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PubMed2004

Genetic polymorphisms of CYP2A13 and its relationship to nasopharyngeal carcinoma in the Cantonese population.

Nasopharyngeal carcinoma (NPC) is characterized by a high prevalence in Southern China, especially among Cantonese individuals of the Guangdong Province. Epidemiological studies have suggested that frequent exposure to high levels of nitrosamine from preserved foods such as salted fish could be a risk factor for NPC. Cytochrome P450 encompasses a family of enzymes that metabolize carcinogens and CYP2A13, a member of this family, is expressed predominantly in the respiratory tract with the highest levels in the nasal mucosa. In an effort to test whether a correlation exists between CYP2A13 genetic polymorphism and the risk of developing NPC, we sequenced all nine exons and the exon-intron junctions of the CYP2A13 gene in 45 NPC patients. We identified a total of 21 single nucleotide polymorphism (SNPs), including 7 novel SNPs. The most frequent functional variant allele was 74A-1757G-3375T-7233G with a haplotype frequency of 7.8% in the 45 NPC cases. In addition, a stop codon mutation was detected in one case. We then selected the 3 most frequent SNPs and one stop codon mutation to expand our study to a case-control analysis within the Cantonese population. A novel haplotype consisting 8 SNPs in introns, and four additional novel SNPs were identified; but no correlation between CYP2A13 genetic polymorphism and individual susceptibility to NPC was observed.

Journal Article↗
PubMed2004

Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels.

Association studies are used to identify genetic determinants of complex human traits of medical interest. With the large number of validated single nucleotide polymorphisms (SNPs) currently available, two limiting factors in association studies are genotyping capability and costs. Pooled DNA genotyping has been proposed as an efficient means of screening SNPs for allele frequency differences in case-control studies and for prioritising them for subsequent individual genotyping analysis. Here, we apply quantitative pooled genotyping followed by individual genotyping and replication to identify associations with human serum high-density lipoprotein (HDL) cholesterol levels. The DNA from individuals with low and high HDL cholesterol levels was pooled separately, each pool was amplified by polymerase chain reaction in triplicate and each amplified product was separately hybridised to a high-density oligonucleotide array. Allele frequency differences between case and control groups with low and high HDL cholesterol levels were estimated for 7,283 SNPs distributed across 71 candidate gene regions spanning a total of 17.1 megabases. A novel method was developed to take advantage of independently derived haplotype map information to improve the pooled estimates of allele frequency differences. A subset of SNPs with the largest estimated allele frequency differences between low and high HDL cholesterol groups was chosen for individual genotyping in the study population, as well as in a separate replication population. Four SNPs in a single haplotype block within the cholesteryl ester transfer protein (CETP) gene interval were significantly associated with HDL cholesterol levels in both populations. Our study is among the first to demonstrate the application of pooled genotyping followed by confirmation with individual genotyping to identify genetic determinants of a complex trait.

Case-Control Studies↗
PubMed2026

Multi-omics analysis identifies key genes and functional loci affecting teat number in American Large White and Landrace pigs and their application in optimizing genomic selection models.

BACKGROUND: Teat number is a crucial economic trait in pigs. It directly affects the ability of sows to lactate, which in turn influences the survival and health of piglets. The teat number of French Large White pigs is close to 16, while the teat number of American Large White and Landrace pigs is about 14. In order to improve the teat number of American Landrace and Large White pigs through molecular approaches and precise breeding techniques, we genotyped 2,131 American Landrace and 4,564 American Large White with teat number phenotype using a 50 K SNP chip. Then, the SNP-chip data was imputed to the level of whole-genome sequencing (iWGS). Based on iWGS data, we conducted GWAS to identify novel, significant SNPs associated with teat number and to incorporate them into genomic selection. RESULTS: In Landrace pigs, significant SNPs for TTN mapped to SSC2, SSC7, SSC8, and SSC14; the SSC8 and SSC14 effects are novel. LTN mapped to SSC7, RTN to SSC7 and SSC8. The lead SSC7 SNP explained 2.60% of TTN phenotypic variance. In Large White pigs, significant SNPs were detected on SSC7 and SSC10 for TTN; SSC7, SSC10, and SSC12 for LTN; and SSC7 and SSC10 for RTN. The most significant locus on SSC7 accounted for 2.99% of the phenotypic variance in TTN. Additionally, a multi-population meta-analysis detected significant novel SNPs for LTN on SSC1 and SSC8. By utilizing Bayesian fine mapping, the most precise QTL confidence interval on SSC7 for both TTN and RTN in Large White pigs was reduced to 40 kb. By integrating functional gene annotation with RNA-seq and ATAC-seq data from Erhualian and Bamaxiang pigs mammary placodes at embryonic day 26, we prioritized PTPN13, TRPV3, ZDHHC13, and BRD2 as novel candidate genes for teat number. We then incorporated the significant SNPs to GBLUP and benchmarked genomic-selection accuracy. In both breeds, fitting the top SNP as fixed maximized prediction for TTN and RTN, whereas treating all significant loci as an additional random effect optimized LTN. CONCLUSIONS: Our findings provide a theoretical basis for dissecting new key genes affecting teat number and for advancing molecular breeding of teat number in pigs.

Animals↗
PubMed2026

SNP genotyping in Pseudotsuga menziesii and Pinus radiata using targeted genotyping-by-sequencing (GBS): improved Bayesian SNP calling using a beta-binomial distribution and other optimized input parameters.

BACKGROUND: Single-nucleotide polymorphism markers (SNPs) have important applications in gene conservation, breeding, and fundamental genetics research. Our long-term goal is to develop routine approaches for SNP genotyping in forest trees. Ideally, these approaches would be inexpensive, able to accommodate a wide range of samples and SNPs, available through commercial providers, and produce high-quality SNP data. RESULTS: Using targeted genotyping-by-sequencing (GBS), we developed SNP assays for two highly heterozygous tree species, Douglas-fir (Pseudotsuga menziesii) and radiata pine (Pinus radiata). Using Douglas-fir haploid and diploid data, we optimized Bayesian SNP calling by testing four input parameters: (1) allele and genotype prior probabilities, (2) Rho, the beta-binomial dispersion parameter, (3) estimated read error (BayesReadError), and (4) the logPO cutoff used to filter low confidence SNP calls. logPO is the Bayesian posterior odds ratio for a called SNP. Compared to assuming a binomial distribution of read counts (Rho = 0), the beta-binomial distribution (Rho = 0.33) substantially reduced call error and heterozygote undercalling. Compared to the other Bayesian parameters, genotype priors had little effect on genotyping success. For Douglas-fir, we tested 5,360 SNP assays, and then studied the performance of the best 4,000. For radiata pine, we tested 6,000 SNP assays, and then studied the performance of the best 4,570. In Douglas-fir and radiata pine, our Bayesian approach resulted in median call rates of 95% to 98% for the top-ranked SNPs, with an estimated call error of 1.60% for known homozygous genotypes and 2.27% for known heterozygotes. In radiata pine, median and mean call rates were above 91% for GBS and SNP genotyping using an Axiom fixed genotyping array. Additionally, the median correspondence between the GBS and Axiom genotypes was about 98% overall (mean 96%). CONCLUSIONS: By optimizing Bayesian SNP calling, selecting the best 4-5 K SNPs, and excluding samples with low DNA amounts, we substantially reduced call error and heterozygote undercalling, resulting in SNP genotypes that were nearly identical to genotypes obtained using the Axiom array. Furthermore, genotyping performance should increase even further if our SNP rankings were used to develop less complex probe pools that target fewer SNPs.

Pinus↗
PubMed2005

Higher order lipase gene association with plasma triglycerides.

Lipoprotein lipase, HL, and endothelial lipase (EL) are proteoglycan-bound enzymes that regulate plasma lipoprotein levels through coordinated triglyceride (TG) lipase and phospholipase activity. We hypothesized that single nucleotide polymorphisms (SNPs) in lipase genes would have higher order impact on plasma lipoproteins beyond the influence of individual SNPs. In a sample of asymptomatic Caucasian subjects (n = 738), we used a two-stage approach, first identifying groups of subjects with similar multilocus lipase genotypes and then characterizing the relationships between genotype groups and plasma lipids. Using complementary methods, including a permutation test procedure and a mixed-effects modeling approach, we found a higher order interaction between four SNPs in three lipase genes (EL 2,237 3' untranslated region, EL Thr111Ile, HL -514C/T, and LPL HindIII) and plasma TG levels. Subjects who were heterozygous for all four lipase SNPs had significantly higher plasma TG levels beyond the effect of individual lipase SNPs and environmental factors, even after correcting for multiple comparisons. In conclusion, lipase genes had synergistic association with plasma TG beyond individual gene effects. Higher order multilocus genotype contributions to dyslipidemia and atherosclerotic cardiovascular disease need to be considered a priori because they may have an important effect even in the absence of significant main effects of the individual genes.

Adult↗
PubMed2006

High-density genotyping and functional SNP localization in the CETP gene.

The cholesteryl ester transfer protein gene (CETP) has been the subject of hundreds of genetic analyses that typically focus on a small number of polymorphisms within a single ethnic group. Furthermore, the extent of DNA beyond the transcribed sequence from which single nucleotide polymorphisms (SNPs) may influence CETP expression has not been well defined. To better understand the role of natural variation in modulating CETP and high density lipoprotein-cholesterol (HDL-C) levels, dense genotyping of CETP and regions up to 15 kb on either side of the gene was carried out on >2,000 individuals. A complex, nonlinear set of linkage disequilibrium bins was found, with many bins interspersed along the DNA sequence and spread over large regions of the gene. Bins assigned based on large numbers of individuals matched the small subset of SNPs that had been assigned to bins previously with a small number of individuals. Associations of known functional SNPs with HDL-C were found, but there were suggestions that there are additional functional SNPs not characterized previously. Narrowing of the set of likely functional SNPs was accomplished by comparing associations observed in different ethnic groups. The promoter SNP most highly associated with HDL-C that is likely to be functional, position -4,502, alters a consensus transcription factor binding site.

Black or African American↗
PubMed2006

Positive association of obesity with single nucleotide polymorphisms of syndecan 3 in the Korean population.

CONTEXT: Very recently the unforeseen role of syndecan 3 (SDC3), a family of membrane-bound heparin sulfate proteoglycans, in the regulation of energy balance has been discovered in the Sdc3 null female mice. OBJECTIVE: The objective of the study was to test the hypothesis that single nucleotide polymorphisms (SNPs) in SDC3 are associated with obesity in the Korean population. DESIGN/SETTING/SUBJECTS: We conducted a population-based cohort study consisting of 229 control and 245 study subjects and a second independent study consisting of 192 control and 115 study subjects. MAIN OUTCOME MEASUREMENT: Body mass index (BMI) was measured. RESULTS: First, Sdc3 mRNA expression in the brain of ob/ob mice was profoundly increased, compared with control mice. Next, all three nonsynonymous SNPs [T271I (rs2282440, C>T), D245N (rs4949184, C>T), and V150I (rs2491132, C>T)] in the SDC3 gene in control female subjects (BMI < 23, n = 229) and obese female subjects (BMI > 30, n = 245) were genotyped. We demonstrated the presence of clear ethnic differences in three nonsynonymous SDC3 SNPs among African-Americans, Chinese, Europeans, and Koreans. Of three SNPs in SDC3, rs4949184 was not associated with obesity and the other two SNPs (rs2282440 and rs2491132) were strongly associated with obesity (P < 0.0001), and the results were confirmed in the second independent study group. Haplotype analysis also revealed strong association with obesity (chi2 = 76.92, P < 0.000001). CONCLUSIONS: There are ethnic differences in the SDC3 polymorphisms, and the polymorphisms are strongly associated with obesity.

Adult↗
PubMed2004

Matrix metalloproteinase-9 coding sequence single-nucleotide polymorphisms in caucasians with intracranial aneurysms.

OBJECTIVE: There are several lines of evidence suggesting that matrix metalloproteinases (MMPs), particularly MMP-9, are involved in the pathogenesis of intracranial aneurysms. Some studies have demonstrated that genetic variants in the promoter region of the MMP-9 gene are associated with aneurysms. We performed a case-control study to investigate whether single-nucleotide polymorphisms (SNPs) within the coding region of the MMP-9 gene might affect the development of intracranial aneurysms. METHODS: All 13 exons and the 3' untranslated region of the MMP-9 gene were analyzed by direct sequencing in a study group that comprised 40 Caucasian patients with at least one intracranial aneurysm and 44 Caucasian controls. Genotypes were determined, and those that were in Hardy-Weinberg disequilibrium were analyzed in another sample of 40 cases and 40 controls. Differences among the genotype frequencies of the identified polymorphisms were investigated. RESULTS: Seven SNPs were identified in the coding region, two were identified in the adjacent intronic sequences, and two were identified in the 3' untranslated region. Genotype frequencies of four SNPs were demonstrated to be in Hardy-Weinberg disequilibrium in both analyzed study samples. Therefore, an accurate estimation of haplotype frequencies was not possible. No difference in genotype frequencies between cases and controls was detected at any of the 11 SNPs. CONCLUSION: SNPs of the coding region and the 3' untranslated region of the MMP-9 gene are not associated with intracranial aneurysms in Caucasians.

3' Untranslated Regions↗
PubMed2005

Possible influence of delta-aminolevulinic acid dehydratase polymorphism and susceptibility to renal toxicity of lead: a study of a Vietnamese population.

We examined six newly identified polymorphisms in the delta-aminolevulinic acid dehydratase (ALAD) single-nucleotide polymorphisms (SNPs) to determine if these SNPs could modify the relationship between blood lead (PbB) and some renal parameters. This is a cross-sectional study of 276 lead-exposed workers in Vietnam. All workers were measured for PbB, urinary retinol-binding protein (URBP), urinary alpha1-microglobulin (Ualpha1m), urinary beta2-microglobulin (Ubeta 2m), urinary N-acetyl-beta -d-glucosaminidase (NAG), urinary aminolevulinic acid (ALAU), serum alpha1-microglobulin (Salpha1m), serum beta2-microglobulin (Sbeta 2m), and urinary albumin (Ualb). The six SNPs were Msp and Rsa in exon 4, Rsa39488 in exon 5, HpyIV and HpyCH4 in intron 6, and Sau3A in intron 12. Analysis of covariance (ANCOVA) with interaction of PbB times SNPs were applied to examine modifying effect of the SNPs on the association of renal parameters and PbB, adjusting for potential confounders of age, gender, body mass index, and exposure duration. HpyCH4 was found to be associated with certain renal parameters. For HpyCH4 1-1, an increase of 1 microg/dL PbB caused an increase of 1.042 mg/g creatinine (Cr) U alpha1m, 1.069 mg/g Cr Ubeta 2m, 1.038 mg/g Cr URBP, and 1.033 mg/g Cr Ualb, whereas in HpyCH4 1-2, an increase of 1 microg/dL PbB resulted in an increase of only 1.009 mg/g Cr Ualpha1m, 1.012 mg/g Cr Ubeta 2m, 1.009 mg/g Cr URBP, and 1.007 mg/g Cr Ualb. HpyCH4 SNP appeared to modify the lead toxicity to kidney with wild-type allele being more susceptible than variants. The mechanism for this effect is not clear. Further studies are needed to confirm this observation.

Adult↗
PubMed2004

The thiazide-sensitive Na(+)-Cl(-) cotransporter gene, C1784T, and adrenergic receptor-beta3 gene, T727C, may be gene polymorphisms susceptible to the antihypertensive effect of thiazide diuretics.

The response of blood pressure to thiazide diuretics (TZDs) differs among individuals. The prediction of the antihypertensive effect of TZDs is important for realizing individualized therapy in the management of hypertension. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) susceptible to the antihypertensive effect of TZDs, particularly focusing on genes related to water-electrolyte absorption in the kidney. Seventy-six outpatients (mean age, 65.4+/-9.0 years) with essential hypertension (EHT) taking TZDs were retrospectively assessed. We defined as responders (R) those whose mean blood pressure was lowered by more than 5 mmHg after the use of TZDs. Forty-eight SNPs in 17 genes (ADD1, GNB3, TSC [SLC12A3], MLR [NR3C2], NCX1 [SLC8A1], WNK1, WNK4, AGT, ACE, AT1 [AGTR1], CYP11B2, ADRB1, ADRB2, ADRB3, ADRA1A, ADRA1B, ADRA2A) were genotyped in the 76 patients. The SNPs in TSC, MLR, NCX1, WNK1, and WNK4 were identified by direct sequencing and those with minor frequencies of greater than 5% were genotyped in this study. The comparison of polymorphism prevalence between R and non-responders (NR) showed significant differences in TSC C1784T (C allele vs. T allele, odds ratio (OR)=3.81, p =0.016, confidence interval (CI): 1.25-11.63) and ADRB3 T727C (Trp64Arg) (T allele vs. C allele, OR=4.59, p =0.005, CI: 1.54-13.68). The blood pressure (BP) in patients homozygous for the major alleles of both TSC C1784T and ADRB3 T727C were significantly reduced by TZD treatment; however, the BP in those homozygous for the minor allele and heterozygous (TSC C1784T: TT+CT; ADRB3 T727C: CC+CT) for both SNPs were not significantly changed after TZD treatment. Both newly detected TSC C1784T and ADRB3 T727C are gene polymorphisms susceptible to the antihypertensive effect of TZDs in patients with EHT. Thus, the prediction of BP reduction by TZDs may be possible by evaluating these two SNPs.

Benzothiadiazines↗
PubMed2003

Analysis of genetic variation in the GenomEUtwin project.

Multiallelic short tandem repeat polymorphisms, or microsatellites, are useful markers in genome wide scans to identify chromosomal regions containing genes underlying disease loci. The biallelic single nucleotide polymorphism (SNP) can be used to fine map previously identified large candidate regions or to test functional candidate genes by association analysis. In the GenomEUtwin project the population based impact of susceptibility genes for six multifactorial traits will be studied. A genome wide panel of informative human microsatellite markers will be analyzed by fluorescent capillary electrophoresis in well characterized twin and population samples. Contrary to microsatellites, selection of the most informative panels of SNPs is hampered by imperfect data on the allele frequencies and population distribution of SNPs markers in the databases. Therefore, selection of SNPs requires a substantial amount of bioinformatics, and, the SNPs need to be validated experimentally in the relevant populations prior to genotyping large sample sets. In the GenomEUtwin project, large scale genotyping of SNPs will be performed using the SNPstreamUHT and MassARRAY genotyping systems that are based on the primer extension reaction principle combined with fluorescent and mass spectrometric detection, respectively. Production of the genotyping data will be a joint effort by GenomEUtwin partners at the University of Helsinki, the National Public Health Institute in Helsinki, Finland and Uppsala University, Sweden. All genotyping data will be stored in a common database established specifically for the GenomEUtwin project, from where it can be accessed by the twin research centres that provided the samples for genotyping.

Databases, Genetic↗
PubMed2005

Relationship between single nucleotide polymorphisms in leptin, IL6 and adiponectin genes and their circulating product in morbidly obese subjects before and after gastric banding surgery.

BACKGROUND: Certain adipose-produced signals are secreted in proportion to body fat mass and are involved in regulation of the energy metabolism of the whole body. Leptin, IL6 and adiponectin can be considered as adiposity signals. Several Single Nucleotide Polymorphisms (SNPs) in genes encoding for these molecules are known to influence their concentration in situations of stable weight. We hypothesized that polymorphism effects could be better detected in a situation of negative energy balance and that modified concentrations of adiposity signal genes could change the dynamics of weight gain in obese subjects. METHODS: 65 obese patients undergoing gastric banding surgery were genotyped for LEP+19A-->G, LEP-2548G-->C, IL6-174G-->C, APM1-11377C-->G and PM1-11391G-->A common SNPs. BMI and concentrations of leptin, IL6 and adiponectin were measured before surgery and after 1 year. RESULTS: All SNPs except IL6-174G-->C SNP were associated with modifications of the circulating concentrations of signals produced by adipose tissue at baseline. During weight loss, variant genotype carriers of LEP -2548 and +19 SNPs were characterized by a trend towards less decrease in circulating leptin. Weight loss was associated with an increase in IL6 concentration (16.9%+/-12.2) in the IL6-174 C/C genotype carriers, whereas the C/G or G/G genotypes carriers showed a decrease in IL6 (19.9%+/-5.2, P=0.001). CONCLUSION: We observed that the SNPs studied could modulate the concentration of adiposity signals not only at baseline but also during weight loss. Such variations may be sensed by the homeostatic feedback system that controls energy balance and may in turn contribute to some disturbances in weight regulation.

Adiponectin↗
PubMed2004

Polymorphisms in the P-selectin (CD62P) and P-selectin glycoprotein ligand-1 (PSGL-1) genes and coronary heart disease.

P-selectin and its ligand, PSGL-1, are cell adhesion molecules that facilitate interaction of platelets, leukocytes and endothelial cells. Polymorphisms of these genes have been reported to be associated with coronary heart disease (CHD). In the present study, we characterized the entire coding regions of P-selectin and PSGL-1 genes in CHD patients and healthy controls. The 17 exons of the P-selectin gene and exon 2 of the PSGL-1 gene were screened for single nucleotide polymorphisms (SNPs) by exon re-sequencing in 88 CHD patients and 96 controls. For rapid genotyping of the SNPs we developed PCR techniques with sequence-specific primers (PCR-SSP). By using PCR-SSPs we genotyped 261 CHD patients and 214 controls for 5 SNPs in P-selectin and 2 SNPs in PSGL-1. In addition to the already described SNPs in P-selectin (S290N, N562D, V599L and T715P), we identified a novel SNP in exon 5 (V168M). The P-selectin 715P allele was more frequent among CHD patients with hypercholesterolemia compared to patients with normal cholesterol levels. A SNP (M621) in the PSGL-1 gene was found close to the P-selectin binding site and the 621 allele revealed a higher prevalence in the control group indicating a protective effect of the mutation. The molecular characterization of P-selectin and PSGL-1 in a case-control study including CHD patients and healthy controls revealed evidence for association of the genes with development of the disease. However, the functional role of the gene variants should be elucidated by further experimental data.

Adult↗
PubMed2005

Mutation analysis of the MCHR1 gene in human obesity.

OBJECTIVE: The importance of the melanin-concentrating hormone (MCH) system for regulation of energy homeostasis and body weight has been demonstrated in rodents. We analysed the human MCH receptor 1 gene (MCHR1) with respect to human obesity. DESIGN: This consisted of genomic screening of 13.4 kb encompassing the MCHR1 in extremely obese German children and adolescents and association analyses for two coding single nucleotide polymorphisms (SNPs). To confirm initial positive association results, additional association studies and transmission disequilibrium tests in further German, Danish, French and American samples were conducted. Selected SNPs were investigated using functional in vitro studies and reporter gene assays. METHODS: Single-stranded conformation polymorphism analysis, re-sequencing, PCR-restriction fragment length polymorphism analyses, tetra-primer amplification refractory mutation systems, matrix-assisted laser desorption/ionization time of flight mass spectrometry and reporter gene assays were carried out as well as measuring inositol phosphate formation, inhibition of cAMP formation and activation of p42/44 MAP kinase. RESULTS: We identified 11 infrequent variations and two SNPs in the MCHR1 coding sequence and 18 SNPs (eight novel) in the flanking sequence. Association and transmission disequilibrium with obesity were detected for several SNPs in independent study groups of German obese children and adolescents and controls. In two German samples, encompassing 4056 and 295 individuals, trends towards association with obesity were detected. Findings in a second epidemiological German sample and in Danish, French and American samples were negative. Functional in vitro studies as well as reporter gene assays revealed no significant results. CONCLUSION: Our initial association of MCHR1 alleles/haplotype detected might be related to juvenile-onset obesity, conditional on a particular genetic and/or environmental background. Alternatively, we could not exclude the possibility that the initially detected association represented a false positive finding.

Adolescent↗
PubMed2005

LightTyper platform for high-throughput clinical genotyping.

DNA sequence variations due to single nucleotide changes or polymorphisms (SNPs) have demonstrated an association with certain diseases as causative agents or surrogate biomarkers. Identification and genotyping of SNPs requires reliable and robust technologies. Multiple genotyping platforms are available to detect SNPs. Although many of these platforms meet the requirements of the research environment, technologies have also emerged for high-throughput clinical genotyping as well. The LightTyper is one such platform, providing SNP identification by employing melting curve analysis of fluorescently labeled probes. The LightTyper has been used to identify SNPs associated with myocardial infarction, developing and validating assays for approximately 100 SNPs in 30 candidate genes. The LightTyper is also amenable to the use of assays already developed for the LightCycler, which is widely used in clinical laboratories. The initial experience presented here suggests the potential use of the LightTyper for high-throughput clinical genotyping.

Animals↗
PubMed2002

Novel single nucleotide polymorphisms in the CYP2D6 gene associated with CYP2D6*2 and/or CYP2D6*10 alleles.

Novel single nucleotide polymorphisms (SNPs) were found in introns 1, 3, 4, 5, and 7 of the gene encoding cytochrome (CYP) 2D6 in 90 Japanese subjects. Some of these SNPs were associated with C2850T and/or C100T, which are key SNPs for CYP2D6(*)2 and CYP2D6(*)10, respectively. The SNPs in the CYP2D6 gene (ACCESSION NUMBER, M33388) were designated as follows: SNP, MPJ6_2D6010 (IVS1-138C>G) associated with C2850T; SNP, MPJ6_2D6012 (IVS1-41T>G) associated with C100T, C2850T and G4180C; SNP, MPJ6_2D6016 (IVS3+32A>G); SNP, MPJ6_2D6017 (IVS4-17C>G); SNP, MPJ6_2D6018 (IVS4-17C>T); SNP, MPJ6_2D6020 (IVS5+46G>A); SNP, MPJ6_2D6021 (IVS5-49T>C); SNP, MPJ6_2D6023 (IVS7+40A>C) associated with both C100T, C2850T and G4180C; SNP, MPJ6_2D6024 (IVS7+64T>C); and SNP, MPJ6_2D6025 (IVS7-9C>T) associated with C2850T. These SNPs are convenient for allele typing and should be further investigated for their potential effects on transcription, such as splicing.

Journal Article↗
PubMed2002

Eleven novel single nucleotide polymorphisms in the NR1I2 (PXR) gene, four of which induce non-synonymous amino acid alterations.

Eleven novel single nucleotide polymorphisms (SNPs) were found in the NR1I2 (PXR/SXR) gene from 205 Japanese subjects. The detected SNPs were as follows: 1) SNP, MPJ6_1I2001; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-TTTCTACCTCTAC/TTATTGAAAGGGC-3'. 2) SNP, MPJ6_1I2004; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-AGGCCCAAATGTG/AAGTGATGCATAG-3'. 3) SNP, MPJ6_1I2007; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-TGCCAGGCCTGCC/TGCCTGCGCAAGT-3'. 4) SNP, MPJ6_1I2008; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-GAGTGAGCAGTGG/CGCGCGCGGGCGG-3'. 5) SNP, MPJ6_1I2010; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-CAGAGGAGCAGCG/AGATGATGATCAG-3'. 6) SNP, MPJ6_1I2011; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-CTGGAAGTGGCCA/GGGAGGTTCAAAG-3'. 7) SNP, MPJ6_1I2013; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-TCTTCCTCTCGCC/TCCCAACTTCTGG-3'. 8) SNP, MPJ6_1I2017; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-ATTGAATGCAATC/TGGCCCCAGCCTG-3'. 9) SNP, MPJ6_1I2018; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-GGTGAGCACAGCA/GGGGGGTGAGGAC-3'. 10) SNP, MPJ6_1I2019; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-GAGCTCCGCAGCA/GTCAATGCTCAGC-3'. 11) SNP, MPJ6_1I2021; GENE NAME, NR1I2; ACCESSION NUMBER, AF364606; LENGTH, 25 bases; 5'-GGTGACACCTCCG/AAGAGGCAGCCAG-3'. The frequencies were 0.0293 for MPJ6_1I2021, 0.0073 for MPJ6_1I2011, and 0.0024 for the other 9 SNPs. All SNPs were found as heterozygous. Among these SNPs, MPJ6_1I2007, MPJ6_1I2010, MPJ6_1I2017 and MPJ6_1I2019 induce non-synonymous amino acid alterations (R98C, R148Q, R381W and I403V, respectively, in PAR1).

Journal Article↗
PubMed2004

Novel nonsynonymous single nucleotide polymorphisms in the CYP2D6 gene.

Cytochrome P450 (CYP) 2D6 is an important drug-metabolizing enzyme, and its gene is known to be highly polymorphic. Here, we report five novel nonsynonymous single nucleotide polymorphisms (SNPs), and 65 other sequence variations detected from the gene coding for cytochrome P450 (CYP) 2D6 in 254 Japanese subjects. Two of the novel nonsynonymous SNPs were associated with the *10 key SNP, C100T. Among the 65 variations, 23 were novel, including 12 SNPs in 5'-flanking, 1 in 5'-untranslated, and 10 in intronic regions. The nonsynonymous SNPs in the CYP2D6 gene were as follows: 73 C>T (Arg25Trp, exon 1), 972 C>T (Ala90Val, exon 2), 1611 T>A (Phe120Ile, exon 3), 1720 A>C (Glu156Ala, exon 3), 3172 A>C (Glu334Ala, exon 7). The SNPs, 73C>T, 972 C>T, 1611 T>A, 1720 A>C and 3172 A>C were linked with *10, *1, *10, *1 and *2, respectively.

Amino Acid Substitution↗