using simulated data, we evaluate the performance of two MCMC-based linkage-analysis programs--lm_markers from the MORGAN package and SimWalk2--under a variety of analysis conditions. Pedigrees consisted of 14, 52, or 98 individuals in 3, 5, or 6 generations, respectively, with increasing amounts of missing data in larger pedigrees. One hundred replicates of markers and trait data were simulated on a 100-cM chromosome, with up to 10 multiallelic and up to 200 diallelic markers used simultaneously for computation of multipoint LOD scores. Exact computation was available for comparison in most situations, and comparison with a perfectly informative marker or interprogram comparison was available in the remaining situations. Our results confirm the accuracy of both programs in multipoint analysis with multiallelic markers on pedigrees of varied sizes and missing-data patterns, but there are some computational differences. In contrast, for large numbers of dense diallelic markers, only the lm_markers program was able to provide accurate results within a computationally practical time. Thus, programs in the MORGAN package are the first available to provide a computationally practical option for accurate linkage analyses in genome scans with both large numbers of diallelic markers and large pedigrees.

Alleles↗

CoPE: a collaborative pedigree drawing environment.

SUMMARY: We developed a collaborative pedigree environment called CoPE. This environment includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. AVAILABILITY: At http://www.infobiogen.fr/services/CoPE

Pedigree↗

A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags.

A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.

Base Sequence↗

Peditree: pedigree database analysis and visualization for breeding and science.

At the Wageningen Laboratory of Plant Breeding, a software package has been developed to query a simple structured database with variety pedigree data. The package, called Peditree, creates a tree-shaped representation of pedigree information and has several visualization and lookup options. Estimates of inbreeding coefficient within a pedigree or coefficients of coancestry among pedigrees can be obtained. Furthermore trait data--if available--can be linked, displayed within the pedigree tree, and used to highlight pedigree entries that comply with set criteria.

Animals↗

Four pedigrees of the cation-leaky hereditary stomatocytosis class presenting with pseudohyperkalaemia. Novel profile of temperature dependence of Na+-K+ leak in a xerocytic form.

We report four pedigrees of the group of Na(+)-K(+)-leaky red cell disorders of the 'hereditary stomatocytosis' class. Each showed pseudohyperkalaemia because of temperature-dependent loss of K(+) from red cells on storage of whole blood at room temperature. All pedigrees showed an abnormality in the temperature dependence of the 'passive leak' of the membrane to K(+). Two pedigrees, both of which showed a compensated haemolytic state with dehydrated red cells and target cells on the blood film, showed a novel pattern, in which the profile was flat between 37 degrees C and about 32 degrees C then dropped as the temperature was reduced to zero. The third showed the 'shallow slope' profile, with stomatocytes on the blood film and very markedly abnormal intracellular Na(+) and K(+) levels. Minimal haemolysis was present. The fourth pedigree, of Asian origin, showed the shoulder pattern (minimum at 32 degrees C, maximum at 12 degrees C) with essentially normal haematology. Both of these latter two forms have previously been seen in other pedigrees. The first variant represents a novel kind of temperature dependence of the passive leak found in these pedigrees presenting with pseudohyperkalaemia.

Adult↗

Ascertainment in the sequential sampling of pedigrees.

One aim in the analysis of pedigree data may be to infer the mode of inheritance of a characteristic. If only "interesting" pedigrees are analysed, the ascertainment bias may lead to some modes of inheritance being unintentionally preferred. Also, it is clearly most efficient in attempting to make such inferences, if a decision on whether to continue sampling a pedigree is made conditional on the types of individuals who have been observed; an a priori decision to examine 500 members of a pedigree may lead to much wasted effort, since the pedigree may prove to be largely uninformative. The present paper shows that provided all observed families are included in the analysis, even those which appeared "uninteresting" or "sporadic" and were not sampled further, and provided a decision to continue sampling is made conditional on types observed up to that point, the correct likelihood for the mode of inheritance may be easily computed. This opens the way for a more detailed study of the wider problem of optimal samplings rules on pedigrees.

Computers↗

Classification and genetic features of neonatal haemochromatosis: a study of 27 affected pedigrees and molecular analysis of genes implicated in iron metabolism.

Neonatal haemochromatosis (NH) is a severe and newly recognised syndrome of uncertain aetiology, characterised by congenital cirrhosis or fulminant hepatitis and widespread tissue iron deposition. NH occurs in the context of maternal disease including viral infection, as a complication of metabolic disease in the fetus, and sporadically or recurrently, without overt cause, in sibs. Although an underlying genetic basis for NH has been suspected, no test is available for predictive analysis in at risk pregnancies. As a first step towards an understanding of the putative genetic basis for neonatal haemochromatosis, we have conducted a systematic study of the mode of transmission of this disorder in a total of 40 infants born to 27 families. We have moreover carried out a molecular analysis of candidate genes (beta(2)-microglobulin, HFE, and haem oxygenases 1 and 2) implicated in iron metabolism. No pathogenic mutations in these genes were identified that segregate consistently with the disease phenotype in multiplex pedigrees. However, excluding four pedigrees with clear evidence of maternal infection associated with NH, a pedigree showing transmission of maternal antinuclear factor and ribonucleoprotein antibodies to the affected infants, and two families with possible matrilineal inheritance of disease in maternal half sibs, a large subgroup of the affected pedigrees point to the inheritance of an autosomal recessive trait. This included 14 pedigrees with affected and unaffected infants and a single pedigree where all four affected infants were the sole offspring of consanguineous but otherwise healthy parents. We thus report three distinct patterns of disease transmission in neonatal haemochromatosis. In the differentiation of a large subgroup showing transmission of disease in a manner suggesting autosomal recessive inheritance, we also provide the basis for further genome wide studies to define chromosomal determinants of iron storage disease in the newborn.

Adolescent↗

The impact of pedigree structure on heritability estimates for pulse pressure in three studies.

OBJECTIVES: Pulse pressure (PP) is a measure of large artery stiffness and has been shown to be an important predictor of cardiovascular morbidity and mortality. The aims of the present study were to investigate the heritability of PP in three studies, the Diabetes Heart Study (DHS), the Insulin Resistance Atherosclerosis Family Study (IRAS FS), and the NHLBI Family Heart Study (FHS), to estimate the residual heritability after inclusion of a common set of covariates, and to investigate the impact of pedigree structure on estimating heritability. METHODS AND RESULTS: DHS is primarily a sibling pair nuclear family study design, while both IRAS FS and FHS have large pedigrees. Heritability estimates of log-transformed PP were obtained using variance component models. After adjusting for age, gender, ethnicity/center, height, diabetes status, and mean arterial pressure (MAP), heritability estimates of PP were 0.40 +/- 0.08 , 0.22 +/- 0.05, and 0.19 +/- 0.03 in DHS, IRAS FS, and FHS, respectively. The heritability estimate from DHS was significantly different from both IRAS FS and FHS (both p values <0.05). A random re-sampling technique (modified bootstrap) was used to explore the heritability in the IRAS FS and FHS data when these pedigrees were trimmed to mimic the DHS pedigree structure. The re-sampling method (mimicking a sibling pair nuclear family design in all studies) yielded PP heritability estimates of 0.37, 0.34, and 0.27 in DHS, IRAS FS, and FHS, respectively. There was no significant difference among the heritability estimates from the three studies based on the re-sampling method. CONCLUSION: We have shown that PP has a moderately heritable component in three different studies. These data illustrate the influence of pedigree structure can have on estimating heritability. Thoughtful comparisons of heritability estimates must consider study design factors such as pedigree structure.

Adolescent↗

Examination of ELN as a candidate gene in the Utah intracranial aneurysm pedigrees.

BACKGROUND AND PURPOSE: A study of intracranial aneurysm (IA) sibpairs suggested association of an ELN haplotype with IA risk. Subsequent linkage analysis of the ELN region on chromosome 7q11 in high-risk Utah IA pedigrees significantly confirmed linkage between IA and the ELN region. METHODS: We have investigated the ELN gene as a potential candidate gene for IA in Utah pedigrees. One IA case from each pedigree, who shared an ELN region haplotype segregating in the pedigree, was screened for mutation. The promoter region, 34 exons, and the 3'UTR (UnTranslated Region) of the ELN gene were screened for variants using DHPLC. RESULTS: Variants were observed in the promoter region, exons 4 and 6, and the 3'UTR. Variants in exon 6 and in one 3'UTR position were unique to Utah. The remaining variants were absent in the controls. There was no evidence for segregation of the ELN variants found in IA cases with the hypothesized chromosome 7 haplotypes segregating in pedigrees. CONCLUSIONS: Our analysis does not support ELN as the gene responsible for familial IA in the linked Utah IA pedigrees.

3' Untranslated Regions↗

Ethical and methodological issues in pedigree stroke research.

BACKGROUND: Stroke is a complex genetic disorder with a variable phenotype. Investigations of heritable factors in complex genetic disorders use pedigree and genetic techniques, which pose different ethical and methodological challenges than those routinely encountered in therapeutic research. Building consensus on acceptable research practices in this field is vital to the success of multicentered collaborations. SUMMARY OF REVIEW: We review important ethical and methodological concerns related to the collection, storage, and release of pedigree research information. The human studies aspects of pedigree research are complicated methodologically because individuals can be active or passive participants and pedigrees can be proband derived, partially validated, or fully validated. Current research ethics frameworks do not work well outside of a dyadic researcher-subject relationship. Privacy and confidentiality for family members must be considered in pedigree research. Investigators should anticipate potential conflicts of interest among family members when designing a pedigree research protocol. CONCLUSIONS: We propose a "proband-initiated contact" methodology in which the proband or the proband's designate allows identification of potential families without breaching the privacy of individuals in the family. In situations in which family history data are collected without direct contact between researchers and individuals in the proband's family, an Institutional Review Board may waive consent by family members after appropriate review of the protocol and application of rules for granting waivers of consent. Certificates of Confidentiality should be considered.

Confidentiality↗

Pedigree and marker information requirements to monitor genetic variability.

There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals.

Animals↗

Evaluating outlier loci and their effect on the identification of pedigree errors.

Homozygosity outlier loci, which show patterns of variation that are extremely divergent from the rest of the genome, can be evaluated by comparison of the homozygosity under Hardy-Weinberg proportions (the sum of the squares of allele frequencies) with the expected homozygosity under neutrality. Such outlier loci are potentially under selection (balancing selection or directional selection) when genome-wide effects (such as bottleneck and rapid population growth) are excluded. Outlier loci show skewed allele frequencies with respect to neutrality and may therefore affect the identification of pedigree errors. However, choosing neutral markers (excluding outlier loci) for the identification of pedigree errors has been neglected thus far. Our results showed that 4.1%, 5.5%, and 1.5% of the microsatellite markers, Illumina single-nucleotide polymorphisms (SNPs), and Affymetrix SNPs, respectively, on the autosomes appear to be under balancing selection (p or=40%) appear to be under balancing selection. Pedigree structure errors in 15 of 143 pedigrees were detected using microsatellite markers from the autosomes and/or selected SNPs from chromosomes 1 to 18 of the Illumina and/or selected SNPs from chromosomes 1 to 16 of the Affymetrix. Outlier loci did not make a major difference to the identification of pedigree errors. The Collaborative Study on the Genetics of Alcoholism data has pedigree errors and some of them may be due to sample mix up.

Alcoholism↗

Collection of pedigree data for genetic analysis in isolate populations.

Pedigree data are useful for a wealth of research purposes in human population biology and genetics. The collection of extended pedigrees represents the most powerful sampling design for quantitative genetic and linkage studies of both normal and disease-related quantitative traits. In this paper we outline an approach for collecting pedigree data in stable isolate populations. As an example, the pedigree for the Jirel population, which was obtained using the methods presented, is described. The Jirel pedigree contains 2,000 study participants and more than 62,000 pairwise relationships that are informative for genetic analysis. Once such pedigrees are genetically characterized by a genome scan for a given trait, they become an invaluable resource for future genetic studies of any quantitative trait.

Female↗

Effect of incomplete pedigrees on estimates of inbreeding and inbreeding depression for days to first service and summit milk yield in Holsteins and Jerseys.

A method to measure completeness of pedigree information is applied to populations of Holstein (registered and grade) and Jersey (largely registered) cows. Inbreeding coefficients where missing ancestors make no contribution were compared to a method using average relationships for missing ancestors. Estimated inbreeding depression was from an animal model that simultaneously adjusted for breeding values. Inbreeding and its standard deviation increased with more information, from 0.04 +/- 0.84 to 1.65 +/- 2.05 and 2.06 +/- 2.22 for grade Holsteins with <31%, 31 to 70%, and 71 to 100% complete five-generation pedigrees. Inbreeding from the method of average relationships for missing ancestors was 2.75 +/- 1.06, 3.10 +/- 2.21, and 2.89 +/- 2.37 for the same groups. Pedigrees of registered Holsteins and Jerseys were over 97% and over 89% complete, respectively. Inbreeding depression in days to first service and summit milk yield was estimated from both methods. Inbreeding depression for days to first service was not consistently significant for grade Holsteins and ranged from -0.37 d/1% increase in inbreeding (grade Holstein pedigrees <31% complete) to 0.15 d for grade Holstein pedigrees >70% complete. Estimates were similar for both methods. Inbreeding depression for registered Holsteins and Jerseys were positive (undesirable) but not significant for days to first service. Inbreeding depressed summit milk yield significantly in all groups by both methods. Summit milk yield declined by -0.12 to -0.06 kg/d per 1% increase in inbreeding in Holsteins and by -0.08 kg/1% increase in inbreeding in Jerseys. Pedigrees of grade animals are frequently incomplete and can yield misleading estimates of inbreeding depression. This problem is not overcome by inserting average relationships for missing ancestors in calculation of inbreeding coefficients.

Animals↗