Published Articles

The following is a list of peer reviewed publications in which Golden Helix SVS software has been cited. This list was composed using Google™ Scholar. Updated: June 3, 2008.

SNP & Variation Suite - HelixTree

2008

  • Abatepaulo ARR et al. (2008) Detection of SNPs in bovine immune-response genes that may mediate resistance to the cattle tick Rhipicephalus (Boophilus) microplus. Animal Genetics. 39 (3): 328–329.
  • Amos CI et al. (2008) Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nature Genetics 40(5):616-22.
  • Ashworth JJ et al. (2008) Polymorphisms spanning the 0N exon and promoter of the estrogen receptor-beta (ERβ) gene ESR2 are associated with venous ulceration. Clinical Genetics, 73(1):55-61.
  • Cogulu O et al. (2008) Role of angiotensin-converting enzyme gene polymorphisms in children with sepsis and septic shock. Pediatrics International, doi:10.1111/j.1442-200X.2008.02583.x.
  • Hellard SL et al. (2008) Association between the insulin-induced gene 2 (INSIG2) and weight gain in a German sample of antipsychotic-treated schizophrenic patients: perturbation of SREBP-controlled lipogenesis in drug-related metabolic adverse effects? Molecular Psychiatry, doi: 10.1038/sj.mp.4002133.
  • Liu YJ et al. (2008) Genome-wide association scans identified CTNNBL1 as a novel gene for obesity. Human Molecular Genetics, doi:10.1093/hmg/ddn072.
  • Paiva L et al. (2008) Polymorphism of glutathione transferase Omega 1 in a population exposed to a high environmental arsenic burden. Pharmacogenetics & Genomics 18(1):1-10.
  • Pushpakom SP et al. (2008) Polymorphisms in COL15 Gene Are Not Associated with Systemic Sclerosis. The Journal of Rheumatology 35(2):251-3.
  • Smith, R.B. Warren, et al. (2008) Polymorphisms in the PTPN22 region are associated with psoriasis of early onset. British Journal of Dermatology 158 (5): 962–968.
  • Sun YV et al. (2008) Imputing missing genotypic data of single-nucleotide polymorphisms using neural networks. European Journal of Human Genetics 16: 487–495.
  • Tian C et al. (2008) Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genetics 4(1):e5.
  • Voetsch B et al. (2008) Role of promoter polymorphisms in the plasma glutathione peroxidase (GPx-3) gene as a risk factor for cerebral venous thrombosis. Stroke 39(2):303-7.
  • Yang H et al. (2008) Evaluation of Genetic Variants in MicroRNA-Related Genes and Risk of Bladder Cancer. Cancer Research 68: 2530-2537.
  • Yang H et al. (2008) Profiling of Genetic Variations in Inflammation Pathway Genes in Relation to Bladder Cancer Predisposition. Clinical Cancer Research 14: 2236-2244.
  • Zhu Y et al. (2008) Modulation of DNA damage/DNA repair capacity by XPC polymorphisms. DNA Repair 7(2): 141-148.

2007

  • Beretta L , et al. (2007) Interleukin-1 gene complex polymorphisms in systemic sclerosis patients with severe restrictive lung physiology. Human Immunology 68(7):603-609.
  • Chen M , et al. (2007) High-order interactions among genetic polymorphisms in nucleotide excision repair pathway genes and smoking in modulating bladder cancer risk. Carcinogenesis 28(10):2160.
  • Chinoy H , et al. (2007) Interferon-gamma and interleukin-4 gene polymorphisms in Caucasian idiopathic inflammatory myopathy patients in UK. British Medical Journal 66(7):970-973.
  • Chinoy H , et al. (2007) Tumour necrosis factor- single nucleotide polymorphisms are not independent of HLA class I in UK Caucasians with adult onset idiopathic inflammatory myopathies. Rheumatology.
  • Chinoy H , et al. (2007) STK15 F31I polymorphism is associated with increased uterine cancer risk: A pilot study. Rheumatology 46(4):604.
  • Corella D , et al. (2007) APOA5 gene variation modulates the effects of dietary fat intake on body mass index and obesity risk in the Framingham Heart Study. Journal of Molecular Medicine 85 (2): 119 – 128.
  • Dessai M , et al. (2007) An association analysis of the HLA gene region in latent autoimmune diabetes in adults. Diabetologia 50 (1): 68-73.
  • Donn R , et al. (2007) Glucocorticoid receptor gene polymorphisms and susceptibility to rheumatoid arthritis. Clinical Endocrinology 67(3):342–345.
  • Engels EA , et al. (2007) Systematic Evaluation of Genetic Variants in the Inflammation Pathway and Risk of Lung Cancer. Cancer Research 67(13):6520.
  • Glorioso N , et al. (2007) Association of ATP1A1 and Dear Single-Nucleotide Polymorphism Haplotypes with Essential Hypertension. Circulation Research 100(10):1522.
  • Hinks A , et al. (2007) Investigation of genetic variation across the protein tyrosine phosphatase gene in patients with rheumatoid arthritis in the UK. Annals of Rheumatic Diseases 66: 683 – 686.
  • Ho PYPC , et al. (2007) HLA-Cw6 and HLA-DRB1*07 together are associated with less severe joint disease in psoriatic arthritis. British Medical Journal 66(6):807-811.
  • Ho PYPC , et al. (2007) Investigating the role of the HLA-Cw*06 and HLA-DRB1 genes in susceptibility to psoriatic arthritis: comparison with psoriasis and undifferentiated inflammatory arthritis. British Medical Journal.
  • Huang M , et al. (2007) High-Order Interactions among Genetic Variants in DNA Base Excision Repair Pathway Genes and Smoking in Bladder Cancer Susceptibility. Cancer Epidemiology Biomarkers & Prevention 16: 84-91.
  • Kaushal R , et al. (2007) Association of ALOX5AP with ischemic stroke: a population-based case-control study. Human Genetics 121 (5): 601-607.
  • Knafo A , et al (2007) Individual Differences in Allocation of Funds in the Dictator Game Associated with Length of the Arginine Vasopressin 1a Receptor (AVPR1a) RS3 Promoter-region and Correlation between RS3 Length and Hippocampal mRNA. Genes, Brain and Behavior.
  • Lencz T, Lambert C , et al. (2007) Runs of Homozygosity Reveal Highly Penetrant Recessive Loci in Schizophrenia. Proceedings of the National Academy of Sciences.
  • Lencz T , et al. (2007) Converging evidence for a pseudoautomal cytokin receptor gene locus in schizophrenia. Molecular Psychiatry 12: 572 – 580.
  • Lin J , et al. (2007) Mutagen Sensitivity and Genetic Variants in Nucleotide Excision Repair Pathway: Genotype-Phenotype Correlation. Cancer Epidemiology Biomarkers & Prevention 16(10):2065.
  • Miyajima F , et al. (2007) Brain-derived neurotrophic factor polymorphism Val66Met influences cognitive abilities in the elderly. Genes, Brain and Behavior.
  • Nielsen DA , et al. (2007) The BiolAD-DB System: An Informatics System for Clinical and Genetic Data. Molecular Diagnosis & Therapy 11(1):15-19.
  • Banerji N , et al. (2007) Association of Germ-line Polymorphisms in the Feline p53 Gene with Genetic Predisposition to Vaccine-Associated Feline Sarcoma. Journal of Heredity 98(5):421 – 427.
  • Rukin N , et al. (2007) Prostate cancer susceptibility is mediated by interactions between exposure to ultraviolet radiation and polymorphisms in the 5 haplotype block of the vitamin D receptor gene. Cancer Letters 247 (2): 328 – 335.
  • Shen J , et al. (2007) Interleukin1ß Genetic Polymorphisms Interact with Polyunsaturated Fatty Acids to Modulate Risk of the Metabolic Syndrome. Journal of Nutrition 137(8):1846.
  • Sun YV, Cai Z et al. (2007) Classification of rheumatoid arthritis status with candidate gene and genome-wide single-nucleotide polymorphisms using random forests. BMC Proceedings 1 (Suppl 1):S62.
  • Taylor M , et al. (2007) Management, presentation and interpretation of genome scans using GSCANDB. Bioinformatics 23(12):1545.
  • Tejedor T , et al. (2007) Introgression of Alectoris chukar Genes into a Spanish Wild Alectoris rufa Population. Journal of Heredity 98 (2): 179-182.
  • Voetsch B , et al. (2007) Promoter Polymorphisms in the Plasma Glutathione Peroxidase (GPx-3) Gene. A Novel Risk Factor for Arterial Ischemic Stroke Among Young Adults and Children. Stroke 38: 41.
  • Wang W , et al (2007) Genetic Variants in Cell Cycle Control Pathway Confer Susceptibility to Lung Cancer. Clinical Cancer Research 13(19):5974.
  • Warren L , et al. (2007) Use of pairwise marker combination and recursive partitioning in a pharmacogenetic genome-wide scan. The Pharmacogenomics Journal 7: 180 - 189.
  • Zhang H , et al. (2007) The OPRD1 and OPRK1 loci in alcohol or drug dependence: OPRD1 variation modulates substance dependence risk. Molecular Psychiatry.

2006

  • Brown JJ , et al. (2006) TNF-a SNP haplotype frequencies in equidae. Tissue Antigens 67 (5):377-382.
  • Bugeja MJ , et al. (2006) An investigation of polymorphisms in the 17q11. 2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians. BMC Medical Genetics 7 (1):64.
  • Calle R , et al. (2006) Paraoxonase 2 (PON2) polymorphisms and development of renal dysfunction in type 2 diabetes: UKPDS 76. Diabetologia 49 (12):2892-2899.
  • Chinoy H , et al. (2006) Monocyte chemotactic protein-1 single nucleotide polymorphisms do not confer susceptibility for the development of adult onset polymyositis/dermatomyositis in UK Caucasians. Rheumatology.
  • Chinoy H , et al. (2006) In adult onset myositis, the presence of interstitial lung disease and myositis specific/associated antibodies are governed by HLA class II haplotype, rather than by myositis subtype. Arthritis Research & Therapy 8: R13.
  • Desai M , et al. (2006) The Variable Number of Tandem Repeats Upstream of the Insulin Gene Is a Susceptibility Locus for Latent Autoimmune Diabetes in Adults. Diabetes 55 (6):1890-1894.
  • Eyre S , et al. (2006) Association of the FCRL3 gene with rheumatoid arthritis: a further example of population specificity? Arthritis Research & Therapy 8: R117.
  • Gu J , et al. (2006) Polymorphisms of STK15 (Aurora-A) gene and lung cancer risk in Caucasians. Carcinogenesis 28 (2): 350 – 355.
  • Hallman D , et al. (2006) Longitudinal analysis of haplotypes and polymorphisms of the APOA5 and APOC3 genes associated with variation in serum triglyceride levels: the Bogalusa Heart Study. Human Molecular Genetics 55 (12): 1574 – 1581.
  • Hinks A , et al. (2006) Fine mapping of genes within the IDDM8 region in rheumatoid arthritis. Arthritis Research & Therapy 8: R145.
  • Huang R and Poduslo SE (2006) CYP19 haplotypes increase risk for AlzheimerÆs disease. Journal of Medical Genetics 43 (8):42.
  • Jones DC , et al. (2006) Nature of allelic sequence polymorphism at the KIR3DL3 locus. Immunogenetics 58 (8):614-627.
  • Klos KLE , et al. (2006) Consistent Effects of Genes Involved in Reverse Cholesterol Transport on Plasma Lipid and Apolipoprotein Levels in CARDIA Participants. Arteriosclerosis, Thrombosis, and Vascular Biology 26 (8):1828.
  • Lamb RM, Zeggini E, and Abinun BM (2005) Toll-like receptor 4 (TLR4) gene polymorphisms and susceptibility to juvenile idiopathic arthritis. Annals of the Rheumatic Diseases.
  • Lotsch J , et al. (2006) Modulation of the central nervous effects of levomethadone by genetic polymorphisms potentially affecting its metabolism, distribution, and drug action. Clinical Pharmacology & Therapeutics 79 (1):72-89.
  • Lai CQ , et al. (2006) Dietary Intake of n-6 Fatty Acids Modulates Effect of Apolipoprotein A5 Gene on Plasma Fasting Triglycerides, Remnant Lipoprotein Concentrations, and Lipoprotein Particle Size. The Framingham Heart Study. Circulation.
  • Lim JE , et al. (2006) Allelic expression of serotonin transporter (SERT) mRNA in human pons: lack of correlation with the polymorphism SERTLPR. Molecular Psychiatry 11:649-662.
  • Moon S , et al. (2006) Associations Between G/A1229, A/G3944, T/C30875, C/T48200 and C/T65013 Genotypes and Haplotypes in the Vitamin D Receptor Gene, Ultraviolet Radiation and Susceptibility to Prostate Cancer. Annals of Human Genetics 70 (2): 226 – 236.
  • Nam RK , et al. (2006) Variants of the hK2 Protein Gene (KLK2) Are Associated with Serum hK2 Levels and Predict the Presence of Prostate Cancer at Biopsy. Clinical Cancer Research 12 (21):6452.
  • Pal P , et al. (2006) Variants in the HEPSIN gene are associated with prostate cancer in men of European origin. Human Genetics 120 (2):187-192.
  • Pinsonneault JK, Papp AC, and Sadee W (2006) Allelic mRNA expression of X-linked monoamine oxidase a (MAOA) in human brain: dissection of epigenetic and genetic factors. Human Molecular Genetics 15 (17):2636.
  • Plant D , et al. (2006) The CX3CL1ûCX3CR1 system and psoriasis. Experimental Dermatology 15 (11):900-903.
  • Saeed M , et al. (2006) Paraoxonase cluster polymorphisms are associated with sporadic ALS. Neurology 67 (5):771.
  • Shephard N , et al (2006) Will the real disease gene please stand up? BMC Genetics 6 (Suppl1): S66.
  • Woo D , et al. (2006) Association of Phosphodiesterase 4D With Ischemic Stroke A Population-Based Case-Control Study. Stroke 37: 371.
  • Wu X , et al. (2006) Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. American Journal of Human Genetics 78 (3):464-479.
  • Zeggini E , et al. (2006) Association of HLA-DRB1* 13 with susceptibility to uveitis in juvenile idiopathic arthritis in two independent data sets. Rheumatology 45 (8):972.
  • Zeggini E , et al. (2006) Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition. BMC Genetics 6: 21.
  • Zhu Y , et al. (2006) Genotypes, haplotypes, and diplotypes of XPC and risk of bladder cancer. Carcinogenesis.

2005

  • Barton A , et al. (2005) Investigation of the SLC22A4 gene (associated with rheumatoid arthritis in a Japanese population) in a United Kingdom population of rheumatoid arthritis patients. Arthritis Rheum 52 (3):752-758.
  • Bugeja MJ , et al. (2005) An investigation of NOS2A promoter polymorphisms in Australian multiple sclerosis patients. European Journal of Human Genetics 13:815-822.
  • Bull SB, John S, and Briollais L (2005) Fine Mapping by Linkage and Association in Nuclear Family and Case-Control Designs. Genetic Epidemiology 29 (1):S48-S58.
  • Carroll WD , et al. (2005) Maternal glutathione S-transferase GSTP 1 genotype is a specific predictor of phenotype in children with asthma. Pediatric Allergy and Immunology 16 (1):32-39.
  • Ho P , et al (2005) Evidence for common genetic control in pathways of inflammation for Crohn’s disease and psoriatic arthritis. Arthritis Rheum 52 (11):3596-3602.
  • Kuo NW , et al. (2005) TNF-857T, A Genetic Risk Marker for Acute Anterior Uveitis. Investigative Ophthalmology & Visual Science 46 (5):1565-1571.
  • Lamb R , et al. (2005) Toll-like receptor 4 gene polymorphisms and susceptibility to juvenile idiopathic arthritis. Annals of Rheumatic Diseases 64: 767 – 769.
  • Liang D , et al (2005) Variations within OLF1/EBF-associated zinc finger protein gene confer susceptibility to lupus nephritis in Chinese population. Zhonghua Yi Xue Za Zhi 85 (14):949-954.
  • Lovatt T , et al. (2005) Polymorphism in the nuclear excision repair geneERCC 2/XPD: association between an exon 6-exon 10 haplotype and susceptibility to cutaneous basal cell carcinoma. Human Mutation 25 (4):353-359.
  • Moore RM , et al. (2005) Selecting cases from nuclear families for case-control association analysis. BMC Genetics 6 (Suppl 1): S105.
  • Potter C , et al. (2005) TNFR2 is not associated with rheumatoid arthritis susceptibility in a Caucasian population. Arthritis & Rheumatism 52 (8): 2579-2581.
  • Spraggs CF , et al. (2005) Pharmacogenetics and obesity: common gene variants influence weight loss response of the norepinephrine/dopamine transporter inhibitor GW320659 in obese subjects. Pharmacogenetics and Genomics 15 (12):883-889.
  • Stephens R , et al. (2005) Polymorphisms in IGF-Binding Protein 1 Are Associated With Impaired Renal Function in Type 2 Diabetes. Diabetes 54: 3547 – 3553.
  • Woo D , et al. (2005) Association of Apolipoprotein E4 and Haplotypes of the Apolipoprotein E Gene With Lobar Intracerebral Hemorrhage. Stroke 36: 1874.
  • Young S , et al. (2005) Recursive partitioning analysis of complex disease pharmacogenetic studies. I. Motivation and overview. Pharmacogenomics 6 (1):65-75.
  • Zaykin D , et al. (2005) Large recursive partitioning analysis of complex disease pharmacogenetic studies. II. Statistical considerations. Pharmacogenomics 6 (1):77-89.
  • Zeggini E , et al. (2005) Large-scale studies of the association between variation at the TNF/LTA locus and susceptibility to type 2 diabetes. Diabetologia 48 (10):2013-2017.
  • Zeggini E , et al. (2005) Examining the relationships between the Pro12Ala variant in PPARG and Type 2 diabetes-related traits in UK samples. Diabet Med 22 (12):1696-1700.

2004

  • Barrows C , et al. (2004) The sumatriptan/naratriptan aggregated patient(SNAP) database: aggregation, validation and application. Cephalalgia 24 (7):586-595.
  • Barton A , et al. (2004) Haplotype analysis in simplex families and novel analytic approaches in a case-control cohort reveal no evidence of association of the CTLA-4 gene with rheumatoid arthritis. Arthritis & Rheumatism 50 (3):748-752.
  • Barton A , et al (2004) Polymorphisms in the tumour necrosis factor gene are not associated with severity of inflammatory polyarthritis. Annals of the Rheumatic Diseases 63 (3):280.
  • Barton A , et al. (2004) A functional haplotype of the PADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population. Arthritis and Rheumatism 50 (4):1117-1121.
  • Barton A , et al. (2004) Association of protein kinase C alpha (PRKCA) gene with multiple sclerosis in a UK population. Brain 127 (8):1717-1722.
  • Bodiwala D , et al. (2004) Polymorphisms in the vitamin D receptor gene, ultraviolet radiation, and susceptibility to prostate cancer. Environmental and Molecular Mutagenesis 43 (2):121-127.
  • Jones PW , et al. (2004) p16 INK4a polymorphism: Associations with tumour progression in patients with sporadic colorectal cancer. International Journal of Oncology 25:1447-1452.
  • John S , et al. (2004) Whole-Genome Scan, in a Complex Disease, Using 11, 245 Single-Nucleotide Polymorphisms: Comparison with Microsatellites. The American Journal of Human Genetics 75 (1):54-64.
  • Klotsman M , et al. (2004) A case-based evaluation of SRD5A1, SRD5A2, AR, and ADRA1A as candidate genes for severity of BPH. The Pharmacogenomics Journal 4:251-259.
  • Lai CQ , et al. (2004) Influence of the APOA5 locus on plasma triglyceride, remnant-like particles, lipoprotein subclasses and cardiovascular disease risk in the Framingham Heart Study. The Journal of Lipid Research.
  • Lanier ER , et al. (2004) Antiviral efficacy of abacavir in antiretroviral therapyexperienced adults harbouring HIV-1 with specific patterns of resistance to nucleoside reverse transcriptase inhibitors. Antivir Ther 9 (1):37-45.
  • Liew CF , et al. (2004) Analysis of the contribution to type 2 diabetes susceptibility of sequence variation in the gene encoding stearoyl-CoA desaturase, a key regulator of lipid and carbohydrate metabolism. Diabetologia 47 (12):2168-2175.
  • Limmroth V (2004) Poster sessions. Journal of Neurology 251.
  • Report C (2004) Linkage and association studies of discoidin domain receptor 1 (DDR1) single nucleotide polymorphisms (SNPs) in juvenile oligoarthritis. Rheumatology 43 (9):1138-1141.
  • Simister RJ, et al. (2004) Abnormalities in Cardiac Rhythm Revealed in Patients with Refractory Epilepsy. Journal of Neurology Neurosurgery and Psychiatry 75: 516 – 522.
  • Strange RC , et al. (2004) Susceptibility to Basal Cell Carcinoma: Associations with PTCH Polymorphisms. Annals of Human Genetics 68 (6):536-545.
  • Strange RC , et al. (2004) PTCH Polymorphism Is Associated With the Rate of Increase in Basal Cell Carcinoma Numbers During Follow-Up. Environmental and Molecular Mutagenesis 44:469-476.
  • Strange RC , et al. (2004) Susceptibility to Basal Cell Carcinoma: Associations with PTCH Polymorphisms. Annals of Human Genetics 68 (6):536-545.
  • Strange RC , et al. (2004) PTCH Polymorphism Is Associated With the Rate of Increase in Basal Cell Carcinoma Numbers During Follow-Up. Environmental and Molecular Mutagenesis 44:469-476.

2003

  • Bodiwala D , et al. (2003) Associations between prostate cancer susceptibility and parameters of exposure to ultraviolet radiation. Cancer Letters 200 (2):141-148.
  • Bodiwala D , et al. (2003) Susceptibility to prostate cancer: studies on interactions between UVR exposure and skin type. Carcinogenesis 24 (4):711-717.
  • Dow D , et al. (2003) Gene polymorphisms and response to treatment. United States Patent 20030100479.
  • Eyre S , et al. (2006) Investigation of the MHC2TA gene, associated with rheumatoid arthritis in a Swedish population, in a UK rheumatoid arthritis cohort. Arthritis & Rheumatism 54 (11):3417-3422.
  • Jaakkola E , et al. (2003) Genetics: Non-HLA genes. Rheumatology.
  • Lai CQ , et al. (2003) The APOA5 locus is a strong determinant of plasma triglyceride concentrations across ethnic groups in Singapore. The Journal of Lipid Research 44 (12):2365-2373.

PBAT

  • I. Ionita-Laza, C. Lange, et. al. (2008) On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test. Genetic Epidemiology. 32(3): 273 - 284.
  • Lasky-Su J, et al. (2008) On the Replication of Genetic Associations: Timing Can Be Everything! The American Journal of Human Genetics, 82(4): 849-858, doi:10.1016/j.ajhg.2008.01.018.
  • Hunninghake GM et al. (2008) Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Journal of Allergy and Clinical Immunology, doi:10.1016/j.jaci.2008.03.015.
  • Herbert A, et al. (2006) A Common Genetic Variant Is Associated with Adult and Childhood Obesity. Science 312: 279-283.