Research Topics
Genomes and Genes
Species | David ContiSummaryAffiliation: University of Southern California Country: USA Publications
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Publications
Meta-analysis of 8q24 for seven cancers reveals a locus between NOV and ENPP2 associated with cancer developmentAbra G Brisbin
Department of Health Sciences Research, Mayo Clinic, Rochester, USA
BMC Med Genet 12:156. 2011..However, the abundance of associations around 128 Mb on chromosome 8 could mask the appearance of a weaker, but important, association elsewhere on 8q24...- Variation in genetic admixture and population structure among Latinos: the Los Angeles Latino eye study (LALES)Corina J Shtir
Department of Preventive Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
BMC Genet 10:71. 2009..Sensitivity of ancestry estimates to relative sample size was considered... 
Comparison of missing data approaches in linkage analysisChao Xing
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
BMC Genet 4:S44. 2003..Therefore, we compare here six methods of imputing missing repeated phenotypes on results from genome-wide linkage analyses of four quantitative traits from the Framingham Heart Study cohort...- Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasisJoshua Millstein
National Oceanic and Atmospheric Administration National Marine Fisheries Service, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
BMC Genet 6:S147. 2005..The strongest effect was for SNP B03T3056, which had a median p-value of 1.98 x 10(-34). No two- or three-locus effects were found in more than one replicate... - Prevalence of common disease-associated variants in Asian IndiansTrevor J Pemberton
Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
BMC Genet 9:13. 2008.... - Snagger: a user-friendly program for incorporating additional information for tagSNP selectionChristopher K Edlund
Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
BMC Bioinformatics 9:174. 2008..Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important... 
Bayesian modeling of complex metabolic pathwaysDavid V Conti
Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089 9011, USA
Hum Hered 56:83-93. 2003..The new analyses are structured in a manner that attempts to take advantage of prior knowledge of the metabolism of these classes of compounds and the various genes that regulate these pathways...- SNPs, haplotypes, and model selection in a candidate gene region: the SIMPle analysis for multilocus dataDavid V Conti
Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
Genet Epidemiol 27:429-41. 2004..Using simulations, we demonstrate the utility of the SIMPle model to identify crucial SNPs and underlying haplotype structures across a variety of causal models and genetic architectures... - Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessationDavid V Conti
Department of Preventive Medicine, Keck School of Medicine, Zilkha Neurogenetics Institute, University of Southern California, 1501 San Pablo Street, ZNI 445, Los Angeles, CA 90089, USA
Hum Mol Genet 17:2834-48. 2008..0002) and an impact on withdrawal symptoms at target quit date (TQD) (P = 0.0009). Overall, while our results indicate strong evidence for CHRNB2 in ability to quit smoking, these results require replication in an independent sample... - Efficient genome-wide association testing of gene-environment interaction in case-parent triosW James Gauderman
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033, USA
Am J Epidemiol 172:116-22. 2010..This 2-step scan for G x E interaction is independent of any prior scan that may have been conducted for genetic main effects, and thus has the potential to uncover new genes in a GWAS that have not been previously identified... - Bayesian spatial modeling of haplotype associationsDuncan C Thomas
University of Southern California, Los Angeles, CA 90089 9011, USA
Hum Hered 56:32-40. 2003..We conclude with a discussion of the implications of these methods for modeling cryptic relatedness, haplotype blocks, and haplotype tagging SNPs, and suggest a Bayesian framework for the HapMap project... 
Role of inducible nitric oxide synthase in asthma risk and lung function growth during adolescenceTalat Islam
Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, 1540 Alcazar Street, CHP 236, Los Angeles, CA 90033, USA
Thorax 65:139-45. 2010..Because nitrosative stress affects respiratory health, it was hypothesised that variants in NOS2A are associated with asthma incidence and lung function growth during adolescence...- Detecting gene-environment interactions using a combined case-only and case-control approachDalin Li
Department of Preventive Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
Am J Epidemiol 169:497-504. 2009..Increased power or increased robustness to violations of the independence assumption may be obtained with more appropriate prior specification. The authors use an example data analysis to demonstrate the advantages of this approach... - Genetic variability in the MTHFR gene and colorectal cancer risk using the colorectal cancer family registryA Joan Levine
USC Keck School of Medicine, Department of Preventive Medicine, Genetic Epidemiology, NRT 1450 Biggy Street, Room 1509A, Los Angeles, CA 90033, USA
Cancer Epidemiol Biomarkers Prev 19:89-100. 2010..The MTHFR C677T TT genotype is associated with a 15% to 18% reduction in colorectal cancer risk, but it is not clear if other variants of the gene are associated with colorectal cancer risk... - A survey of current Bayesian gene mapping methodsJohn Molitor
Department of Preventive Medicine, University of Southern California, 1540 Alcazar Street, CHP 220, Los Angeles, CA 90089 9011, USA
Hum Genomics 1:371-4. 2004..This review attempts to summarise some of the currently available methods and the software available to implement these methods... - Discovery of complex pathways from observational dataJames W Baurley
Department of Preventive Medicine, University of Southern California, Los Angeles, USA
Stat Med 29:1998-2011. 2010..Our method can correctly identify the risk factors and interactions involved in the simulated pathway. We apply our framework to an asthma case-control data set with polymorphisms in 12 genes... - Intercellular adhesion molecule-1 and childhood asthmaYu Fen Li
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CHP 236, Los Angeles, CA 90033, USA
Hum Genet 117:476-84. 2005..3, 95% CI 0.1-0.8), as compared with two copies of the AGA haplotype. Consistent with information on variant function, the 241A and 469G variants may indicate haplotypes that are associated with reduced risk for asthma... - Using extreme phenotype sampling to identify the rare causal variants of quantitative traits in association studiesDalin Li
Medical Genetics Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
Genet Epidemiol 35:790-9. 2011..Finally, we expanded the current analysis and design framework to accommodate the CMC approach where multiple rare-variants in the same gene region are analyzed jointly... - Effect of tidal volume in children with acute hypoxemic respiratory failureRobinder G Khemani
Department of Anesthesia and Critical Care Medicine, Children s Hospital Los Angeles, 4650 Sunset Blvd, Mail Stop 12, Los Angeles, CA 90027, USA
Intensive Care Med 35:1428-37. 2009..To validate lung injury severity markers such as oxygenation index (OI), PaO2/FiO2 (PF) ratio, and lung injury score (LIS)... - Interleukin-6-related genotypes, body mass index, and risk of multiple myeloma and plasmacytomaWendy Cozen
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MC 9175, Los Angeles, CA 90089 9175, USA
Cancer Epidemiol Biomarkers Prev 15:2285-91. 2006..These results suggest that IL-6 promoter genotypes may be associated with increased risk of plasma cell neoplasms... - Water intake and bladder cancer risk in Los Angeles CountyXuejuan Jiang
USC Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
Int J Cancer 123:1649-56. 2008..Similarly, the protection from water intake was confined to women who did not experience nocturia and to men who did. Results from our study suggest that water intake may be associated with a slight reduction in bladder cancer risk... - Sequence variant on 3q28 and urinary bladder cancer risk: findings from the Los Angeles-Shanghai bladder case-control studyMariana C Stern
Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, USA
Cancer Epidemiol Biomarkers Prev 18:3057-61. 2009..045). Our results suggest that a TP63 gene variant may increase susceptibility for the development of urinary bladder tumors with low risk of progression... - Genes involved with folate uptake and distribution and their association with colorectal cancer riskJane C Figueiredo
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1450 Biggy Street Room 1509J, Los Angeles, CA 90033, USA
Cancer Causes Control 21:597-608. 2010..In conclusion, we found no significant evidence that genetic variants in FOLR1, GGH, FPGS and SLC19A1 are associated with the risk of colorectal cancer... - Genetic variation in the vitamin D receptor (VDR) and the vitamin D-binding protein (GC) and risk for colorectal cancer: results from the Colon Cancer Family RegistryJenny N Poynter
Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
Cancer Epidemiol Biomarkers Prev 19:525-36. 2010..Overall, our results do not provide evidence for a role of common genetic variants in VDR or GC in susceptibility to CRC... - A candidate gene study of folate-associated one carbon metabolism genes and colorectal cancer riskA Joan Levine
USC Keck School of Medicine, Department of Preventive Medicine, Genetic Epidemiology, NRT 1450 Biggy Street Room 1509A, Los Angeles, CA 90033, USA
Cancer Epidemiol Biomarkers Prev 19:1812-21. 2010..Folate-associated one-carbon metabolism (FOCM) may play an important role in colorectal carcinogenesis. Variation in FOCM genes may explain some of the underlying risk of colorectal cancer... - Hypertension, diuretics and antihypertensives in relation to bladder cancerXuejuan Jiang
Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
Carcinogenesis 31:1964-71. 2010..7 pg/g Hb) compared with individuals without hypertension (79.8 pg/g Hb) (P = 0.009). In conclusion, untreated hypertension was associated with a reduced risk of bladder cancer... - Risk of urinary bladder cancer is associated with 8q24 variant rs9642880[T] in multiple racial/ethnic groups: results from the Los Angeles-Shanghai case-control studyVictoria K Cortessis
Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Ave, MC 9175, Los Angeles, CA 90089, USA
Cancer Epidemiol Biomarkers Prev 19:3150-6. 2010..Recent genome-wide association studies of urinary bladder cancer report risk to be associated with the T allele of rs9642880 on 8q24 among individuals of European descent... - Use of pathway information in molecular epidemiologyDuncan C Thomas
Department of Preventive Medicine, University of Southern California, 1540 Alcazar St, CHP 220, Los Angeles, CA 90089 9011, USA
Hum Genomics 4:21-42. 2009..The review concludes with some thoughts about potential uses of pathways in genome-wide association studies... - Genetic variations on chromosomes 5p15 and 15q25 and bladder cancer risk: findings from the Los Angeles-Shanghai bladder case-control studyManuela Gago-Dominguez
Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 9175, USA
Carcinogenesis 32:197-202. 2011..26; 95% CI, 1.04-1.54; P = 0.017). Our results support 5p15 and 15q25 as susceptibility regions for bladder cancer risk... - Variation in folate pathway genes and distal colorectal adenoma risk: a sigmoidoscopy-based case-control studyA Joan Levine
Department of Preventive Medicine, Genetic Epidemiology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
Cancer Causes Control 22:541-52. 2011..Folate-associated one-carbon metabolism (FOCM) is an important pathway in colorectal neoplasia risk but data on genetic variation in this pathway are largely limited to studies of single SNPs in selected genes... - Glutathione S-transferase P1, maternal smoking, and asthma in children: a haplotype-based analysisYu Fen Li
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
Environ Health Perspect 116:409-15. 2008..Glutathione S-transferase P1 (GSTP1) plays a role in a spectrum of respiratory diseases; however, the effects of sequence variation across the entire locus in asthma pathogenesis have yet to be determined... - Comprehensive evaluation of ESR2 variation and ovarian cancer riskCeleste Leigh Pearce
USC Norris Comprehensive Cancer Center and Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
Cancer Epidemiol Biomarkers Prev 17:393-6. 2008..28-11.73; P = 0.016). Haplotype D was also reported by the BPC3 to be associated with increased risk of breast cancer. This haplotype warrants further investigation to rule out any effect with invasive ovarian cancer risk... - Common genetic variation in the sex steroid hormone-binding globulin (SHBG) gene and circulating shbg levels among postmenopausal women: the Multiethnic CohortChristopher A Haiman
University of Southern California Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, California 90089, USA
J Clin Endocrinol Metab 90:2198-204. 2005.... - Age-related smoking progression among adolescents in ChinaWei Sun
Keck School of Medicine, University of Southern California, Los Angeles, California, USA
J Adolesc Health 39:686-93. 2006..This study examined the differences in smoking progression between middle and upper school students... - XRCC1, XRCC3, and XPD polymorphisms as modifiers of the effect of smoking and alcohol on colorectal adenoma riskMariana C Stern
University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Avenue, Room 5421A, Los Angeles, CA 90089, USA
Cancer Epidemiol Biomarkers Prev 15:2384-90. 2006..04). Our data suggest that the effects of smoking and alcohol may vary depending on the genetic background of proteins that participate in the base excision repair and nucleotide excision repair pathways... - Testing association between disease and multiple SNPs in a candidate geneW James Gauderman
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
Genet Epidemiol 31:383-95. 2007..We observe stronger evidence of an association using the PC approach (p = 0.044) than using either a genotype-based (p = 0.13) or haplotype-based (p = 0.052) approach... - Alcohol consumption and risk of bladder cancer in Los Angeles CountyXuejuan Jiang
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
Int J Cancer 121:839-45. 2007..Alcohol consumption was strongly associated with a reduced risk of bladder cancer. The effect was modified by the type of alcoholic beverage, cigarette smoking and frequency of urination... - The effect of montelukast and low-dose theophylline on cardiovascular disease risk factors in asthmaticsHooman Allayee
Department of Preventive Medicine, USC Keck School of Medicine, 2250 Alcazar St, IGM 206, Los Angeles, CA 90033, USA
Chest 132:868-74. 2007..We sought to determine whether montelukast, a cysteinyl LT antagonist, and low-dose theophylline affected serum inflammatory and lipid CVD risk factors in a recently completed clinical trial in asthmatic patients... - Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigationJuan Pablo Lewinger
Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089 9011, USA
Genet Epidemiol 31:871-82. 2007..We show that the ranking by posterior expectations performs better at selecting the true positive association than a simple ranking of p-values if at least some of the prior covariates have predictive value... - DNA repair single-nucleotide polymorphisms in colorectal cancer and their role as modifiers of the effect of cigarette smoking and alcohol in the Singapore Chinese Health StudyMariana C Stern
Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Room 5421A, Los Angeles, CA 90089, USA
Cancer Epidemiol Biomarkers Prev 16:2363-72. 2007..8; 95% CI, 1.0-8.1). Our results support a role for reactive oxygen species as relevant genotoxins that may account for the effects of both smoking and alcohol on colorectal cancer risk... - Variants on 9p24 and 8q24 are associated with risk of colorectal cancer: results from the Colon Cancer Family RegistryJenny N Poynter
Department of Preventive Medicine, University of Southern California, 1441 Eastlake Avenue, NOR4411A, Los Angeles, CA 90089 9175, USA
Cancer Res 67:11128-32. 2007..These data suggest that common variants may play important roles in the risk of CRC... - Commentary: the concept of 'Mendelian Randomization'Duncan C Thomas
Department of Preventive Medicine, University of Southern California, Los Angeles, CA 9089-9011, USA
Int J Epidemiol 33:21-5. 2004 - Complex system approaches to genetic analysis Bayesian approachesMelanie A Wilson
Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
Adv Genet 72:47-71. 2010..In particular, we highlight the ability of Bayesian methods to construct complex probability models via a hierarchical structure and to account for uncertainty in model specification by averaging over large spaces of alternative models... - DNA repair gene XRCC1 and XPD polymorphisms and risk of prostate cancerBenjamin A Rybicki
Department of Biostatistics and Research Epidemiology, Henry Ford Health System, Detroit, Michigan, USA
Cancer Epidemiol Biomarkers Prev 13:23-9. 2004.... - Testing association and linkage using affected-sib-parent study designsJoshua Millstein
National Oceanic and Atmospheric Administration National Marine Fisheries Service, Alaska Fisheries Science Center, Seattle, Washington 98115, USA
Genet Epidemiol 29:225-33. 2005..8% by FBAT, and 82.5% by our joint test of linkage and association. Our model can also be used to obtain tests of linkage conditional on association and association conditional on linkage, which can be helpful in fine mapping... - A testing framework for identifying susceptibility genes in the presence of epistasisJoshua Millstein
National Oceanic and Atmospheric Administration National Marine Fisheries Service, Alaska Fisheries Science Center, Seattle, WA 98115, USA
Am J Hum Genet 78:15-27. 2006..In an independent data set consisting primarily of African American and Asian American children, these three genes also showed a significant association with asthma status (P = .0008)... - Association of prostate cancer risk and aggressiveness to androgen pathway genes: SRD5A2, CYP17, and the ARMine S Cicek
Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
Prostate 59:69-76. 2004..CONCLUSIONS: These findings suggest that the SRD5A2 V89L variant may influence risk of developing prostate cancer, especially among men with a younger age of diagnosis or more aggressive disease... - Relationship between methylenetetrahydrofolate reductase C677T and A1298C genotypes and haplotypes and prostate cancer risk and aggressivenessMine S Cicek
Department of Cancer Biology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
Cancer Epidemiol Biomarkers Prev 13:1331-6. 2004..47, 95% CI 0.29-0.76; P = 0.002). Our findings suggest that 677T and 1298A, or another variant on their haplotype, may be associated with a reduced risk of progression to more advanced prostate cancer... - Hierarchical modeling of linkage disequilibrium: genetic structure and spatial relationsDavid V Conti
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 44106, USA
Am J Hum Genet 72:351-63. 2003..This work demonstrates that hierarchical modeling of linkage disequilibrium is a valuable and flexible approach for fine-scale mapping... - Comprehensive evaluation of the association between prostate cancer and genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2Anu Loukola
Amersham Biosciences, Sunnyvale, CA 94085, USA
Eur J Hum Genet 12:321-32. 2004..02). Undertaking a two-phase study comprising SNP discovery, haplotype tagging, and association analyses allowed us to more fully decipher the relation between CYP17A1, CYP3A4, and SRD5A2 and prostate cancer... - CYP3A4 and CYP3A5 genotypes, haplotypes, and risk of prostate cancerSarah J Plummer
Department of Cancer Biology, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio, USA
Cancer Epidemiol Biomarkers Prev 12:928-32. 2003..07; 95% CI, 0.01-0.51; P=0.009). These findings suggest that the CYP3A4 and CYP3A5 variants, or other alleles on the haplotypes they help distinguish, are associated with prostate cancer risk and aggressiveness... - Prostate cancer aggressiveness locus on chromosome segment 19q12-q13.1 identified by linkage and allelic imbalance studiesPhillippa J Neville
Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA
Genes Chromosomes Cancer 36:332-9. 2003..06). These data provide strong evidence that we have mapped a prostate tumor aggressiveness locus to chromosome segments 19q12-q13.11 that may play a role in both familial and non-familial forms of prostate cancer... - Prostate cancer aggressiveness locus on chromosome 7q32-q33 identified by linkage and allelic imbalance studiesPhillippa J Neville
Department of Cancer Biology, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
Neoplasia 4:424-31. 2002..05). These data imply that we have localized a prostate cancer tumor aggressiveness loci to chromosome 7q32-q33 that is involved in familial and nonfamilial forms of prostate cancer... - Genetic dissection of complex traits with chromosome substitution strains of miceJonathan B Singer
Broad Institute, Cambridge, MA 02142, USA
Science 304:445-8. 2004..These results demonstrate that CSSs greatly facilitate the detection and identification of genes that control the wide diversity of naturally occurring phenotypic variation in the A/J and C57BL/6J inbred strains...
Research Grants
- HIERARCHICAL MODELING OF INTERACTIONS IN GENOME-WIDE AND PATHWAY-BASED STUDIESDavid V Conti; Fiscal Year: 2010..By identifying both genetic and environmental factors, we will make progress in understanding the underlying mechanism that leads to disease and potentially identify ways in which to both prevent and treat complex diseases. ..