Mixed effects modeling of proliferation rates in cell-based models: Consequence for pharmacogenomics and Cancer

PLoS Genetics

Volumn 8, Issue 2, 2012, Pages

  Im, Hae Kyung ^a   Gamazon, Eric R ^a   Stark, Amy L ^a   Huang, R Stephanie ^a   Cox, Nancy J ^a   Dolan, M Eileen ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CELL GROWTH; CELL LINE; CELL PROLIFERATION; DATA BASE; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC VARIABILITY; GROWTH RATE; HAPLOTYPE MAP; HUMAN; MIXED EFFECTS MODEL AVERAGING; NEOPLASM; PHARMACOGENOMICS; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; LYMPHOCYTE ACTIVATION; METABOLISM; PHARMACOGENETICS; TUMOR CELL LINE;

CELL LINE, TUMOR; CELL PROLIFERATION; DATABASES, GENETIC; GENE EXPRESSION; GENE EXPRESSION PROFILING; HAPMAP PROJECT; HUMANS; LYMPHOCYTE ACTIVATION; NEOPLASMS; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84859185340     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002525     Document Type: Article

References (51)

1. International HapMap Consortium (2003) The international hapmap project. Nature 426: 789-96.
2. International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million snps. Nature 449: 851-61.
3. Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-73.
4. Welsh M, Mangravite L, Medina M, Tantisira K, Zhang W, et al. (2009) Pharmacogenomic discovery using cell-based models. PHARMACOLOGICAL REVIEWS 61: 413.
5. Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, et al. (2010) Scan: Snp and copy number annotation. Bioinformatics 26: 259-262.
6. Gamazon ER, Duan S, Zhang W, Huang RS, Kistner EO, et al. (2010) Pacdb: a database for cell-based pharmacogenomics. Pharmacogenet Genomics 20: 269-273.
7. Thorn CF, Klein TE, Altman RB, (2005) Pharmgkb: the pharmacogenetics and pharma-cogenomics knowledge base. Methods Mol Biol 311: 179-91.
8. Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, et al. (2001) Integrating genotype and phenotype information: an overview of the pharmgkb project. pharmacogenetics research network and knowledge base. The Pharmacogenomics Journal 1: 167-70.
9. Wheeler HE, Gamazon ER, Stark AL, ODonnell PH, Gorsic LK, et al. (2011) Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. The Pharmacogenomics Journal.
10. Wen Y, Gorsic LK, Wheeler HE, Ziliak DM, Huang RS, et al. (2011) Chemotherapeutic- induced apoptosis: a phenotype for pharmacogenomics studies. Pharmacogenet Genomics 21.
11. Smirnov DA, Morley M, Shin E, Spielman RS, Cheung VG, (2009) Genetic analysis of radiation-induced changes in human gene expression. Nature 459: 587-591.
12. Stark AL, Zhang W, Mi S, Duan S, O'Donnell PH, et al. (2010) Heritable and non-genetic factors as variables of pharmacologic phenotypes in lymphoblastoid cell lines. The Pharmacogenomics Journal 10: 505.
13. Stark A, Zhang W, Zhou T, O'Donnell P, Beiswanger C, et al. (2010) Population differences in the rate of proliferation of international hapmap cell lines. The American Journal of Human Genetics.
14. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, et al. (2008) Genetic analysis of human traits in vitro: Drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 4: e1000287 doi:10.1371/journal.pgen.1000287.
15. Brauer M, Huttenhower C, Airoldi E, Rosenstein R, Matese J, et al. (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Molecular Biology of the Cell 19: 352.
16. Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T, (2010) Interdependence of cell growth and gene expression: origins and consequences. Science 330: 1099-102.
17. Klumpp S, Zhang Z, Hwa T, (2009) Growth rate-dependent global effects on gene expression in bacteria. Cell 139: 1366-1375.
18. Whitfield M, George L, Grant G, Perou C, (2006) Common markers of proliferation. Nat Rev Cancer 6: 99-106.
19. Ross D, Scherf U, Eisen M, Perou C, Rees C, et al. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nature genetics 24: 227-235.
20. Rhodes D, Yu J, Shanker K, Deshpande N, Varambally R, et al. (2004) Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA 101: 9309.
21. Starmans MHW, Krishnapuram B, Steck H, Horlings H, Nuyten DSA, et al. (2008) Ro- bust prognostic value of a knowledge-based proliferation signature across large patient microarray studies spanning different cancer types. Br J Cancer 99: 1884.
22. Damasco C, Lembo A, Somma MP, Gatti M, Cunto FD, et al. (2011) A signature inferred from drosophila mitotic genes predicts survival of breast cancer patients. PLoS ONE 6: e14737 doi:10.1371/journal.pone.0014737.
23. Dai H, (2005) A cell proliferation signature is a marker of extremely poor outcome in a subpopulation of breast cancer patients. Cancer Res 65: 4059-4066.
24. Rosenwald A, Wright G, Wiestner A, Chan WC, Connors JM, et al. (2003) The pro-liferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma. Cancer Cell 3: 185-197.
25. Huang RS, Duan S, Bleibel W, Kistner E, Zhang W, et al. (2007) A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proceedings of the National Academy of Sciences 104: 9758.
26. Huang RS, Duan S, Shukla SJ, Kistner EO, Clark TA, et al. (2007) Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach. The American Journal of Human Genetics 81: 427-437.
27. Zhang W, Duan S, Kistner E, Bleibel W, Huang RS, et al. (2008) Evaluation of genetic variation contributing to differences in gene expression between populations. The American Journal of Human Genetics 82: 631-640.
28. Leek J, Storey J, (2008) A general framework for multiple testing dependence. Proceedings of the National Academy of Sciences 105: 18718.
29. Huang DW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using david bioinformatics resources. Nat Protoc 4: 44-57.
30. Huang DW, Sherman BT, Lempicki RA, (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
31. Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, et al. (2008) Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res 10: R65.
32. Whitfield M, Sherlock G, Saldanha A, Murray J, Ball C, et al. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Molecular Biology of the Cell 13: 1977.
33. Chang H, Sneddon J, Alizadeh A, Sood R, West R, et al. (2004) Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol 2: e7 doi:10.1371/journal.pbio.0020007.
34. Nicolae D, Gamazon E, Zhang W, Duan S, Dolan M, et al. (2010) Trait-associated snps are more likely to be eqtls: Annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888 doi:10.1371/journal.pgen.1000888.
35. Gamazon ER, Huang RS, Cox NJ, Dolan ME, (2010) Chemotherapeutic drug susceptibility associated snps are enriched in expression quantitative trait loci. Proc Natl Acad Sci USA 107: 9287-9292.
36. Nica AC, Montgomery SB, Dimas AS, Stranger BE, ClaudeBeazley, et al. (2010) Candidate causal regulatory effects by integration of expression qtls with complex trait genetic associations. PLoS Genet 6: e1000895 doi:10.1371/journal.pgen.1000895.
37. Fehrmann R, Jansen RC, Veldink JH, Westra HJ, Arends D, et al. (2011) Trans-eqtls reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the hla. PLoS Genet pp. e1002197 doi:10.1371/journal.pgen.1002197.
38. Jaeger E, Webb E, Howarth K, Carvajal-Carmona L, Rowan A, et al. (2007) Common genetic variants at the crac1 (hmps) locus on chromosome 15q13. 3 inuence colorectal cancer risk. Nat Genet 40: 26-28.
39. Ho J, Choi S, f Lee Y, Hui T, Cherny S, et al. (2011) Replication study of snp associations for colorectal cancer in hong kong chinese. Br J Cancer 104: 369-375.
40. Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, et al. (2008) Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet 40: 631-637.
41. Uemura T, Shiozaki K, Yamaguchi K, Miyazaki S, Satomi S, et al. (2009) Contribution of sialidase neu1 to suppression of metastasis of human colon cancer cells through desia-lylation of integrin 4. Oncogene.
42. Knuesel MT, Meyer KD, Bernecky C, Taatjes DJ, (2009) The human cdk8 subcomplex is a molecular switch that controls mediator coactivator function. Genes & Development 23: 439-451.
43. Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, et al. (2008) Cdk8 is a colorectal cancer oncogene that regulates-catenin activity. Nature 455: 547-551.
44. Çalşkan M, Cusanovich DA, Ober C, Gilad Y, (2011) The effects of ebv transformation on gene expression levels and methylation profiles. Human molecular genetics 20: 1643-52.
45. Bates D, Maechler M, Bolker B, (2011) lme4: Linear mixed-effects models using S4 classes. URL http://CRAN.R-project.org/package=lme4. R package version 0.999375-38.
46. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/. ISBN 3-900051-07-0.
47. Leek JT, sva: Surrogate Variable Analysis. Key: sva.package Annotation: R package version 1.1.0.
48. Dabney A, Storey JD, with assistance from Gregory R Warnes (2010) qvalue: Q-value estimation for false discovery rate control. URL http://CRAN.R-project.org/package=qvalue. R package version 1.24.0.
49. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-5.
50. Wickham H, (2009) ggplot2: elegant graphics for data analysis. Springer New York. URLhttp://had.co.nz/ggplot2/book.
51. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) Plink: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81: 559-575.