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Genetic analysis with hierarchical models.

During the Genetic Analysis Workshop 9 presentations [Goldin et al., 1995] a brief discussion took place about the value of empirical-Bayes methods in genetic analysis. Due to the informal nature of this discussion, the improvements available for analyzing data with this approach--and with the broader class of hierarchical models--were not clearly presented. As a methodologic contribution, I further explore how one can use this potentially valuable technique in analysis of genetic data, including data similar to those given in GAW10.

Bayes Theorem↗

[Statistical genetic analysis of some problem behaviors during sleep in childhood--estimation of genetic and environmental factors influencing multiple health phenomena simultaneously].

This study was conducted to clarify the genetic and environmental factors for some problem behaviors during sleep in childhood, namely sleep talking, half-sleeping, night terrors and nocturnal enuresis. The subjects were 881 pairs of twins, consisting of 609 monozygotic (279 male-male, 330 female-female) and 272 dizygotic (86 male-male, 84 female-female, 102 opposite-sexed). They were all applicants to the junior high school affiliated with Tokyo University from 1981 to 1998. The twins' mothers had previously completed a medical questionnaire and had been interviewed by three to five interviewers. With regard to the above mentioned four traits, they selected one answer from the choices 'often', 'sometimes' 'never' and 'unknown' for each twin. The interviewer checked the answers and, where necessary, explained the meaning of any terms such as "night terrors". Genetic analysis was performed as follows. First the answers were summarized in the form of a 2 x 2 contingency table; 'often' and 'sometimes' were included in one category. Then, tetrachoric correlations of the contingency table were calculated according to zygosity using the program package PRELIS2. Furthermore, covariance structure analysis was performed for several genetic models using the program package LISREL8. The results were as follows. Univariate genetic analysis showed that all four traits were under genetic control. Sleep talking, half-sleeping and night terrors were under strong or moderate genetic control. As to nocturnal enuresis, the genetic effect was moderate and shared environmental factors played an important role. Sex difference was observed in the case of half-sleeping and enuresis. Moreover these traits tended to occur together, and sleep talking, half-sleeping and night terrors shared common genetic and environmental factors in addition to specific genetic and environmental factors.

Child↗

An integrated system for genetic analysis.

BACKGROUND: Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. DESCRIPTION: We have developed an Integrated Genotyping System (IGS) to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. CONCLUSION: IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

Chromosome Mapping↗

Application of DNA typing methods and genetic analysis to epidemiology and taxonomy of Saccharomyces isolates.

We have previously described differences in phenotype and virulence among clinical and nonclinical isolates of Saccharomyces. To further characterize these isolates, a comparison of restriction fragment length polymorphism (RFLP) patterns and genetic analysis were done. The cellular DNA of each of 49 clinical and 11 nonclinical isolates of Saccharomyces was digested with the endonuclease EcoRI, and the resultant fragments were separated by electrophoresis. Sixty isolates were grouped on the basis of the presence (group B) or absence (group A) of a 3-kb band. Group A contained 43 isolates (35 clinical and 8 nonclinical isolates) in 31 discernible subgroups, and group B had 17 isolates (14 clinical and 3 nonclinical isolates) in 10 subgroups. Interestingly, six of eight known vaginal isolates were group B, with four of those six being identical. Virulence of isolates was associated with membership in group A (P = 0.03). Comparison of known members of sibling species within the genus Saccharomyces, which cannot be distinguished by standard biochemical tests, showed that S. paradoxus, S. bayanus, and S. cerevisiae could be differentiated by RFLP analysis. Genetic analysis of the isolates forming viable spores showed that most group A isolates were diploid and members of the species S. cerevisiae. Those group A and B isolates unable to form viable spores may be diploid hybrids between Saccharomyces species. The group B isolates that formed viable spores were tetraploid and may also be interspecific hybrids. Overall, clinical isolates of Saccharomyces were very heterogeneous and exhibited little clonality. RFLP pattern analysis could be a useful method of demonstrating transmission in patients with infection or between environmental sources and patients.

DNA, Fungal↗

Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus.

An unusual system of genetic exchange exists in the purple nonsulfur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs. This paper presents the results of gene cloning, analysis, and mutagenesis experiments that show that GTA resembles a defective prophage related to bacteriophages from diverse genera of bacteria, which has been adopted by R. capsulatus for genetic exchange. A pair of cellular proteins, CckA and CtrA, appear to constitute part of a sensor kinase/response regulator signaling pathway that is required for expression of GTA structural genes. This signaling pathway controls growth-phase-dependent regulation of GTA gene messages, yielding maximal gene expression in the stationary phase. We suggest that GTA is an ancient prophage remnant that has evolved in concert with the bacterial genome, resulting in a genetic exchange process controlled by the bacterial cell.

Amino Acid Sequence↗

Common disease analysis using Multivariate Adaptive Regression Splines (MARS): Genetic Analysis Workshop 12 simulated sequence data.

A newly developed modern analytic approach, Multivariate Adaptive Regression Splines (MARS), was used to identify both genetic and non-genetic factors involved in the etiology of a common disease. We tested this method on the simulated data provided by the Genetic Analysis Workshop (GAW) 12 in problem 2 for the isolated population. MARS simultaneously analyzes all inputs, in this case DNA sequence variants and non-genetic data, and selectively prunes away variables contributing insignificantly to fit by internal cross-validation to arrive at a generalizable predictive model of the response. The relevant factors identified, by means of an importance value computed by MARS, were assumed to be associated with risk to the disease. The application of a series of subsequent models identified the quantitative traits and a single major gene contributing directly to risk liability using five sets of 7,000 individuals.

Genetic Predisposition to Disease↗

Genetic analysis of tumorigenesis: XII. Genetic control of the anchorage requirement in CHEF cells.

Chinese hamster somatic cell hybrids between diploid anchorage-independent CHEF/204Bu50 cells and diploid anchorage dependent CHEF/205-30 cells are anchorage dependent but can segregate subclones at low frequency which reexpress anchorage independence. Thus, anchorage independence, like other characteristics of the transformed phenotype, is suppressed in these hybrids. Anchorage-independent subclones were recovered from the anchorage-dependent hybrids under conditions which favored the retention of most chromosomes. Karyotype analysis of suppressed hybrids and their anchorage-independent subclones showed that segregation of anchorage dependence was correlated with the loss of one copy of chromosome 1 in CHEF Chinese hamster hybrids. Thus, suppression of anchorage independence has a chromosomal basis. Several genetic models are considered for the origin of anchorage-independent subclones from suppressed Chinese hamster hybrids.

Animals↗

A genetic analysis of retinitis pigmentosa.

Genetic analysis of 457 patients with retinitis pigmentosa (RP) included categorisation of families by recognised mendelian pattern of inheritance and formal segregation analysis of all informative sibships. Of the 368 probands a surprisingly high 18% (68) had significant congenital loss of hearing and were diagnosed as having Usher syndrome. The RP probands were categorised as: 21.7% autosomal dominant, 9.0% X-linked, 16.0% autosomal recessive, 3.3% genetic type uncertain, and 50.0% simplex. Segregation analysis reflected this high proportion of simplex cases, accounting for reduced penetrance in dominant families; only 20% remain classified as sporadic (possibly nongenetic). In the matings between normal persons estimates of the segregation ratio also indicate lower values than expected. Unlike in RP sibship, segregation in the Usher syndrome is consistent with the hypothesis of recessive inheritance. Therefore RP with significant hearing loss segregates as expected, while even if a proband is classified as a dominant or recessive the recurrence risk for the RP phenotype may be below mendelian expectation.

Female↗

Description of the Genetic Analysis Workshop 11 Collaborative Study on the Genetics of Alcoholism.

Problem 1 of Genetic Analysis Workshop 11 consists of data from a family study of the genetics of alcoholism and related traits contributed by the six centers making up the National Institute for Alcohol Abuse and Alcoholism sponsored by the Collaborative Study on the Genetics of Alcoholism (COGA). The family data included 1,214 members of 105 pedigrees ascertained for having three or more individuals affected with alcoholism. Data available to workshop participants included clinical phenotypes, personality measures, smoking behavior, event-related potentials, platelet monamine oxidase B activity, and a genome scan of 296 markers.

Alcoholism↗

Multiplexed genetic analysis using an expanded genetic alphabet.

BACKGROUND: All states require some kind of testing for newborns, but the policies are far from standardized. In some states, newborn screening may include genetic tests for a wide range of targets, but the costs and complexities of the newer genetic tests inhibit expansion of newborn screening. We describe the development and technical evaluation of a multiplex platform that may foster increased newborn genetic screening. METHODS: MultiCode PLx involves three major steps: PCR, target-specific extension, and liquid chip decoding. Each step is performed in the same reaction vessel, and the test is completed in approximately 3 h. For site-specific labeling and room-temperature decoding, we use an additional base pair constructed from isoguanosine and isocytidine. We used the method to test for mutations within the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The developed test was performed manually and by automated liquid handling. Initially, 225 samples with a range of genotypes were tested retrospectively with the method. A prospective study used samples from >400 newborns. RESULTS: In the retrospective study, 99.1% of samples were correctly genotyped with no incorrect calls made. In the perspective study, 95% of the samples were correctly genotyped for all targets, and there were no incorrect calls. CONCLUSIONS: The unique genetic multiplexing platform was successfully able to test for 31 targets within the CFTR gene and provides accurate genotype assignments in a clinical setting.

Autoanalysis↗

[Molecular genetic analysis of hobo mobile genetic element polymorphism in the genome of Drosophila melanogaster line subjected to long-term selection].

The distribution of mobile genetic element hobo was examined in Drosophila melanogaster lines HA (high male mating activity) and LA (low male mating activity) before and after their isogenization using Southern blot hybridization. The probe containing a full-size hobo copy was shown to produce polymorphic multilocus hybridization with chromosomal DNA. The polymorphism was line-specific. A comparison of hybridization patterns in isogenic and original lines showed that isogenization in dysgenic crosses resulted in the appearance of additional hobo localization sites in LA but not in HA. The hobo destabilization in the LA genome correlated with genetic instability and the ability to induce H-E hybrid dysgenesis. The results obtained are discussed in relation to the possible role of hobo in inducing genetic variability in lines with low male mating activity, which may counteract deleterious consequences of inbreeding and selection in the negative direction.

Animals↗

The nature of extraversion: a genetical analysis.

A biometrical-genetical analysis of twin data to elucidate the determinants of variation in extraversion and its components, sociability and impulsiveness, revealed that both genetical and environmental factors contributed to variation in extraversion, to the variation and covariation of its component scales, and to the interaction between subjects and scales. A large environmental correlation between the scales suggested that environmental factors may predominate in determining the unitary nature of extraversion. The interaction between subjects and scales depended more on genetical factors, which suggests that the dual nature of extraversion has a strong genetical basis. A model assuming random mating, additive gene action, and specific environmental effects adequately describes the observed variation and covariation of sociability and impulsiveness. Possible evolutionary implications are discussed.

Adult↗

Current perspectives on the genetic analysis of autism.

Although no definitive genetic mutations leading to autism susceptibility have been established, the field has many new resources to tackle this difficult problem. Numbers of families at many research sites are now large, and new collaborations among these groups will allow for collections of subjects with enough statistical power to detect relatively small gene effects. New technological advances in genotyping will allow for more fine-grained genetic analysis, and more sophisticated techniques have been developed to address the vast amounts of data acquired. Researchers have also begun to focus on intermediate phenotypes associated with autism, such as elevated serotonin, increased head circumference, social difficulties, or language impairment or delay. These phenotypes may help to stratify affected cases into more genetically homogeneous subgroups, and may also occur in their clinically unaffected relatives. The study of intermediate phenotypes may allow investigators to find common gene variants that lead to autism susceptibility. Here we discuss the major intermediate phenotypes, and give an overview of current genetic analysis techniques.

Autistic Disorder↗

Haplotype sharing analysis with SNPs in candidate genes: the Genetic Analysis Workshop 12 example.

Haplotype sharing analysis was used to investigate the association of affection status with single nucleotide polymorphism (SNP) haplotypes within candidate gene 1 in one sample each from the isolated and the general population of Genetic Analysis Workshop (GAW) 12 simulated data. Gene 1 has direct influence on affection and harbors more than 70 SNPs. Haplotype sharing analysis depends heavily on previous haplotype estimation. Using GENEHUNTER haplotypes, strong evidence was found for most SNPs in the isolated population sample, thus providing evidence for an involvement of this gene, but the maximum -log(10)(p) values for the haplotype sharing statistics (HSS) test statistic did not correspond to the location of the true variant in either population. In comparison, transmission disequilibrium test (TDT) analysis showed the strongest results at the disease-causing variant in both populations, and these were outstanding in the general population. In this example, TDT analysis appears to perform better than HSS in identifying the disease-causing variant, using SNPs within a candidate gene in an outbred population. Simulations showed that the performance of HSS is hampered by closely spaced SNPs in strong linkage disequilibrium with the functional variant and by ambiguous haplotypes.

Chromosome Mapping↗

Genetic Analysis Workshop II: segregation and three-locus linkage analysis.

Data stimulated for Genetic Analysis Workshop II were analyzed using PAP. Segregation analysis showed a simple recessive mode of inheritance for data set 2 while no conclusions could be made about the mode of inheritance for data set 3. Pairwise linkage analysis suggested three linkage groups, but three-locus analysis did not provide strong evidence for the gene order within these groups. For three of the four three-locus comparisons performed, three-locus analysis suggested the simulated order. In only one case did the pairwise analysis suggest the simulated order, indicating the necessity for multi-locus analysis for gene order.

Chromosome Mapping↗