Set Of Genetic Markers Research Articles

Species identification of two sympatric hakes by allozymic markers

Samples were collected from hake species Merluccius australis and M. hubbsi in the south west Atlantic Ocean. Enzyme electrophoretic analysis of the eye, liver and muscle revealed 5 out of 33 genetic loci with species-specific allelic frequencies. These five loci provide a set of genetic markers for individual classification.

Combining multiple phenotypic traits optimally for detecting linkage with sib-pair observations.

A number of investigators have proposed regression methods for testing linkage between a phenotypic trait and a genetic marker with sib-pair observations. Xu et al. [Am J Hum Genet 67:1025-8, 2000] studied a unified method for testing linkage, which tends to be more powerful than existing procedures. Often there are multiple traits, which are linked to a common set of genetic markers. In this paper, we present a simple generalization of the unified test to combine information from multiple traits optimally. We use the simulated Genetic Analysis Workshop 12 data to illustrate this methodology and show the advantage of using the combined tests over the single-trait tests. For the four quantitative traits (Q1,...,Q4) studied, our linkage results suggest that major loci affecting Q1 and Q2 localize at or near markers D02G172, D19G032, and D09G122, while loci affecting Q3 and Q4 localize at or near markers D09G122 and D17G051.

The Score Statistic of the LD-Lod Analysis: Detecting Linkage Adaptive to Linkage Disequilibrium

We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers.

Microsatellite Analysis of Genetic Variation in Sturgeon: New Primer Sequences forScaphirhynchusandAcipenser

Low levels of genetic variation at traditional molecular markers have hampered genetic research within the family Acipenseridae. In an effort to develop a large set of polymorphic genetic markers, 172 clones were sequenced from three subgenomic libraries of shovelnose sturgeon Scaphirhynchus platorynchus; the libraries were enriched for two dinucleotide and one tetranucleotide microsatellite motifs (CA, GA, and TAGA). Primers were designed for 113 of the sequences and tested against shovelnose sturgeon, pallid sturgeon S. albus, white sturgeon Acipenser transmontanus, lake sturgeon A. fulvescens, and green sturgeon A. medirostris. Of the 113 primer sets tested, 96% amplified in one or more species (58 dimeric and 50 tetrameric). In Scaphirhynchus species, 93% of all loci amplified, and 76% were polymorphic. Within the individual Acipenser species, 65–80% of loci amplified, with 42–58% being polymorphic. Polymorphic systems for Scaphirhynchus species predominately displayed simple, disomic banding patterns, while those for Acipenser species typically displayed banding patterns characteristic of tetraploid or higher polyploid levels. These new microsatellite loci provide a group of genetic markers that are detectable with noninvasive sampling and that should prove useful in the preservation of threatened and endangered sturgeon species worldwide.

Association Mapping in Structured Populations

The use, in association studies, of the forthcoming dense genomewide collection of single-nucleotide polymorphisms (SNPs) has been heralded as a potential breakthrough in the study of the genetic basis of common complex disorders. A serious problem with association mapping is that population structure can lead to spurious associations between a candidate marker and a phenotype. One common solution has been to abandon case-control studies in favor of family-based tests of association, such as the transmission/disequilibrium test (TDT), but this comes at a considerable cost in the need to collect DNA from close relatives of affected individuals. In this article we describe a novel, statistically valid, method for case-control association studies in structured populations. Our method uses a set of unlinked genetic markers to infer details of population structure, and to estimate the ancestry of sampled individuals, before using this information to test for associations within subpopulations. It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations.

Build Your Own Map

Biotech Software & Internet ReportVol. 1, No. 3 Views from the WebBuild Your Own MapDarryl NishimuraDarryl NishimuraSearch for more papers by this authorPublished Online:5 Jul 2004https://doi.org/10.1089/152791600414415AboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetails Volume 1Issue 3Jun 2000 To cite this article:Darryl Nishimura.Build Your Own Map.Biotech Software & Internet Report.Jun 2000.68-70.http://doi.org/10.1089/152791600414415Published in Volume: 1 Issue 3: July 5, 2004PDF download

Corticobasal degeneration shares a common genetic background with progressive supranuclear palsy.

Corticobasal degeneration is a sporadic form of tauopathy, involving the cerebral cortex and extrapyramidal motor system. A series of affected subjects was genotyped for a set of genetic markers along the tau protein gene. A specific haplotype is significantly overrepresented in patients versus controls. This haplotype is the same already reported in association with progressive supranuclear palsy. These data show that corticobasal degeneration and progressive supranuclear palsy, in addition to several clinical, pathological, and molecular features, may have the same genetic background.

Corticobasal degeneration shares a common genetic background with progressive supranuclear palsy

Corticobasal degeneration is a sporadic form of tauopathy, involving the cerebral cortex and extrapyramidal motor system. A series of affected subjects was genotyped for a set of genetic markers along the tau protein gene. A specific haplotype is significantly overrepresented in patients versus controls. This haplotype is the same already reported in association with progressive supranuclear palsy. These data show that corticobasal degeneration and progressive supranuclear palsy, in addition to several clinical, pathological, and molecular features, may have the same genetic background. Ann Neurol 2000;47:374–377

Corticobasal degeneration shares a common genetic background with progressive supranuclear palsy

Corticobasal degeneration is a sporadic form of tauopathy, involving the cerebral cortex and extrapyramidal motor system. A series of affected subjects was genotyped for a set of genetic markers along the tau protein gene. A specific haplotype is significantly overrepresented in patients versus controls. This haplotype is the same already reported in association with progressive supranuclear palsy. These data show that corticobasal degeneration and progressive supranuclear palsy, in addition to several clinical, pathological, and molecular features, may have the same genetic background.

Genetic markers in ribosomal DNA for the identification of members of the genus Anisakis (Nematoda: Ascaridoidea) defined by polymerase-chain-reaction-based restriction fragment length polymorphism

Polymerase-chain-reaction-based restriction fragment length polymorphism analysis was performed to establish genetic markers in rDNA, for the identification of the three sibling species of the Anisakis simplex complex and morphologically differentiated Anisakis species, i.e. Anisakis physeteris, Anisakis schupakovi, Anisakis typica and Anisakis ziphidarum. Different restriction patterns were found between A. simplex sensu stricto and Anisakis pegreffii with two of the restriction endonucleases used ( HinfI and TaqI), between A. simplex sensu stricto and A. simplex C with one endonuclease ( HhaI), and between A. simplex C and Aniskis pegreffii with three endonucleases ( HhaI, HinfI and TaqI), while no variation in patterns was detected among individuals within each species. The species A. physeteris, A. schupakovi, A. typica and A. ziphidarum were found to be different from each other and different from the three sibling species of the A. simplex complex by distinct fragments using 10–12 of the endonucleases tested. The polymorphisms obtained by restriction fragment length polymorphisms have provided a new set of genetic markers for the accurate identification of sibling species and morphospecies.

Molecular epidemiology and evolutionary genetics of Leishmania parasites

In order to illustrate the relevance of the concepts and methods of evolutionary genetics in the understanding of the epidemiology of pathogenic agents, we develop in this paper the case of the Leishmania, a genus of parasitic protozoa. An extensive study of various natural populations of Leishmania in different countries (Old and New World) was carried out by using Multilocus Enzyme Electrophoresis (MLEE) and Random Amplified Polymorphic DNA fingerprinting (RAPD) as genetic markers. The data have been interpreted in evolutionary genetic terms. The main benefit of this approach has been to better define the concept of species in the genus Leishmania, on rigorous phylogenetic bases. As a matter of fact, a sound taxonomical background is a prerequisite for any epidemiological approach. Since the biological concept of species is difficult or impossible to apply for most pathogenic microorganisms, we recommend relying on criteria of both phylogenetic discreteness and of epidemiological/medical relevance to describe new species of Leishmania. Through this approach, for example, we have shown that the species status of L. (V.) peruviana can be supported. On the contrary, we have been unable to clearly distinguish L. (V.) panamensis from L. (V.) guyanensis with genetic tools. Additionally, we have shown that the epidemiological inferences based on a limited set of genetic markers can be misleading. As a matter of fact, we have demonstrated that a collection of L. (L.) infantum stocks identified as zymodeme `MON 1' by other authors present additional genetic heterogeneity and do not correspond to a distinct `Discrete Typing Unit' DTU, and are actually polyphyletic. Lastly, in the samples that were conveniently designed, we have confirmed that Leishmania parasites have a basically clonal population structure. As the clonal model specifies it, occasional bouts of genetic exchange remain nevertheless possible. Telling comparisons are drawn with the evolutionary genetics of other pathogens Trypanosoma cruzi and Trypanosoma congolense.

The human genome project and the future of diagnostics, treatment, and prevention

During the past 5 years, the Human Genome Project has had a tremendous influence on the field of genetics. This influence will soon become extended across the whole of biology and medicine. After centuries of description, we are now on the eve of truly understanding the cellular processes in the human body. Up until the late 1980s, tracing the causes of genetic disease involved time-consuming linkage analysis in families, by limited sets of genetic markers. At the end of that decade a more comprehensive approach was tabled—the Human Genome Project—the mapping of all our 80 000–100 000 genes and the decoding of our complete DNA sequence of 3 billion bp.

Low-Copy Repeats Mediate the Common 3-Mb Deletion in Patients with Velo-cardio-facial Syndrome

Velo-cardio-facial syndrome (VCFS) is the most common microdeletion syndrome in humans. It occurs with an estimated frequency of 1 in 4, 000 live births. Most cases occur sporadically, indicating that the deletion is recurrent in the population. More than 90% of patients with VCFS and a 22q11 deletion have a similar 3-Mb hemizygous deletion, suggesting that sequences at the breakpoints confer susceptibility to rearrangements. To define the region containing the chromosome breakpoints, we constructed an 8-kb-resolution physical map. We identified a low-copy repeat in the vicinity of both breakpoints. A set of genetic markers were integrated into the physical map to determine whether the deletions occur within the repeat. Haplotype analysis with genetic markers that flank the repeats showed that most patients with VCFS had deletion breakpoints in the repeat. Within the repeat is a 200-kb duplication of sequences, including a tandem repeat of genes/pseudogenes, surrounding the breakpoints. The genes in the repeat are GGT, BCRL, V7-rel, POM121-like, and GGT-rel. Physical mapping and genomic fingerprint analysis showed that the repeats are virtually identical in the 200-kb region, suggesting that the deletion is mediated by homologous recombination. Examination of two three-generation families showed that meiotic intrachromosomal recombination mediated the deletion.

A system for rapid generation of coat color-tagged knockouts and defined chromosomal rearrangements in mice.

Gene targeting in mouse embryonic stem (ES) cells can be used to generate single gene mutations or defined multi-megabase chromosomal rearrangements when applied with the Cre- loxP recombination system. While single knockouts are essential for uncovering functions of cloned genes, chromosomal rearrangements are great genetic tools for mapping, mutagenesis screens and functional genomics. The conventional approach to generate mice with targeted alterations of the genome requires extensive molecular cloning to build targeting vectors and DNA-based genotyping for stock maintenance. Here we describe the design and construction of a two-library system to facilitate high throughput gene targeting and chromo-somal engineering. The unique feature of these libraries is that once a clone is isolated, it is essentially ready to be used for insertional targeting in ES cells. The two libraries each bear a complementary set of genetic markers tailored so that the vector can be used for Cre- loxP -based chromosome engineering as well as single knockouts. By incorporating mouse coat color markers into the vectors, we illustrate a widely applicable method for stock maintenance of ES cell-derived mice with single gene knockouts or more extensive chromosomal rearrangements.

Anxiety proneness linked to epistatic loci in genome scan of human personality traits.

A genome-wide scan between normal human personality traits and a set of genetic markers at an average interval of 13 centimorgans was carried out in 758 pairs of siblings in 177 nuclear families of alcoholics. Personality traits were measured by the Tridimensional Personality Questionnaire. We detected significant linkage between the trait Harm Avoidance, a measure of anxiety proneness, and a locus on chromosome 8p21-23 that explained 38% of the trait variance. There was significant evidence of epistasis between the locus on 8p and others on chromosomes 18p, 20p, and 21q. These oligogenic interactions explained most of the variance in Harm Avoidance. There was suggestive evidence of epistasis in other personality traits. These results confirm the important influence of epistasis on human personality suggested by twin and adoption studies.

Genetic Heterogeneity ofLeucostomaSpecies in Michigan Peach Orchards

ABSTRACT The pathogens causing perennial canker of peach, Leucostoma spp., were characterized in Michigan orchards to identify which species and subgroups (cryptic species) were prevalent on a highly susceptible peach cultivar, Loring, and a less susceptible cultivar, Redhaven. Four hundred and three strains of Leucostoma were isolated from cankers in three southwest Michigan orchards where 'Loring' occurred adjacent to 'Redhaven' in side-by-side plots. Based on colony morphology and small nuclear rDNA size polymorphisms, three cryptic species were detected; 89% of the isolates were identified as L. persoonii phenetic group 1, 10% were L. cincta group 4, and 1% were L. persoonii group 2. Pathogen profiles differed significantly between cankers on small branches of 'Loring' and 'Redhaven', and between cankers on small branches and trunks. Of 1,232 random pairings among isolates of L. persoonii group 1, 95% were vegetatively incompatible. A minimum of 11 and a maximum of 17 maternal lines were identified based upon mitochondrial DNA restriction fragment length polymorphisms among 69 isolates of L. persoonii group 1 from one split-cultivar block of 72 trees. Vegetative compatibility loci were randomly associated with maternal lines. Evidence of clonality was absent in L. persoonii group 1, as no correlation occurred between these two sets of independent genetic markers and no genotype was over-represented. The number of cryptic species, the number of maternal lines, and the frequency of incompatibility within maternal lines indicate that considerable genetic variation exists within the Leucostoma populations in Michigan peach orchards, and that sexual recombination is common.

Genetic epidemiology of parasitic protozoa and other infectious agents: the need for an integrated approach

This paper emphasises the relevance of the concepts and methods of evolutionary genetics for studying the epidemiology of parasitic protozoa and other pathogenic agents. Population genetics and phylogenetic analysis both contribute to identifying the relevant evolutionary and epidemiologically discrete units of research (Discrete typing units = DTUs), that can be equated to distinct phylogenetic lines. It is necessary (i) to establish that a given species ∗∗ ∗∗ Words marked by an asterix are defined in the glossary at the end of the text. represents a reliable DTU; (ii) to see whether a given species ∗ is further structured into lower DTUs that correspond to either clonal ∗ lineages or to cryptic species ∗, and could exhibit distinct biomedical properties (virulence, resistance to drugs, etc). DTUs at the species ∗ and subspecies ∗ level can be conveniently identified by specific genetic markers or sets of genetic markers (“tags”) for epidemiological follow-up. For any kind of pathogen (protozoa, fungi, bacteria, viruses), DTUs represent the relevant units of research, not only for epidemiology, but also, for other applied researches (clinical study, pathogenicity, vaccine and drug design, immunology, etc). The development of an “integrated genetic epidemiology of infectious diseases”, that would explore the respective role of, and the interactions between, the genetic diversity (and its biological consequences) of the pathogen, the host and the vector (in the case of vector-borne diseases) is called for.

Are genotypes of Trypanosoma cruzi involved in the challenge of chagasic cardiomyopathy?

Myocardial damage in Chagas' disease differs, depending on the particular Trypanosoma cruzi stock. It is reasonable to expect that the extent of phylogenetic divergence between lineages will have an impact on the biological properties of the parasite. The aim of the present work was to evaluate this impact on the cardiac damage produced by this protozoan. Heart histopathologic lesions were studied in mice infected with 15 cloned stocks of T. cruzi of various origins pertaining to 3 major clones or genotypes (19, 20, and 39) that share 3 different profiles for a given set of genetic markers. Sets of mice were infected intraperitoneally with 10(6) blood trypomastigotes of each of the T. cruzi clones. The macroscopy study showed a cardiac index (CI) higher than 0.6 (cardiomegaly) in 5 of the 15 stocks studied (33.33%). Inflammatory infiltrates appeared in stocks pertaining to the three genotypes studied without relation to the genetic pattern. Pseudocysts were present at higher levels (83%) in stocks pertaining to genotype 39. A lower rate could be seen in stocks pertaining to genotype 19 (50%). Only one stock pertaining to genotype 20 presented myocardial parasites (20%). Hearts were also studied for lesions in the different cardiac chambers. Inflammatory foci as well as pseudocysts appeared mainly in ventricles, with the left ventricle sharing the highest percentage of pathologic findings. In summary, in spite of the similar inflammatory pattern demonstrated for all stocks studied, the parasite's presence seemed to be related to the genotype of reference, but no relation could be demonstrated with the genetic distances.

Isolation ofCryptococcus neoformanschromosome-specific probes using expressed sequence tags

Clinical and environmental isolates of Cryptococcus neoformans exhibit a high degree of karyotypic variability. Analysis of the molecular basis of karyotypic differences requires a large set of chromosome-specific probes. We have determined the chromosomal distribution of a set of randomly selected C. neoformans cDNA clones and have explored the feasibility of identifying these clones through partial DNA sequencing. Forty-four randomly selected cDNA clones were labelled and hybridized to PFGE blots of C. neoformans. Expressed sequence tags were generated by sequencing the 5'-end of each clone. Thirty-five clones hybridized to single bands on PFGE blots. At least seven chromosomes were recognized by these probes. Homology searches identified potential homologs of several groups of proteins not previously studied in C. neoformans. PFGE hybridization and sequencing of random cDNA clones is an efficient method for identifying chromosomal-specific probes in fungi that lack extensive sets of genetic markers.

Genetic mapping of new morphological, isozyme and RAPD markers in Vicia faba L. using trisomics

Thirteen F2 families of faba bean (Vicia faba L.), descended from plants trisomic for chromosomes 3, 4, 5 and 6, have been analyzed for morphological, isozyme and RAPD markers. This allowed the establishment of linkage relationships among these markers as well as the assignment of some markers and/or linkage groups to their respective chromosomes. The linkage analysis of partially overlapping sets of informative genetic markers for the data pooled from 13 F2 families has revealed 48 linkage groups, six of which have been precisely assigned to specific chromosomes. A statistical procedure to analyze the data of joint segregation analysis in families derived from trisomic plants has been developed.