scholarly journals Analysis of CYP2D6 Allele Frequencies and Identification of Novel SNPs and Sequence Variations in Sardinians

ISRN Genetics ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Matteo Falzoi ◽  
Luigi Pira ◽  
Paolo Lazzari ◽  
Luca Pani
Keyword(s):  
Enzyme Level ◽  
Gene Copy Number ◽  
Drug Level ◽  
Caucasian Population ◽  
Allele Frequencies ◽  
Gene Copy ◽  
Sequencing Analysis ◽  
Gene Deletions ◽  
Allele Specific ◽  
Dna Sequencing Analysis

The CYP2D6 enzyme is involved in the metabolism of many commonly prescribed drugs. The presence of polymorphisms in the CYP2D6 gene may modulate the enzyme level and activity affecting individual responses, to pharmacological treatment in drug level, response and adverse reactions. Aims. This study aimed to analyze the determination of allele frequencies in Sardinians and the comparison to frequencies found in the Caucasian Population. Methods and Materials. We used a Long PCR strategy coupled to direct genomic DNA sequencing analysis. An amplification allele-specific was carried out to infer the correct allelic phase. The TaqMan Gene Copy Number Assay (Applied Biosystems) was used to verify the presence of gene deletions/multiplications. Results and Conclusions. Our results indicated that CYP2D6 allele frequencies in Sardinians differed from those previously detected in the Caucasian Population. Moreover, three new SNPs and four novel haplotypes were identified.

scholarly journals RPW8/HR Repeats Predict NLR-dependent Hybrid Performance

2019 ◽  
Author(s):  
Cristina A. Barragan ◽  
Rui Wu ◽  
Sang-Tae Kim ◽  
Wanyan Xi ◽  
Anette Habring ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Gene Copy ◽  
Hybrid Necrosis ◽  
Resistance Proteins ◽  
Broad Spectrum Resistance ◽  
Structural Differences ◽  
Allele Specific ◽  
Complex Manner

SummaryHybrid offspring can look very different from their parents, including having greatly increased or decreased fitness. In many plant species, conflicts between divergent elements of the immune system can cause hybrids to express autoimmunity, a generally deleterious syndrome known as hybrid necrosis. We are investigating multiple hybrid necrosis cases in Arabidopsis thaliana that are caused by allele-specific interactions between different variants at two unlinked resistance (R) gene clusters. One is the RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7) cluster, which encodes an intracellular nucleotide binding site-leucine rich repeat (NLR) immune receptors that confer strain-specific resistance to oomycetes. The other is the RESISTANCE TO POWDERY MILDEW 8 (RPW8)/HOMOLOG OF RPW8 (HR) locus, which encodes atypical resistance proteins that can confer broad-spectrum resistance to filamentous pathogens. There is extensive structural variation in the RPW8/HR cluster, both at the level of gene copy number and at the level of C-terminal protein repeats of unknown function. We demonstrate that the number of RPW8/HR repeats correlate, albeit in a complex manner, with the severity of hybrid necrosis when these alleles are combined with specific RPP7 variants. This observation suggests that gross structural differences, rather than individual amino acid polymorphisms, guide the genetic interaction between RPW8/HR and RPP7 alleles. We discuss these findings in light of the similarity of RPW8/HR proteins with pore-forming toxins, MLKL and HET-S, from mammals and fungi.

scholarly journals Genetic Factors Associated with Elevated Carbapenem Resistance in KPC-Producing Klebsiella pneumoniae

2010 ◽  
Vol 54 (10) ◽  
pp. 4201-4207 ◽  
Author(s):  
Brandon Kitchel ◽  
J. Kamile Rasheed ◽  
Andrea Endimiani ◽  
Andrea M. Hujer ◽  
Karen F. Anderson ◽  
...  
Keyword(s):  
United States ◽  
Klebsiella Pneumoniae ◽  
Copy Number ◽  
Gene Copy Number ◽  
Carbapenem Resistance ◽  
The United States ◽  
Gene Copy ◽  
Sequencing Analysis ◽  
Low Level ◽  
High Level

ABSTRACT In the United States, the most prevalent mechanism of carbapenem resistance among Enterobacteriaceae is the production of a Klebsiella pneumoniae carbapenemase (KPC). KPC-producing isolates often exhibit a range of carbapenem MICs. To better understand the factors that contribute to overall carbapenem resistance, we analyzed 27 KPC-producing K. pneumoniae isolates with different levels of carbapenem resistance, 11 with low-level (i.e., meropenem or imipenem MIC ≤ 4 μg/ml), 2 with intermediate-level (i.e., meropenem and imipenem MIC = 8 μg/ml), and 14 with high-level (i.e., imipenem or meropenem MIC ≥ 16 μg/ml) carbapenem resistance, that were received from throughout the United States. Among 14 isolates that exhibited high-level carbapenem resistance, Western blot analysis indicated that 10 produced an elevated amount of KPC. These isolates either contained an increased bla KPC gene copy number (n = 3) or had deletions directly upstream of the bla KPC gene (n = 7). Four additional isolates lacked elevated KPC production but had high-level carbapenem resistance. Porin sequencing analysis identified 22 isolates potentially lacking a functional OmpK35 and three isolates potentially lacking a functional OmpK36. The highest carbapenem MICs were found in two isolates that lacked both functioning porins and produced elevated amounts of KPC. The 11 isolates with low-level carbapenem resistance contained neither an upstream deletion nor increased bla KPC copy number. These results suggest that both bla KPC copy number and deletions in the upstream genetic environment affect the level of KPC production and may contribute to high-level carbapenem resistance in KPC-producing K. pneumoniae, particularly when coupled with OmpK36 porin loss.

scholarly journals Characterization of single gene copy number variants in schizophrenia

2019 ◽  
Author(s):  
Jin P. Szatkiewicz ◽  
Menachem Fromer ◽  
Randal J. Nonneman ◽  
NaEshia Ancalade ◽  
Jessica S. Johnson ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Copy Number ◽  
Single Gene ◽  
Copy Number Variants ◽  
Gene Copy Number ◽  
Added Value ◽  
Gene Copy ◽  
Specific Gene ◽  
Potential Contribution ◽  
Gene Deletions

AbstractGenetic studies of schizophrenia (SCZ) have now implicated numerous genomic loci that contribute to risk including several copy number variants (CNV) of large effect and hundreds of associated loci of small effect. However, in only a few cases has a specific gene been clearly identified. Rare CNV that affect only a single gene offer a potential avenue to discovering specific SCZ risk genes. Here, we use CNV generated from exome-sequencing of 4,913 SCZ cases and 6,188 controls in a homogenous Swedish cohort to assess the contribution of single-gene deletions and duplications to SCZ risk. As previously seen, we found an excess of rare deletions (p = 0.0004) and duplications (p = 0.0006) in SCZ cases compared to controls. When limiting to only single-gene CNV we identified nominally significant excess of deletions (p = 0.04) and duplications (p = 0.03). In an effort to increase the number of single-gene CNV, we reduced strict filtering criteria but required support from two independent CNV calling methods to create an expanded set that showed a significant burden of deletions in 11 out of 22 gene sets previously implicated in SCZ and in the combined set of genes across those sets (p = 0.008). Finally, for the significantly enriched set of voltage-gated calcium channels, we performed an extensive validation of all deletions generated from exome-sequencing as well as any deletion with evidence from previously analyzed genotyping arrays. In total, 4 exonic, single-gene deletions validated in cases and none in controls (p = 0.039), of which all were identified by exome-sequencing. Broadly, these results point to the potential contribution of single-gene CNV to SCZ and the added value of a deeper dive into CNV calls from exome-sequencing.

Novel hemophilia B mouse models exhibiting a range of mutations in the Factor IX gene

Blood ◽  
2004 ◽  
Vol 104 (9) ◽  
pp. 2767-2774 ◽  
Author(s):  
Denise E. Sabatino ◽  
Elina Armstrong ◽  
Shyrie Edmonson ◽  
Yi-Lin Liu ◽  
Marc Pleimes ◽  
...  
Keyword(s):  
Mouse Models ◽  
Viral Vector ◽  
Translation Termination ◽  
Gene Copy Number ◽  
Large Deletion ◽  
Factor Ix ◽  
Hemophilia B ◽  
Gene Copy ◽  
Missense Mutations ◽  
Gene Deletions

Abstract Animal models have been critical to the development of novel therapeutics in hemophilia. A deficiency of current murine models of hemophilia B is that they are all due to gene deletions, a type of mutation that is relatively rare in the human hemophilia population. We generated mice with a range of mutations in the Factor IX (F.IX) gene; these more faithfully reflect the types of mutations that cause disease in the human population. Transgenic mice expressing either wild-type human F.IX (hF.IX), or F.IX variants with premature translation termination codons, or missense mutations, under the control of the murine transthyretin promoter, were generated and crossed with mice carrying a large deletion of the murine F.IX gene. Gene copy number, F.IX transcript levels in the liver, intrahepatocyte protein expression, and circulating levels of F.IX protein in the mice were determined and compared with data generated by transient transfection assays using the same F.IX variants. Mice were injected with a viral vector expressing hF.IX and displayed a range of immune responses to the transgene product, depending on the underlying mutation. These new mouse models faithfully mimic the mutations causing human disease, and will prove useful for testing novel therapies for hemophilia. (Blood. 2004;104:2767-2774)

scholarly journals Functional interactions between unlinked muscle genes within haploinsufficient regions of the Drosophila genome.

Genetics ◽  
1988 ◽  
Vol 119 (1) ◽  
pp. 105-121
Author(s):  
T Homyk ◽  
C P Emerson
Keyword(s):  
Muscle Development ◽  
Gene Copy Number ◽  
Large Family ◽  
Mutant Gene ◽  
Genetic Interactions ◽  
Gene Copy ◽  
Drosophila Genome ◽  
Gene Products ◽  
New Genes ◽  
Allele Specific

Abstract Mutations in 13 genes affecting muscle development in Drosophila have been examined in pairwise combinations for evidence of genetic interactions. Heterozygous combinations of mutations in five genes, including the gene coding for myosin heavy chain, result in more severe phenotypes than respective single heterozygous mutant controls. The various mutant interactions include examples showing allele-specific intergenic interactions, gene specific interactions, and allele-specific intragenic complementations, suggesting that some interactions result from the manner in which mutant gene products associate. Interactions that result from alterations in "+" gene copy number were also uncovered, suggesting that normal myofibril development requires that the relative amounts of respective gene products produced be tightly regulated. The importance of the latter parameter is substantiated by the finding that all five interacting loci map to disperse haploinsufficient or haplolethal regions of the genome. The implications of the present findings are discussed in relation to pursuing the phenomena involving genetic interactions to identify new genes encoding interacting myofibrillar proteins, to examine the nature of intermolecular interactions in mutant and normal development and to decipher the quantitative and temporal regulation of a large family of functionally related gene products.

scholarly journals Expression of the mef(E) Gene Encoding the Macrolide Efflux Pump Protein Increases in Streptococcus pneumoniae with Increasing Resistance to Macrolides

2005 ◽  
Vol 49 (11) ◽  
pp. 4635-4640 ◽  
Author(s):  
Aleksandra K. Wierzbowski ◽  
Dave Boyd ◽  
Michael Mulvey ◽  
Daryl J. Hoban ◽  
George G. Zhanel
Keyword(s):  
Streptococcus Pneumoniae ◽  
Efflux Pump ◽  
Blot Hybridization ◽  
Gene Copy Number ◽  
Southern Blot Hybridization ◽  
Macrolide Resistance ◽  
Start Codon ◽  
Gene Copy ◽  
Sequencing Analysis ◽  
E Gene

ABSTRACT Active macrolide efflux is a major mechanism of macrolide resistance in Streptococcus pneumoniae in many parts of the world, especially North America. In Canada, this active macrolide efflux in S. pneumoniae is predominantly due to acquisition of the mef(E) gene. In the present study, we assessed the mef(E) gene sequence as well as mef(E) expression in variety of low- and high-level macrolide-resistant, clindamycin-susceptible (M-phenotype) S. pneumoniae isolates (erythromycin MICs, 1 to 32 μg/ml; clindamycin MICs, ≤0.25 μg/ml). Southern blot hybridization with mef(E) probe and EcoRI digestion and relative real-time reverse transcription-PCR were performed to study the mef(E) gene copy number and expression. Induction of mef(E) expression was analyzed by Etest susceptibility testing pre- and postincubation with subinhibitory concentrations of erythromycin, clarithromycin, azithromycin, telithromycin, and clindamycin. The macrolide efflux gene, mef(E), was shown to be a single-copy gene in all 23 clinical S. pneumoniae isolates tested, and expression post-macrolide induction increased 4-, 6-, 20-, and 200-fold in isolates with increasing macrolide resistance (erythromycin MICs 2, 4, 8, and 32 μg/ml, respectively). Sequencing analysis of the macrolide efflux genetic assembly (mega) revealed that mef(E) had a 16-bp deletion 153 bp upstream of the putative start codon in all 23 isolates. A 119-bp intergenic region between mef(E) and mel was sequenced, and a 99-bp deletion was found in 11 of the 23 M-phenotype S. pneumoniae isolates compared to the published mega sequence. However, the mef(E) gene was fully conserved among both high- and low-level macrolide-resistant isolates. In conclusion, increased expression of mef(E) is associated with higher levels of macrolide resistance in macrolide-resistant S. pneumoniae.

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