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At least 181 records · Page 10Linked to original sources

Congenital central hypoventilation syndrome: inheritance and relation to sudden infant death syndrome.

We evaluated the families of 50 children with idiopathic congenital central hypoventilation syndrome (CCHS) to 1) test genetic hypotheses, 2) explore the relationship to Hirschsprung disease (HD), and 3) examine other clinical findings including sudden infant death syndrome (SIDS) in relatives of CCHS patients. A questionnaire was administered to parents of each proband to determine a detailed pedigree and medical history for 3 generations including 1,482 relatives. The data were analyzed under the unified mixed model method (assumes individual genotype composed of multifactorial [MF] and major locus [ML] components). Analysis was made of the Total dataset and on subdivided data sets: HIR1 = families of probands with HD (n = 8) vs. HIR2 = families of probands without HD; then under a premise that severe, chronic constipation may be a milder form of HD (i.e., ganglion cells present but dysfunctional), CON1 = families of probands with HD or constipation (n = 13) vs. CON2 = families of probands without HD or constipation. By statistical genetic analysis of the Total, HIR1, and CON1 datasets, the MF and ML hypotheses were about equally likely, with the MF model slightly more parsimonious. Although HIR2 and CON2 datasets indicated no familiality, statistical evidence of heterogeneity between the results of HIR1 and HIR2, or between CON1 and CON2 was lacking. A SIDS incidence of 11.2/1,000 was documented among the relatives of CON1 vs. 1.8/1,000 among relatives of CON2. Our results are consistent with familiality by either MF or ML models. Recurrence risk is likely < 5%. The relationship of CCHS to the high familial incidence of SIDS is intriguing and demands further investigation.

Female↗

Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations.

Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform in-depth analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development. The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale case-based diagnostic analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser ( https://dbmi-bgm.github.io/udn-browser/ ). These results show that case-level diagnostic efforts should be supplemented by a joint genomic analysis across cohorts.

Humans↗

Estimating the correlation of pairwise relatedness along chromosomes.

The 'spatial' pattern of the correlation of pairwise relatedness among loci within a chromosome is an important aspect for an insight into genomic evolution in natural populations. In this article, a statistical genetic method is presented for estimating the correlation of pairwise relatedness among linked loci. The probabilities of identity-in-state (IIS) are related to the probabilities of identity-by-descent (IBS) for the two- and three-loci cases. By decomposing the joint probabilities of two- or three-loci IBD, the probability of pairwise relatedness at a single locus and its correlation among linked loci can be simultaneously estimated. To provide effective statistical methods for estimation, weighted least square (LS) and maximum likelihood (ML) methods are evaluated through extensive Monte Carlo simulations. Results show that the ML method gives a better performance than the weighted LS method with haploid genotypic data. However, there are no significant differences between the two methods when two- or three-loci diploid genotypic data are employed. Compared with the optimal size for haploid genotypic data, a smaller optimal sample size is predicted with diploid genotypic data.

Animals↗

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↗

Statistical testing of genetic linkage under heterogeneity.

Recent advances in human genetics have led to a renewed interest in statistical methods for the detection of linkage from family data--for example, between marker loci and disease traits. Statistical analysis of linkage between two loci is carried out almost exclusively by means of the lod (log-odds) score test, equivalent to a likelihood ratio test. The current practice is to declare genetic linkage between loci when the maximum lod score exceeds 3. As will be discussed here, the lod-score approach is not appropriate for the detection of linkage from heterogeneous data, e.g., when families consist of a mixture of linked and unlinked types. Heterogeneity may arise, for example, when rare mutations at different genetic loci are responsible for the same disease trait. As an alternative approach to account for possible heterogeneity in the detection of linkage, we propose the application of large-sample test statistics that are members of Neyman's class of C(alpha), or partial score tests. The convergence of the proposed test statistics to their asymptotic distributions is investigated via Monte Carlo simulation for typical study designs applicable in human genetics.

Biometry↗

Interaction of genetics and epidemiology in the literature.

To evaluate the extent of interaction between genetics and epidemiology in studies reported in the literature, we reviewed all the "familial/genetic" papers published in a standard epidemiology journal (American Journal of Epidemiology, AJE) and all the "epidemiology" papers published in a standard human genetics journal (American Journal of Human Genetics, AJHG) between 1966 and 1984. A variety of medline subject headings were used in this search. Computerized listings of titles, subject headings, and abstracts were reviewed. It could be shown that familial/genetic papers constituted 4.3% of all papers published in AJE and epidemiology papers constituted 16.4% of papers published in AJHG. Over time, familial/genetic studies published in AJE increased both in number and in proportion of all papers, and more family studies are using complex statistical genetic techniques. On the other hand, epidemiology papers published in AJHG did not increase in number over time, and actually decreased in relation to all papers. These papers were mostly either descriptive (eg, defining frequencies of Mendelian traits in populations) or analytical (eg, defining risk factors for chromosomal abnormalities, and other reproductive outcomes). This analysis suggests that epidemiologic methods have been widely used in the genetic literature, and that genetic methods are gaining more access to the recent epidemiology literature. Because of increasing recognition of the role of genetic factors in disease, there is a growing need to incorporate both genetic and epidemiologic methods in etiologic studies of complex disorders.

Epidemiology↗

Genetic design of solids possessing a random-particulate microstructure.

There exists a variety of difficulties in the computational design of macroscopic solid material properties formed by doping a homogeneous base matrix material with randomly distributed particles having different properties. Three primary problems are (1) the wide array of free microdesign variables, such as particle topology, property phase contrasts and volume fraction, which render the associated objective functions to be highly non-convex; (2) that the associated objective functions are not differentiable with respect to design variables, primarily due to prescribed constraints, such as prespecified restrictions on the microscale stress-field behaviour; and (3) the effective responses of various finite-sized samples, of equal volume but of different random particle distributions, exhibit mutual fluctuations, leading to amplified noise in optimization strategies where objective function sensitivities or comparisons are needed. The focus of this paper is the development of a statistical genetic algorithm which can handle difficulties due to non-convexity, lack of regularity and size effects. Theoretical properties of the overall approach are investigated. Semi-analytical and large-scale numerical examples, involving finite-element type discretizations, are given to illustrate its practical application.

Computer-Aided Design↗

Statistical aspects of genetic mapping in autopolyploids.

Many plant species of agriculture importance are polyploid, having more than two copies of each chromosome per cell. In this paper, we describe statistical methods for genetic map construction in autopolyploid species with particular reference to the use of molecular markers. The first step is to determine the dosage of each DNA fragment (electrophoretic band) from its segregation ratio. Fragments present in a single dose can be used to construct framework maps for individual chromosomes. Fragments present in multiple doses can often be used to link the single chromosome maps into homologous groups and provide additional ordering information. Marker phenotype probabilities were calculated for pairs of markers arranged in different configurations among the homologous chromosomes. These probabilities were used to compute a maximum likelihood estimator of the recombination fraction between pairs of markers. A likelihood ratio test for linkage of multidose markers was derived. The information provided by each configuration and power and sample size considerations are also discussed. A set of 294 RFLP markers scored on 90 plants of the species Saccharum spontaneum L. was used to illustrate the construction of an autopolyploid map. Previous studies conducted on the same data revealed that this species of sugar cane is an autooctaploid with 64 chromosomes arranged into eight homologous groups. The methodology described permitted consolidation of 54 linkage groups into ten homologous groups.

Chromosomes↗

Mating system and the evolution of quantitative traits: an experimental study of Mimulus guttatus.

The mating system of a population profoundly influences its evolution. Inbreeding alters the balance of evolutionary forces that determine the amount of genetic variation within a population. It redistributes that variation among individuals, altering heritabilities and genetic correlations. Inbreeding even changes the basic relationships between these genetic statistics and response to selection. If populations differing only in mating system are exposed to the same selection pressures, will they respond in qualitatively different ways? Here, we address this question by imposing selection on an index of two negatively correlated traits (flower size and development rate) within experimental populations that reproduce entirely by outcrossing, entirely by self-fertilizing, or by a mixture of outcrossing and selfing. Entirely selfing populations responded mainly by evolving larger flowers whereas outcrossing populations also evolved more rapid development. Divergence occurred despite an equivalent selection regime and no direct effect of mating system on fitness. The study provides an experimental demonstration of how the interaction of selection, genetic drift, and mating system can produce dramatic short-term changes in trait means, variances, and covariances.

Crosses, Genetic↗

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.

Alleles↗

Understanding Genomic Landscapes of Differentiation in Round-Tailed Horned Lizards (Phrynosoma modestum).

Population divergence is promoted by divergent selection and inhibited by gene flow, but the mechanisms of and relationship between these two processes remain poorly understood. Developing a well-informed hypothesis of the selective pressures underlying divergence in a natural population requires a thorough understanding of both species structure and demographic history. In this study, we assess whole-genome sequences of round-tailed horned lizards (Phrynosoma modestum) from throughout the species range and combine phylogenetic analyses with genomic landscape scans to understand how current genetic diversity has been influenced by demographic histories and evolutionary pressures. Maximum likelihood (ML) phylogenetic analysis supports two lineages within the species, corresponding to a North/South population divide that developed around 7&#x2005;million years ago (Ma) and displays little migration. However, intermediate genealogical divergence index values between the two lineages ultimately leave us unable to recommend a full taxonomic distinction. Genome-wide scans of population genetic statistics identified islands of divergence exhibiting differentiation patterns linked to models of reproductive isolation and within-population selection. Significantly negative values of Tajima's D and positive selection statistics in these islands offer support for selection acting on P. modestum, but patterns may also stem from recent population expansions. We posit that selection within populations has played a large role in shaping genomic divergence across the species' range. Taken together, our results provide perspective into how variable selective pressures shape the genomics of two divergent populations currently maintaining species integrity, despite significant signatures of geographic structure and divergence.

Animals↗

Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group.

Large-scale genotyping is required to generate dense identity-by-descent maps to map genes for human complex disease. In some studies the number of genotypes needed can approach or even exceed 1 million. Generally, linkage and linkage disequilibrium analyses depend on clear allele identification and subsequent allele frequency estimation. Accurate grouping or categorization of each allele in the sample (allele calling or binning) is therefore an absolute requirement. Hence, a genotyping system that can reliably achieve this is necessary. In the case of affected sib-pair analysis without parents, the need for accurate allele calling is even more critical. We describe methods that permit precise sizing of alleles across multiple gels using the fluorescence-based, Applied Biosystems (ABI) genotyping technology and discuss ways to reduce genotyping error rates. Using database utilities, we show how to minimize intergel allele size variation, to combine data effectively from different models of ABI sequencing machines, and automatically bin alleles. The final data can then be converted into a format ready for analysis by statistical genetic packages such as MENDEL.

Alleles↗

[Molecular genetics methods in the study of hereditary essential hypertension].

The main task in hypertension research is to explain genetic causes of a raised blood pressure. It is anticipated that advances in this area will promote not only a better understanding of the pathophysiology of hypertension but will make a more aimed approach to early diagnosis, prevention and therapy of essential hypertension possible. The greatest problems in investigations of the heredity of hypertension are; a) in cardiovascular control mechanisms several genes participate; b) factors of the external environment which act on a long-term basis interfere with the relationship of the genotype and phenotype individually, within the family and regionally; c) the blood pressure is a continuous variable and the definition of the phenotype of hypertension is inaccurate; d) inadequate number of family members where hypertension segregates. New methods in molecular biology and statistical genetics made it possible to assess a number of highly polymorphous genetic signs in several candidate genes and the subsequent investigation of their possible role in the pathogenesis of hypertension. The majority of hitherto accomplished studies was concentrated on genes coding different components of the renin-angiotensin system: renin, ACE, angiotensinogen and angiotensin II receptors. So far the most promising, though not consistent, results were obtained for angiotensinogen and the insulin receptor. Work focused on the relationship of the polymorphism of genes for ANF, growth hormone and kallikrein to essential hypertension is negative. The genetic heterogeneity of the human population, physiological differences in the genesis of high blood pressure in different ethnical groups and inaccurate measurements of specific phenotypes can contribute to different results of different studies.

Genes↗

Genetic epidemiology of familial aggregation of cancer.

Literature pertaining to genetic epidemiological studies of familial cancer has been reviewed from a historical perspective. Although interest in the question of heritability of cancer was extant at least as early as the beginning of the nineteenth century, early investigators were unable to produce consistent and meaningful evidence pertaining to the issue because of unsystematic methods of data collection and inadequate methods of data analysis. During the early twentieth century, developments in the fields of genetics, statistics, and epidemiology provided concepts and methods that permitted investigators to recognize important deficiencies in past studies, and to design others in which the critical comparisons could be made between patient groups and control groups. Registries of cancer incidence in large populations became available in several countries in the middle twentieth century, providing a standard "control group" for comparison. Large surveys of site-specific cancer experience in families, rigorously designed and analyzed, found for most kinds of cancers a two- to threefold increased risk for close relatives of propositi. These studies also reemphasized the great difficulty in obtaining even minimally complete family health history information, and the importance of verifying all reported cases with medical or vital records. Although clinical and laboratory investigation will be necessary to understand the mechanisms by which human genes may predispose to cancer, epidemiological approaches can estimate the extent to which genetic etiological factors may be present in a population, whether a general population or one defined by other factors under investigation. Population-based studies are already of practical significance to the clinical geneticist in the estimation of risk of eventual cancer development in unaffected family members, and can be expected to continue to identify specific groups and characteristics associated with genetic cancer predisposition. Finally, segregation and linkage analysis and their present applications to family studies of cancer were reviewed. As a result of the increasing number of DNA polymorphisms that are becoming available due to developments in molecular biology, the human gene map can be expected to be well defined in the near future, and investigation of families using segregation and linkage analysis will then be instrumental in defining the role of heredity in the development of cancer in human populations.

Age Factors↗

[A clinico-genetic analysis of functional temporomandibular joint lesions in children].

The authors review the results of a clinical genealogic investigation of 130 families with children suffering from abnormalities of the temporomandibular joints presenting as recurrent subluxations and/or arthrosis. A genetic statistic study, carried out by proband Weinberg's method in sibs families, has lead the authors to a conclusion on the monogenic autosomal dominant type of inheriting the temporomandibular joint abnormalities. A high incidence of diseases due to connective tissue failure in the body (lower limb varicose veins, spinal deformations, platypodia, hernias, hemorrhoids, etc.) in the families with children suffering from temporomandibular joint abnormalities has permitted the authors regard recurrent subluxations and/or arthrosis of the temporomandibular joints as a component of the total involvement of the connective tissue.

Adolescent↗

Mitochondrial DNA phylogeography reveals the existence of an Evolutionarily Significant Unit of the sand goby Pomatoschistus minutus in the Adriatic (Eastern Mediterranean).

The sand goby Pomatoschistus minutus is a major component of marine shelf and estuarine food webs and an important study organism in behavioural research. Yet, despite the sand goby's significance, its past and present patterns of migration and gene flow are poorly understood. Here we use the mtDNA control region and parts of the flanking tRNA genes of 63 fish from six localities in the Adriatic (Eastern Mediterranean), Western Mediterranean, Atlantic, and North Sea to investigate the phylogeography of this gobiid. Phylogenetic analyses and population genetics statistics reveal the existence of an Evolutionarily Significant Unit, sensu Moritz (1994), in the Adriatic and another in the Western Mediterranean, Atlantic, and North Sea. A possible biogeographical scenario for the separation of the ancestral population is that sand gobies in the Adriatic and Western Mediterranean split between 10,000 and 5000 years ago when due to the rise in sea temperature they migrated northwards and were bisected by the Italian peninsula. A testable prediction of this scenario is that sand gobies from the Western Mediterranean, Adriatic, and Aegean form three reciprocally monophyletic groups which are the descendants of a three-way diversification event.

Analysis of Variance↗

Population genomics: genome-wide sampling of insect populations.

Modern population genetics underwent a major paradigm shift during the last decade of the 20th century with the discovery that thousands of genes of known function and position in a genome can be analyzed simultaneously in a single individual. The impact of this technology on insect population genetics is potentially profound. Sampling distributions of genetic statistics can now be derived from many individual loci or among many segregating sites within a gene. Inferences regarding random mating, gene flow, effective population sizes, disequilibrium, and relatedness among populations can now be based on patterns of variation at many loci. More importantly, genome-wide sampling enables population geneticists to distinguish effects that act on the whole genome from those that act on individual loci or nucleotides. We introduce the term "population genomics" to describe the process of simultaneous sampling of numerous variable loci within a genome and the inference of locus-specific effects from the sample distributions. The four critical assumptions implicit in the population genomics approach are explained in detail. Studies adopting this paradigm are reviewed, and the steps necessary to complete a population genomics study are outlined.

Animals↗

Population genetic data on loci LDLR, GYPA, HBGG, D7S8 and GC in the Bangkok population compared with rural Thais from Trat province.

Prior to the introduction of any DNA marker as a tool for person identification and paternity test in certain ethnic groups, a population genetic database should be constructed. Using multiplex primers in single tube polymerase chain amplification, 5 loci of unrelated genes in the PM Amplitype kit (Perkin Elmer) were studied in two Thai population groups: 228 DNA samples were extracted from blood collected at the Borai rural area in Trat province; another 123 DNA samples were collected at the outpatient clinic, Department of Forensic Medicine, King Chulalongkorn Memorial Hospital, Bangkok. Analysis of alleles and genotypes was performed after reversed dot blot hybridization of PCR products to allelic sequence specific probes immobilized on the membrane strip followed by nonradioisotopic detection according to the manufacturer's protocol. Population genetic statistic parameters including discrimination power (DP), the probability of matching (PM), power of exclusion for trio (PE trio) and typical paternity index (PI typical) were computed. Both Thai population groups showed no significant deviation from the Hardy Weinberg Expectation (HWE). The combined DP of all 5 loci in the PM Amplitype markers was 0.993636 for rural Thais and 0.994409 for Thais from Bangkok. The combined PM for rural Thais and those living in Bangkok was 0.006364 and 0.005591, respectively. The combined PE trio was 0.696825 and 0.698875 in both Thai population groups and the combined PI typical values were < 1.0. In conclusion, person identification using PM Amplitype DNA markers was efficient and satisfactory within certain limits. Hence, the application of PM Amplitype DNA markers for paternity tests should be cautiously considered and applied in combination with other parameters.

Alleles↗