Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues

Rockman, 2002, Abundant raw material for cis-regulatory evolution in humans, Mol Biol Evol, 19, 1991, 10.1093/oxfordjournals.molbev.a004023

Bray, 2003, Cis-acting variation in the expression of a high proportion of genes in human brain, Hum Genet, 113, 149, 10.1007/s00439-003-0956-y

Yan, 2002, Allelic variation in human gene expression, Science, 297, 1143, 10.1126/science.1072545

Yan, 2004, Allelic variations in gene expression, Curr Opin Oncol, 16, 39, 10.1097/00001622-200401000-00008

Pastinen, 2006, Influence of human genome polymorphism on gene expression, Hum Mol Genet, 15, R9, 10.1093/hmg/ddl044

Cheung, 2003, Natural variation in human gene expression assessed in lymphoblastoid cells, Nat Genet, 33, 422, 10.1038/ng1094

Rockman, 2005, Ancient and recent positive selection transformed opioid cis-regulation in humans, PLoS Biol, 3, e387, 10.1371/journal.pbio.0030387

Johnson, 2005, Polymorphisms affecting gene regulation and mRNA processing: broad implications for pharmacogenetics, Pharmacol Ther, 106, 19, 10.1016/j.pharmthera.2004.11.001

Wang, 2005, Multidrug resistance polypeptide 1 (MDR1, ABCB1) variant 3435C>T affects mRNA stability, Pharmacogenet Genom, 15, 693, 10.1097/01.fpc.0000178311.02878.83

Zhang, 2005, Allelic expression imbalance of human mu opioid receptor (OPRM1) caused by variant A118G, J Biol Chem, 280, 32618, 10.1074/jbc.M504942200

Lim, 2006, Allelic expression of serotonin transporter (SERT) mRNA in human pons: lack of correlation with the polymorphism SERTLPR, Mol Psychiatry, 11, 649, 10.1038/sj.mp.4001797

Pinsonneault, 2006, Allelic mRNA expression of X-linked monoamine oxidase a (MAOA) in human brain: dissection of epigenetic and genetic factors, Hum Mol Genet, 15, 2636, 10.1093/hmg/ddl192

Lim, 2007, Tryptophan hydroxylase 2 (TPH2) haplotypes predict levels of TPH2 mRNA expression in human pons, Mol Psychiatry, 12, 491, 10.1038/sj.mp.4001923

Pinsonneault, 2004, Genetic variants of the human H+/Dipeptide transporter PEPT2: analysis of haplotype functions, J Pharmacol Exp Ther, 311, 1088, 10.1124/jpet.104.073098

Wang, 2006, Highly variable mRNA expression and splicing of L-type voltage-dependent calcium channel alpha subunit 1C in human heart tissues, Pharmacogenet Genom, 16, 735, 10.1097/01.fpc.0000230119.34205.8a

Zhang, 2007, Novel polymorphisms in the human dopamine D2 receptor gene affect gene expression, splicing, and neuronal activity, PNAS, 104, 20552, 10.1073/pnas.0707106104

Bray, 73, A haplotype implicated in schizophrenia susceptibility is associated with reduced COMT expression in human brain., Am J Hum Genet, 152-, 161

Knight, 2003, In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading, Nat Genet, 33, 469, 10.1038/ng1124

Ge, 2005, Survey of allelic expression using EST mining, Genome Res, 15, 1584, 10.1101/gr.4023805

Lin, 2005, Allelic variation in gene expression identified through computational analysis of the dbEST database, Genomics, 86, 518, 10.1016/j.ygeno.2005.05.004

Cowles, 2002, Detection of regulatory variation in mouse genes, Nat Genet, 32, 432, 10.1038/ng992

Liu, 2005, Identification of the control region for tissue-specific imprinting of the stimulatory G protein alpha-subunit, Proc Natl Acad Sci U S A, 102, 5513, 10.1073/pnas.0408262102

Singer-Sam, 1992, Parental imprinting studied by allele-specific primer extension after PCR: paternal X chromosome-linked genes are transcribed prior to preferential paternal X chromosome inactivation, Proc Natl Acad Sci U S A, 89, 10469, 10.1073/pnas.89.21.10469

Pastinen, 2004, A survey of genetic and epigenetic variation affecting human gene expression, Physiol Genom, 16, 184, 10.1152/physiolgenomics.00163.2003

He, 2005, Allelic variation in gene expression in thyroid tissue, Thyroid, 15, 660, 10.1089/thy.2005.15.660

Pant, 2006, Analysis of allelic differential expression in human white blood cells, Genome Res, 16, 331, 10.1101/gr.4559106

Cirulli, 2007, In vitro assays fail to predict in vivo effects of regulatory polymorphisms, Hum Mol Genet, 16, 1931, 10.1093/hmg/ddm140

Wilkins, 2007, Extreme context specificity in differential allelic expression, Hum Mol Genet, 16, 537, 10.1093/hmg/ddl488

Bray, 2005, Haplotypes at the dystrobrevin binding protein 1 (DTNBP1) gene locus mediates risk for schizophrenia through reduced DTNBP1 expression, Hum Mol Genet, 14, 1947, 10.1093/hmg/ddi199

Bray, 2004, The serotonin-2A receptor gene locus does not contain common polymorphism affecting mRNA levels in adult brain, Mol Psychiatry, 9, 109, 10.1038/sj.mp.4001366

Fukuda, 2006, Monoallelic and unequal allelic expression of the HTR2A gene in human brain and peripheral lymphocytes, Biol Psychiatry, 60, 1331, 10.1016/j.biopsych.2006.06.024

Sayed-Tabatabaei, 2006, ACE polymorphisms, Circ Res, 98, 1123, 10.1161/01.RES.0000223145.74217.e7

Rovin, 1999, A novel polymorphism in the MCP-1 gene regulatory region that influences MCP-1 expression, Biochem Biophys Res Commun, 259, 344, 10.1006/bbrc.1999.0796

Nakayama, 1999, T-786–>C mutation in the 5′-flanking region of the endothelial nitric oxide synthase gene is associated with coronary spasm, Circulation, 99, 2864, 10.1161/01.CIR.99.22.2864

Hiroi, 1999, Polymorphisms in the SOD2 and HLA-DRB1 genes are associated with nonfamilial idiopathic dilated cardiomyopathy in Japanese, Biochem Biophys Res Commun, 261, 332, 10.1006/bbrc.1999.1036

Xu, 2002, Transcriptional regulation of the human manganese superoxide dismutase gene: the role of specificity protein 1 (Sp1) and activating protein-2 (AP-2), Biochem J, 362, 401, 10.1042/bj3620401

Miklos, 2005, Moments of the Boltzmann distribution for RNA secondary structures, Bull Math Biol, 67, 1031, 10.1016/j.bulm.2004.12.003

Lengauer, 1998, Genetic instabilities in human cancers, Nature, 396, 643, 10.1038/25292

Duan, 2003, Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor, Hum Mol Genet, 12, 205, 10.1093/hmg/ddg055

Howe, 2001, The cyclin D1 alternative transcripts (a) and (b) are expressed in normal and malignant lymphocytes and their relative levels are influenced by the polymorphism at codon 241, Haematologica, 86, 563

Nackley, 2006, Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure, Science, 314, 1930, 10.1126/science.1131262

Sam, 2005, Increased reactive oxygen species production and functional alterations in antioxidant enzymes in human failing myocardium, J Card Fail, 11, 473, 10.1016/j.cardfail.2005.01.007

Valenti, 2004, The mitochondrial superoxide dismutase A16V polymorphism in the cardiomyopathy associated with hereditary haemochromatosis, J Med Genet, 41, 946, 10.1136/jmg.2004.019588

Hung, 2004, Genetic polymorphisms of MPO, COMT, MnSOD, NQO1, interactions with environmental exposures and bladder cancer risk, Carcinogenesis, 25, 973, 10.1093/carcin/bgh080

Xu, 2007, The role of a single-stranded nucleotide loop in transcriptional regulation of the human sod2 gene, J Biol Chem, 282, 15981, 10.1074/jbc.M608979200

Ginsberg, 2003, PKA-dependent binding of mRNA to the mitochondrial AKAP121 protein, J Mol Biol, 327, 885, 10.1016/S0022-2836(03)00173-6

Huang, 1999, Decreased expression of manganese superoxide dismutase in transformed cells is associated with increased cytosine methylation of the SOD2 gene, DNA Cell Biol, 18, 643, 10.1089/104454999315051

Chasman, 2004, Pharmacogenetic study of statin therapy and cholesterol reduction, J Am Med Assoc, 291, 2821, 10.1001/jama.291.23.2821

Kathiresan, 2008, Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans, Nat Gen, 40, 189, 10.1038/ng.75

Eubank, 2003, M-CSF induces vascular endothelial growth factor production and angiogenic activity from human monocytes, J Immunol, 171, 2637, 10.4049/jimmunol.171.5.2637

Zuker, 2003, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res, 31, 3406, 10.1093/nar/gkg595