OBJECTIVETo elucidate the development of mapping and localization of susceptible genes on chromosomes to asthma related phenotypes.

DATA SOURCESPublished articles about susceptibility genes for asthma related phenotypes were selected using PubMed.

STUDY SELECTIONUsing methods of candidate gene positional clone and genome-wide scan with linkage and association analysis to determine the location in the genome of susceptibility genes to asthma and asthma related phenotypes.

RESULTSThere are multiple regions in the genome harboring susceptibility genes to asthma and asthma related phenotypes, including chromosomes 5, 11, 12, 6, 2, 3, 13, 7, 14, 9, 19 and 17. Many of these regions contain candidate genes involved in asthma development and progression. Some susceptible genes may affect the phenotype expression or response to therapy. In addition, the interaction of multiple genes with the environment may contribute to the susceptibility to asthma.

CONCLUSIONSAs an essential step toward cloning the susceptible genes to asthma, fine mapping and localization on chromosomes are definitely needed. Novel powerful tools for gene discovery and the integration of genetics, biology and bioinformatics should be pursued.

Asthma ; genetics ; Chromosome Mapping ; methods ; Genetic Predisposition to Disease ; genetics ; Humans

Chromosome Mapping ; Genome-Wide Association Study ; methods ; Humans

A method was proposed for the detection of outliers and influential observations in the framework of a mixed linear model, prior to the quantitative trait locus (QTL) mapping analysis. We investigated the impact of outliers on QTL mapping for complex traits in a mouse BXD population, and observed that the dropping of outliers could provide the evidence of additional QTL and epistatic loci affecting the 1stBrain-OB and the 2ndBrain-OB in a cross of the abovementioned population. The results could also reveal a remarkable increase in estimating heritabilities of QTL in the absence of outliers. In addition, simulations were conducted to investigate the detection powers and false discovery rates (FDRs) of QTLs in the presence and absence of outliers. The results suggested that the presence of a small proportion of outliers could increase the FDR and hence decrease the detection power of QTLs. A drastic increase could be obtained in the estimates of standard errors for position, additive and additivex environment interaction effects of QTLs in the presence of outliers.
Animals ; Chromosome Mapping ; methods ; Mice ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Quantitative Trait Loci

This paper presents a description of the rules of construction and function of genome as well as evolutional relationship between organisms, and opens out the essence of life through introducing the progress in genome of model organism. The other purpose of this review is to highlight the status and function of model organism in the research of comparing genomics so as to provide the model of cycle for researches into high creature life, especially human beings life.
Animals ; Chromosome Mapping ; Genes ; genetics ; Genome ; Genomics ; methods ; trends ; Human Genome Project ; Humans ; Models, Animal

An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.
Biological Evolution ; Chromosome Mapping ; methods ; Evolution, Molecular ; Genetic Variation ; genetics ; Genome, Plant ; Oryza ; genetics ; Polyploidy

OBJECTIVETo define the origin and the precise location of the aberrant fragments on the short arm of the chromosome 8 in a mentally retarded boy, and to understand the mechanism, the characteristic clinical features and the recurrent risk associated with this abnormality.

METHODSHigh-resolution chromosomal banding was performed to analyze the karyotype of the patient and his parents, array comparative genomic hybridization (array-CGH) was employed to investigate the precise location of the aberrant fragments, and quantitative real-time PCR was used to confirm the results.

RESULTSThe rearranged chromosome 8 in the patient was inverted and duplicated for region 8p11.2-p23.1, and deleted for region 8p23.1-pter. In between, a 5.70 Mb single copy region was present, which was delimited by the two olfactory receptor (OR) gene clusters.

CONCLUSIONThis is a case of classic inv dup del(8p) syndrome, which is characterized by severe mental retardation, brain malformation and specific facial dysmorphism, and is induced by non-allelic homologous recombination (NAHR) between the OR genes on 8p23.1. Prenatal diagnosis should be performed to monitor the recurrent risk of inv dup del(8p), as well as the other three harmful consequences resulted from the same NAHR mechanism. To the best of our knowledge, this is the first case of inverted duplicated 8p syndrome identified in Mainland China.

Abnormalities, Multiple ; genetics ; China ; Chromosome Aberrations ; classification ; Chromosome Banding ; methods ; Chromosome Deletion ; Chromosome Inversion ; Chromosome Mapping ; Chromosomes, Human, Pair 8 ; Cytogenetic Analysis ; methods ; Cytogenetics ; methods ; Gene Duplication ; Humans ; In Situ Hybridization, Fluorescence ; Infant ; Karyotyping ; methods ; Male ; Multigene Family ; Syndrome

A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that nucleotides have an inner abstract characteristic, the determinative degree, which reflects genetic code phenomenological properties and is adjusted to nucleotides physical properties. We consider each codon position independently, which gives three separate walks characterized by different angles and lengths, and that such an object is called triander which reflects the "strength" of branch. A general method for identifying DNA sequence "by triander" which can be treated as a unique "genogram" (or "gene passport") is proposed. The two- and three-dimensional trianders are considered. The difference of sequences fine structure in genes and the intergenic space is shown. A clear triplet signal in coding sequences was found which is absent in the intergenic space and is independent from the sequence length. This paper presents the topological classification of trianders which can allow us to provide a detailed working out signatures of functionally different genomic regions.
Algorithms ; Base Sequence ; Chromosome Mapping ; methods ; Codon ; genetics ; DNA ; genetics ; Molecular Sequence Data ; Nucleotides ; genetics ; Sequence Analysis, DNA ; methods

OBJECTIVETuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis (M. tuberculosis) multilocus sequence analysis (MLSA) was established for the phylogenetic and epidemiology analysis.

METHODSTo establish the scheme of M. tuberculosis MLSA, the genome of H37Rv, CCDC5079 and CCDC5180 were compared, and some variable genes were chosen to be the MLSA typing scheme. 44 M. tuberculosis clinical isolates were typed by MLSA, IS6110-RFLP, and soligotyping, to evaluate the MLSA methods.

RESULTSAfter comparison of the genome, seven high discrimination gene loci (recX, rpsL, rmlC, rpmG1, mprA, gcvH, ideR) were chosen to be the MLSA typing scheme finally. 11 variable SNP sites of those seven genes were found among the 44 M. tuberculosis isolate strains and 11 sequence types (STs) were identified. Based on the Hunter-Gaston Index (HGI), MLSA typing was not as good for discrimination at the strain level as IS6110-RFLP, but the HGI was much better than that of spoligotyping. In addition, the MEGA analysis result of MLSA data was similar to spoligotyping/PGG lineage, showing a strong phylogenetic signal in the modern strains of M. tuberculosis. The MLSA data analysis by eBURST revealed that 4 sequence types (ST) came into a main cluster, showing the major clonal complexes in those 44 strains.

CONCLUSIONMLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.

Chromosome Mapping ; Chromosomes, Bacterial ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Genotype ; Multilocus Sequence Typing ; methods ; Mycobacterium tuberculosis ; genetics ; metabolism

OBJECTIVETo improve the experimental method of DXS52 (St14) and apply it to genetic testing for hemophilia A (HA).

METHODSPCR of DXS52 and agarose gel electrophoresis were performed for genetic testing in 61 non-inversion HA families. Linkage analysis of 7 loci within the FVIII gene including Bcl I, Hind III, Xba I, STR1, STR13, STR22 and STR24 were also carried out for the 61 families.

RESULTSDXS52 can provide information in 43 out of 61 families and the diagnostic rate was 70.5%. Eight families can be diagnosed only by DXS52 locus, accounting for 13.1%. Two families were found to have recombination between DXS52 and FVIII.

CONCLUSIONThe new experimental conditions can reach accurate and clear results in DXS52 genetic testing. This gene maker has high diagnostic rate, so it is an indispensable linkage analysis method in HA gene diagnosis. More caution should be paid when using the extragenic locus DXS52 to perform gene diagnosis because of its high recombinant rate with FVIII.

Chromosome Mapping ; methods ; Chromosomes, Human, X ; Factor VIII ; genetics ; Female ; Genetic Linkage ; Genetic Markers ; Hemophilia A ; diagnosis ; genetics ; Humans ; Male

Molecular genetic map is a fundamental organizational tool for genomic research. However, a genetic linkage map for Bupleurum chinense DC. has not been developed. In this study, with the theory of pseudo-testcross, 96 F1 plants from an intraspecific cross of B. chinense were used as mapping populations. Twenty eight ISSR (inter-simple sequence repeat) primers and 44 SSR (simple sequence repeat) primers were used to detect the polymorphisms between the parental plants, and of them, 28 ISSRs and 14 SSRs were selected to analyze the F1 populations. The map consisted of 13 linkage groups which included 80 (72 ISSRs and 8 SSRs) loci, and covered 2 633.9 cM with an average density of 33.4 cM. All 13 linkage groups consisted of 2-31 loci ranging in length from 15.4-1295.7 cM. This map will provide a basis for studies on gene mapping, map-based cloning and maker-assisted selection of important traits in B. chinense.
Bupleurum ; genetics ; Chromosome Mapping ; methods ; DNA, Plant ; genetics ; Genetic Linkage ; Microsatellite Repeats ; Plants, Medicinal ; genetics ; Polymorphism, Genetic