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At least 163 records · Page 9Linked to original sources
PubMed1998

Clonal and chronological genetic analysis of multifocal cancers of the bladder and upper urinary tract.

Recent molecular genetic studies have suggested that multifocal urothelial cancers are derived from an identical progenitor cell. However, the clonal origin of multifocal urothelial cancers of a low-grade superficial type has not been fully defined. Using microsatellite markers, we examined genetic alterations at 20 loci on eight chromosomal arms (2q, 4p, 4q, 8p, 9p, 9q, 11p, and 17p) in 87 metachronous and/or synchronous multifocal urothelial cancers, which included 84 low-grade superficial papillary tumors from 29 patients. Judging from the patterns of loss of heterozygosity, microsatellite shifts, and the subchromosomal partial deletion, multifocal tumors in at least 20 (80%) of the 25 evaluable patients were considered to be derived from a single progenitor cell, although the possibility remained that multifocal tumors in a small subset of patients might develop from distinct progenitor cells due to field cancerization. In 13 of the 20 patients, a chronological genetic analysis was available: genetic heterogeneity was detected in 3 (23%) patients, and an apparent accumulated pattern of genetic alterations was detected in only 1 (8%) patient. In the 20 patients with multifocal tumors of an identical clonal origin, discordant microsatellite alterations were observed, with significantly lower frequencies on chromosome 9 compared to those on the other chromosomes tested. The results indicate that most multifocal low-grade superficial urothelial cancers are genetically stable despite their incidence of frequent recurrence, and genetic divergence occurs in a subset of patients. This heterotopic spread and genetic divergence may occur long before the clinical manifestation of multiplicity from a single transformed cell. These data support the previous view that heterotopic spread of transformed progenitor cells and genetic divergence occur after chromosome 9 alterations in most of low-grade superficial urothelial cancers.

Chromosome Aberrations↗
PubMed2003

Genetic analysis of males from intracytoplasmic sperm injection couples.

A total of 392 men referred for intracytoplasmic sperm injection (ICSI) participated in genetic analysis. The control group consisted of 100 normal fertile males. Chromosome and DNA analyses were performed to investigate the frequency of Y-chromosome microdeletions and CFTR mutations (the controls underwent DNA analysis only). An abnormal karyotype was found in 4.6% of all males, but the frequency among men with azoospermia was higher, at 11.7%. Y-chromosome microdeletions were found only among men with azoospermia (6.5%) and men with extreme oligospermia (2%). Compound heterozygosity for CFTR mutations was found in men with azoospermia (3.9%) and congenital bilateral absence of vas deferens (CBAVD) only. We conclude that all couples referred for ICSI should be offered chromosome analysis. DNA analysis for Y-chromosome microdeletions should be reserved for men with azoospermia or extreme oligospermia (<1 x 106 spermatozoa). Analysis for CFTR mutations should be limited to those with obstructive azoospermia or those with a family history of cystic fibrosis.

Adult↗
PubMed2005

Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14.

The data provided to the Genetic Analysis Workshop 14 (GAW 14) was the result of a collaboration among several different groups, catalyzed by Elizabeth Pugh from The Center for Inherited Disease Research (CIDR) and the organizers of GAW 14, Jean MacCluer and Laura Almasy. The DNA, phenotypic characterization, and microsatellite genomic survey were provided by the Collaborative Study on the Genetics of Alcoholism (COGA), a nine-site national collaboration funded by the National Institute of Alcohol and Alcoholism (NIAAA) and the National Institute of Drug Abuse (NIDA) with the overarching goal of identifying and characterizing genes that affect the susceptibility to develop alcohol dependence and related phenotypes. CIDR, Affymetrix, and Illumina provided single-nucleotide polymorphism genotyping of a large subset of the COGA subjects. This article briefly describes the dataset that was provided.

Alcoholism↗
PubMed2002

Non-parametric exploratory analysis of the covariance structure for genetic analysis of repeated measures and other function-value traits.

In the analysis of longitudinal data, before assuming a parametric model, an idea of the shape of the variance and correlation functions for both the genetic and environmental parts should be known. When a small number of observations is available for each subject at a fixed set of times, it is possible to estimate unstructured covariance matrices, but not when the number of observations over time is large and when individuals are not measured at all times. The non-parametric approach, based on the variogram, presented by Diggle & Verbyla (1998), is specially adapted for exploratory analysis of such data. This paper presents a generalization of their approach to genetic analyses. The methodology is applied to daily records for milk production in dairy cattle and data on age-specific fertility in Drosophila.

Animals↗
PubMed1996

Genetic analysis of cholinergic nerve terminal function in invertebrates.

Genetic analysis of nerve terminal function is proving fruitful and studies on invertebrates are making a substantial impact. In this survey, particular emphasis has been placed on cholinergic chemical synaptic transmission. The advanced genetics of Drosophila melanogaster and Caenorhabditis elegans with their rich diversity of behavioural and biochemical mutants is providing new insights into the functions of key molecular components of synapses. A 'space-invader' mutant of Periplaneta americana permits investigations of competition between neurons during synaptogenesis and its impact on neurotransmitter release. The growing importance of the C. elegans genome as a major research resource is emphasized in this survey.

Acetylcholine↗
PubMed2003

Causes of stability of aggression from early childhood to adolescence: a longitudinal genetic analysis in Dutch twins.

This study investigated the contribution of genetic and environmental influences on the stability of aggressive behavior from early childhood to adolescence. Two developmental models, the simplex model and the common factor model, were tested to study the underlying processes of stability and change. Measures of aggressive behavior (AGG) were obtained from maternal CBCL data as part of a large ongoing longitudinal study of the Netherlands Twin Registers (NTR) and included data from 6488 three-year-old twin pairs, 5475 seven-year-old twin pairs, 2983 ten-year-old twin pairs, and 1509 twelve-year-old twin pairs. AGG showed moderate to high stability during childhood. The stability coefficients ranged from 0.41 to 0.77 across varying intervals. Averaged across boys and girls, genetic factors accounted for approximately 65% of the total stability. Longitudinal genetic analysis indicated a simplex model for genetic effects, which suggests a dynamic development process consisting of transmission of existing genetic effects interacting with new genetic influences. This is especially true at age 7, when the influence of new genetic factors was large. Shared environmental factors accounted for approximately 25% of phenotypic stability, and it seemed that a stable set of the same shared environmental factors underlay the development of AGG. Nonshared environmental factors, when important, are age specific. Sex-specific differences for stability were identified. For boys, genetic influences were greater, whereas for girls shared environmental factors were more important. These data support the idea that both genetic and environmental influences play a role in the stability of AGG from age 3 to 12.

Aggression↗
PubMed2005

Construction of the model for the Genetic Analysis Workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype.

The Genetic Analysis Workshop 14 simulated dataset was designed 1) To test the ability to find genes related to a complex disease (such as alcoholism). Such a disease may be given a variety of definitions by different investigators, have associated endophenotypes that are common in the general population, and is likely to be not one disease but a heterogeneous collection of clinically similar, but genetically distinct, entities. 2) To observe the effect on genetic analysis and gene discovery of a complex set of gene x gene interactions. 3) To allow comparison of microsatellite vs. large-scale single-nucleotide polymorphism (SNP) data. 4) To allow testing of association to identify the disease gene and the effect of moderate marker x marker linkage disequilibrium. 5) To observe the effect of different ascertainment/disease definition schemes on the analysis. Data was distributed in two forms. Data distributed to participants contained about 1,000 SNPs and 400 microsatellite markers. Internet-obtainable data consisted of a finer 10,000 SNP map, which also contained data on controls. While disease characteristics and parameters were constant, four "studies" used varying ascertainment schemes based on differing beliefs about disease characteristics. One of the studies contained multiplex two- and three-generation pedigrees with at least four affected members. The simulated disease was a psychiatric condition with many associated behaviors (endophenotypes), almost all of which were genetic in origin. The underlying disease model contained four major genes and two modifier genes. The four major genes interacted with each other to produce three different phenotypes, which were themselves heterogeneous. The population parameters were calibrated so that the major genes could be discovered by linkage analysis in most datasets. The association evidence was more difficult to calibrate but was designed to find statistically significant association in 50% of datasets. We also simulated some marker x marker linkage disequilibrium around some of the genes and also in areas without disease genes. We tried two different methods to simulate the linkage disequilibrium.

Computer Simulation↗
PubMed2004

[Clinical and genetic analysis of juvenile parkinsonism in Russia].

Clinical and genetic analysis of juvenile parkinsonism was performed in 26 sibs from 20 families. Heterogeneity of the disorder was observed. Mutations in the parkin gene (locus PARK2, chromosome 6q25.2-27), with the prevalence of deletions over point mutations, have been identified in 41%. The comparative clinical analyses of patients examined confirmed the phenotypical polymorphism of "parkinopathy". We also showed the absence of asymmetric manifestation--an important and underestimated so far sign of the disease. The results of the study may be considered as a valuable clue to the clinical diagnosis of parkin-related juvenile parkinsonism in Russian population and implemented for mutation screening and medico-genetic counseling of affected families.

Adolescent↗
PubMed1993

[Genetic analysis of differences in dopamine metabolism in two Drosophila virilis lines under normal conditions and under heat stress].

The results of genetic analysis of the differences in dopamine (DA) content between two lines of Drosophila virilis in response to heat stress are presented. The gene(s) controlling the differences in DA content under normal conditions is located on the X-chromosome, and the gene(s) controlling the differences in responsiveness of DA system to stress was found to be autosomal. By means of polyacrylamide gel electrophoresis was also examined phenoloxidase activity in these lines under normal conditions and short-term heat stress (60 min, 38 degrees C). Of the five phenol oxidase fractions identified, three were major, A1, A2 and A3 components, and two appeared occasionally. It seems likely that A1 is monophenol oxidase and A2 is diphenol oxidase. It was shown that neither mono, nor diphenol oxidase activities change under heat stress. It was found that D. virilis lines 147 and 101 differ in diphenol oxidase activity under normal conditions. Genetic analysis of these differences revealed that they are controlled by a single gene (or a group of closely linked genes). The gene controlling diphenol oxidase activity in D. virilis is located on the X-chromosome.

Animals↗
PubMed2005

Identification of susceptibility loci for complex diseases in a case-control association study using the Genetic Analysis Workshop 14 dataset.

Although current methods in genetic epidemiology have been extremely successful in identifying genetic loci responsible for Mendelian traits, most common diseases do not follow simple Mendelian modes of inheritance. It is important to consider how our current methodologies function in the realm of complex diseases. The aim of this study was to determine the ability of conventional association methods to fine map a locus of interest. Six study populations were selected from 10 replicates (New York) from the Genetic Analysis Workshop 14 simulated dataset and analyzed for association between the disease trait and locus D2. Genotypes from 45 single-nucleotide polymorphisms in the telomeric region of chromosome 3 were analyzed by Pearson's chi-square tests for independence to test for association with the disease trait of interest. A significant association was detected within the region; however, it was found 3 cM from the documented location of the D2 disease locus. This result was most likely due to the method used for data simulation. In general, this study showed that conventional case-control association methods could detect disease loci responsible for the development of complex traits.

Case-Control Studies↗
PubMed1976

Genetic analysis of enzyme polymorphisms in plaice (Pleuronectes platessa).

Genetic analysis was performed on five enzyme systems (G3PDH; GPI-A; GPI-B; PGM; MDH-A) in plaice (Pleuronectes platessa) collected in spawning condition from the North Sea. Conventional crosses, induced gynogenesis and induced triploidy were performed. The data conclusively demonstrated the inheritance of isozymes by co-dominant alleles at individual loci for each system. No linkage was observed but tests did not include MDH nor the possibility of linkage between G3PDH and GPI-A. Some anomalous segregation ratios were observed, particularly a deficiency of heterozygotes for GPI-A, but the data were largely in conformity with Mendelian expectations. At the PGM locus, five independent anomalous individuals were scored and interpreted as mutations with a mutation rate of 1.1 X 10(-3) per gamete. Recombination with the centromere was assessed and induced triploidy and cross-over values of 41 per cent for PGM, 19 per cent for MDH-A and 9 per cent for GPI-B were derived on the assumption of complete interference. Amongst the parent fish, genotypic and phenotypic frequencies were largely consistent with the expectations of the Hardy-Weinberg Law, and allelic frequencies were not significantly different between year of collection or location of collection ground.

Animals↗
PubMedDate not supplied

Genetic analysis of a group of mentally retarded children.

Genetic analysis of 169 mentally retarded (MR) children from Madras, revealed chromosomal abnormalities in 17%. Down syndrome was the major chromosomal anomaly (24/169 = 14.2%). These included three cases of trisomy-21 mosaics, and one case of de novo Robertsonian translocation. MR children with chromosomal abnormalities were either mildly or moderately retarded. Syndromes with known etiology occurred in 3% of the MR cases. Microcephaly, neonatal anoxia, perinatal stress and pharmacological attempt for abortion were found to be important pathogenic factors associated with MR. Most of the microcephalics (11/169 = 6.5%) were severely retarded, whereas those associated with neonatal anoxia and perinatal stress were either mildly or moderately retarded. Birth-order effects were found only among Down syndrome patients. Segregation analysis of the three groups of proband families (viz. mild, moderate and severe MR) indicated that autosomal recessive mode of inheritance is compatible in moderate and severe MR proband families. The proportion of X-linked instances of MR is estimated to be about 22% of the cases.

Child↗
PubMed1992

Pathway recognition by neuronal growth cones: genetic analysis of neural cell adhesion molecules in Drosophila.

Genetic analysis has finally come of age in the study of neural cell adhesion molecules and their function during growth cone guidance in Drosophila. Recent studies have shown that fasciclin II, a neural cell adhesion molecule of the immunoglobulin superfamily, functions as a recognition molecule for the MP1 axon pathway, thus serving as the first molecular confirmation for the existence of functional labels on specific axon pathways in the developing organism.

Animals↗
PubMed2024

Exploring the potential of genetic analysis in historical blood spots for patients with iodine-deficient goiter and thyroid carcinomas in Switzerland and Germany (1929-1989).

Iodine deficiency-induced goiter continues to be a global public health concern, with varying manifestations based on geography, patient's age, and sex. To gain insights into clinical occurrences, a retrospective study analyzed medical records from patients with iodine deficiency-induced goiter or thyroid cancer who underwent surgery at the Community Hospital in Riehen, Switzerland, between 1929 and 1989. Despite today's adequate iodine supplementation, a significant risk for iodine-independent goiter remains in Switzerland, suggesting that genetic factors, among others, might be involved. Thus, a pilot study exploring the feasibility of genetic analysis of blood spots from these medical records was conducted to investigate and enhance the understanding of goiter development, potentially identify genetic variations, and explore the influence of dietary habits and other environmental stimuli on the disease.Blood prints from goiter patients' enlarged organs were collected per decade from medical records. These prints had been made by pressing, drawing, or tracing (i.e., pressed and drawn) the removed organs onto paper sheets. DNA analysis revealed that its yields varied more between the prints than between years. A considerable proportion of the samples exhibited substantial DNA degradation unrelated to sample collection time and DNA mixtures of different contributors. Thus, each goiter imprint must be individually evaluated and cannot be used to predict the success rate of genetic analysis in general. Collecting a large sample or the entire blood ablation for genetic analysis is recommended to mitigate potential insufficient DNA quantities. Researchers should also consider degradation and external biological compounds' impact on the genetic analysis of interest, with the dominant contributor anticipated to originate from the patient's blood.

Humans↗
PubMed2004

Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.).

BACKGROUND: Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species. RESULTS: Seven hundred clones containing microsatellite sequences from a Tsp-AG/TC microsatellite enriched library were identified and one-hundred and forty-four primer pairs designed and synthesized. When 67 microsatellite markers were tested on a panel of melon and other cucurbit accessions, 65 revealed DNA polymorphisms among the melon accessions. For some cucurbit species, such as Cucumis sativus, up to 50% of the melon microsatellite markers could be readily used for DNA polymophism assessment, representing a significant reduction of marker development costs. A random sample of 25 microsatellite markers was extracted from the new microsatellite marker set and characterized on 40 accessions of melon, generating an allelic frequency database for the species. The average expected heterozygosity was 0.52, varying from 0.45 to 0.70, indicating that a small set of selected markers should be sufficient to solve questions regarding genotype identity and variety protection. Genetic distances based on microsatellite polymorphism were congruent with data obtained from RAPD marker analysis. Mapping analysis was initiated with 55 newly developed markers and most primers showed segregation according to Mendelian expectations. Linkage analysis detected linkage between 56% of the markers, distributed in nine linkage groups. CONCLUSIONS: Genomic library microsatellite enrichment is an efficient procedure for marker development in melon. One-hundred and forty-four new markers were developed from Tsp-AG/TC genomic library. This is the first reported attempt of successfully using enriched library for microsatellite marker development in the species. A sample of the microsatellite markers tested proved efficient for genetic analysis of melon, including genetic distance estimates and identity tests. Linkage analysis indicated that the markers developed are dispersed throughout the genome and should be very useful for genetic analysis of melon.

Chromosome Mapping↗
PubMed1997

Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometry.

The ability to analyze multiple polymorphic sites rapidly and accurately is crucial in all areas of genetic analysis. We have developed an approach for the detection of multiple point mutations, using allele-specific, mass-labeled, peptide nucleic acid (PNA) hybridization probes, and direct analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The composite mass spectra produced contain peaks of distinct masses corresponding to each allele present, resulting in a mass spectral "fingerprint" for each DNA sample. The hybridization characteristics of PNA:DNA duplexes were found to be highly dependent on both base content and sequence. Results from the analysis of four polymorphic sites contained in exon 4 of the human tyrosinase gene show that this approach is simple, rapid, and accurate with potential applications in many areas of genetic analysis.

Alleles↗
PubMed2025

Genetic analysis in African ancestry populations reveals genetic contributors to lung cancer susceptibility.

Striking disparities in lung cancer exist, with Black/African American individuals disproportionately affected by lung cancer, yet the genetic architecture in African ancestry individuals is poorly understood. We aimed to address this by performing a comprehensive genetic association study of lung cancer, incorporating local ancestry, across 6,490 African ancestry individuals (2,390 individuals with lung cancer and 4,100 control subjects). We identified a single genome-wide significant (p < 5 &#xd7; 10-8) locus, 15q25.1 (lead SNP rs17486278, OR [95% CI] = 1.34 [1.23-1.45], p = 4.52 &#xd7; 10-12), that has consistently shown a strong association with lung cancer across populations. Additionally, we identified nine suggestive (p < 1 &#xd7; 10-6) loci. Four of these loci (3p12.1, 8q22.2, 14q11.2, and 18q22.3) have no prior reported associations with lung cancer. We performed a multi-ancestry lung cancer meta-analysis using prior large-scale summary statistics from European and Asian ancestry populations, incorporating our African ancestry results. The meta-analysis identified 17 genome-wide significant loci, including an association with locus 4q35.2 (p = 1.22 &#xd7; 10-8), a genomic region that has been previously linked to forced expiratory volume. Genome-wide SNP-based heritability for lung cancer was 16% among African ancestry individuals. Follow-up in silico functional analyses identified genetically regulated gene expression (GReX) of nine genes (AC012184.3, ADK, CCDC12, CHRNA3, EML4, PSMA4, SNRNP200, TMEM50A, and ZYG11A) associated with lung cancer risk and biological pathways relevant to cancer and lung function. Cumulatively, these findings further elucidate the genetic architecture of lung cancer in African ancestry individuals, confirming prior loci and revealing new loci.

Female↗
PubMed1984

Genetic Analysis Workshop II: results of incorporating a linkage disequilibrium parameter.

The corporation of a linkage disequilibrium parameter, delta, into linkage analysis is illustrated for data from Genetic Analysis Workshop II. Points from a joint likelihood surface are calculated and displayed on a recombination fraction-linkage disequilibrium grid using a simple modification of LIPED. The approach is shown to increase the power of linkage analysis and the power of tests for heterogeneity of linkage for the simulated examples.

Computer Simulation↗