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PubMed2000

Multiple-changepoint testing for an alternating segments model of a binary sequence.

A binary sequence may give the appearance of being composed of alternating segments with relatively high and relatively low probability of success. Determining whether such an alternating pattern is significant is a multiple-changepoint problem where the number of segments and their success probabilities are unknown, with the added constraint of segment alternation. A dynamic programming method for determining the optimal segmentation into a given number of segments is provided. Given this, a variation on the simulation method of Venter and Steel (1996, Computational Statistics and Data Analysis 22, 481-504) may be employed to test the null hypothesis of a homogeneous sequence as well as to estimate the number and location of changepoints. A sample application, the assessment of the possibility of genetic recombination in HIV sequences, is presented.

Base Sequence↗
PubMed2006

Viva la Familia Study: genetic and environmental contributions to childhood obesity and its comorbidities in the Hispanic population.

BACKGROUND: Genetic and environmental contributions to childhood obesity are poorly delineated. OBJECTIVE: The Viva la Familia Study was designed to genetically map childhood obesity and its comorbidities in the Hispanic population. The objectives of this report were to describe the study design and to summarize genetic and environmental contributions to the phenotypic variation in obesity and risk factors for metabolic diseases in Hispanic children. DESIGN: The Viva la Familia cohort consisted of 1030 children from 319 families selected based on an overweight proband between the ages of 4 and 19 y. In-depth phenotyping to characterize the overweight children and their siblings included anthropometric and body-composition traits by dual-energy X-ray absorptiometry and assessments of diet by 24-h recalls, physical activity by accelerometry, and risk factors for metabolic diseases by standard biochemical methods. Univariate quantitative genetic analysis was used to partition phenotypic variance into additive genetic and environmental components by using the computer program SOLAR. RESULTS: Sex, age, and environmental covariates explained 1-91% of the phenotypic variance. Heritabilities of anthropometric indexes ranged from 0.24 to 0.75. Heritability coefficients for the body-composition traits ranged from 0.18 to 0.35. Diet and physical activity presented heritabilities of 0.32 to 0.69. Risk factors for metabolic diseases were heritable with coefficients ranging from 0.25 to 0.73. Significant genetic correlations between obesity traits and risk factors for metabolic diseases substantiated pleiotropy between traits. CONCLUSION: The Viva la Familia Study provides evidence of a strong genetic contribution to the high prevalence of obesity and its comorbidities in Hispanic children.

Adolescent↗
PubMed2025

Association of HFE genotypes with hemochromatosis-related phenotypes in the All of Us research program.

PURPOSE: Type 1 hereditary hemochromatosis (HH) can result in iron overload and liver disease if not detected and treated early. Most cases are found among people homozygous for HFE p.Cys282Tyr variants. Compound heterozygosity with the HFE p.His63Asp variant is associated with disease to a lesser degree. We sought to examine the association of HFE variation with HH-related phenotypes and assess the prevalence of testing and diagnosis of HH using All of Us data. METHODS: We used data from 133,978 participants with genetic information linked to medical records. For different HFE genotypes, we examined the prevalence of HH diagnosis codes and related biochemical and clinical phenotypes. RESULTS: Among participants who were p.Cys282Tyr homozygotes, the prevalence of HH diagnosis codes was 22.6% among males and 15.6% among females. Serum transferrin-iron saturation measures were available only for 31.4% of males and 21.1% of females who were p.Cys282Tyr homozygotes. Liver disease, including cirrhosis or hepatocellular carcinoma, was present more among males who were p.Cys282Tyr homozygotes compared with males with no p.Cys282Tyr or p.His63Asp variants (15.5% vs 8.5%, P = .0001). Of the 71 participants who were p.Cys282Tyr homozygotes with indication of liver disease, 32 (45.1%) did not have a serum transferrin-iron saturation measure, and 37 (52.1%) did not have diagnosis codes for HH. CONCLUSION: Limited serum transferrin-iron saturation measures or HH diagnosis codes among p.Cys282Tyr homozygotes, even those with liver disease, suggests potential undertesting and underdiagnosis of type 1 HH in clinical practice and a need for improved awareness, education, and testing around HH.

C282Y homozygosity↗
PubMedDate not supplied

[Problems of variability in weightlessness].

The genetic (cytogenetic) effects of microgravity have been under study for about 30 years. This line of research developed through three periods. Initially, biologists raised the question whether microgravity may act as a lethal factor or a strong mutagen. Many flight experiments gave a negative answer to it. The major goal of the second period was to identify the effects of microgravity at the chromosomal and cellular levels. Such effects, statistically significant although small in value, were detected in Tradescantia paludosa and Drosophila melanogaster microspores. These findings were confirmed by American and--later--by European investigators. The third period addresses the entire problem of variability in microgravity. This approach can be implemented on the basis of a comprehensive program of research that will include experiments at different levels: from the gene to the population level. The basic objective of the program is to clarify the role of the genetic apparatus in the adaptation of living systems to microgravity and, consequently, to determine the role of gravity in the evolution of life on the Earth.

Adaptation, Biological↗
PubMed2002

Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia.

Prior evidence has supported the existence of multiple susceptibility genes for schizophrenia. Multipoint linkage analysis of the 270 Irish high-density pedigrees that we have studied, as well as results from several other samples, suggest that at least one such gene is located in region 6p24-21. In the present study, family-based association analysis of 36 simple sequence-length-polymorphism markers and of 17 SNP markers implicated two regions, separated by approximately 7 Mb. The first region, and the focus of this report, is 6p22.3. In this region, single-nucleotide polymorphisms within the 140-kb gene DTNBP1 (dystrobrevin-binding protein 1, or dysbindin) are strongly associated with schizophrenia. Uncorrected, empirical P values produced by the program TRANSMIT were significant (P<.01) for a number of individual SNP markers, and most remained significant when the data were restricted to include only one affected offspring per nuclear family per extended pedigree; multiple three-marker haplotypes were highly significant (P=.008-.0001) under the restricted conditions. The pattern of linkage disequilibrium is consistent with the presence of more than one susceptibility allele, but this important issue is unresolved. The number of markers tested in the adjacent genes, all of which are negative, is not sufficient to rule out the possibility that the dysbindin gene is not the actual susceptibility gene, but this possibility appears to be very unlikely. We conclude that further investigation of dysbindin is warranted.

Animals↗
PubMed2026

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.

A pangenome reference overcomes the inherent limitation of any individual reference genome by integrating the variation present in a population. We present the Human Pangenome Reference Consortium's (HPRC) Release 2 (HPRC2), an openly available, second phase pangenome that is an approximately fivefold expansion in genome number over HPRC Release 1 (HPRC1) and measurable improvement in genome completeness, contiguity, and accuracy. Selecting samples with a principled algorithm prioritising common variant coverage, HPRC2 contributes 460 haplotypes that together capture over 99% of common variation observed in the All of Us Research Program v8 cohort. Combining high-coverage long and ultra-long reads with modern assemblers and polishers, we produce thousands of telomere-to-telomere (T2T) chromosomes, and relative to HPRC1 halve the number of structurally unreliable regions as well as individual base errors per haplotype. We complement the assemblies with whole genome multiple alignments and gene annotations, and derive formal pangenome coordinate systems for addressing off-reference variation, demonstrating that individual human genomes contain more than one hundred thousand variants not succinctly described with respect to existing reference genomes. We also present the first matched long-read backed pantranscriptome and panepigenome at this scale, provide continuous local-ancestry estimates spanning every genome, and outline a host of new tools and applications that leverage the pangenome resource for improved genomics analysis.

Journal Article↗
PubMed1995

Association of protein polymorphism among pepper (Capsicum annuum L.) inbred lines with agronomic performance of their crosses.

The genetic variation of 10 morphologically similar pepper (Capsicum annuum L.) inbred lines has been analyzed by two-dimensional electrophoresis with immobilized pH gradient (IPG-DALT) of seed proteins. For all pairs of inbred lines genetic distance indices were calculated on the basis of the IPG-DALT analysis and a genetic tree was constructed. The protein polymorphism data of the 10 inbred lines were integrated into a pepper breeding program to validate the assumption that there is a higher chance of achieving better hybrid performance when the genetic distance between the parents is as great as possible. Field trials were performed in Turkey and consisted of a total of 27 crossings based on 9 inbred lines. Fifteen hybrids exceeded the crop yield of the better parent and 8 additional hybrids exceeded the mean crop yield of both parents. The genetic distance indices of the parental inbred lines based on protein polymorphism data were not significantly correlated to heterosis performance of the experimental hybrids (r = 0.20), indicating that protein polymorphism data add little to the prediction of single cross hybrid performance. Nevertheless, protein polymorphism data support the breeder in being more effective in finding out the best inbred combinations, because most of the less promising crossings can be omitted from the expensive and time-consuming performance tests. Those hybrids whose distance indices exceeded the mean of all 27 distance values (0.52) were superior to the mean value of all heterosis performances by 19%.(ABSTRACT TRUNCATED AT 250 WORDS)

Capsicum↗
PubMed2025

Genome-wide association study of copy number variations in Parkinson's disease.

OBJECTIVE: To investigate the impact of copy number variations (CNVs) on Parkinson's disease (PD) pathogenesis using genome-wide data and explore their role in sporadic PD. METHODS: We analyzed CNV data from 11,035 PD patients (including 2,731 early-onset PD (EOPD)) and 8,901 controls from the COURAGE-PD consortium using a sliding window CNV-GWAS and genome-wide burden analysis. The independent dataset from the Global Parkinson Genetics Program (GP2) consisted of 23,089 cases and 18,824 controls were used to validate our initial findings. RESULTS: The exploratory dataset identifies multiple CNV regions associated with PD risk. The nominated CNV loci were not confirmed in an independent dataset, except that only a deletion in the PRKN gene, a well-established EOPD locus, remained genome-wide significant and robustly supported. CNV burden analysis showed a higher prevalence of CNVs in PD-related genes in patients compared to controls (OR=1.56 [1.18-2.09], p=0.0013), with PRKN showing the highest burden (OR=1.47 [1.10-1.98], p=0.026). Patients with CNVs in PRKN had an earlier disease onset. Burden analysis with controls and EOPD patients showed similar results. INTERPRETATION: The largest CNV-based GWAS on PD highlights both the promise and pitfalls of array-based CNV detection in PD and underscores the relevance of whole-genome sequencing approaches in resolving the role of CNV in PD. The array-based findings are prone towards false positive findings that might arise either from platform limitations and/or cohort biases. Future studies require improved genotyping resolution and rigorous cross-cohort validation to reliably assess CNV contributions to PD risk.

Journal Article↗
PubMed1984

Date of conception and prevention of neural tube defects.

The authors studied the time of conception of 280 fetuses and liveborns with anencephaly or spina bifida seen in a French Canadian population during a period of six years. There is an evident seasonal variation in the conception of NTD fetuses. Using a wave statistical model applied to data recorded over a six year period the authors have rejected the "no variation between the six two-month intervals" hypothesis at a P less than or equal to 0.005 level. It is postulated that, in any vitamin intake or environmental program to prevent NTD in families at risk, one must take into account the annual and seasonal variations, ethnic groups identity and the date of conception in the choice of control mothers.

Canada↗
PubMed1999

Interspecific and progeny relationships in the genus Stylosanthes inferred from chloroplast DNA sequence variation.

The chloroplast trnL (UAA) intron and trnL (UAA)-trnF (GAA) intergenic spacer region have been sequenced from 37 samples, 36 of which representing 19 Stylosanthes species and one from the related genus Zornia. The DNA sequences were used to study phylogenetic relationships in the tropical forage legume genus Stylosanthes, by means of parsimony analysis using the heuristic search method of the computer program PAUP. The resulting cladograms divide Stylosanthes into four separate clades. Within the clades, species are poorly resolved owing to low sequence divergence. Small intra-specific chloroplast DNA variation is observed in S. humilis, S. scabra and the species complex S. guianensis. Variation between S. humilis populations is considered to be geographically structured. The overall results agree well with previously established inter-specific relationships and provide evidence for the genetic origin of the alloploid species S. hamata, S. scabra, S. ingrata, S. sympodialis, S. subsericea, S. capitata and S. fruticosa. This understanding of evolutionary relationships in Stylosanthes, in combination with biogeographical concepts provides a way of discerning isolated habitats in Central and South America, which may therefore contribute to strategies of plant collecting.

Base Sequence↗
PubMed2004

Immunity and vaccine control of Echinococcus granulosus infection in animal intermediate hosts.

Much progress has been made with characterisation of the EG95 vaccine which can be used to prevent hydatid infection in animal intermediate hosts of Echinococcus granulosus. The vaccine comprises a single recombinant oncosphere antigen and the adjuvant Quil A. It induces complement-fixing antibodies that kill the invading oncosphere early in an infection. In the majority of vaccinated animals, no hydatid cysts occur following a challenge infection. However, a small number of viable cysts may occur in some vaccinated animals. The vaccine has proved effective in vaccine trials carried out in sheep in New Zealand, Australia, Argentina, Chile and China as well as in goats and cattle. Investigations of the genetic diversity of the gene encoding EG95 have identified no unequivocal variation within the G1 strain parasites; however DNA sequence diversity within the EG95 family of genes has been found in G6/G7 parasites. GMP production scale-up of the vaccine has been undertaken in New Zealand and China and it is expected that the vaccine will be become available through these sources for implementation as part of hydatid control programs worldwide.

Animals↗
PubMed2005

Molecular mapping of sorghum genes expressing tolerance to damage by greenbug (Homoptera: Aphididae).

Genetic linkage maps are fundamental for the localization of genes conferring tolerance to greenbug, Schizaphis graminum (Rondani), feeding damage in sorghum, Sorghum bicolor (L.) Moench. Thirteen linkage groups (LGs) containing 60 simple sequence repeat (SSR) loci were mapped by using a set of sorghum recombinant inbred lines (RILs) obtained from the cross '96-4121' (greenbug-tolerant parent) x Redlan (greenbug-susceptible parent). The LG spanned a distance of 603.5 cM, with the number of loci per LG varying from 2 to 14. Seventeen additional SSR loci were unlinked at a log of odds value of 3.0. Based on chlorophyll loss occurring after greenbug feeding, visual damage ratings, and soil plant analysis development (SPAD), chlorophyll-loss indices were recorded for each RIL and for the parents used in the cross. Composite-interval mapping identified three quantitative trait loci (QTLs) associated with biotype I and five QTLs associated with biotype K. The amount of phenotypic variation explained by these QTLs ranged from 9 to 19.6%. The identification of QTLs that influence greenbug tolerance will not only facilitate the use of marker-assisted selection in sorghum breeding programs but also will provide a solid foundation for detailed characterization of individual loci implicated in greenbug tolerance in sorghum.

Animals↗
PubMed1982

Lymphocyte proteins in Huntington's disease: quantitative analysis by use of two-dimensional electrophoresis and computerized densitometry.

We used quantitative two-dimensional electrophoresis to study lymphocyte proteins in Hungtington's disease. Three hundred and six polypeptides from 14C-labeled, phytohemagglutinin-stimulated lymphocytes were measured for variation in relative spot density and 186 for variation in spot position by use of a computer program requiring operator interaction. Each polypeptide was measured in a total of 30 electrophoretograms from 28 individuals, including 13 with Huntington's disease, 2 at risk for it, and 13 controls. The study included two sets of identical twins and, as neurological controls, individuals with neurofibromatosis, Alzheimer's disease, or Shy-Drager syndrome. Seven protein polymorphisms were identified among the 186 most dense polypeptides of each gel, corresponding to a minimum average heterozygosity of 1.4%. Stringent criteria were used to define polymorphic proteins, including observation of at least one individual with each of two homozygous phenotypes and one with the heterozygous phenotype, demonstration of the expected gene dosage relationship by quantitative densitometry, consistency with genetic relationships, and reproducibility. One polymorphic protein showed three electrophoretically variant alleles. Our identification of seven polymorphisms among the 186 proteins measured on a single electrophoretogram illustrates the potential of this technique for performing linkage analysis in diseases of genetic origin. However, we observed no quantitative or positional protein variations that were characteristic of (i.e. specific for) Huntington's disease.

Blood Proteins↗
PubMed1999

Candidate gene markers associated with somatotropic axis and milk selection.

One of the obstacles to progress in dairy cattle selection is that milk production traits are only expressed after the first calving. However, the use of the quantitative trait loci (QTL) technology will improve the efficiency of dairy industry with a positive image for the consumers. QTL are part of the genome showing a preponderant action and explaining the major part of variation of the trait production. At the present time, the two major strategies developed to detect such QTL are the candidate gene approach and the positional genetics approach. The somatotropic axis contains the most promising candidates in this respect, as it strongly regulates milk production. Then, the identification of favorable QTL associated with the somatotropic axis that are significantly correlated with genetic merits for milk production could lead to more effective selection programs.

Animals↗
PubMed2003

Community-acquired poliovirus infection in children with primary immunodeficiencies in Tunisia.

The global polio eradication program recommends the use of massive vaccination campaigns with live vaccine through National Immunization Days (NIDs) to displace the wild virus from the community. Immunodeficient patients may be indirectly infected and become chronic excretors and potential reservoirs of polioviruses, a concern for the posteradication era. This prospective study aimed to assess the risk of community-acquired infection of immunodeficient patients following NIDs, the dynamics of viral excretion and the genetic variation of excreted viruses. Sixteen children with various primary immunodeficiencies, who did not receive the vaccine during the campaign, were investigated. Stool samples were collected weekly, shortly after the NIDs, during at least 3 months, and were processed for viral isolation. Isolates were characterized by three intratypic differentiation methods and partial sequencing of the VP1/2A region. Polioviruses were detected in 4 out of 16 patients (serotype 1 in 3 patients and serotype 3 in 1 patient). Sequencing revealed more than 99% homology with homotypic Sabin strains, suggesting recent infection. Duration of viral excretion ranged from 1 to 7 weeks. Nine out of eleven isolates from the three poliovirus serotype 1-infected patients disclosed a non-Sabin-like phenotype by enzyme-linked immunosorbent assay and had recurrent mutations within or close to the neutralizing antigenic sites. In summary, the risk of secondary infection in immunodeficient patients is within the range previously reported for the general population. Although none of the four infected patients developed prolonged viral excretion, particular viral variants were selected and may be of epidemiological significance.

Child↗
PubMed2005

Genetic differentiation among geographic populations of Gonatocerus ashmeadi, the predominant egg parasitoid of the glassy-winged sharpshooter, Homalodisca coagulata.

The aim of genetically comparing different populations of the same species of natural enemies is to identify the strain that is most adapted to the environment where it will be released. In the present study, Inter-Simple Sequence Repeat-Polymerase Chain Reaction (ISSR-PCR) was utilized to estimate the population genetic structure of Gonatocerus ashmeadi (Girault) (Hymenoptera: Mymaridae), the predominant egg parasitoid of Homalodisca coagulata (Say) (Homoptera:Cicadellidae), the glassy-winged sharpshooter. Six populations from throughout the U.S. and a population from Argentina identified as near G. ashmeadi were analyzed. Four populations (California; San Antonio, Texas; Weslaco, Texas [WTX-2]; and Florida) were field collected and two (Louisiana and Weslaco, Texas [WTX-1]) were reared. Three ISSR-PCR reactions were pooled to generate 41 polymorphic markers among the six U.S. populations. Nei's expected heterozygosity values (h), including the reared population from Louisiana, were high (9.01-14.3%) for all populations, except for a reared population from WTX-1 (2.9%). The total genetic diversity value (Ht) for the field populations was high (23%). Interestingly, the Florida population that was collected from one egg mass (siblings) generated the greatest number of polymorphic markers (20) and was observed with the highest gene diversity value (14.3%). All populations, except WTX-2 generated population-specific markers. Comparison of genetic differentiation estimates, which evaluate the degree of genetic subdivision, demonstrated good agreement between G(ST) and theta values, 0.38 and 0.50, respectively for field populations, and 0.44 and 0.50, respectively for all populations. Genetic divergence (D) indicated that the WTX-1 population was the most differentiated. Average D results from the Argentina population support the taxonomic data that it is a different species. The present results estimate the population genetic structure of G. ashmeadi, demonstrating genetic divergence and restricted gene flow (Nm = 0.83) among populations. These results are of interest to the Pierce's disease/glassy-winged sharpshooter biological control program because the key to successful biological control may not be in another species, but instead in different geographic races or biotypes.

Animals↗
PubMed2006

Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology.

BACKGROUND: In experimental biology, including retrovirology and molecular biology, replicate measurement sessions very often show similar proportional differences between experimental conditions, but different absolute values, even though the measurements were presumably carried out under identical circumstances. Although statistical programs enable the analysis of condition effects despite this replication error, this approach is hardly ever used for this purpose. On the contrary, most researchers deal with such between-session variation by normalisation or standardisation of the data. In normalisation all values in a session are divided by the observed value of the 'control' condition, whereas in standardisation, the sessions' means and standard deviations are used to correct the data. Normalisation, however, adds variation because the control value is not without error, while standardisation is biased if the data set is incomplete. RESULTS: In most cases, between-session variation is multiplicative and can, therefore, be removed by division of the data in each session with a session-specific correction factor. Assuming one level of multiplicative between-session error, unbiased session factors can be calculated from all available data through the generation of a between-session ratio matrix. Alternatively, these factors can be estimated with a maximum likelihood approach. The effectiveness of this correction method, dubbed "factor correction", is demonstrated with examples from the field of molecular biology and retrovirology. Especially when not all conditions are included in every measurement session, factor correction results in smaller residual error than normalisation and standardisation and therefore allows the detection of smaller treatment differences. Factor correction was implemented into an easy-to-use computer program that is available on request at: biolab-services@amc.uva.nl?subject=factor. CONCLUSION: Factor correction is an effective and efficient way to deal with between-session variation in multi-session experiments.

Female↗