R Stephanie Huang

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. pmc The regulatory effect of miRNAs is a heritable genetic trait in humans
    Paul Geeleher
    Department of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    BMC Genomics 13:383. 2012
  2. pmc Genetic variation that predicts platinum sensitivity reveals the role of miR-193b* in chemotherapeutic susceptibility
    Dana Ziliak
    Section of Hematology Oncology, The University of Chicago, Chicago, Illinois 60637, USA
    Mol Cancer Ther 11:2054-61. 2012
  3. pmc Population differences in microRNA expression and biological implications
    R Stephanie Huang
    Section of Hematology Oncology, University of Illinois at Chicago, Chicago, IL, USA
    RNA Biol 8:692-701. 2011
  4. 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
  5. pmc Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity
    Christine M Hartford
    Department of Pediatrics, University of Chicago, IL 60637, USA
    Blood 113:2145-53. 2009
  6. 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
  7. 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
  8. pmc Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach
    R Stephanie Huang
    Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 81:427-37. 2007
  9. 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
  10. 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

Collaborators

Detail Information

Publications34

  1. pmc The regulatory effect of miRNAs is a heritable genetic trait in humans
    Paul Geeleher
    Department of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    BMC Genomics 13:383. 2012
    ..Given a gene expression dataset, Cheng et al. defined the regulatory effect score (RE-score) of a miRNA as the difference in the gene expression rank of targets of the miRNA compared to non-targeted genes...
  2. pmc Genetic variation that predicts platinum sensitivity reveals the role of miR-193b* in chemotherapeutic susceptibility
    Dana Ziliak
    Section of Hematology Oncology, The University of Chicago, Chicago, Illinois 60637, USA
    Mol Cancer Ther 11:2054-61. 2012
    ..Our findings highlight a potential mechanism of action for a previously observed genotype-survival outcome association. Further examination of miR-193b* in platinum sensitivity in ovarian cancer is warranted...
  3. pmc Population differences in microRNA expression and biological implications
    R Stephanie Huang
    Section of Hematology Oncology, University of Illinois at Chicago, Chicago, IL, USA
    RNA Biol 8:692-701. 2011
    ....
  4. 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...
  5. pmc Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity
    Christine M Hartford
    Department of Pediatrics, University of Chicago, IL 60637, USA
    Blood 113:2145-53. 2009
    ..These unique genetic signatures comprise novel genes that can now be studied further in functional studies...
  6. 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...
  7. 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...
  8. pmc Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach
    R Stephanie Huang
    Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 81:427-37. 2007
    ..Our whole-genome approach can be used to elucidate the expression of quantitative trait loci contributing to a wide range of cellular phenotypes...
  9. 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
    ....
  10. 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...
  11. 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...
  12. 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...
  13. pmc Expression and alternative splicing of folate pathway genes in HapMap lymphoblastoid cell lines
    Shiwei Duan
    The University of Chicago, Chicago, IL 60637, USA
    Pharmacogenomics 10:549-63. 2009
    ..In this study, we evaluate the genetic regulation for expression and alternative splicing of folate related genes in HapMap lymphoblastoid cell lines (LCLs) of individuals of European and African descent...
  14. 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...
  15. 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...
  16. pmc Identification of genomic regions contributing to etoposide-induced cytotoxicity
    Wasim K Bleibel
    Department of Medicine, University of Chicago, 5841 S Maryland Ave, Box MC2115, Chicago, IL 60637, USA
    Hum Genet 125:173-80. 2009
    ..Our findings suggest that susceptibility to etoposide-induced cytotoxicity is heritable and using an integrated genomics approach we identified both genomic regions and SNPs associated with the cytotoxic phenotypes...
  17. pmc Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans
    R Stephanie Huang
    Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Box MC2115, Chicago, IL 60637, USA
    Mol Cancer Ther 7:3038-46. 2008
    ..The identification of concentration specific genetic signatures allows for potential integration of pharmacokinetics, pharmacodynamics, and pharmacogenetics in tailoring chemotherapy...
  18. 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
    ....
  19. pmc Approaches to the discovery of pharmacogenomic markers in oncology: 2000-2010-2020
    R Stephanie Huang
    Department of Medicine, University of Chicago, IL 60637, USA
    Pharmacogenomics 11:471-4. 2010
    ....
  20. pmc Genetic variants contributing to daunorubicin-induced cytotoxicity
    R Stephanie Huang
    Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
    Cancer Res 68:3161-8. 2008
    ..005 and P = 0.0008, respectively), and rs1551315 trends toward significance (P = 0.089). This unbiased method can be used to elucidate genetic variants contributing to a wide range of cellular phenotypes...
  21. pmc Pharmacogenetics and pharmacogenomics: a bridge to individualized cancer therapy
    Liming Weng
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Pharmacogenomics 14:315-24. 2013
    ..Furthermore, examples are also provided for the role of PGx in new anticancer drug development by revealing novel druggable targets...
  22. 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...
  23. pmc Population differences in the rate of proliferation of international HapMap cell lines
    Amy L Stark
    Department of Human Genetics, University of Chicago, IL 60637, USA
    Am J Hum Genet 87:829-33. 2010
    ..0001). Therefore, studies that separate HapMap panels into discovery and replication sets must take this into consideration...
  24. pmc Gene set enrichment analyses revealed differences in gene expression patterns between males and females
    Wei Zhang
    Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    In Silico Biol 9:55-63. 2009
    ..Gender-specific patterns of gene expression also appeared to be different between these two populations...
  25. pmc Pharmacogenetics and pharmacogenomics of anticancer agents
    R Stephanie Huang
    Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    CA Cancer J Clin 59:42-55. 2009
    ....
  26. 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...
  27. pmc Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data
    Eric R Gamazon
    Department of Medicine, University of Chicago Chicago, IL, USA
    Front Genet 3:202. 2012
    ..Finally, we provide an R code to compute the empirical false discovery rate when p-values for the observed and simulated phenotypes are available...
  28. 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...
  29. 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
    ....
  30. pmc Pharmacogenomic discovery using cell-based models
    Marleen Welsh
    Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
    Pharmacol Rev 61:413-29. 2009
    ..The primary focus is recent progress in the pharmacogenomic discovery area through ex vivo models...
  31. doi request reprint 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. ..
  32. doi request reprint An integrated genomic approach to the assessment and treatment of acute myeloid leukemia
    Lucy A Godley
    Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    Semin Oncol 38:215-24. 2011
    ..With these expectations comes the hope that such an approach will lead to decreased toxicities and prolonged survival for patients...
  33. pmc Pharmacogenomics discovery and implementation in genome-wide association studies era
    Xiuqin Ni
    Department of Anatomy, Harbin Medical University Daqing, Daqing, Heilongjiang Province, China
    Wiley Interdiscip Rev Syst Biol Med 5:1-9. 2013
    ..Furthermore, investigation of the complex interactions among genetic and epigenetic factors on the whole-genome scale will become the post-GWAS research focus for pharmacologic complex traits...
  34. pmc Variants at 6q21 implicate PRDM1 in the etiology of therapy-induced second malignancies after Hodgkin's lymphoma
    Timothy Best
    Committee on Cancer Biology, University of Chicago, Chicago, Illinois, USA
    Nat Med 17:941-3. 2011
    ..These data suggest a new gene-exposure interaction that may implicate PRDM1 in the etiology of radiation therapy-induced SMNs...