Genotyping and haplotyping of CYP2C19 functional alleles on thin-film biosensor chips

Nakamoto, Kaori; Kidd, Judith R.; Jenison, Robert; Klaassen, Curtis D.; Wan, Yu‐Jui Yvonne; Kídd, Kenneth K.; Zhong, Xiao Bo

doi:10.1097/fpc.0b013e32801152c2

Cited by 19 publications

(13 citation statements)

References 56 publications

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“…As an supplemental step in our assessment of panel performance in this study, we compared the allele frequencies observed here with reference allele frequencies abstracted from multiple sources including the primary literature, The International HapMap Project, 1000 Genomes Project (Pilot 1 Low Coverage Panel), dbSNP, PharmGKB, the Environmental Genome Project, and SNP500Cancer [17 - 22]. Of the 173 diallelic, non-CNV markers targeted by the panel, we were able to abstract allele frequencies from European-descent populations for 109 (63%).…”

Section: Resultsmentioning

confidence: 99%

“…Tests of HWE for triallelic SNPs were calculated manually using Pearson’s chi-squared test. ADME Core Panel marker allele frequencies for comparison with the present study were abstracted from the primary literature, The International HapMap Project, 1000 Genomes Project, dbSNP, PharmGKB, the Environmental Genome Project, and SNP500Cancer [17 - 22]. All frequencies were selected from populations of European-descent, similar to the study population described here.…”

Section: Methodsmentioning

confidence: 99%

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Assessment of a Pharmacogenomic Marker Panel in a Polypharmacy Population Identified from Electronic Medical Records

et al. 2013

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We genotyped 326 “frequently medicated” individuals of European-descent in Vanderbilt’s biorepository linked to de-identified electronic medical records, BioVU, on the ADME Core Panel to assess quality and performance of the assay. We compared quality control metrics and determined the extent of direct and indirect marker overlap between the ADME Core Panel and the Illumina Omni1-Quad. We found the quality of the ADME Core Panel data to be high, with exceptions in select copy number variants (CNVs) and markers in certain genes (notably CYP2D6). Most of the common variants on the ADME panel are genotyped by the Omni1, but absent rare variants and CNVs could not be accurately tagged by single markers. Finally, our frequently medicated study population did not convincingly differ in allele frequency from reference populations, suggesting that heterogeneous clinical samples (with respect to medications) follow similar allele frequency distributions in pharmacogenetics genes as their appropriate reference populations.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Assessment of a Pharmacogenomic Marker Panel in a Polypharmacy Population Identified from Electronic Medical Records

et al. 2013

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“…Thin-film biosensor chips are capable of transducing specific molecular interactions into signals that can be visualized by the naked eye or by simple digital-imaging systems because mass deposited on the thin-film surface by enzymatic catalysis alters the wavelength of light reflected by the optical layer resulting in a perceived colour change on the surface [41]. The assay has been described for SNP detection for several animal and plant species and is reported to be robust, exhibit high sensitivity and specificity, and is flexible from low to high throughput [42–44]. We are currently examining the feasibility of using this platform for a multiplexed version of the VPMT.…”

Section: Summary and Future Developmentmentioning

confidence: 99%

The Vector Population Monitoring Tool (VPMT): High-Throughput DNA-Based Diagnostics for the Monitoring of Mosquito Vector Populations

Bass

Nikou

Vontas

et al. 2010

Malaria Research and Treatment

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Regular monitoring of mosquito vector populations is an integral component of most vector control programmes. Contemporary data on mosquito species composition, infection status, and resistance to insecticides are a prerequisite for effective intervention. For this purpose we, with funding from the Innovative Vector Control Consortium (IVCC), have developed a suite of high-throughput assays based on a single “closed-tube” platform that collectively comprise the “Vector Population Monitoring Tool” (VPMT). The VPMT can be used to screen mosquito disease vector populations for a number of traits including Anopheles gambiae s.l. and Anopheles funestus species identification, detection of infection with Plasmodium parasites, and identification of insecticide resistance mechanisms. In this paper we focus on the Anopheles-specific assays that comprise the VPMT and include details of a new assay for resistance todieldrin Rdl detection. The application of these tools, general and specific guidelines on their use based on field testing in Africa, and plans for further development are discussed.

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“…The promoter SNPs were genotyped on thin-film biosensor chips using technology described previously (Nakamoto et al, 2007). Sequences for capture probes (P1) and detection probes (P2) are listed in Supplemental Table S3.…”

Section: Methodsmentioning

confidence: 99%

Genetic Polymorphisms in the TATA Box and Upstream Phenobarbital-Responsive Enhancer Module of the UGT1A1 Promoter Have Combined Effects on UDP-Glucuronosyltransferase 1A1 Transcription Mediated by Constitutive Androstane Receptor, Pregnane X Receptor, or Glucocorticoid Receptor in Human Liver

Li¹,

Buckley²,

Wang³

et al. 2009

Drug Metab Dispos

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ABSTRACT:Transcription of UDP-glucuronosyltransferase (UGT) 1A1 is regulated by the transcription factors, constitutive androstane receptor (CAR), pregnane X receptor (PXR), glucocorticoid receptor (GR), hepatocyte nuclear factor (HNF) 1␣, and HNF4␣. The purpose of this study was to determine whether the genetic polymorphisms in the RNA polymerase II core promoter and the upstream phenobarbital-responsive element module (PBREM) of the UGT1A1 promoter have combined effects on UGT1A1 transcription mediated by the transcription factors. A polymorphism of A(TA) 5-8 TAA in the UGT1A1 TATA box and a single nucleotide polymorphism of ؊3279T>G in PBREM were genotyped in 98 human liver samples. Relative mRNA levels of CAR, PXR, GR, HNF1␣, HNF4␣, and UGT1A1 were quantified by a multiplex branched DNA technique. Correlations of mRNA levels between UGT1A1 and the transcription factors were established in liver samples with different combined genetic polymorphisms. Correlation of mRNA levels between UGT1A1 and CAR, PXR, or GR, but not HNF1␣ or HNF4␣, was abolished in the samples with the combined genotype of TA7/7 plus ؊3279G/G, which was also associated with significantly lower UGT1A1 mRNA levels compared with other combined genotypes. Correlations of mRNA levels between UGT1A1 and CAR or PXR were reduced but not abolished in the samples with the combined genotype of TA6/7 plus ؊3279 G/G, which showed significantly lower UGT1A1 mRNA levels compared with the combined genotype of TA6/7 plus ؊3279T/G and other genotypes containing TA6/6. In conclusion, the combined genotypes containing A(TA) 7 TAA and ؊3279G decrease UGT1A transcription mediated by CAR, PXR, or GR but not by HNF1␣ or HNF4␣.

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Genotyping and haplotyping of CYP2C19 functional alleles on thin-film biosensor chips

Abstract: This assay can be applied in pharmacogenomic studies in both basic research and clinical laboratories. It is also an ideal technology for pharmacogenomic tests in both developed and developing countries.

Cited by 19 publications

References 56 publications

Assessment of a Pharmacogenomic Marker Panel in a Polypharmacy Population Identified from Electronic Medical Records

Assessment of a Pharmacogenomic Marker Panel in a Polypharmacy Population Identified from Electronic Medical Records

The Vector Population Monitoring Tool (VPMT): High-Throughput DNA-Based Diagnostics for the Monitoring of Mosquito Vector Populations

Genetic Polymorphisms in the TATA Box and Upstream Phenobarbital-Responsive Enhancer Module of the UGT1A1 Promoter Have Combined Effects on UDP-Glucuronosyltransferase 1A1 Transcription Mediated by Constitutive Androstane Receptor, Pregnane X Receptor, or Glucocorticoid Receptor in Human Liver

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