Nancy J Cox

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. pmc Integrative analyses of genetic variation, epigenetic regulation, and the transcriptome to elucidate the biology of platinum sensitivity
    Bonnie LaCroix
    Section of Hematology Oncology, Department of Medicine, University of Chicago, 900 E 57th Street, KCBD room 7148, Chicago, IL, 60637, USA
    BMC Genomics 15:292. 2014
  2. pmc Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS
    Dan L Nicolae
    Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 6:e1000888. 2010
  3. pmc A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 7:e1001292. 2011
  4. pmc The role of inflammatory pathway genetic variation on maternal metabolic phenotypes during pregnancy
    Margrit Urbanek
    Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
    PLoS ONE 7:e32958. 2012
  5. pmc Copy number polymorphisms and anticancer pharmacogenomics
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
    Genome Biol 12:R46. 2011
  6. pmc Genetic architecture of transcript-level variation in humans
    Shiwei Duan
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 82:1101-13. 2008
  7. pmc Variation in the perilipin gene (PLIN) affects glucose and lipid metabolism in non-Hispanic white women with and without polycystic ovary syndrome
    Toshihide Kawai
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Diabetes Res Clin Pract 86:186-92. 2009
  8. pmc The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study
    Margrit Urbanek
    Division on Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Hum Mol Genet 22:3583-96. 2013
  9. pmc SCAN: SNP and copy number annotation
    Eric R Gamazon
    Department of Medicine, The University of Chicago, Chicago, IL, USA
    Bioinformatics 26:259-62. 2010
  10. pmc A genome-wide integrative study of microRNAs in human liver
    Eric R Gamazon
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    BMC Genomics 14:395. 2013

Collaborators

Detail Information

Publications110 found, 100 shown here

  1. pmc Integrative analyses of genetic variation, epigenetic regulation, and the transcriptome to elucidate the biology of platinum sensitivity
    Bonnie LaCroix
    Section of Hematology Oncology, Department of Medicine, University of Chicago, 900 E 57th Street, KCBD room 7148, Chicago, IL, 60637, USA
    BMC Genomics 15:292. 2014
    ..Using genome-wide genetic, gene expression, and microRNA expression (miRNA) data, we developed an integrative approach to investigate the genetic and epigenetic basis of chemotherapeutic sensitivity...
  2. pmc Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS
    Dan L Nicolae
    Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 6:e1000888. 2010
    ....
  3. pmc A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 7:e1001292. 2011
    ....
  4. pmc The role of inflammatory pathway genetic variation on maternal metabolic phenotypes during pregnancy
    Margrit Urbanek
    Division of Endocrinology, Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
    PLoS ONE 7:e32958. 2012
    ....
  5. pmc Copy number polymorphisms and anticancer pharmacogenomics
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
    Genome Biol 12:R46. 2011
    ..We developed a genome-wide method to identify CNVs that contribute to heterogeneity in drug response, focusing on drugs that are widely used in anticancer treatment regimens...
  6. pmc Genetic architecture of transcript-level variation in humans
    Shiwei Duan
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 82:1101-13. 2008
    ..We highlight in the EPHX1 gene a deleterious nonsynonymous SNP that is distantly associated with gene expression of ORMDL3, a susceptibility gene for asthma...
  7. pmc Variation in the perilipin gene (PLIN) affects glucose and lipid metabolism in non-Hispanic white women with and without polycystic ovary syndrome
    Toshihide Kawai
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Diabetes Res Clin Pract 86:186-92. 2009
    ..59], P=0.022). It was also associated with increased LDL (P=0.007) and total cholesterol levels (P=0.042). These results suggest that genetic variation in PLIN may affect glucose and lipid metabolism in women both with and without PCOS...
  8. pmc The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study
    Margrit Urbanek
    Division on Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Hum Mol Genet 22:3583-96. 2013
    ..This region has previously been shown to be associated with birth weight in Europeans. The current study suggests that association of this locus with birth weight is secondary to an effect on fat as opposed to lean body mass...
  9. pmc SCAN: SNP and copy number annotation
    Eric R Gamazon
    Department of Medicine, The University of Chicago, Chicago, IL, USA
    Bioinformatics 26:259-62. 2010
    ....
  10. pmc A genome-wide integrative study of microRNAs in human liver
    Eric R Gamazon
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    BMC Genomics 14:395. 2013
    ..The study of microRNAs in human liver tissue promises to clarify the therapeutic and diagnostic value of this important regulatory mechanism of gene expression...
  11. pmc Fine mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers
    Yonglan Zheng
    Department of Medicine, Center for Clinical Cancer Genetics and Global Health, The University of Chicago, Chicago, IL 60637, USA
    Carcinogenesis 34:1520-8. 2013
    ..Future studies and new GWAS in women of African ancestry hold promise to discover additional variants for breast cancer susceptibility with clinical implications throughout the African diaspora. ..
  12. pmc Genetic susceptibility to type 2 diabetes and breast cancer risk in women of European and African ancestry
    Ningqi Hou
    Department of Health Studies, University of Chicago, Chicago, Illinois 60637, USA
    Cancer Epidemiol Biomarkers Prev 21:552-6. 2012
    ..Epidemiologic studies have reported a positive association between type 2 diabetes (T2D) and breast cancer risk, independent of body weight...
  13. pmc Population-specific GSTM1 copy number variation
    R Stephanie Huang
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, 5841 S Maryland Ave, PB Box MC2115, Chicago, IL 60637, USA
    Hum Mol Genet 18:366-72. 2009
    ..In conclusion, HapMap rs366631 is a pseudo-SNP that can be used as a GSTM1 deletion marker. Both the pseudo-SNP allele frequency and GSTM1 upstream region CNV show population-specific patterns between CEU and YRI samples...
  14. pmc Identification of common genetic variants that account for transcript isoform variation between human populations
    Wei Zhang
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, Box MC6091, 5841 S Maryland Ave, Chicago, IL 60637, USA
    Hum Genet 125:81-93. 2009
    ..Our findings provide new insights into the complexity of the human genome as well as the health disparities between the two populations...
  15. pmc Comprehensive survey of SNPs in the Affymetrix exon array using the 1000 Genomes dataset
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 5:e9366. 2010
    ....
  16. ncbi request reprint Relationship of calpain-10 genotype to phenotypic features of polycystic ovary syndrome
    David A Ehrmann
    Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
    J Clin Endocrinol Metab 87:1669-73. 2002
    ..In addition to its association with insulin levels in African-Americans, the 112/121-haplotype combination was associated with an approximate 2-fold increase in risk of PCOS in both African-Americans and whites...
  17. pmc Mixed effects modeling of proliferation rates in cell-based models: consequence for pharmacogenomics and cancer
    Hae Kyung Im
    Department of Health Studies, University of Chicago, Chicago, Illinois, USA
    PLoS Genet 8:e1002525. 2012
    ..This resource should enable researchers to explore the mediating effects of proliferation rate on other phenotypes...
  18. pmc Identification of genetic variants and gene expression relationships associated with pharmacogenes in humans
    Rong Stephanie Huang
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
    Pharmacogenet Genomics 18:545-9. 2008
    ..Our objective was to identify single nucleotide polymorphisms (SNPs) that potentially affected the expression of these genes or potential SNP-gene interactions involved to improve our understanding of genetic effects on drug therapy...
  19. pmc PACdb: a database for cell-based pharmacogenomics
    Eric R Gamazon
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Pharmacogenet Genomics 20:269-73. 2010
    ..PACdb will be regularly updated to include more drugs and new datasets (e.g. baseline microRNA levels). PACdb will be linked into PharmGKB to benefit the next wave of pharmacogenetic and pharmacogenomic discovery...
  20. pmc Genetic architecture of microRNA expression: implications for the transcriptome and complex traits
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, University of Chicago, IL 60637, USA
    Am J Hum Genet 90:1046-63. 2012
    ..This study extends our understanding of the genetic regulation of the transcriptome and suggests that genetic variation might underlie observed relationships between miRNAs and mRNAs more commonly than has previously been appreciated...
  21. pmc Trans-population analysis of genetic mechanisms of ethnic disparities in neuroblastoma survival
    Eric R Gamazon
    Section of Genetic Medicine, University of Chicago, 900 E 57th St, Rm 3220F, Chicago, IL 60637, USA
    J Natl Cancer Inst 105:302-9. 2013
    ..We sought to investigate the relationship between genetic variation and the disparities in survival observed in neuroblastoma...
  22. pmc Evaluation of genetic variation contributing to differences in gene expression between populations
    Wei Zhang
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 82:631-40. 2008
    ..We also provide an evaluation of the contributions of genetic variation and nongenetic factors to the population differences in gene expression...
  23. ncbi request reprint Relationship of insulin receptor substrate-1 and -2 genotypes to phenotypic features of polycystic ovary syndrome
    David A Ehrmann
    Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
    J Clin Endocrinol Metab 87:4297-300. 2002
    ..Thus, individuals with the common IRS-2 Gly/Gly genotype may be at increased risk of developing type 2 diabetes...
  24. pmc Evaluation of 19 susceptibility loci of breast cancer in women of African ancestry
    Dezheng Huo
    Department of Health Studies, University of Chicago, 5841 South Maryland Avenue, MC 2007, Chicago, IL 60637, USA
    Carcinogenesis 33:835-40. 2012
    ..Further fine-mapping studies in women of African ancestry will be needed to reveal additional and causal variants for breast cancer...
  25. ncbi request reprint Identification of type 2 diabetes genes in Mexican Americans through genome-wide association studies
    M Geoffrey Hayes
    Department of Medicine, University of Chicago, 5841 S Maryland Ave, MC6091, Chicago, IL 60637, USA
    Diabetes 56:3033-44. 2007
    ..The objective of this study was to identify DNA polymorphisms associated with type 2 diabetes in a Mexican-American population...
  26. pmc Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci
    Eric R Gamazon
    Sections of Genetic Medicine and Hematology Oncology, Department of Medicine, Pharmacogenomics, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:9287-92. 2010
    ....
  27. pmc Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue
    Federico Innocenti
    Cancer Research Center, Committee on Clinical Pharmacology and Pharmacogenomics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 7:e1002078. 2011
    ..In general, the work presented here will be valuable for future efforts to precisely identify and functionally characterize genetic contributions to a variety of complex traits...
  28. pmc Platinum sensitivity-related germline polymorphism discovered via a cell-based approach and analysis of its association with outcome in ovarian cancer patients
    R Stephanie Huang
    Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
    Clin Cancer Res 17:5490-500. 2011
    ..Cell-based approaches were used to identify genetic markers predictive of patients' risk for poor response prior to chemotherapy...
  29. pmc Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set
    Dan L Nicolae
    Department of Statistics, The University of Chicago, Chicago, Illinois, USA
    PLoS Genet 2:e67. 2006
    ....
  30. pmc Variants affecting exon skipping contribute to complex traits
    Younghee Lee
    Department of Medicine, The University of Chicago, Chicago, IL, USA
    PLoS Genet 8:e1002998. 2012
    ..We find that SNPs we would predict to affect exon skipping are enriched among the set of SNPs reported to be associated with complex human traits...
  31. ncbi request reprint Association testing of the positional and functional candidate gene SLC1A1/EAAC1 in early-onset obsessive-compulsive disorder
    Diane E Dickel
    Department of Human Genetics, University of Chicago, Chicago, IL, USA
    Arch Gen Psychiatry 63:778-85. 2006
    ....
  32. pmc A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity
    R Stephanie Huang
    Section of Hematology Oncology, Biostatistics Consulting Laboratory, Department of Health Studies, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 104:9758-63. 2007
    ..This unbiased method can be used to elucidate genetic variants contributing to a wide range of cellular phenotypes induced by chemotherapeutic agents...
  33. pmc Identification of novel germline polymorphisms governing capecitabine sensitivity
    Peter H O'Donnell
    Section of Hematology Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, USA
    Cancer 118:4063-73. 2012
    ....
  34. pmc Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans
    Heather E Wheeler
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 6:e21920. 2011
    ..Although our results require further study, we have identified variants and genes associated with chemotherapeutic susceptibility in African Americans by using an approach that incorporates local ancestry information...
  35. pmc Germline polymorphisms discovered via a cell-based, genome-wide approach predict platinum response in head and neck cancers
    Dana Ziliak
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Transl Res 157:265-72. 2011
    ....
  36. pmc Quantitative allelic test--a fast test for very large association studies
    Sang Mee Lee
    Department of Health Studies, University of Chicago, Chicago, Illinois, United States of America
    Genet Epidemiol 37:831-9. 2013
    ..We show the asymptotic equivalence of the proposed test to linear regression results. We also reduce a generalized linear regression problem to the comparison of two groups, which can handle nonnormal and survival time phenotypes. ..
  37. pmc Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies
    M Geoffrey Hayes
    Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
    Diabetes 62:3282-91. 2013
    ..These results suggest that the genetic architecture underlying glucose metabolism may differ, in part, in pregnancy. ..
  38. pmc Spoiling the whole bunch: quality control aimed at preserving the integrity of high-throughput genotyping
    Anna Pluzhnikov
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 87:123-8. 2010
    ..We describe how to detect and correct this bias by utilizing additional sources of information, including raw signal-intensity data...
  39. pmc Insulin gene mutations as a cause of permanent neonatal diabetes
    Julie Støy
    Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 104:15040-4. 2007
    ..One of the human mutations we report here is identical to that in the Akita mouse. The identification of insulin mutations as a cause of neonatal diabetes will facilitate the diagnosis and possibly, in time, treatment of this disorder...
  40. pmc Replication analysis for severe diabetic retinopathy
    Michael A Grassi
    Section of Ophthalmology and Visual Science, University of Chicago, Chicago, Illinois 60637, USA
    Invest Ophthalmol Vis Sci 53:2377-81. 2012
    ....
  41. ncbi request reprint Genome-wide scan for type 2 diabetes loci in Hong Kong Chinese and confirmation of a susceptibility locus on chromosome 1q21-q25
    Maggie C Y Ng
    Howard Hughes Medical Institute, University of Chicago, 5841 S Maryland Ave, MC1028, Chicago, IL 60637, USA
    Diabetes 53:1609-13. 2004
    ..9 cM) and suggest the locations of other loci that may contribute to the development of type 2 diabetes in Hong Kong Chinese...
  42. pmc A pharmacogene database enhanced by the 1000 Genomes Project
    Eric R Gamazon
    Department of Medicine, The University of Chicago, Illinois, USA
    Pharmacogenet Genomics 19:829-32. 2009
    ..Our database provides a convenient portal for immediate utilization of the newly released 1000 Genomes Project data in pharmacogenetic studies...
  43. ncbi request reprint Patterns of linkage disequilibrium in the type 2 diabetes gene calpain-10
    M Geoffrey Hayes
    Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 507, Chicago, Illinois 60637, USA
    Diabetes 54:3573-6. 2005
    ..These observations further suggest that there are one or more relatively common alleles increasing risk of type 2 diabetes in this local region...
  44. pmc Obesity-associated variants within FTO form long-range functional connections with IRX3
    Scott Smemo
    1 Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA 2
    Nature 507:371-5. 2014
    ..Our data suggest that IRX3 is a functional long-range target of obesity-associated variants within FTO and represents a novel determinant of body mass and composition. ..
  45. pmc Institutional Profile: University of Chicago Center for Personalized Therapeutics: research, education and implementation science
    M Eileen Dolan
    Committee on Clinical Pharmacology and Pharmacogenomics, 900 E 57th Street, KCBD 7100, University of Chicago, Chicago, IL 60637, USA
    Pharmacogenomics 14:1383-7. 2013
    ..The mission of the Center is to facilitate research, education and implementation of pharmacogenomics to realize the true potential of personalized medicine and improve the lives of patients. ..
  46. pmc SCAN: a systems biology approach to pharmacogenomic discovery
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
    Methods Mol Biol 1015:213-24. 2013
    ..In particular, this public resource implements a systems biology approach to pharmacogenomic discovery. ..
  47. ncbi request reprint Fine mapping and positional candidate studies on chromosome 5p13 identify multiple asthma susceptibility loci
    Thorsten Kurz
    Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
    J Allergy Clin Immunol 118:396-402. 2006
    ..Genome-wide linkage scans to identify asthma susceptibility loci have revealed many linked regions, including a broad region on chromosome 5p...
  48. pmc Comprehensive evaluation of the contribution of X chromosome genes to platinum sensitivity
    Eric R Gamazon
    Section of Genetic Medicine, Department of Medicine, The University of Chicago, 900 E 57 street, KCBD room 7148, Chicago, IL 60637, USA
    Mol Cancer Ther 10:472-80. 2011
    ....
  49. pmc Genome-wide meta-analysis for severe diabetic retinopathy
    Michael A Grassi
    Section of Ophthalmology and Visual Science, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
    Hum Mol Genet 20:2472-81. 2011
    ..5 Mb, a gain/loss site. In summary, this study nominates several novel genetic loci associated with the sight-threatening complications of diabetic retinopathy and anticipates future large-scale consortium-based validation studies...
  50. pmc On sharing quantitative trait GWAS results in an era of multiple-omics data and the limits of genomic privacy
    Hae Kyung Im
    Department of Health Studies, University of Chicago, Chicago, IL, 60637, USA
    Am J Hum Genet 90:591-8. 2012
    ..These findings emphasize the need to devise a mechanism that allows data sharing that will facilitate scientific progress without sacrificing privacy protection...
  51. ncbi request reprint Haplotype structure and phylogenetic shadowing of a hypervariable region in the CAPN10 gene
    Vanessa J Clark
    Department of Human Genetics, University of Chicago, 507F CLSC, 920 E 58th Street, Chicago, IL 60637, USA
    Hum Genet 117:258-66. 2005
    ..These elements are postulated to be the targets of long-standing balancing selection...
  52. pmc Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study
    Minoli A Perera
    Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA
    Lancet 382:790-6. 2013
    ..We aimed to identify additional variants contributing to warfarin dose requirements in African Americans...
  53. pmc Cancer pharmacogenomics: strategies and challenges
    Heather E Wheeler
    Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, 900 East 57th Street, Chicago, Illinois 60637, USA
    Nat Rev Genet 14:23-34. 2013
    ..We discuss the application of germline genetics analysis methods to cancer pharmacogenomics with a focus on the special considerations for study design...
  54. pmc Poly-omic prediction of complex traits: OmicKriging
    Heather E Wheeler
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
    Genet Epidemiol 38:402-15. 2014
    ..Using clinical statin response, we show improved prediction over existing methods. We provide an R package to implement OmicKriging (http://www.scandb.org/newinterface/tools/OmicKriging.html). ..
  55. pmc Lack of association between common single nucleotide polymorphisms in the TERT-CLPTM1L locus and breast cancer in women of African ancestry
    Yonglan Zheng
    Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD Building 8113D, Chicago, IL 60637, USA
    Breast Cancer Res Treat 132:341-5. 2012
    ....
  56. pmc Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of Paclitaxel-induced sensory peripheral neuropathy
    Heather E Wheeler
    Sections of Hematology Oncology and Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Clin Cancer Res 19:491-9. 2013
    ....
  57. pmc Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases
    Younghee Lee
    Center for Biomedical Informatics, The University of Chicago, Chicago, Illinois, USA
    J Am Med Inform Assoc 20:619-29. 2013
    ..Physical protein interactions have been utilized to increase our understanding of human Mendelian disease loci but have yet to be fully exploited for complex traits...
  58. pmc Exprtarget: an integrative approach to predicting human microRNA targets
    Eric R Gamazon
    Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 5:e13534. 2010
    ..We also developed an online database, ExprTargetDB, of human miRNA targets predicted by our approach that integrates gene expression profiling into a broader framework involving important features of miRNA target site predictions...
  59. pmc Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study: common genetic variants in GCK and TCF7L2 are associated with fasting and postchallenge glucose levels in pregnancy and with the new consensus definition of gestational diabetes mellitus from the I
    Rachel M Freathy
    Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
    Diabetes 59:2682-9. 2010
    ..We hypothesized that these variants are associated with quantitative measures of glycemia in pregnancy...
  60. ncbi request reprint Relationship of EGFR mutations, expression, amplification, and polymorphisms to epidermal growth factor receptor inhibitors in the NCI60 cell lines
    Wanqing Liu
    Department of Medicine, The University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
    Clin Cancer Res 13:6788-95. 2007
    ..We aimed to determine if there are interactions between EGFR expression, mutations, polymorphisms, and gene amplification, and whether these factors are associated with variability in response to EGFR inhibitors...
  61. pmc Factors that impact susceptibility to fiber-induced health effects
    Jennifer E Below
    Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, Illinois 60637, USA
    J Toxicol Environ Health B Crit Rev 14:246-66. 2011
    ....
  62. pmc Comprehensive genetic analysis of cytarabine sensitivity in a cell-based model identifies polymorphisms associated with outcome in AML patients
    Eric R Gamazon
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Blood 121:4366-76. 2013
    ..015), likely as a result of greater treatment-related mortality (P = .0037) in patients with acute myeloid leukemia (AML). This multicenter AML02 study trial was registered at www.clinicaltrials.gov as #NCT00136084...
  63. ncbi request reprint A 48-hour exposure of pancreatic islets to calpain inhibitors impairs mitochondrial fuel metabolism and the exocytosis of insulin
    Yun Ping Zhou
    Departments of Medicine, Neurobiology, Pharmacology and Physiology, Biochemistry and Molecular Biology, Human Genetics, and the Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
    Metabolism 52:528-34. 2003
    ....
  64. pmc Rational inferences about departures from Hardy-Weinberg equilibrium
    Jacqueline K Wittke-Thompson
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 76:967-86. 2005
    ..We illustrate how the analytic framework and software can be used to help investigators interpret DHW in the context of association studies of common diseases...
  65. ncbi request reprint Genome-wide linkage analysis of families with obsessive-compulsive disorder ascertained through pediatric probands
    Gregory L Hanna
    Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48109 0390, USA
    Am J Med Genet 114:541-52. 2002
    ..73 on 19q. The maximum multipoint LOD score with a recessive model was 1.40 on 6p. The results provide suggestive evidence for linkage on 9p and identify regions requiring further study with much larger samples...
  66. pmc Genomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the combined sample
    Brian K Suarez
    Department of Psychiatry and Genetics, Washington University, St Louis, MO, USA
    Am J Hum Genet 78:315-33. 2006
    ..3-p15.2, 5p15.2-q13.3, 10p15.3-p14, 10q25.3-q26.3, and 11p13-q23.3. The highest increase in Z(lr) scores was observed for 5p14.1-q12.1, where the maximum Z(lr) increased from 2.77 initially to 3.80 after fine mapping in the EA families...
  67. ncbi request reprint The allelic architecture of human disease genes: common disease-common variant...or not?
    Jonathan K Pritchard
    Department of Human Genetics, University of Chicago, 920 E 58th St CLSC 507, Chicago IL 60637, USA
    Hum Mol Genet 11:2417-23. 2002
    ..We also show that the predicted frequency spectrum of disease variants at a gene depends crucially on the method of ascertainment, for example from prior linkage scans or from surveys of functional candidate loci...
  68. ncbi request reprint Mapping genes influencing type 2 diabetes risk and BMI in Japanese subjects
    Naoko Iwasaki
    Diabetes Center, Tokyo Women s Medical University, Tokyo, Japan
    Diabetes 52:209-13. 2003
    ..Thus, our results may replicate findings in other studies. They may also indicate new regions of the genome that are involved in the regulation of blood glucose levels or body weight...
  69. ncbi request reprint Variants within the calpain-10 gene on chromosome 2q37 (NIDDM1) and relationships to type 2 diabetes, insulin resistance, and impaired acute insulin secretion among Scandinavian Caucasians
    Søren K Rasmussen
    Steno Diabetes Center and Hagedorn Research Institute, Gentofte, Denmark
    Diabetes 51:3561-7. 2002
    ....
  70. ncbi request reprint Genetic variants in the calpain-10 gene and the development of type 2 diabetes in the Japanese population
    Naoko Iwasaki
    Diabetes Center, Tokyo Women s Medical University, 8 1 Kawada cho, Shinjuku ku, Tokyo, 162 8666, Japan
    J Hum Genet 50:92-8. 2005
    ..82 and 0.80, respectively; P=0.04 and 0.02). Thus, variation in the calpain-10 gene may affect risk of type 2 diabetes in Japanese, especially in older individuals...
  71. pmc Fine mapping and positional candidate studies identify HLA-G as an asthma susceptibility gene on chromosome 6p21
    Dan Nicolae
    Department of Statistics, The University of Chicago, Chicago, IL, USA
    Am J Hum Genet 76:349-57. 2005
    ....
  72. ncbi request reprint Genome-wide scan for metabolic syndrome and related quantitative traits in Hong Kong Chinese and confirmation of a susceptibility locus on chromosome 1q21-q25
    Maggie C Y Ng
    Departmetn of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, SAR
    Diabetes 53:2676-83. 2004
    ..Our results confirm the findings of previous studies on diabetes and related phenotypes. We also suggest the locations of other loci that may contribute to the development of MES in Hong Kong Chinese...
  73. ncbi request reprint Calpain 10 and genetics of type 2 diabetes
    Nancy J Cox
    University of Chicago, Department of Human Genetics, 507H CLSC, 920 E 58th Street, Chicago, IL 60637, USA
    Curr Diab Rep 2:186-90. 2002
    ..We review the results of follow-up studies on the CAPN10 finding, and consider the issues inherent in conclusively establishing that particular genetic variation affects a complex phenotype...
  74. ncbi request reprint Linkage of calpain 10 to type 2 diabetes: the biological rationale
    Nancy J Cox
    Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
    Diabetes 53:S19-25. 2004
    ....
  75. ncbi request reprint Association of the calpain-10 gene with type 2 diabetes mellitus in a Mexican population
    Laura Del Bosque-Plata
    Department of Biochemistry, Medicine and Human Genetics, The University of Chicago, 5841 S Maryland Ave, MC1028, Chicago, IL 60637, USA
    Mol Genet Metab 81:122-6. 2004
    ..15, 95% CI=0.57-2.34). The results suggest that variation in CAPN10 affects risk of type 2 diabetes in the mestizo population of central Mexico (Mexico City and Orizaba) and in Mexican Americans (Starr County, Texas)...
  76. ncbi request reprint GEL: a novel genotype calling algorithm using empirical likelihood
    Dan L Nicolae
    Department of Statistics, The University of Chicago
    Bioinformatics 22:1942-7. 2006
    ..Therefore, the factors that need to be evaluated in assessing the performance of an algorithm are the missing data (call) and error rates, but also the heterozygous proportions in missing data and errors...
  77. ncbi request reprint Association of the calpain-10 gene with type 2 diabetes in Europeans: results of pooled and meta-analyses
    Takafumi Tsuchiya
    Departments of Medicine and Human Genetics, The University of Chicago, 5841 S Maryland Ave, MC1027, Chicago, IL 60637, USA
    Mol Genet Metab 89:174-84. 2006
    ..68 (1.33-2.11), P=0.00001). The pooled and meta-analyses as well as the linkage disequilibrium and haplotype diversity studies suggest a role for genetic variation in CAPN10 affecting risk of T2D in Europeans...
  78. ncbi request reprint Association studies of variants in the genes involved in pancreatic beta-cell function in type 2 diabetes in Japanese subjects
    Norihide Yokoi
    Division of Cellular and Molecular Medicine, Kobe University Graduate School of Medicine, Kobe 650 0017, Japan
    Diabetes 55:2379-86. 2006
    ..This is the largest association study so far conducted on these genes in Japanese and provides valuable information for comparison with other ethnic groups...
  79. pmc Transmission disequilibrium testing of the chromosome 15q11-q13 region in autism
    Soo Jeong Kim
    Department of Psychiatry, College of Medicine, University of Florida, Gainesville, Florida, USA
    Am J Med Genet B Neuropsychiatr Genet 147:1116-25. 2008
    ..Further investigation of the 15q11-q13 region with denser genotyping in a larger sample set may be necessary to determine whether this region confers risk to autism, indicated by association, or to specific autism phenotypes...
  80. ncbi request reprint Variation in the calpain-10 gene affects blood glucose levels in the British population
    Stephen Lynn
    School of Clinical Medical Sciences, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, UK
    Diabetes 51:247-50. 2002
    ..002). We conclude that genetic variation in the CAPN10 gene influences blood glucose levels in nondiabetic British subjects and that this is due, at least in part, to the effects of calpain-10 on the early insulin secretory response...
  81. pmc Meta-analysis of 23 type 2 diabetes linkage studies from the International Type 2 Diabetes Linkage Analysis Consortium
    Weihua Guan
    Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109 2029, USA
    Hum Hered 66:35-49. 2008
    ..The International Type 2 Diabetes Linkage Analysis Consortium was formed to localize type 2 diabetes predisposing variants based on 23 autosomal linkage scans...
  82. ncbi request reprint Interpreting P values in pharmacogenetic studies: a call for process and perspective
    Michael L Maitland
    J Clin Oncol 25:4513-5. 2007
  83. ncbi request reprint MERLIN...and the geneticist's stone?
    Dan L Nicolae
    Nat Genet 30:3-4. 2002
  84. ncbi request reprint Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1
    James B Potash
    Department of Psychiatry, Johns Hopkins University, Baltimore, Maryland 21287 7419, USA
    Am J Med Genet B Neuropsychiatr Genet 147:59-67. 2008
    ..Further work is needed to confirm these results and uncover the functional variation underlying the association signal...
  85. pmc A statistical method for identification of polymorphisms that explain a linkage result
    Lei Sun
    Department of Statistics, University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 70:399-411. 2002
    ..We extend our method to larger sibships and apply it to an NIDDM1 data set...
  86. ncbi request reprint Role of calpain-10 gene variants in familial type 2 diabetes in Caucasians
    Steven C Elbein
    Department of Medicine, University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, Arkansas 72205, USA
    J Clin Endocrinol Metab 87:650-4. 2002
    ..However, CAPN10 influences insulin sensitivity and glucose homeostasis in nondiabetic members of kindreds at high risk for T2DM...
  87. ncbi request reprint Insulin resistance is attenuated in women with polycystic ovary syndrome with the Pro(12)Ala polymorphism in the PPARgamma gene
    Manami Hara
    Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
    J Clin Endocrinol Metab 87:772-5. 2002
    ..03) and 2 h (688 +/- 103 vs. 10190 +/- 99 pmol/liter; P = 0.04) time points during the oral glucose tolerance test. We conclude that Pro(12)Ala in PPARG is a modifier of insulin resistance in Caucasian women with PCOS...
  88. pmc Geographic and haplotype structure of candidate type 2 diabetes susceptibility variants at the calpain-10 locus
    Stephanie M Fullerton
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 70:1096-106. 2002
    ..These results suggest a history of positive natural selection at the locus, resulting in significant geographic differences in polymorphism frequencies. The relationship of these differences to disease risk is discussed...
  89. ncbi request reprint Variation within the type 2 diabetes susceptibility gene calpain-10 and polycystic ovary syndrome
    Lema Haddad
    Complex Traits Analysis Group, Department of Medicine, Imperial College Genetics and Genomics Research Institute, Imperial College School of Medicine, London W12 0NN, UK
    J Clin Endocrinol Metab 87:2606-10. 2002
    ..40-1.71). No associations were seen with intermediate traits of relevance to diabetes and PCOS pathogenesis. We have found no evidence from these analyses that CAPN10 gene variation influences susceptibility to PCOS...
  90. pmc Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus
    Martin Mehlmann
    Department of Chemistry and Biochemistry, University of Colorado, UCB215, Boulder, CO 80303, USA
    J Clin Microbiol 44:2857-62. 2006
    ..A detailed experimental evaluation of the selected sequences is described in a companion paper. The software is freely available under the General Public License at http://www.colorado.edu/chemistry/RGHP/software/...
  91. pmc Evaluation of MChip with historic subtype H1N1 influenza A viruses, including the 1918 "Spanish Flu" strain
    Chad L Moore
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, CO 80309, USA
    J Clin Microbiol 45:3807-10. 2007
    ..An artificial neural network trained with temporally related A/H1N1 viruses identified A/Brevig Mission/1/1918 as influenza virus A/H1N1 with 94% probability...
  92. ncbi request reprint Risk of influenza A (H5N1) infection among poultry workers, Hong Kong, 1997-1998
    Carolyn Buxton Bridges
    Influenza Branch, Division of Viral and Rickettsial Diseases, MS A 32, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, Georgia 30333, USA
    J Infect Dis 185:1005-10. 2002
    ..More-intensive poultry exposure, such as butchering and exposure to ill poultry, was associated with having anti-H5 antibody. These findings suggest an increased risk for avian influenza infection from occupational exposure...
  93. ncbi request reprint Evidence for gene-environment interactions in a linkage study of asthma and smoking exposure
    Susan Colilla
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    J Allergy Clin Immunol 111:840-6. 2003
    ..Asthma, a common and chronic disease of the airways, has a multifactorial cause involving both genetic and environmental factors. As a result, mapping genes that influence asthma susceptibility has been challenging...
  94. pmc Lack of evidence for human-to-human transmission of avian influenza A (H9N2) viruses in Hong Kong, China 1999
    Timothy M Uyeki
    Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    Emerg Infect Dis 8:154-9. 2002
    ..No serologic evidence of H9N2 infection was found in family members or health-care workers who had close contact with the H9N2-infected children, suggesting that these H9N2 viruses were not easily transmitted from person to person...
  95. ncbi request reprint Loci on chromosomes 6q and 6p interact to increase susceptibility to bipolar affective disorder in the national institute of mental health genetics initiative pedigrees
    Thomas G Schulze
    Genetic Basis of Mood and Anxiety Disorders, Mood and Anxiety Program, Bethesda, USA
    Biol Psychiatry 56:18-23. 2004
    ....
  96. pmc Concordant gene expression in leukemia cells and normal leukocytes is associated with germline cis-SNPs
    Deborah French
    Department of Pharmaceutical Sciences, St Jude Children s Research Hospital, Memphis, Tennessee, United States of America
    PLoS ONE 3:e2144. 2008
    ....
  97. pmc Evidence for a susceptibility locus on chromosome 10p15 in early-onset obsessive-compulsive disorder
    Gregory L Hanna
    Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48105, USA
    Biol Psychiatry 62:856-62. 2007
    ..The goal of this study was to identify chromosomal regions likely to contain susceptibility loci for obsessive-compulsive disorder (OCD)...
  98. pmc Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance
    Michael B Townsend
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado, Boulder, CO 80309, USA
    J Clin Microbiol 44:2863-71. 2006
    ..In the overwhelming majority of cases in which incomplete subtyping was observed, the failure was due to the nucleic acid amplification step rather than limitations in the microarray...
  99. ncbi request reprint Polygenic virulence factors involved in pathogenesis of 1997 Hong Kong H5N1 influenza viruses in mice
    Hualan Chen
    Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road, N E, MS G16, Atlanta, GA 30333, USA
    Virus Res 128:159-63. 2007
    ..Multiple genes are involved in virulence of Hong Kong H5N1 influenza A viruses for mice with the presence of lysine at aa627 in the PB2 gene exhibiting a significantly larger effect than the HA and NA genes...
  100. pmc Gender-specific differences in expression in human lymphoblastoid cell lines
    Wei Zhang
    Department of Medicine, University of Chicago, Chicago, Ilinois 60637, USA
    Pharmacogenet Genomics 17:447-50. 2007
    ..A Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that two known pathways are over-represented: adherens junction and cytokine-cytokine receptor interaction...
  101. pmc Diagnostic microarray for influenza B viruses
    Daniela M Dankbar
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, Colorado 80309, USA
    Anal Chem 79:2084-90. 2007
    ..Furthermore, application of a trained artificial neural network to the pattern of relative fluorescence signals resulted in correct lineage assignment for 94% of 50 applicable influenza B viruses, with no false assignments...