Identification of 20 novel SNPs in the guanine nucleotide binding protein alpha 12 gene locus

Iida, Aritoshi; Saito, Susumu; Sekine, Akihiro; Tabei, Wataru; Kataoka, Yukie; Nakamura, Yusuke

doi:10.1007/s10038-004-0167-y

Cited by 4 publications

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References 30 publications

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“…As a result, we identified a total of 7552 genetic variations that include 6733 SNP and 819 genetic variations of other types. ( 7–28 ) Simultaneously, we constructed fine‐scale and high‐density SNP maps at these genomic loci (Fig. 1).…”

Section: Identification Of 7552 Genetic Variations Within 267 Genes Rmentioning

confidence: 99%

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Japanese single nucleotide polymorphism database for 267 possible drug‐related genes

et al. 2005

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A combination of genetic variations and various environmental factors define unique human characteristics, including individual responsiveness to drugs, severity of disease and susceptibility to common diseases. Among the genetic differences present in human populations, polymorphisms in genes that encode various enzymes, transporters and receptors involved in the metabolism of drugs are considered to be medically important because some can affect therapeutic efficacy of drugs and risk of adverse reaction.(1,2) For example, it is known that some genetic variations in the thiopurine S-methyltransferase gene cause severe adverse drug reactions to anticancer drugs or immunosuppressants, (3,4) and variations in the dihydropyrimidine dehydrogenase, uridine diphosphate glycosyltransferase 1A1, and glutathione S-transferase genes are correlated with serious toxicities following administration of 5-fluorouracil, irinotecan and cisplatin, respectively. In the year 2000, the Japanese single nucleotide polymorphism (SNP) database (JSNP) project was launched to build the infrastructure for genome-wide association studies of common diseases and drug reactions (efficacy as well as adverse reaction) as a part of the Japanese Millennium Genome project.(6) Simultaneously, we also began to screen genetic variations in the genomic regions corresponding to genes encoding various enzymes, transporters and receptors involved in drug reactions. Consequently, we identified a total of 7552 genetic variations among 267 gene loci, and constructed comprehensive SNP maps. The first phase of the SNP database of representative drug-related genes is now complete. In this review, we introduce the outline of our database with several distinctive features that have been established: 1 Unique database of drug-related genes. As we almost completely screened the genomic regions covering drug-related genes, we were able to find SNP that may influence the quality or quantity of gene products by association studies, if some of them affect the efficacy or adverse reactions of the drugs. 2 Real SNP. A certain proportion of SNP deposited to the dbSNP database at the National Center for Biotechnology Information (NCBI) are not real SNP, but misidentified SNP due to sequencing errors. However, all genetic variations that we identified by means of a combination of polymerase chain reaction (PCR) and direct sequencing are really polymorphic among the Japanese population. 3 Population-based database. This is a specialized database for the Japanese population. The presence or absence of SNP as well as their allelic frequencies are significantly different among different ethnic groups. (29,30) However, as the international HapMap data showed the very high similarity between the Japanese and Han Chinese populations, our data should be useful for other Asian populations, and should also be a good reference for people in other countries. Subjects and strategySamples of peripheral blood were obtained with written informed consent from 48 Japanese volunteers for the...

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Section: Identification Of 7552 Genetic Variations Within 267 Genes Rmentioning

confidence: 99%

“…Consequently, we identified a total of 7552 genetic variations among 267 gene loci, and constructed comprehensive SNP maps. ( 7–28 ) The first phase of the SNP database of representative drug‐related genes is now complete. In this review, we introduce the outline of our database with several distinctive features that have been established:…”

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Japanese single nucleotide polymorphism database for 267 possible drug‐related genes

et al. 2005

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“…[58] About 20 novel SNPs in the guanine nucleotide binding protein alpha 12-gene locus have been identified in Japanese population. [59] The SNP of growth hormone receptor (GHR) are unevenly distributed in various ethnic groups as evidenced by a study conducted in Chinese Hans ethnic population. [60] Signals of differential demographic history in African-American, East-Asian and European-American populations have been reported by the mathematical formulation for the SNP allele frequency spectrum.…”

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Contribution of genomics, proteomics, and single-nucleotide polymorphism in toxicology research and Indian scenario

et al. 2005

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Advancement in the molecular tools used in toxicology has provided immense information about the cellular and global structure and function of toxicant-responsive genes. Now, it has become possible to assess the functional activity of genes and proteins involved in various toxicological pathways, which were not possible with the conventional methods. Many genes are known to have a greater influence on the susceptibility to environmental agents than others; therefore, identification and characterization of polymorphism in such genes for the determination of early, late, or no response of an individual for the toxicant-induced diseases has also become mandatory. Toxicogenomics, a newly born discipline of toxicology, comprises of two major facets, one, how various genes in the genome respond to environmental toxicants and stressors and second, how toxicants modify the function and expression of specific genes in the genome. Toxicogenomics play an important role in the identification and characterization of molecular biomarkers to predict cellular toxicity and to determine the efficacy and exposure in the toxicity trials at an early stage. Genome and proteome-wide expression profiles in combination with conventional toxicology are being used to classify compounds, predict the mechanism of toxicity of newer compounds and determine the susceptibility of an individual for the toxic responses. Single-nucleotide polymorphism in toxicant-responsive genes is being used to obtain basic information of the genetic variation and its role in the functional protein expression. Various national and international government and private organizations have launched several programs on gene-environment interactions. Council of Scientific and Industrial Research (CSIR), New Delhi, India, has also launched a program on 'toxicogenomics of genetic polymorphism in Indian population to industrial chemicals for development of biomarkers' to provide better ventures and facilities to researchers in order to understand the environmentgenome interactions. In this review, the contribution of genomics, proteomics, and SNPs in toxicology along with its current status in India has been discussed.

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“…As a part of this program, we previously reported SNPs in genomic regions corresponding to genes encoding GPCRs and other known drug targets and constructed fine-scale SNP maps containing more than 1,100 SNPs in 63 genes (Iida et al 2003(Iida et al , 2004a(Iida et al , 2004bSaito et al 2003b). We further extended our SNP discoveries of the GPCRs in 96 chromosomes from healthy Japanese donors and here report a total of 156 novel SNPs and 32 genetic variations of other types for 29 additional members of the GPCR gene family GPR5-9, GPR11-18, GPR20, GPR21-27, GPR29-31, GPR34, GPR35, and GPR37, GPR39, and GPR40.…”

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Identification of 156 novel SNPs in 29 genes encoding G-protein coupled receptors

Iida¹,

Nakamura

2005

J Hum Genet

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We have been performing extensive screening on single nucleotide polymorphisms (SNPs) in and around genes encoding drug metabolizing enzymes, transporters, and receptors and have constructed the high-density SNP maps of such gene regions. In addition to genetic information reported earlier, we identified a total of 390 genetic variations, 358 SNPs and 32 genetic variations of other types, detected in 29 genes encoding G-protein coupled receptors in Japanese populations. Following a comparison of our data with SNPs in the dbSNP database in the US National Center for Biotechnology Information, 156 SNPs from these gene loci are considered to be novel. The fine-scale SNP maps constructed in this study should serve an important resource for studies of linkage-disequilibrium mapping for complex genetic diseases and drug-response phenotypes.

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Identification of 20 novel SNPs in the guanine nucleotide binding protein alpha 12 gene locus

Cited by 4 publications

References 30 publications

Japanese single nucleotide polymorphism database for 267 possible drug‐related genes

Japanese single nucleotide polymorphism database for 267 possible drug‐related genes

Contribution of genomics, proteomics, and single-nucleotide polymorphism in toxicology research and Indian scenario

Identification of 156 novel SNPs in 29 genes encoding G-protein coupled receptors

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