scholarly journals Cross-validation of technologies for genotyping CYP2D6 and CYP2C19

2019 ◽  
Author(s):  
Beatriz Carvalho Henriques ◽  
Amanda Buchner ◽  
Xiuying Hu ◽  
Vasyl Yavorskyy ◽  
Yabing Wang ◽  
...  
Keyword(s):  
Copy Number Variant ◽  
Data Interpretation ◽  
Gene Duplications ◽  
Cytochrome P450 Enzymes ◽  
Extra Copy ◽  
Single Nucleotide ◽  
Therapeutic Drugs ◽  
Two Samples ◽  
Genes Encoding ◽  
Polymerase Chain

AbstractBackgroundCYP2D6 and CYP2C19 are cytochrome P450 enzymes involved in the metabolism of many medications from multiple therapeutic classes. Associations between patterns of variants (known as haplotypes) in the genes encoding them (CYP2D6 and CYP2C19) and enzyme activities are well described. The genes in fact comprise 21% of biomarkers in drug labels. Despite this, genotyping is not common, partly attributable to its challenging nature (CYP2D6 having >100 haplotypes, including those with sequence from an adjacent pseudogene, and gene duplications). We cross-validated different methodologies for identifying haplotypes in these genes against each other.MethodsNinety-two samples with a variety of CYP2D6 and CYP2C19 genotypes according to prior AmpliChip CYP450 and TaqMan CYP2C19*17 data were selected from the Genome-based therapeutic drugs for depression (GENDEP) study. Genotyping was performed with TaqMan copy number variant (CNV) and single nucleotide variant (SNV) analysis, the next generation sequencing-based Ion S5 AmpliSeq Pharmacogenomics Panel, PharmacoScan, long-range polymerase chain reaction (L-PCR) followed by amplicon analysis, and Agena for CYP2C19. Variant pattern to haplotype translation was automated.ResultsThe inter-platform concordance for CYP2C19 was high (up to 100% for available data). For CYP2D6, the IonS5-PharmacoScan concordance was 94% for a range of variants tested apart from those with at least one extra copy of a CYP2D6 gene (occurring at a frequency of 3.8%, 33/853), or those with substantial sequence derived from pseudogene, known as hybrids (3%, 26/853).ConclusionsInter-platform concordance for CYP2C19 was high, and, moreover, the Ion S5 and PharmacoScan data were 100% concordant with that from a TaqMan CYP2C19*2 assay. We have also demonstrated feasibility of using an NGS platform for genotyping CYP2D6 and CYP2C19, with automated data interpretation methodology. This points the way to a method of making CYP2D6 and CYP2C19 genotyping more readily accessible.

scholarly journals Methodology for clinical genotyping of CYP2D6 and CYP2C19

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Beatriz Carvalho Henriques ◽  
Avery Buchner ◽  
Xiuying Hu ◽  
Yabing Wang ◽  
Vasyl Yavorskyy ◽  
...  
Keyword(s):  
Copy Number Variant ◽  
Cytochrome P450 Enzymes ◽  
Clinical Implementation ◽  
Clinical Workflow ◽  
Single Nucleotide ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Therapeutic Drugs ◽  
Automated Translation ◽  
Polymerase Chain

AbstractMany antidepressants, atomoxetine, and several antipsychotics are metabolized by the cytochrome P450 enzymes CYP2D6 and CYP2C19, and guidelines for prescribers based on genetic variants exist. Although some laboratories offer such testing, there is no consensus regarding validated methodology for clinical genotyping of CYP2D6 and CYP2C19. The aim of this paper was to cross-validate multiple technologies for genotyping CYP2D6 and CYP2C19 against each other, and to contribute to feasibility for clinical implementation by providing an enhanced range of assay options, customizable automated translation of data into haplotypes, and a workflow algorithm. AmpliChip CYP450 and some TaqMan single nucleotide variant (SNV) and copy number variant (CNV) data in the Genome-based therapeutic drugs for depression (GENDEP) study were used to select 95 samples (out of 853) to represent as broad a range of CYP2D6 and CYP2C19 genotypes as possible. These 95 included a larger range of CYP2D6 hybrid configurations than have previously been reported using inter-technology data. Genotyping techniques employed were: further TaqMan CNV and SNV assays, xTAGv3 Luminex CYP2D6 and CYP2C19, PharmacoScan, the Ion AmpliSeq Pharmacogenomics Panel, and, for samples with CYP2D6 hybrid configurations, long-range polymerase chain reactions (L-PCRs) with Sanger sequencing and Luminex. Agena MassARRAY was also used for CYP2C19. This study has led to the development of a broader range of TaqMan SNV assays, haplotype phasing methodology with TaqMan adaptable for other technologies, a multiplex genotyping method for efficient identification of some hybrid haplotypes, a customizable automated translation of SNV and CNV data into haplotypes, and a clinical workflow algorithm.

The Association of CYP2D6*4 and POR*28 Polymorphisms on Mirtazapine Plasma Level in Subjects with Major Depressive Disorder and Anxiety Disorders

2020 ◽  
Vol 23 (10) ◽  
pp. 1032-1040
Author(s):  
Fezile Ozdemir ◽  
Emrah Dural ◽  
Nilay Sedes Baskak ◽  
Yağmur Kır ◽  
Bora Baskak ◽  
...  
Keyword(s):  
Plasma Level ◽  
Plasma Levels ◽  
Psychiatric Patients ◽  
Nucleotide Polymorphisms ◽  
Major Depressive ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Genes Encoding ◽  
Study Population ◽  
Polymerase Chain

Aims and Objective: The plasma level of mirtazapine (MIR) varies between individuals primarily depending on the differences in metabolism during pharmacotherapy. CYP2D6 takes the role as a major enzyme in MIR metabolism and POR enzyme donates an electron to CYP2D6 for its activity. Single nucleotide polymorphisms in the genes encoding pharmacokinetic enzymes may cause changes in enzyme activity, leading to differences in metabolism of the drug. Our aim was to assess the influence of CYP2D6*4 and POR*28 polymorphisms on MIR plasma levels in Turkish psychiatric patients. Materials and Methods: The association between genetic variations and plasma level of MIR was investigated on 54 patients. CYP2D6*4 and POR*28 polymorphisms were analysed using Polymerase Chain Reaction- Restriction Fragment Length Polymorphism (PCR-RFLP) and plasma MIR levels were measured using HPLC. Results: Allele frequencies of CYP2D6*4 and POR*28 were 0.11 and 0.39, respectively in the study population. The results showed that CYP2D6*4 allele carriers have higher C/D MIR levels while POR*28 allele carriers have lower C/D MIR levels. Combined genotype analyses also revealed that individuals with CYP2D6*1/*1 - POR*28/*28 genotype have a statistically lower C/D MIR level (0.95 ng/ml/dose) when compared with individuals with CYP2D6*1/*1 - POR*1/*1 genotype (1.52 ng/ml/dose). Conclusion: Our results indicate that CYP2D6*4 and POR*28 polymorphisms may have a potential in the explanation of differences in plasma levels in MIR treated psychiatric patients. A combination of these variations may be beneficial in increasing drug response and decreasing adverse drug reactions in MIR psychopharmacotherapy.

Evaluation of Ficolin-3 (FCN3) 1637delC (rs28357092) Frameshift Mutation in Iranian Type 2 Diabetic Subjects

2018 ◽  
Author(s):  
Shaghayegh Pishkhan Dibazar ◽  
Ahmad Zavaran Hosseini ◽  
Fatemeh Yari ◽  
Shirin Fateh ◽  
Mohammad Reza Deyhim
Keyword(s):  
Healthy Subjects ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphism ◽  
Salting Out ◽  
Single Nucleotide ◽  
Three Samples ◽  
Two Samples ◽  
Polymerase Chain ◽  
Type 2 Diabetic

Background and Aims: Ficolins are proteins that bind to carbohydrates, act as opsonins and play an important role in innate immunity. Polymorphism in ficolin-3 gene (FCN3) can lead to complement deficiency and increase the risk of some disorders such as diabetes. The aim of this study was to investigate the frequency of FCN3 + 1637delC as a single nucleotide polymorphism (SNP) in this gene in healthy and diabetic subjects of Iran. Materials and Methods: Blood was taken from 36 diabetics and 37 healthy subjects who had referred to the Iranian Blood Transfusion Organization. Blood sugar was analyzed using a calorimetric method. After DNA extraction using salting out method, polymerase chain reaction (PCR) was carried out and the restriction fragment length polymorphism (RFLP) method was accomplished using ApaI restriction enzyme. Consequently, the resulted fragments were evaluated using electrophoresis on 2% L-agarose gel. Results: Evaluation of the results indicated that the heterozygote form of SNP FCN3 + 1637delC was seen in three samples (8.1%) of the studied healthy subjects and in two samples (5.6%) of the diabetic individuals. Besides, the homozygous form of the mutation was not seen in the studied healthy and diabetic subjects. Conclusion: Results of this study showed that FCN3 variant of SNP FCN3 + 1637delC was not considered as a risk factor for type 2 diabetes mellitus (T2DM) in Iranian subjects.

Involvement of MTHFR and TPMT genes in susceptibility to childhood acute lymphoblastic leukemia (ALL) in Mexicans

2016 ◽  
Vol 31 (1) ◽  
Author(s):  
Ossyneidee Gutiérrez-Álvarez ◽  
Ismael Lares-Asseff ◽  
Carlos Galaviz-Hernández ◽  
Elio-Aarón Reyes-Espinoza ◽  
Horacio Almanza-Reyes ◽  
...  
Keyword(s):  
Essential Role ◽  
Case Control Study ◽  
Lymphoblastic Leukemia ◽  
Case Control ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Genes Encoding ◽  
Polymerase Chain ◽  
Control Study

AbstractFolate metabolism plays an essential role in the processes of DNA synthesis and methylation. Deviations in the folate flux resulting from single-nucleotide polymorphisms in genes encoding folate-dependent enzymes may affect the susceptibility to leukemia. This case-control study aimed to assess associations amongDNA samples obtained from 70 children with ALL and 152 age-matched controls (range, 1–15 years) were analyzed by real-time reverse transcription polymerase chain reaction (RT-qPCR) to detect: The frequency of the: The

scholarly journals Pharmacogenetic Markers of Treatment Response of Imatinib Mesylate in Chronic Myeloid Leukemia Brazilian Patients

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5458-5458
Author(s):  
Natália M Vieira ◽  
Renata Leite ◽  
Fabíola Reginato ◽  
Marília Zandoná ◽  
Tito Vanelli Costa ◽  
...  
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Imatinib Mesylate ◽  
Myeloid Leukemia ◽  
Conflicts Of Interest ◽  
Response To Treatment ◽  
Nucleotide Polymorphisms ◽  
Metabolizing Enzymes ◽  
Single Nucleotide ◽  
Genes Encoding ◽  
Polymerase Chain

Abstract The treatment of chronic myeloid leukemia (CML) was revolutionized by the introduction of imatinib mesylate (IM). However, approximately 20% of patients are non-responsive and interpatient variability in response to IM is still a phenomenon lacking explanation. Single nucleotide polymorphisms (SNPs) located in genes encoding proteins involved in IM pharmacokinetics are potentially involved in the causes of this variation. In this study, we investigated the association of SNPs in the genes encoding IM metabolizing enzymes CYP3A4 (rs35599367 and rs2740574) and CYP3A5 (rs776746) and efflux transporter proteins ABCB1 (rs3213619, rs1128503, rs2032582 and rs1045642), ABCG2 (rs2231142) and ABCC4 (rs9561765) with response to treatment and with IM plasma through levels and hair concentrations. The analyzed sample was constituted of 182 CML patients on IM treatment. DNA samples were genotyped for the nine SNPs using real-time polymerase chain reaction. Hair and plasma trough IM concentrations were measured through liquid chromatography coupled to mass spectrometry methods. Clinical response was defined according to the European Leukemia Net guidelines. The number of responders to standard IM therapy was 104. A trend to a higher frequency of CYP3A4 *22 (rs35599367) allele carriers was observed among responders to IM (12.5 vs. 3.4% of non-responders, P = 0.087), although no significant differences in plasma or hair concentrations between genotypes were found. Pharmacogenetics may become a valuable approach to optimize therapy with IM in CML, but many factors still need to be clarified to make possible its application in clinical practice. Disclosures No relevant conflicts of interest to declare.

scholarly journals Validation of methodology for efficient genotyping of CYP2D6 and CYP2C19

2021 ◽  
Author(s):  
Beatriz Carvalho Henriques ◽  
Amanda Buchner ◽  
Xiuying Hu ◽  
Yabing Wang ◽  
Vasyl Yavorskyy ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Copy Number Variant ◽  
Large Datasets ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Polymerase Chain ◽  
Consensus Genotypes ◽  
Hybrid Genes

Abstract There are some data associating variants in the CYP2D6 and/or CYP2C19 genes with concentration-to-dose ratios, efficacy, and retention in treatments. However, much of the above arises from relatively small studies or large datasets with limited genotyping methodologies. Our aim was to develop and validate comprehensive and accurate genotyping methodology for these two genes to facilitate regenotyping in large datasets and hence the generation of more accurate clinical associations. TaqMan copy number variant (CNV) assays for CYP2D6 were used to identify samples from a relevant large dataset (GENDEP study, N = 853) with particularly challenging genotypes to call. These and those representing as broad a range of CYP2D6 and CYP2C19 genotypes as possible by prior available data (AmpliChip CYP450 and TaqMan CYP2C19*17) were chosen for further analysis (N = 96). Genotyping techniques employed were: Luminex CYP2D6 xTAGv3 and Luminex CYP2C19 xTAGv3, PharmacoScan, the Ion S5 AmpliSeq Pharmacogenomics Panel, TaqMan single nucleotide variant (SNV) assays, and, for the CYP2D6 hybrids, long-range polymerase chain reactions (L-PCRs) with Sanger sequencing. Agena was also used for CYP2C19. The TaqMan SNV assays were able to assist with identifying which gene was duplicated or in tandem for multiple copy variants. A multiplex assay was adaptable for analysis of CYP2D6 hybrid genes, with Sanger sequencing data being consistent with the data arising; we provide these data for efficient genotyping of such CYP2D6 hybrid genes with adaptable multiplex methods. Consensus genotypes generated to date resulted in revision of assigned enzyme activity score for 28/96(29%) and 2/93 samples (2.2%) for CYP2D6 and CYP2C19, respectively.

Structure, expression, chromosomal location and product of the gene encoding Adh2 in Petunia.

Genetics ◽  
1993 ◽  
Vol 133 (4) ◽  
pp. 999-1007
Author(s):  
R G Gregerson ◽  
L Cameron ◽  
M McLean ◽  
P Dennis ◽  
J Strommer
Keyword(s):  
Chromosomal Location ◽  
Higher Plants ◽  
Gene Encoding ◽  
Genomic Libraries ◽  
Regulatory Strategy ◽  
Adh1 Gene ◽  
Adh Genes ◽  
Genes Encoding ◽  
Adh Gene ◽  
Polymerase Chain

Abstract In most higher plants the genes encoding alcohol dehydrogenase comprise a small gene family, usually with two members. The Adh1 gene of Petunia has been cloned and analyzed, but a second identifiable gene was not recovered from any of three genomic libraries. We have therefore employed the polymerase chain reaction to obtain the major portion of a second Adh gene. From sequence, mapping and northern data we conclude this gene encodes ADH2, the major anaerobically inducible Adh gene of Petunia. The availability of both Adh1 and Adh2 from Petunia has permitted us to compare their structures and patterns of expression to those of the well-studied Adh genes of maize, of which one is highly expressed developmentally, while both are induced in response to hypoxia. Despite their evolutionary distance, evidenced by deduced amino acid sequence as well as taxonomic classification, the pairs of genes are regulated in strikingly similar ways in maize and Petunia. Our findings suggest a significant biological basis for the regulatory strategy employed by these distant species for differential expression of multiple Adh genes.

scholarly journals Genetic Variants in Smoking-Related Genes in Two Smoking Cessation Programs: A Cross-Sectional Study

2021 ◽  
Vol 18 (12) ◽  
pp. 6597
Author(s):  
Gloria Pérez-Rubio ◽  
Luis Alberto López-Flores ◽  
Ana Paula Cupertino ◽  
Francisco Cartujano-Barrera ◽  
Luz Myriam Reynales-Shigematsu ◽  
...  
Keyword(s):  
Smoking Cessation ◽  
Cross Sectional Study ◽  
Nucleotide Polymorphisms ◽  
Sectional Study ◽  
Cross Sectional ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Quitting Smoking ◽  
Genes Encoding ◽  
Genomic Regions

Previous studies have identified variants in genes encoding proteins associated with the degree of addiction, smoking onset, and cessation. We aimed to describe thirty-one single nucleotide polymorphisms (SNPs) in seven candidate genomic regions spanning six genes associated with tobacco-smoking in a cross-sectional study from two different interventions for quitting smoking: (1) thirty-eight smokers were recruited via multimedia to participate in e-Decídete! program (e-Dec) and (2) ninety-four attended an institutional smoking cessation program on-site. SNPs genotyping was done by real-time PCR using TaqMan probes. The analysis of alleles and genotypes was carried out using the EpiInfo v7. on-site subjects had more years smoking and tobacco index than e-Dec smokers (p < 0.05, both); in CYP2A6 we found differences in the rs28399433 (p < 0.01), the e-Dec group had a higher frequency of TT genotype (0.78 vs. 0.35), and TG genotype frequency was higher in the on-site group (0.63 vs. 0.18), same as GG genotype (0.03 vs. 0.02). Moreover, three SNPs in NRXN1, two in CHRNA3, and two in CHRNA5 had differences in genotype frequencies (p < 0.01). Cigarettes per day were different (p < 0.05) in the metabolizer classification by CYP2A6 alleles. In conclusion, subjects attending a mobile smoking cessation intervention smoked fewer cigarettes per day, by fewer years, and by fewer cumulative pack-years. There were differences in the genotype frequencies of SNPs in genes related to nicotine metabolism and nicotine dependence. Slow metabolizers smoked more cigarettes per day than intermediate and normal metabolizers.

scholarly journals scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gavin W. Wilson ◽  
Mathieu Derouet ◽  
Gail E. Darling ◽  
Jonathan C. Yeung
Keyword(s):  
Genetic Variants ◽  
False Positive ◽  
Variant Calling ◽  
Call Rate ◽  
Rna Seq ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Variant Call ◽  
Two Samples ◽  
Co Detection

AbstractIdentifying single nucleotide variants has become common practice for droplet-based single-cell RNA-seq experiments; however, presently, a pipeline does not exist to maximize variant calling accuracy. Furthermore, molecular duplicates generated in these experiments have not been utilized to optimally detect variant co-expression. Herein, we introduce scSNV designed from the ground up to “collapse” molecular duplicates and accurately identify variants and their co-expression. We demonstrate that scSNV is fast, with a reduced false-positive variant call rate, and enables the co-detection of genetic variants and A>G RNA edits across twenty-two samples.

scholarly journals The Yeast Signal Sequence Trap Identifies Secreted Proteins of the Hemibiotrophic Corn Pathogen Colletotrichum graminicola

2008 ◽  
Vol 21 (10) ◽  
pp. 1325-1336 ◽  
Author(s):  
Jorrit-Jan Krijger ◽  
Ralf Horbach ◽  
Michael Behr ◽  
Patrick Schweizer ◽  
Holger B. Deising ◽  
...  
Keyword(s):  
Cell Walls ◽  
Leaf Extract ◽  
Signal Sequence ◽  
Stem Rot ◽  
Colletotrichum Graminicola ◽  
In Planta ◽  
Chain Reaction ◽  
Genes Encoding ◽  
Polymerase Chain

The hemibiotroph Colletotrichum graminicola is the causal agent of stem rot and leaf anthracnose on Zea mays. Following penetration of epidermal cells, the fungus enters a short biotrophic phase, followed by a destructive necrotrophic phase of pathogenesis. During both phases, secreted fungal proteins are supposed to determine progress and success of the infection. To identify genes encoding such proteins, we constructed a yeast signal sequence trap (YSST) cDNA-library from RNA extracted from mycelium grown in vitro on corn cell walls and leaf extract. Of the 103 identified unigenes, 50 showed significant similarities to genes with a reported function, 25 sequences were similar to genes without a known function, and 28 sequences showed no similarity to entries in the databases. Macroarray hybridization and quantitative reverse-transcriptase polymerase chain reaction confirmed that most genes identified by the YSST screen are expressed in planta. Other than some genes that were constantly expressed, a larger set showed peaks of transcript abundances at specific phases of pathogenesis. Another set exhibited biphasic expression with peaks at the biotrophic and necrotrophic phase. Transcript analyses of in vitro-grown cultures revealed that several of the genes identified by the YSST screen were induced by the addition of corn leaf components, indicating that host-derived factors may have mimicked the host milieu.

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