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At least 73 records · Page 4Linked to original sources
PubMed2006

Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes.

BACKGROUND: Single nucleotide polymorphisms (SNPs) represent the most abundant type of DNA variation in the vertebrate genome, and their applications as genetic markers in numerous studies of molecular ecology and conservation of natural populations are emerging. Recent large-scale sequencing projects in several fish species have provided a vast amount of data in public databases, which can be utilized in novel SNP discovery in salmonids. However, the suggested duplicated nature of the salmonid genome may hamper SNP characterization if the primers designed in conserved gene regions amplify multiple loci. RESULTS: Here we introduce a new intron-primed exon-crossing (IPEC) method in an attempt to overcome this duplication problem, and also evaluate different priming methods for SNP discovery in Atlantic salmon (Salmo salar) and other salmonids. A total of 69 loci with differing priming strategies were screened in S. salar, and 27 of these produced approximately 13 kb of high-quality sequence data consisting of 19 SNPs or indels (one per 680 bp). The SNP frequency and the overall nucleotide diversity (3.99 x 10-4) in S. salar was lower than reported in a majority of other organisms, which may suggest a relative young population history for Atlantic salmon. A subset of primers used in cross-species analyses revealed considerable variation in the SNP frequencies and nucleotide diversities in other salmonids. CONCLUSION: Sequencing success was significantly higher with the new IPEC primers; thus the total number of loci to screen in order to identify one potential polymorphic site was six times less with this new strategy. Given that duplication may hamper SNP discovery in some species, the IPEC method reported here is an alternative way of identifying novel polymorphisms in such cases.

Animals↗
PubMed1999

Duplication of 7p21.2-->pter due to maternal 7p;21q translocation: implications for critical segment assignment in the 7p duplication syndrome.

We describe a 1-year-old boy with mental and physical retardation, a large anterior fontanel, brachycephaly with flat occiput, short and stubby fingers, generalized hypotonia, ocular hypertelorism, low-nasal bridge, long philtrum, high-narrow palate, apparently low-set ears, and a small mandible. Cytogenetic analysis utilizing high resolution chromosome banding technique showed an unbalanced karyotype consisting of 46,XY,add(21)(q22.3) that originated from maternal balanced translocation between chromosomes 7 and 21. Fluorescence in situ hybridization (FISH) using micro-dissected library probe pool from chromosome 7 confirmed the additional material on 21q was derived from chromosome 7. Our results indicated that the patient had an unbalanced translocation, 46,XY, der(21)t(7;21)(p21.2;q22.3)mat, which resulted in duplication for distal 7p. Our patient is similar to reported cases with a 7p15-->pter or larger duplication of 7p, suggesting that the critical segment causing the characteristic phenotype of 7p duplication syndrome, including large anterior fontanel, exists at 7p21.2 or 7p21.2-->pter.

Abnormalities, Multiple↗
PubMed1987

Partial duplication 8p due to interstitial duplication: inv dup(8)(p21.1----p22). Further delineation of the phenotype from birth to adulthood.

We report on 2 patients, less than age 5 years, and one adult patient with partial duplication 8p, due to interstitial duplication of bands 8p21.1-22. The phenotype in young and adult patients with this chromosomal unbalance syndrome is further documented. In young patients the craniofacial manifestations are very similar to trisomy 8 mosaicism. However, mental retardation is much more pronounced in 8p21-22 duplication than in trisomy 8 mosaicism. The phenotypic changes observed in adult patients are probably secondary and they are due to the great neurologic deficit with generalized spasticity and hypertonia.

Adult↗
PubMed1994

Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region. Molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication.

The correlation of many HLA-associated autoimmune and genetic diseases with the polymorphic complement C4 genes may be attributed to the presence of disease susceptibility genes in the close proximity of C4. We have cloned and characterized a pair of partially duplicated genes, RP1 and RP2, located 611 base pairs upstream of the human C4A and C4B genes, respectively. The putative RP protein, consisting of 364 amino acid residues, is basic and highly hydrophilic. There is a bipartite nuclear localization signal at residues 114-131 and therefore RP may be a nuclear protein. Northern blot analysis suggested that RP is ubiquitously expressed. The 5' region of the RP1 gene is CpG rich, which is a characteristic of housekeeping genes. The RP1 gene contains nine exons. Located in the fourth intron is a cluster of Alu elements, and a newly defined composite retroposon SVA with a SINE, multiple copies of GC-rich VNTRs and an Alu element altogether enclosed by direct terminal repeats. Members of SVA are also present in the complement C2 gene located about 20 kilobases upstream of RP1 in the HLA and in the cytochrome CYP1A1 gene. Determination of the DNA sequences for RP2 from two different HLA haplotypes revealed identical hybrid sequences which resulted from fusion of RP with the tenascin-like Gene X and truncation of the 5' regions of both genes. Cumulative data suggest that the four tandemly arranged genes RP, complement C4, steroid 21-hydroxylase (CYP21), and Gene X altogether form a modular structure, RCCX. The number of RCCX modules varies from one to three or more in the population. Absence of the truncated genes RP2 and Gene XA have been detected in genomes with single RCCX modules. Duplication of the RCCX modules probably occurred before the speciation of great apes and humans as they contain the same breakpoint region of RP and Gene X gene duplication.

Alleles↗
PubMed1998

Direct duplication of 9p22-->p24 in a child with duplication 9p syndrome.

A de novo direct duplication of 9p22-->p24 was shown in a child with a duplication 9p phenotype by GTG banding and fluorescence in situ hybridization (FISH) using a chromosome-9 specific painting probe as well as 6 YAC DNA probes localized to the 9p13-9p23 region. The breakpoints in this patient and previously reported patients suggest that 9p22 may be the critical region for duplication 9p syndrome.

Chromosome Aberrations↗
PubMed2000

The exon 13 duplication in the BRCA1 gene is a founder mutation present in geographically diverse populations. The BRCA1 Exon 13 Duplication Screening Group.

Recently, a 6-kb duplication of exon 13, which creates a frameshift in the coding sequence of the BRCA1 gene, has been described in three unrelated U.S. families of European ancestry and in one Portuguese family. Here, our goal was to estimate the frequency and geographic diversity of carriers of this duplication. To do this, a collaborative screening study was set up that involved 39 institutions from 19 countries and included 3,580 unrelated individuals with a family history of the disease and 934 early-onset breast and/or ovarian cancer cases. A total of 11 additional families carrying this mutation were identified in Australia (1), Belgium (1), Canada (1), Great Britain (6), and the United States (2). Haplotyping showed that they are likely to derive from a common ancestor, possibly of northern British origin. Our results demonstrate that it is strongly advisable, for laboratories carrying out screening either in English-speaking countries or in countries with historical links with Britain, to include within their BRCA1 screening protocols the polymerase chain reaction-based assay described in this report.

Age of Onset↗
PubMed2003

Comparative analysis of MLL partial tandem duplication and FLT3 internal tandem duplication mutations in 956 adult patients with acute myeloid leukemia.

Partial tandem duplication (PTD) of the MLL gene and internal tandem duplication (ITD) of the juxtamembrane region of the FLT3 receptor tyrosine kinase gene have been described in acute myeloid leukemia (AML) patients, preferentially in those with normal cytogenetics. These alterations have been associated with a poor prognosis. In our study, we analyzed the prevalence and the potential prognostic impact of these aberrations in a large unselected and well-defined cohort of 956 patients with AML. Results were correlated with cytogenetic data and clinical outcome. MLL PTD was detected by RT-PCR, subsequent nucleotide sequencing, and Southern blotting. The overall incidence was found to be 5.0% (48/956), whereas FLT3 ITD was detected in 19.2% (184/956). Sixteen cases were positive for both alterations. The rate of MLL PTD in FLT3 ITD positive patients was significantly higher than that in FLT3 ITD negative patients [16/184 (8.7%); 32/772 (4.1%); P = 0.025]. However, both aberrations were highly increased in patients with normal karyotype (MLL PTD 35/431, P = 0.004; FLT3 ITD 132/334, P < 0.001). When restricted to this subgroup, the rate of MLL PTD in patients with FLT3 mutations was not significantly increased. No statistically significant differences were detected between patients positive for MLL PTD and patients negative for MLL PTD in the rate of complete remissions or the overall survival, although we did see a significantly shorter disease-free survival in patients age 60 or younger. In conclusion, although there is an overlap in the mutational spectrum in AML with FLT3 ITD and MLL PTD mutations, our data do not support a common mechanistic basis. Although associated with inferior disease-free survival, the results of this study do not unequivocally support the notion that MLL PTD mutations represent an independent prognostic factor.

Adolescent↗
PubMed1999

Genetic mechanisms for duplication and multiduplication of the human CYP2D6 gene and methods for detection of duplicated CYP2D6 genes.

The polymorphic CYP2D6 gene determines the rates at which several different classes of clinically important drugs are metabolized in vivo. A specific phenotype whereby a subject metabolizes drugs very rapidly (ultrarapid metabolizer, UM) has been shown to be caused by the presence of multiple active CYP2D6 genes on one allele. Hitherto, individuals with 1, 2, 3, 4, 5, or 13 CYP2D6 genes in tandem have been described for various ethnic groups. In the present investigation, we present results from restriction mapping of the CYP2D loci of individuals with two or more consecutive CYP2D6 genes, along with sequence analysis of this gene (CYP2D6*2). Our results indicate that alleles with duplicated or multiduplicated genes have occurred through unequal crossover at a specific breakpoint in the 3'-flanking region of the CYP2D6*2B allele with a specific repetitive sequence. In contrast, alleles with 13 copies of the gene are proposed to have been formed by unequal segregation and extrachromosomal replication of the acentric DNA. We present a rapid and efficient PCR-based allele-specific method for the detection of duplicated, multiduplicated, or amplified CYP2D6 genes.

Alleles↗
PubMed2005

The distributions of the duplicate oestrogen receptors ER-beta a and ER-beta b in the forebrain of the Atlantic croaker (Micropogonias undulatus): evidence for subfunctionalization after gene duplication.

Teleost fishes have three distinct oestrogen receptor (ER) subtypes: ER-alpha, ER-beta a (or ER-gamma) and ER-beta b. ER-beta a and ER-beta b arose from a duplication of an ancestral ER-beta gene early in the teleost lineage. Here, we describe the distribution of the three ER mRNAs in the hypothalamus and cerebellum of the Atlantic croaker to address two issues: the specific functions of multiple ERs in the neuroendocrine system and the evolution and fate of duplicated genes. ER-alpha was detected in nuclei of the preoptic area (POA) and hypothalamus previously shown to possess ER-alphas in teleosts. AcER-beta b, but not ER-beta a, labelling was detected in the magnocellular neurons of the POA, nucleus posterior tuberis, the nucleus recessus posterior and cerebellum. By contrast, acER-beta a, but not ER-beta b, was detected in the dorsal anterior parvocellular POA and suprachiasmatic nucleus. Both ER-betas were found in posterior parvocellular and ventral anterior POA nuclei, the ventral hypothalamus, and periventricular dorsal hypothalamus. The differences we observed in ER subtype mRNA distribution within well-characterized brain nuclei suggest that ER-beta a and ER-beta b have distinct functions in the neuroendocrine control of reproduction and behaviour, and provide evidence that the teleost ER-beta paralogues have partitioned functions of the ancestral ER-beta gene they shared with tetrapods.

Animals↗
PubMed1982

An esterase duplication in Drosophila: differences in expression of duplicate loci within and among related species.

An esterase duplication is described in the sibling species pair Drosophila mojavensis and Drosophila arizonensis. We present evidence for two separate structural loci mapping at a distance of less than 0.16 recombination units from each other. Alleles at the two loci have the same substrate specificities and form small amounts of interlocus heterodimers. One locus (Est-5) is functioning throughout the insect's life cycle and appears at high concentrations in the hemolymph and the fat body. Its duplicate (Est-4) functions only during the late larval stage and is concentrated mainly in the carcass. No null alleles at either locus were observed in population surveys. An examination of 12 other species from the repleta group, to which D. mojavensis and D. arizonesis belong, suggests that Est-5 is universally present, but the activity levels of Est-4 vary among species and may be totally absent in some species. Variation in the level of Est-4 activity does not closely follow the phylogenetic relationship.

Age Factors↗
PubMed1977

Gene duplication in salmonid fishes: evidence for duplicated but catalytically equivalent A4 lactate dehydrogenases.

Skeletal muscle tissues from many species of salmonid fish are known to exhibit a set of three of five isozymes for A4-type lactate dehydrogenase (L-lactate: NAD oxidoreductase, E.C. 1.1.1.27), but the genetic basis for this isozyme system has not previously been assessed. This isozyme system was purified to homogeneity from salmon (Oncorhynchus tshawytscha) and shown to be composed of two polypeptides. Aalpha and Abeta, in binomial tetrameric combinations. Amino acid analysis revealed that Aalpha and Abeta are closely related but genetically distinct proteins, and thus are coded for the recently duplicated structural loci. Catalytic studies on the purified intact salmon isozyme system and on the isozymically pure Aalpha4 and Abeta4 homotetramers from brown trout (Salmo trutta) revealed no significant differences in catalytic properties among these enzymes, suggesting equivalent catalytic function of Aalpha and Abeta. These results, in combination with studies on polypeptide and isozyme ratios, suggest that one of the duplicated loci in salmon may be drifting toward a nonfunctional state by accumulation of mutations in regulatory DNA rather than in the structural gene itself.

Amino Acid Sequence↗
PubMed1978

Effects of chemical and physical mutagens on the frequency of a large genetic duplication in Salmonella typhimurium. II. Stimulation of duplication-loss from merodiploids.

Strains of Salmonella typhimurium which contain a duplication of approximately 30% of the genome may be obtained by a simple selective procedure. These strains are highly unstable, losing the duplication when grown on non-selective medium. In this paper we report that treatment of merodiploid bacteria with mutagenic agents stimulates the rate at which haploid segregants are obtained from merodiploid strains. The mutagens which have been tested for this effect are X-rays, ultraviolet light (UV), ethyl methanesulfonate (EMS), and the azaacridine half-mustard ICR-372.

Aza Compounds↗
PubMed1989

Duplicates or singletons? An analysis of the need for replication in immunoassay and a computer program to calculate the distribution of outliers, error rate and the precision profile from assay duplicates.

The nature, frequency, statistics and methods of detection of both Gaussian and catastrophic errors in immunoassay are described. The method of sequential analysis is applied to the rates of catastrophic errors and is used to calculate the number of results which must be examined in order to achieve a stated confidence that the error rate is acceptable so that a rational decision on use of duplicate or singleton assay can be made. A simple computer program is described, which allows computation of the precision profile and an analysis of errors using accumulated data from duplicate assays. These methods have been applied to an enzyme amplification immunometric assay for thyroid-stimulating hormone (TSH) and an analysis is made of the errors detected in a sample of 1419 patient results.

Chemistry, Clinical↗
PubMed2001

De novo duplication (5)(q31.3q33.3): report of a patient and characterization of the duplicated region using microdissection and FISH.

We report on a 2-year-old boy presenting with growth and psychomotor retardation and facial anomalies, including a flat face with prominent forehead, a flat nasal bridge and flat occiput, unusually long curved eyelashes, and a thin upper lip with down-turned corners of the mouth. Analysis of GTG-banded chromosomes demonstrated that the patient had extra chromosomal material in the long arm of one chromosome 5. This chromosome aberration was characterized further using microdissection and FISH with band-specific probes and a de novo direct duplication (5)(q31.3q33.3) was shown to be present. We have compared this case with others known to be partially trisomic for chromosome 5q reported in the literature.

Abnormalities, Multiple↗