High throughput genotyping for the detection of a single nucleotide polymorphism in NAD(P)H quinone oxidoreductase (DT diaphorase) using TaqMan probes

Shi, Michael; Myrand, Scott P.; Bleavins, Michael R.; Iglesia, Felix A. de la

doi:10.1136/mp.52.5.295

Cited by 76 publications

(51 citation statements)

References 15 publications

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“…Approximately 8% of samples were re-genotyped by PCR-RFLP as a quality check, with complete concordance. Among the five SNPs, three had already been genotyped in some subjects using PCR-RFLP before the 5 0 nuclease assay method, that is, the TaqMan technique, 49 was available to us; so genotyping for these markers was completed by this method. Because two other SNPs (OPRD1^1 and OPRD1^2) have a low frequency ( < 2%) of the homozygote for the minor allele, the TaqMan assay could not cluster the three groups of genotypes (minor allele homozygote, heterozygote, and major allele homozygote) clearly, so the PCR-RFLP method was used to genotype them.…”

Section: Marker Selection and Genotypingmentioning

confidence: 99%

The OPRD1 and OPRK1 loci in alcohol or drug dependence: OPRD1 variation modulates substance dependence risk

et al. 2007

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Eleven single-nucleotide polymorphisms (SNPs) spanning OPRD1 were examined in 1063 European Americans (EAs) (620 cases with substance dependence (SD), including 557 with alcohol dependence (AD), 225 with cocaine dependence (CD) and 111 with opioid dependence (OD), and 443 controls). Nominally significant associations (P < 0.05) of five SNPs with SD were observed; only the association of the non-synonymous variant G80T with OD remained significant after correction for multiple testing using SNPSpD. Haplotype analyses with six tag SNPs indicated that a specific haplotype GCAACT, which harbors G80T G-allele and C921T C-allele, was significantly associated with AD (v 2 = 14.82, degrees of freedom (d.f.) = 1, P < 0.001), CD (v 2 = 9.19, d.f. = 1, P = 0.002) and OD (v 2 = 20.68, d.f. = 1, P < 0.001). Logistic regression analyses, with sex and age being considered, demonstrated that this haplotype had a risk effect on AD (P = 0.03, b = 1.86, odds ratio (OR) = 6.43) and especially on OD (P < 0.001, b = 3.92, OR = 50.57). Moreover, seven SNPs covering OPRK1 were examined in the majority of the above subjects (390 cases, including 327 AD, 177 CD and 97 OD subjects, and 358 controls). Although no significant differences in allele, genotype or haplotype frequency distributions were seen between cases and controls, a specific OPRK1 haplotype, GGCTTCT, was significantly associated with AD (v 2 = 8.12, d.f. = 1, P = 0.004). Logistic regression analyses also revealed its risk effect on AD (P = 0.009, b = 1.06, OR = 2.90). Population stratification artifact was not observed in the sample. Taken together, our findings supported a positive association between OPRD1 variants and SD, and a positive haplotypic association between OPRK1 and AD in EAs.

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Section: Marker Selection and Genotypingmentioning

confidence: 99%

The OPRD1 and OPRK1 loci in alcohol or drug dependence: OPRD1 variation modulates substance dependence risk

et al. 2007

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“…SNPs were genotyped using TaqMan ™ 5′-nuclease assay methods (Livak et al 1995;Shi et al 1999) together with an ABI 7500 Sequence Detector instrument (Applied Biosystems, Foster City, CA) using probes containing the nonfluorescent minor groove binding 3′-quencher MGB (Applied Biosystems). Primer and probe sequences described by Zhang et al (2004) were used for markers rs806379, rs1535255 and rs2023239 (Table I).…”

Section: Genotypingmentioning

confidence: 99%

Association study of the CNR1 gene exon 3 alternative promoter region polymorphisms and substance dependence

Herman

Kranzler

Cubells

et al. 2006

American J of Med Genetics Pt B

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An alternative promoter producing a novel 5′-untranslated region of cannabinoid receptor mRNA has recently been described in CNR1, the gene encoding the cannabinoid receptor protein. Single nucleotide polymorphisms (SNPs) adjacent to this site were reported to be associated with polysubstance abuse (Zhang et al. 2004). We examined the association of 4 SNPs (rs6928499, rs806379, rs1535255, rs2023239) in the distal region of intron 2 of CNR1 both with individual substance dependence diagnoses (i.e., alcohol, cocaine, and opioids), as well as with polysubstance dependence. The study samples consisted of European American and African American subjects with drug and or alcohol dependence (n=895), and controls (n = 472). Subjects were grouped as polysubstance dependent, opioid dependent, cocaine dependent, cannabis dependent and alcohol dependent. There was a modest association of marker rs1535255 with alcohol dependence, respectively (P=0.04), though with correction for multiple phenotype comparisons, this effect was not considered statistically significant. These findings fail to replicate the original report of an association between SNPs adjacent to an alternative CNR1 exon 3 transcription start site and polysubstance abuse.

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“…Aliquots of 1 ll aliquots were dried in 384-well plates. Genotyping was performed by the 5¢ nuclease method (Shi et al 1999) using fluorogenic allele-specific probes. Oligonucleotide primer and probe sets were designed based on gene sequence from the CDS, November 2003.…”

Section: Snp Markersmentioning

confidence: 99%

Haplotype-based analysis of alpha 2A, 2B, and 2C adrenergic receptor genes captures information on common functional loci at each gene

et al. 2004

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The alpha 2-adrenergic receptors (a 2 -AR) mediate physiological effects of epinephrine and norepinephrine. Three genes encode a 2 -AR subtypes carrying common functional polymorphisms (ADRA2A Asn251Lys, ADRA2B Ins/Del301-303 and ADRA2C Ins/Del322-325). We genotyped these functional markers plus a panel of single nucleotide polymorphisms evenly spaced over the gene regions to identify gene haplotype block structure. A total of 24 markers were genotyped in 96 Caucasians and 96 African Americans. ADRA2A and ADRA2B each had a single haplotype block at least 11 and 16 kb in size, respectively, in both populations. ADRA2C had one haplotype block of 10 kb in Caucasians only. For the three genes, haplotype diversity and the number of common haplotypes were highest in African Americans, but a similar number of markers (3-6) per block was sufficient to capture maximum diversity in either population. For each of the three genes, the haplotype was capable of capturing the information content of the known functional locus even when that locus was not genotyped. The a 2 -AR haplotype maps and marker panels are useful tools for genetic linkage studies to detect effects of known and unknown a 2 -AR functional loci.

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High throughput genotyping for the detection of a single nucleotide polymorphism in NAD(P)H quinone oxidoreductase (DT diaphorase) using TaqMan probes

Cited by 76 publications

References 15 publications

The OPRD1 and OPRK1 loci in alcohol or drug dependence: OPRD1 variation modulates substance dependence risk

The OPRD1 and OPRK1 loci in alcohol or drug dependence: OPRD1 variation modulates substance dependence risk

Association study of the CNR1 gene exon 3 alternative promoter region polymorphisms and substance dependence

Haplotype-based analysis of alpha 2A, 2B, and 2C adrenergic receptor genes captures information on common functional loci at each gene

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