DigiTag assay for multiplex single nucleotide polymorphism typing with high success rate

Nishida, Nao; Tanabe, Tetsuya; Hashido, Kento; Hirayasu, Kouyuki; Takasu, Masako; Suyama, Akira; Tokunaga, Katsushi

doi:10.1016/j.ab.2005.08.007

Cited by 12 publications

(7 citation statements)

References 23 publications

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“…A multiplex SNP-typing method designated DigTag2 is suitable for genotyping an intermediate number of SNPs (tens to hundreds of sites) with a high conversion rate (490%), high accuracy and low cost. 28,29 The conversion rate is defined as the proportion of successfully genotyped SNPs among the total number of SNPs examined. The reproducibility of this assay was examined by duplicate experiments, resulting 100% identical between duplicate experiments.…”

Section: Genotypingmentioning

confidence: 99%

Replication of a genome-wide association study of panic disorder in a Japanese population

Otowa

Tanii

Sugaya³

et al. 2009

J Hum Genet

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Panic disorder (PD) is an anxiety disorder characterized by recurrent and unexpected panic attacks, subsequent worry and phobic avoidance. Although a number of association and linkage studies have been conducted, no gene has been identified as a susceptibility locus. We previously conducted a genome-wide association analysis of PD in 200 Japanese patients and the same number of controls, using a 500 K single nucleotide polymorphisms (SNPs) chip. In this study, we report a replication analysis of PD using the DigTag2 assay. The second stage sample consisted of 558 Japanese patients and 566 controls. Thirty-two markers were tested in a replication sample. As a result, no significant association was found after correction for multiple testing. However, the difference was observed at the nominal allele P-value o0.05 for two SNPs (rs6733840 and rs132617). We also conducted haplotype analyses of SNPs in the APOL3 and CLU genes. Our results failed to show any significant association with PD in these genes. Further studies on these variants with a larger sample size may be worth testing to confirm the results. Keywords: genome-wide association study (GWAS); Japanese population; panic disorder; replication; single nucleotide polymorphism (SNP) INTRODUCTIONPanic disorder (PD) is an anxiety disorder characterized by recurrent and unexpected panic attacks, subsequent worry and phobic avoidance. Life prevalence of PD is 1-3% and twice as many women as men suffer from the disorder. 1 The disorder frequently takes a chronic course, with many remissions and relapses. 2 Genetic epidemiological studies including family and twin studies have shown that genetic as well as environmental factors have an important role in the pathogeneses of PD. First-degree relatives of proband with PD have an approximately fivefold increased risk of PD. 3,4 Twin studies show that about 40% of the liability towards PD consists of heritable factors [5][6][7] However, the etiology of PD is currently unknown.

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Section: Genotypingmentioning

confidence: 99%

Replication of a genome-wide association study of panic disorder in a Japanese population

Otowa

Tanii

Sugaya³

et al. 2009

J Hum Genet

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“…The characteristics of DCNs were described previously (18). Briefly, these sequences are designed to have a uniform length, a uniform melting temperature and have no potential for mishybridizations or stable self-folded structures.…”

Section: Methodsmentioning

confidence: 99%

“…The use of DCNs is highly advantageous in that gene expression profiling of different sets of target genes can be performed by using DNA microarrays with the same set of DNA probe sequences. Even an analysis for single nucleotide polymorphism typing can be performed by using the same DNA microarray and basically the similar protocol to gene expression profiling (18,19). …”

Section: Introductionmentioning

confidence: 99%

Multiplex cDNA quantification method that facilitates the standardization of gene expression data

Gotoh

Murakami

Suyama

2011

Nucleic Acids Research

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Microarray-based gene expression measurement is one of the major methods for transcriptome analysis. However, current microarray data are substantially affected by microarray platforms and RNA references because of the microarray method can provide merely the relative amounts of gene expression levels. Therefore, valid comparisons of the microarray data require standardized platforms, internal and/or external controls and complicated normalizations. These requirements impose limitations on the extensive comparison of gene expression data. Here, we report an effective approach to removing the unfavorable limitations by measuring the absolute amounts of gene expression levels on common DNA microarrays. We have developed a multiplex cDNA quantification method called GEP-DEAN (Gene expression profiling by DCN-encoding-based analysis). The method was validated by using chemically synthesized DNA strands of known quantities and cDNA samples prepared from mouse liver, demonstrating that the absolute amounts of cDNA strands were successfully measured with a sensitivity of 18 zmol in a highly multiplexed manner in 7 h.

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“…Several methods have been reported for detection of ligation reaction products. These include: 1) heterogeneous assays that involve affinity capture of the product to a solid surface (e.g., microtiter wells) and detection by colorimetric, fluorimetric or bio(chemi)luminometric assays [Nickerson et al, 1990;Tobe et al, 1996;Samiotaki et al, 1994;Hansen et al, 1995;Tannous et al, 2003]; 2) electrophoretic methods [Baron et al, 1996;Eggerding et al, 1995;Sakthivel et al, 2001;Tobler et al, 2005;Nishida et al, 2005;Grossman et al, 1994]; 3) multiplex assays based on microarrays or spectrally encoded microspheres [Gerry et al, 1999;Consolandi et al, 2004;Li et al, 2006;Soper et al, 2005;Hashimoto et al, 2006;Iannone et al, 2000]; 5) homogeneous assays based on fluorescence resonance energy transfer [Chen et al, 1998;Lopez-Crapez et al, 2001], fluorescence coincidence analysis [Yeh et al, 2006], and nanoparticle reporters [Li et al, 2005].…”

Section: Introductionmentioning

confidence: 99%

Dry-reagent disposable biosensor for visual genotyping of single nucleotide polymorphisms by oligonucleotide ligation reaction: application to pharmacogenetic analysis

et al. 2008

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Most genotyping methods for known single-nucleotide polymorphisms (SNPs) are based on hybridization with allele-specific probes, oligonucleotide ligation reaction (OLR), primer extension or invasive cleavage. OLR offers superior specificity because it involves two recognition events; namely, the hybridization of an allele-specific probe and a common probe to adjacent positions on target DNA. OLR products can be detected by microtiter well-based colorimetric, time-resolved fluorimetric or chemiluminometric assays, electrophoresis, microarrays, microspheres, and homogeneous fluorimetric or colorimetric assays. We have developed a simple, robust, and low-cost disposable biosensor in dry-reagent format, which allows visual genotyping with no need for instrumentation. The OLR mixture contains a biotinylated common probe and an allele-specific probe with a (dA)(20) segment at the 3'-end. OLR products are denatured and applied to the biosensor next to gold nanoparticles that are decorated with oligo(dT) strands. The sensor is immersed in the appropriate buffer and all components migrate by capillary action. The OLR product is captured by immobilized streptavidin at the test zone (TZ) of the sensor and hybridizes with the oligo(dT) strands of the nanoparticles. A characteristic red line is generated due to the accumulation of nanoparticles. The excess nanoparticles are captured by immobilized oligo(dA) at the control zone of the strip, giving a second red line. We have applied successfully the proposed OLR-dipstick assay to the genotyping of four SNPs in the drug-metabolizing enzyme genes CYP2D6 ((*)3 and (*)4) and CYP2C19 ((*)2 and (*)3). The results were in agreement with direct sequencing.

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DigiTag assay for multiplex single nucleotide polymorphism typing with high success rate

Cited by 12 publications

References 23 publications

Replication of a genome-wide association study of panic disorder in a Japanese population

Replication of a genome-wide association study of panic disorder in a Japanese population

Multiplex cDNA quantification method that facilitates the standardization of gene expression data

Dry-reagent disposable biosensor for visual genotyping of single nucleotide polymorphisms by oligonucleotide ligation reaction: application to pharmacogenetic analysis

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