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PubMed1990

Genetic analysis of Leishmania mexicana populations from Texas, Latin America, and the Caribbean.

A genetic analysis using enzyme data of 72 Leishmania mexicana isolated from hosts in Texas, Latin America, and the Caribbean is presented. All isolates from each country were combined and considered as local populations. Allomorph (allele determined by electrophoresis) frequencies for 20 enzyme (loci) were calculated and 7 populations (Texas, Mexico, Belize, Guatemala, Ecuador [EC], Venezuela, and the Dominican Republic [DR]) were compared pairwise in the statistic of genetic identity (I) (level of genetic similarity). All populations were found to be genetically similar with a mean I value for all comparisons of 0.890 +/- 0.067. When DR was included as one of the pair compared, I = 0.811 +/- 0.034. Among comparisons that include EC (excluding EC vs. DR), I = 0.875 +/- 0.026. The mean I for the other comparisons was less than 0.9. The data indicate that the DR population is divergent enough from the others that it can be considered at the subspecies/incipient species level of evolutionary divergence; the EC population is, to a lesser extent, distinct from the others, and the other 5 represent geographic populations of 1 widely distributed species. A diagrammatic representation of the allomorphs among the 72 isolates is included. There were some allomorph/geographical (or local) population relationships noted.

Animals↗
PubMed1999

A study of fluctuating asymmetry in hybrids of dwarf and normal lake whitefish ecotypes (Coregonus clupeaformis) from different glacial races.

Fish ecotypes found in north temperate lakes are increasingly used as model organisms to explore patterns and processes of population divergence that may ultimately cause speciation. Processes involved in their reproductive isolation are, however, still poorly understood. Recent experimental studies on whitefish ecotypes from different glacial races revealed that embryonic mortality of hybrids was 2.4-4.7 times higher than for parental forms. In this study, we compared fluctuating asymmetry (FA) in morphological traits of these same hybrid and pure crosses to test the hypothesis that genetic stress observed in hybrids at embryonic stages is also manifested at later developmental stages. Twelve morphological traits were used to measure asymmetry. Variable degrees of asymmetry were observed depending on traits and crosses, however there was no significant difference in FA among crosses. These results thus provided no evidence in support of the working hypothesis and indicated that genetic stress may differ among life stages. It is more likely that high hybrid embryonic mortality acts together with ecological factors at later stages to increase further the extent of reproductive isolation between sympatric whitefish ecotypes.

Animals↗
PubMed2026

Genetic evidence and cross-species functional characterization implicate CNN2 in age-related macular degeneration susceptibility.

Age-related macular degeneration (AMD) is a leading cause of irreversible visual impairment in the aging population globally. Although genome-wide association studies (GWAS) have identified many AMD susceptibility loci, the genes and mechanisms underlying many of these associations remain unresolved. Here, we integrated expression quantitative trait locus (eQTL) data with AMD GWAS to prioritize nine putative genes. Through in vivo screening in zebrafish, we demonstrated that the downregulation of cnn2 and sarm1 expression led to ocular structural abnormalities and visual functional impairment. Subsequent mouse model studies confirmed that Cnn2 deficiency affected photoreceptor structure and function, impaired contrast sensitivity, and caused abnormalities in cone cell immunostaining. Given that CNN2 is predominantly expressed in endothelial cells, we propose that endothelial dysfunction may cascade to impair photoreceptor function. Collectively, through in silico prioritization and cross-species functional characterization, we identify CNN2 as a candidate susceptibility gene in AMD pathogenesis, providing vital underlying mechanistic insights.

Animals↗
PubMed2006

Is there heterogeneity among syndromes of substance use disorder for illicit drugs?

The use of DSM criteria to evaluate liability to substance use disorders (SUDs) and to identify SUD phenotypes may not provide the sensitivity required to identify genes associated with vulnerability to SUDs. The purpose of this study is to evaluate a number of basic aspects of substance use that may be more proximal than full SUDs to risk genes, some of which may thus have greater potential utility as phenotypes in subsequent molecular genetic analyses. In this paper we present results from the first stage of our planned analyses, focusing on how individual symptoms of abuse and dependence may be used to create alternate phenotypes for SUDs. Specifically, we used factor analysis and biometrical modeling on each symptom of illicit substance abuse and dependence within different types of substances, and compared and contrasted factor patterns and heritabilities across the different substances. These analyses were carried out using a population-based sample of 3372 male-male twin pairs from the Vietnam Era Twin Registry who participated in the Harvard Twin Study of Substance Abuse. We obtained extensive data from these participants on substance use and SUDs via telephone interview in 1992, including data on the illicit substances: opiates, cocaine, cannabis, sedatives, stimulants, and psychedelics. The results indicate that: A) although a one-factor model assuming a single underlying liability for abuse and dependence symptoms and behaviors can be rejected for most substances, there is no uniform support for a two-factor model differentiating between abuse versus dependence; B) patterns of symptoms or behaviors reported by substance users vary across substances; C) not all symptoms or behaviors contribute equally to the presentation of an SUD; and D) the heritability of symptoms or behaviors of substance users varies both within and between substances. These results represent important first steps in facilitating the search for SUD-risk genes in subsequent high-throughput molecular genetic analyses by providing alternate phenotypes that may have both optimal validity and increased heritability.

Adult↗
PubMed2002

Association analysis of candidate genes for neuropsychiatric disease: the perpetual campaign.

Association studies have been proposed to identify the genetic determinants of complex neuropsychiatric traits. Although such studies of candidate genes offer great potential to identify genetic variants that contribute to the expression of psychiatric disease, no consistent associations have been identified. Studies to date have focused on candidate genes that are selected for analysis on the basis of incomplete information about gene function in the brain, therefore the majority of genes expressed in the brain have been ignored. Additionally, most genetic determinants of psychiatric disease will probably be of modest effect and therefore require association studies of large samples. As genomic technologies advance, massive genotyping of large samples should allow identification of alleles that contribute to psychopathology.

Data Interpretation, Statistical↗
PubMed2004

A genome scan for joint-specific hand osteoarthritis susceptibility: The Framingham Study.

OBJECTIVE: Studies investigating hand osteoarthritis (OA) as a single entity have not shown strong linkage of the disease with any chromosomal sites. We undertook this study to test our hypothesis that phenotypes of hand OA may show stronger linkage than has been shown for overall hand OA. METHODS: We performed a factor analysis on measures of hand OA to determine patterns of disease. Using the joint regions identified by this analysis, we performed a genome-wide linkage analysis for OA susceptibility loci using 426 original cohort members and 790 offspring cohort members in 267 pedigrees. Radiographic OA features evaluated included the Kellgren/Lawrence score, osteophytes, and joint space narrowing. Prior to linkage analysis, standardized residuals were computed from regression analysis of each phenotype on age. This was performed separately for each sex and cohort. The variance component model (GeneHunter) was then applied to the normalized scores of the residuals of both sexes and cohorts. RESULTS: There was evidence suggestive of linkage (logarithm of odds [LOD] score >1.5) at 16 sites. Four of these sites had LOD scores >3.0. Two of these sites (identified in the full sample) included a linkage region for OA of the distal interphalangeal (DIP) joint on chromosome 7 (155 cM; LOD score 3.06) and a linkage region for OA of the first carpometacarpal (CMC) joint on chromosome 15 (81 cM; LOD score 6.25). The other 2 sites (identified in women) included a linkage region for OA of the DIP joint on chromosome 1 (202 cM; LOD score 3.03) and a linkage region for OA of the first CMC joint on chromosome 20 (4 cM; LOD score 3.74). CONCLUSION: These data suggest that several chromosomes contain hand OA susceptibility genes and that a joint-specific approach may be more rewarding than a global approach to the genetics of hand OA. Further investigation of these regions is warranted using finer maps and other populations.

Chromosome Mapping↗
PubMed1989

Analysis of the National Toxicology Program data on in vitro genetic toxicity tests using multivariate statistical methods.

A series of multivariate statistical methods have been used to explore the results of a set of four in vitro short-term tests (STT) on 73 chemicals reported by the US National Toxicology Program (NTP). Cluster analysis showed that the mouse lymphoma mutation (MLY) and sister-chromatid exchange (SCE) were similar in performance, as were the Salmonella (STY) and chromosomal aberration test (CHA). The lack of association between tests using the same genetic end-point or at the same phylogenetic level found in previous analyses was confirmed in this study. Factor analysis was used to derive a scale of genetic damage. This measure was contrasted with rodent carcinogenicity; only a limited association was found (rank correlation coefficient, rs = 0.32). Linear discriminant analysis was used to study whether the STTs could be used to complement one another. The combination of STY with the other STTs did not improve significantly the prediction of rodent carcinogenicity of STY alone. In the entire set of chemicals, 33% were negative in STY and positive in at least two other STT, and 11% was negative in STY and positive in the three other tests. SCE and MLY were complementary to STY for identifying the most genotoxic chemicals, but CHA was not a useful complement. The presence of potential electrophilic sites in the chemicals was highly correlated with the STY results, but did not improve the ability of STY to identify genotoxic chemicals or predict rodent carcinogens. In conclusion, the other in vitro STTs did not complement STY for predicting carcinogenicity, but were an important complement for describing the potential genotoxicity of chemicals.

Animals↗
PubMed2006

Genetic and karyotypic structure in the shrews of the Sorex araneus group: are they independent?

The species of the common shrew (Sorex araneus) group are morphologically very similar but exhibit high levels of karyotypic variation. Here we used genetic variation at 10 microsatellite markers in a data set of 212 individuals mostly sampled in the western Alps and composed of five karyotypic taxa (Sorex coronatus, Sorex antinorii and the S. araneus chromosome races Cordon, Bretolet and Vaud) to investigate the concordance between genetic and karyotypic structure. Bayesian analysis confirmed the taxonomic status of the three sampled species since individuals consistently grouped according to their taxonomical status. However, introgression can still be detected between S. antinorii and the race Cordon of S. araneus. This observation is consistent with the expected low karyotypic complexity of hybrids between these two taxa. Geographically based cryptic substructure was discovered within S. antinorii, a pattern consistent with the different postglaciation recolonization routes of this species. Additionally, we detected two genetic groups within S. araneus notwithstanding the presence of three chromosome races. This pattern can be explained by the probable hybrid status of the Bretolet race but also suggests a relatively low impact of chromosomal differences on genetic structure compared to historical factors. Finally, we propose that the current data set (available at http://www.unil.ch/dee/page7010_en.html#1) could be used as a reference by those wanting to identify Sorex individuals sampled in the western Alps.

Animals↗
PubMed1992

Reporting of highly individual genetic typing results: a practical approach.

This paper considers the interpretation of serological typing data as a problem in forensic science, as opposed to a problem in population genetics or statistics. Controversies arising in this area are partly due to an overly narrow perspective that ignores basic forensic science principles. After an initial discussion of the special problem that deoxyribonucleic acid (DNA) blood typing poses to forensic science, the three difficulties common to all the proposed interpretive methods are discussed. These are: predicting genotype incidence from allele frequencies, predicting frequencies for the joint occurrence of genotypes in a number of different genetic marker systems, and determining the appropriate population to use to measure the frequencies. The inability to test assumptions that are inherent in our routine methods is noted. This is a procedural weakness that unnecessarily limits the admissibility of DNA typing evidence in court. A practical solution to this problem is offered that begins with minimal assumptions. Initially a statement is made based on (1) how many reference samples the laboratory has typed and (2) how many of these samples show genotypes corresponding to the case samples. The second stage of the presentation begins with a statement that additional assumptions are necessary to fully interpret the evidence and that although these assumptions are scientifically very reasonable, they cannot be absolutely proven. The presentation can then proceed, if desired, to consideration of the specific assumptions and frequency estimates of any of the methods that have been proposed to date. To follow this approach population data must be kept in a form that allows the simple first-stage statement to be made. This means that each individual's record would include typing results in each genetic marker system. Although this method of data storage differs from that used in most forensic science laboratories, it is exceptionally versatile, and allows great flexibility in data analysis.

Alleles↗
PubMed2005

Early extreme contradictory estimates may appear in published research: the Proteus phenomenon in molecular genetics research and randomized trials.

BACKGROUND AND OBJECTIVE: Divergent results on the same scientific question generate controversy. We hypothesized that controversial data are attractive to investigators and editors, and thus the most extreme, opposite results would appear very early rather than late, as data accumulate, provided data can be generated rapidly. METHODS: We used data from MEDLINE-indexed meta-analyses of case-control studies on genetic associations (retrospective, hypothesis-generating research with usually rapid turnaround) and meta-analyses of randomized trials of health care interventions (prospective, targeted research that usually takes longer) sampled from the Cochrane Library. Using cumulative meta-analysis, we evaluated how the between-study variance for studies on the same question changed over time and at what point the studies with the most extreme results ever observed had been published. RESULTS: The maximal between-study variance was more likely to be recorded early in the 44 eligible meta-analyses of genetic associations than in the 37 meta-analyses of health care interventions (P = .013). At the time of the first heterogeneity assessment, the most favorable-ever result in support of a specific association was more likely to appear than the least favorable-ever result (22 vs. 10, P = .017); the opposite was seen at the second heterogeneity assessment (15 vs. 5, P = .031). Such a sequence of extreme opposite results was not seen in the clinical trials meta-analyses. The estimated between-study variance decreased over time in genetic association studies (P = .010), but not in clinical trials (P = .30). CONCLUSION: In contrast to prospective trials, a rapid early sequence of extreme, opposite results is frequent in retrospective hypothesis-generating molecular research.

Case-Control Studies↗
PubMedDate not supplied

Blood pressure in infant twins: birth to 6 months of age.

To describe the time course of the early development genetic variance for blood pressure, a cohort of twins is being followed from birth to 1 year of age. The present interim report describes systolic and diastolic blood pressure measurements for 102 twin pairs (39 monozygotic (MZ) and 63 dizygotic (DZ) in the newborn period and at 1, 3 and 6 months of age. Mean values for both systolic and diastolic blood pressure were similar regardless of race, sex, zygosity, or chorionicity. Statistically significant genetic variance was detected for systolic blood pressure at 6 months of age but not for diastolic blood pressure at any data point. The data are consistent with the hypothesis that genetic factors that determine within-family similarities of blood pressure may be detected early in life, and support the need for further investigation of both genetic and environmental determinants of blood pressure in young populations.

Blood Pressure↗
PubMed1993

Characterization of differences between whiteflies using RAPD-PCR.

The B biotype of the sweetpotato whitefly, Bemisia tabaci (Gennadius) has caused over $200 million in crop damage in the US during 1992. The taxonomic classification of the A and B biotypes of B. tabaci is unclear. We used RAPD-PCR to demonstrate DNA differences between the A and B biotypes of this insect. All twenty of the RAPD primers tested distinguished readily between the biotypes. DNA extracted from individual eggs and nymphs showed identical differences. RAPD-based genetic similarity statistics indicate that these two biotypes of B. tabaci were no more similar to each other than to two other whitefly species: bayberry whitefly (Parabemisia myricae) or bandedwinged whitefly (Trialeurodes abutilonea). These results indicate that RAPD-PCR may be useful in distinguishing closely related organisms, but may not be useful in determining higher classification of insects. Before the taxonomic status of B. tabaci biotypes A and B can be determined, results from other genetic, morphological and physiological examinations will have to be compared.

Animals↗
PubMed2001

Lod scores for gene mapping in the presence of marker map uncertainty.

Multipoint lod scores are typically calculated for a grid of locus positions, moving the putative disease locus across a fixed map of genetic markers. Changing the order of a set of markers and/or the distances between the markers can make a substantial difference in the resulting lod score curve and the location and height of its maximum. The typical approach of using the best maximum likelihood marker map is not easily justified if other marker orders are nearly as likely and give substantially different lod score curves. To deal with this problem, we propose three weighted multipoint lod score statistics that make use of information from all plausible marker orders. In each of these statistics, the information conditional on a particular marker order is included in a weighted sum, with weight equal to the posterior probability of that order. We evaluate the type 1 error rate and power of these three statistics on the basis of results from simulated data, and compare these results to those obtained using the best maximum likelihood map and the map with the true marker order. We find that the lod score based on a weighted sum of maximum likelihoods improves on using only the best maximum likelihood map, having a type 1 error rate and power closest to that of using the true marker order in the simulation scenarios we considered.

Bias↗
PubMedDate not supplied

An indirect approach to the extensive calculation of relationship coefficients.

A method was described for calculating population statistics on relationship coefficients without using corresponding individual data. It relied on the structure of the inverse of the numerator relationship matrix between individuals under investigation and ancestors. Computation times were observed on simulated populations and were compared to those incurred with a conventional direct approach. The indirect approach turned out to be very efficient for multiplying the relationship matrix corresponding to planned matings (full design) by any vector. Efficiency was generally still good or very good for calculating statistics on these simulated populations. An extreme implementation of the method is the calculation of inbreeding coefficients themselves. Relative performances of the indirect method were good except when many full-sibs during many generations existed in the population.

Biometry↗
PubMed2001

Differences in population structure of the anther smut fungus Microbotryum violaceum on two closely related host species, Silene latifolia and S. dioica.

We investigated the genetic population structure of the sexually transmitted plant pathogen, the fungus Microbotryum violaceum, on the two closely related host species Silene latifolia and S. dioica using microsatellite markers. We found strong deviations from Hardy-Weinberg expectations, with significant heterozygote deficiency in almost all populations. Fungal strains from the two host species were differentiated, and these host races differed in amount of variation within populations and differentiation among populations. Anther smut from S. latifolia harboured significantly less microsatellite diversity and were more genetically differentiated from each other than those from S. dioica. Small effective population sizes, rapid population turnover, and less gene flow among populations could lead to this higher population differentiation and lower within population genetic diversity for anther smut populations on S. latifolia than on S. dioica. These results are in concordance with host ecology because S. latifolia grows in more disturbed habitats than S. dioica and may provide a shorter-lived host environment.

Alleles↗
PubMed1998

[Interpopulation diversity of the gene pool: beta distribution of Wright's F(ST) statistics].

The distribution of FST(i) estimates were studied in representative samples of ith genes for the gene pools of the major human populations, including the populations of Europe, Asia, Africa, Australia, America, North-eastern Eurasia, and five subregions of the latter. An average of 80 FST(i) estimates were analyzed for each sample of marker genes with a level of polymorphism (q) from 0.05 to 0.95. For each gene pool, the empirical distributions of FST(i) estimates were approximated by the main types of theoretical distributions--the normal, chi 2, Weibull, gamma, and beta distributions. In all gene pools, only beta distributions were good approximations of the empirical FST(i) distributions. The parameters of the beta distributions are reported in this study. It was demonstrated that the characteristics of beta distributions for all major gene pools studied could be interpolated to the smaller constituent gene pools. since the use of the traditional parametric tests starts from an assumption of normal distribution, they are inapplicable to analysis of FST statistics. Therefore, the obtained parameters of beta distributions should be used. These parameters allow the confidence intervals of the average FST values to be determined and permit correct comparison between the characteristics of both individual genes and gene pools to be performed.

Africa↗
PubMedDate not supplied

Non-random distribution of various sizes of human Y chromosomes in different ethnic groups.

One hundred and ninety normal males from three ethnically different populations (Caucasians, American blacks and East Indians) were selected to study the frequency distribution of length of the Y chromosome, fluorescent (f) and non-fluorescent (nf) segments as a function of Y/F, f/F and nf/F indices. The QFQ techniques was performed to identify the f and nf segments. The frequency distribution of the total length of Y chromosome was not normally distributed in all three populations (P less than 0.05). Extensive statistical analysis revealed that the non-random distribution of the total length was due to skewness and kurtosis for both the n and nf segments. The clinical implications as well as evolutionary aspects of such variation in ethnic anthropology are discussed.

Black People↗
PubMed2004

Optimizing exact genetic linkage computations.

Genetic linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the probability of data, which is needed for learning linkage parameters, using exact computation procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper, we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of SUPERLINK, which is a fast genetic linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm and hence enlarge the class of problems that can be handled effectively by exact computations.

Algorithms↗