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PubMed2026

Evaluation of the efficacy of optical genome mapping in prenatal diagnosis: a retrospective cohort study.

BACKGROUND: Optical genome mapping (OGM) is an emerging cytogenetic method for concurrently detecting structural variants (SVs) and copy number variants (CNVs). However, its clinical application in prenatal diagnosis remains underexplored. METHODS: This study retrospectively evaluated the clinical validity of OGM in prenatal diagnosis by comparing with two routine genetic testing methods: karyotyping and chromosomal microarray analysis (CMA). Both positive and negative cases detected by routine genetic methods were enrolled to evaluate the technical concordance of OGM and its capability to improve diagnostic rate in negative cases. The exclusion criteria were balanced centromeric translocations, mosaic cases with cellular fractions&#x2009;<&#x2009;20%, and loss of heterozygosity (LOH)&#x2009;<&#x2009;25&#xa0;Mb. All samples subjected to OGM testing were anonymized and analyzed blindly. The results from OGM were compared with those from routine genetic testing, and statistical analyses were performed to assess technical concordance and diagnostic rate. RESULTS: Of 217 samples (166 positive samples and 51 negative samples for routine genetic testing), all were successfully tested with OGM, including 2 umbilical cord blood samples, 4 chorionic villi samples, and 211 cultured amniotic fluid samples. Of the 207 reportable chromosomal aberrations from 166 positive samples, the blinded concordance between OGM and CMA, karyotyping, and combination of karyotyping plus CMA was 97.81%, 96.36%, and 97.10%, respectively. OGM missed six aberrations initially, including one LOH, two marker chromosomes, and three microdeletions. However, after reanalysis, its concordance improved to 100% with CMA and 99.03% with karyotyping plus CMA. OGM also diagnosed one additional case of a 3-kb deletion in 51 negative samples, improving the diagnostic rate by 1.96%. Moreover, OGM reclassified the pathogenicity of two microdeletions from pathogenic to uncertain significance in 2 positive cases. Furthermore, OGM clarified the diagnosis suspected by routine genetic testing and improved diagnostic accuracy in some cases. CONCLUSION: As far as we know, this is the largest retrospective study on OGM in prenatal diagnosis, and it includes a broad range of sample types. The results showed that OGM exhibits high concordance among the tested methods and increases the diagnostic rate. Thus, OGM has the potential to become a first-line technique for prenatal diagnosis in the future.

Humans↗
PubMed2005

Estimating diversifying selection and functional constraint in the presence of recombination.

Models of molecular evolution that incorporate the ratio of nonsynonymous to synonymous polymorphism (dN/dS ratio) as a parameter can be used to identify sites that are under diversifying selection or functional constraint in a sample of gene sequences. However, when there has been recombination in the evolutionary history of the sequences, reconstructing a single phylogenetic tree is not appropriate, and inference based on a single tree can give misleading results. In the presence of high levels of recombination, the identification of sites experiencing diversifying selection can suffer from a false-positive rate as high as 90%. We present a model that uses a population genetics approximation to the coalescent with recombination and use reversible-jump MCMC to perform Bayesian inference on both the dN/dS ratio and the recombination rate, allowing each to vary along the sequence. We demonstrate that the method has the power to detect variation in the dN/dS ratio and the recombination rate and does not suffer from a high false-positive rate. We use the method to analyze the porB gene of Neisseria meningitidis and verify the inferences using prior sensitivity analysis and model criticism techniques.

Bayes Theorem↗
PubMed2004

Mutators in space: the dynamics of high-mutability clones in a two-patch model.

Clones of bacteria possessing high-mutability rates (or mutators) are being observed in an increasing number of species. In a constant environment most mutations are deleterious, and hence the spontaneous mutation rate is generally low. However, mutators may play an important role in the adaptation of organisms to changing environments. To date, theoretical work has focused on temporal variability in the environment, implicitly assuming that environmental conditions are constant through space. Here, we develop a two-patch model to investigate how spatiotemporal environmental variability and dispersal might influence mutator dynamics. Environmental conditions in each patch fluctuate between two states; the rate of fluctuation varies in each patch at differing phase angles. We find that at low and intermediate rates of fluctuation, an increase in dispersal results in a decrease in the density of mutators. However, at high rates of environmental change, dispersal causes an increase in mutator density. For all frequencies of environmental fluctuation these trends are enhanced as the phase angle approaches 180 degrees. We argue that future work, both empirical and theoretical, is needed to improve our understanding of how spatiotemporal variability impacts on mutator densities and dynamics.

Alleles↗
PubMed2001

Platelet-derived growth factor (PDGF) gene delivery for application in periodontal tissue engineering.

BACKGROUND: A challenge in the reconstruction of periodontal structures is the targeted delivery of growth-promoting molecules to the tooth root surface. Polypeptide growth factors such as platelet-derived growth factor (PDGF) stimulate both cementogenesis and osteogenesis. Recent advances in gene therapy offer the advantage of delivering recombinant proteins to tissues for extended periods of time in vivo. METHODS: Recombinant adenoviral vectors encoding for the PDGF-A gene were constructed to allow delivery of PDGF transgenes to cells. The recombinant adenoviruses were assembled using the viral backbone of Ad2/CMV/EGFP and replacing GFP (reporter gene encoding green fluorescent protein driven by the cytomegalovirus promoter [CMV] within adenovirus type 2) with the PDGF-A gene. Root lining cells (cloned cementoblasts) were transduced with Ad2/PDGF-A and evaluated for gene expression, DNA synthesis, and cell proliferation. PDGF-inducible genes, c-myc and osteopontin, were also evaluated following gene delivery of Ad2/PDGF-A. RESULTS: The results revealed high level transduction of cementoblasts by gene transfer for 7 days as evidenced by flow cytometry and Northern blotting. Cementoblast DNA synthesis and subsequent proliferation were stimulated by Ad2/PDGF-A at levels equal to or greater than continuous rhPDGF-AA application. Strong message for the PDGF-A gene and protein as evidenced by Northern blotting and immunocytochemistry was noted. Furthermore, the potent induction of c-myc and osteopontin mRNA was found after PDGF gene delivery to cementoblasts. CONCLUSIONS: These findings demonstrate that gene delivery of platelet-derived growth factor stimulates cementoblast activity that is sustained above that of rhPDGF-AA application. The use of gene therapy as a mode of growth factor delivery offers a novel approach to periodontal tissue engineering.

Adenoviridae↗
PubMed2005

Replication, variation and normalisation in microarray experiments.

INTRODUCTION: Microarray experiments often have complex designs that include sample pooling, biological and technical replication, sample pairing and dye-swapping. This article demonstrates how statistical modelling can illuminate issues in the design and analysis of microarray experiments, and this information can then be used to plan effective studies. METHODS: A very detailed statistical model for microarray data is introduced, to show the possible sources of variation that are present in even the simplest microarray experiments. Based on this model, the efficacy of common experimental designs, normalisation methodologies and analyses is determined. RESULTS: When the cost of the arrays is high compared with the cost of samples, sample pooling and spot replication are shown to be efficient variance reduction methods, whereas technical replication of whole arrays is demonstrated to be very inefficient. Dye-swap designs can use biological replicates rather than technical replicates to improve efficiency and simplify analysis. When the cost of samples is high and technical variation is a major portion of the error, technical replication can be cost effective. Normalisation by centreing on a small number of spots may reduce array effects, but can introduce considerable variation in the results. Centreing using the bulk of spots on the array is less variable. Similarly, normalisation methods based on regression methods can introduce variability. Except for normalisation methods based on spiking controls, all normalisation requires that most genes do not differentially express. Methods based on spatial location and/or intensity also require that the nondifferentially expressing genes are at random with respect to location and intensity. Spotting designs should be carefully done so that spot replicates are widely spaced on the array, and genes with similar expression patterns are not clustered. DISCUSSION: The tools for statistical design of experiments can be applied to microarray experiments to improve both efficiency and validity of the studies. Given the high cost of microarray experiments, the benefits of statistical input prior to running the experiment cannot be over-emphasised.

Algorithms↗
PubMed2004

Microarray data analysis: a hierarchical T-test to handle heteroscedasticity.

The analysis of differential gene expression in microarray experiments requires the development of adequate statistical tools. This article describes a simple statistical method for detecting differential expression between two conditions with a low number of replicates. When comparing two group means using a traditional t-test, gene-specific variance estimates are unstable and can lead to wrong conclusions. We construct a likelihood ratio test while modelling these variances hierarchically across all genes, and express it as a t-test statistic. By borrowing information across genes we can take advantage of their large numbers, and still yield a gene-specific test statistic. We show that this hierarchical t-test is more powerful than its traditional version and generates less false positives in a simulation study, especially with small sample sizes. This approach can be extended to cases where there are more than two groups.

Algorithms↗
PubMed2006

Advances in systems biology: measurement, modeling and representation.

Systems biology is frequently defined as the study of all of the elements in a biological system and their relationship to one another in response to perturbation. Advances in science and technology are enabling the development of this emerging and cross-disciplinary field by allowing researchers to explore how biological components function as a network in cells, tissues and organisms. Recently, pharmaceutical companies have begun to embrace systems approaches in an effort to better understand physiology, pathogenic processes and pharmacological responses. This review focuses on recent advances within three core areas of systems biology: data collection, data analysis, and the integration and sharing of data.

Animals↗
PubMed2006

Parasites as biological tags in population studies of demersal and pelagic fish species.

Among the different techniques applied in a holistic approach for fish stock identification, the use of parasites as "biological tags" is becoming increasingly important. In this presentation, our recent studies on the use of some parasite species, identified by genetic markers, and the parasite/fauna composition, in stock identification of demersal (Merluccius merluccius), small pelagic (Trachurus trachurus), and large pelagic fish species (Xiphias gladius) are reviewed. Different species of Anisakis and Hysterothylacium were genetically identified by the application of genetic (allozyme) markers. Statistically significant differences in the spatial distribution of distinct species of Anisakis were found in the fish considered. As to the species of Hysterothylacium genetically detected, different relative proportions were detected in several Mediterranean and Atlantic samples of swordfish (X. gladius). This study demonstrates the potential value of these anisakid nematodes, at both larval and adult stages, as "biological tags" for these fish species in European waters.

Animals↗
PubMed1990

Linkage strategies for genetically complex traits. II. The power of affected relative pairs.

The power to detect disease-susceptibility loci through linkage analysis using pairs of affected relatives and affected-unaffected pairs is examined. Allelic identity by descent (ibd) for a completely polymorphic marker for sibling, uncle-nephew, grandparent-grandchild, half-sib, and first-cousin pairs is considered. Affected-unaffected pairs generally represent a poor strategy. For single-locus models, ibd depends on lambda R, the risk ratio for type R relatives compared with population prevalence, and the recombination fraction theta. The ibd for grandparent-grandchild pairs is least affected by recombination, followed by sibs, half-sib, uncle-nephew, and first-cousin pairs. For diseases with large lambda values and for small theta values, distant relatives offer greater power. For larger theta values, grandparent-grandchild pairs are best; for small lambda values, sibs are best. Additive and multiplicative multilocus models are considered. For the multiplicative model, the same formulas as in the single-locus model apply, except that lambda iR (for the ith contributing locus) is substituted for lambda R. For the additive model, the deviation from null expectation for ibd is divided among all contributing loci. Compared with the multiplicative model, for an additive model there is usually greater advantage in distant relationships. Multipoint analysis using linked marker loci for affected relative pairs is described. Simultaneous use of multiple markers diminishes the effect of recombination and allows for localization of the disease-susceptibility locus.

Alleles↗
PubMed1978

Frequency distribution and discrimination probability of twelve protein genetic variants in human blood as functions of race, sex, and age.

Fresh blood samples were obtained from 6004 whites, 1025 blacks, 1596 Chicano/Amerindians, and 3053 Asians of California and Hawaii. The samples were typed for ABO and Rh groups and were analyzed electrophoretically for ten genetically determined protein variant systems. The effects of race, age, and sex on phenotypic frequencies within each of the twelve genetic systems were investigated. Large frequency differences were found between races but not between different age and sex subgroups within races. It was also demonstrated that the twelve genetic systems behaved statistically independently. Discrimination probabilities were computed for each of the four ethnic groups. These serve as a measure of the effectiveness of the twelve genetic systems examined in individualizing blood samples. The method is discussed for computing the probability that a randomly chosen individual of a given ethnic group possesses the same blood phenotypes as found in a predetermined sample of blood. The results presented here should prove useful in the investigation of civil and criminal cases involving blood samples.

ABO Blood-Group System↗
PubMed2003

An RAPD (random amplified polymorphic DNA) analysis of genetic population structure of Balea biplicata (Gastropoda: Clausiliidae) in fragmented floodplain forests of the Elster/Saale riparian system.

Eight German populations of the land snail Balea biplicata (Mollusca: Clausiliidae) were studied using the randomly amplified polymorphic DNA-polymerase chain reaction and morphometrics (principal component and discriminant analysis) to examine population structure and gene flow patterns in a fragmented landscape mosaic along the Elster/Saale riparian system, Germany. A variety of population genetic analyses targeting either more on the geographic scale of gene flow (genetic distances, F statistics, Mantel test) or on local genotypic structure (heterozygosity, linkage disequilibrium, bottleneck probability) showed that (1) the population system in total is governed by high gene flow independent of geographic distance, (2) genetic structure on the narrower sampling scale is mainly determined by stochastic processes due to genetic drift in small isolated and frequently recolonized populations, and (3) the morphometrical variation of the populations was related neither to habitat nor to genetic heterogeneity. The potentials for active and passive dispersal capacity of the snails and possible environmental impacts on their population structure are discussed.

Animals↗
PubMed2000

Two-stage global search designs for linkage analysis I: use of the mean statistic for affected sib pairs.

Two-stage global search designs for linkage analysis using pairs of affected relatives were shown by Elston et al. [1996] to typically halve the cost of a study compared to a one-stage design. The statistic used for testing linkage in that study was based on the proportion of pairs sharing no marker alleles identical by descent (IBD). However, it has been established that the mean statistic often has the greatest power for full sib pairs [Blackwelder and Elston, 1985; Schaid and Nick, 1990; Knapp et al. 1994]. In this paper, we study optimal two-stage global search designs, in the case of affected full sib pairs, when using the mean test statistic to test for linkage. When dominant genetic variance is present, using the mean statistic is usually more cost efficient than using the proportion of pairs sharing no maker alleles IBD; in the case when there is no dominant genetic variance, the mean statistic leads to a better design, in the sense of being more cost-saving, provided that the relative risk ratio for first-degree relatives is small. The effect of heterogeneity and markers' informativeness is also investigated, the latter using the Linkage Information Content value for sibs.

Alleles↗
PubMed2000

Genetic structure of reciprocal social behavior.

OBJECTIVE: The study examined the genetic structure of deficits in reciprocal social behavior in an epidemiologic sample of male twins. METHOD: Parents of 232 pairs of 7-15-year-old male twins completed the Social Reciprocity Scale to provide data on their children's reciprocal social behavior. Scale scores were analyzed by using structural equation modeling. RESULTS: Intraclass (twin-twin) correlations for scores on the Social Reciprocity Scale were 0.73 for monozygotic twins (N=98 pairs) and 0.37 for dizygotic twins (N=134 pairs). The best fitting model of causal influences on reciprocal social behavior incorporated additive genetic influences and unique environmental influences. CONCLUSIONS: For school-age boys in the general population, reciprocal social behavior is highly heritable, with a genetic structure similar to that reported for autism in clinical samples. Continuous measures of reciprocal social behavior may be useful for characterizing the broader autism phenotype and may enhance the statistical power of genetic studies of autism.

Adolescent↗
PubMed1998

The genetic code is one in a million.

Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation: erroneous codons are either synonymous or code for an amino acid with chemical properties very similar to those of the one that would have been present had the error not occurred. This work has suggested that the second base of codons is less efficient in this respect, by about three orders of magnitude, than the first and third bases. These results are based on the assumption that all forms of error at all bases are equally likely. We extend this work to investigate (1) the effect of weighting transition errors differently from transversion errors and (2) the effect of weighting each base differently, depending on reported mistranslation biases. We find that if the bias affects all codon positions equally, as might be expected were the code adapted to a mutational environment with transition/transversion bias, then any reasonable transition/transversion bias increases the relative efficiency of the second base by an order of magnitude. In addition, if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.

Amino Acids↗
PubMed1996

Segregation analysis of alcoholism in high density families: a replication.

We have previously reported segregation analysis of alcoholism in 35 multigenerational families, each ascertained through a pair of male alcoholics by using the mixed model implemented by POINTER. This analysis suggested that liability to alcoholism was, in part, controlled by a major effect with or without additional multifactorial effects. The hypothesis that the major effect was explained by a single genetic locus with strictly mendelian transmission was rejected. The purpose of the present analysis was to use the regressive model implemented by the REGD program from the Statistical Analysis for Genetic Epidemiology computer package (S.A.G.E.) to confirm by replication that a major effect was present in these 35 families. Evidence for the major effect found in Pointer was replicated in the present analysis by using S.A.G.E. Also, we found strong evidence for parental effects that were independent of the major locus transmission from ancestral relatives to children. Mendelian transmission of this major effect was rejected when models incorporated parental effects. When the major effect was calculated adjusting for parental phenotypes, the relative risk of affection for children was about twice as high with affected parents vs. unaffected parents.

Adolescent↗
PubMed2025

RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico.

UNLABELLED: The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO&#x2009;=&#x2009;0.333-0.264) and did not reveal population differentiation within our samples (F ST&#x2009;=&#x2009;-&#xa0;0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.

Caribbean Fisheries↗
PubMed1993

BSB: a new mouse model of multigenic obesity.

We report here a new mouse model of multigenic obesity. Backcross progeny ((C57BL/6J x Mus spretus)F1 x C57BL/6J), designated as BSB mice, range from 1% to 50% body fat. Since both parental strains are relatively lean, the wide range of the phenotype in the BSB mice indicates the involvement of multiple genes to produce obesity. Obesity in BSB mice results from increases in both intra-abdominal and subcutaneous fat and is associated with hyperinsulinemia, hyperglycemia, and hyperlipidemia. Female and male BSB mice do not differ in the degree of obesity obtained. Stimulated plasma corticosterone levels are reduced in obese male and female mice. The development of appropriate genetic markers and statistical methods have made it feasible to analyze quantitative polygenic traits in animal models by employing F2 or backcross progeny. Thus, this BSB model is uniquely suited to the genetic analysis of the multifactorial quantitative trait of obesity and its associated phenotypes.

Animals↗