'Particle genetics': Treating every cell as unique

Trends in Genetics

Volumn 30, Issue 2, 2014, Pages 49-56

  Yvert, Gaël ^a  

^a UNIVERSITÉ DE LYON   (France)

Author keywords

Complex traits; GWAS; Probabilistic trait locus (PTL); QTL; Single cell; Stochasticity

Indexed keywords

DEVELOPMENTAL GENETICS; DNA POLYMORPHISM; FLUCTUATING ASYMMETRY; GENE LOCUS; GENETIC ASSOCIATION; GENOTYPE PHENOTYPE CORRELATION; HAPLOINSUFFICIENCY; HUMAN; LOSS OF FUNCTION MUTATION; MUTATIONAL ANALYSIS; NONHUMAN; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROBABILISTIC TRAIT LOCUS; PROBABILITY; PROMOTER REGION; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; REVIEW; SOMATIC MUTATION;

COMPLEX TRAITS; GWAS; PROBABILISTIC TRAIT LOCUS (PTL); QTL; SINGLE CELL; STOCHASTICITY;

ANIMALS; GENETIC ASSOCIATION STUDIES; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; SINGLE-CELL ANALYSIS;

EID: 84892968392     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2013.11.002     Document Type: Review

References (50)

1. Bloom J.S., et al. Finding the sources of missing heritability in a yeast cross. Nature 2013, 494:234-237.
2. Eichler E.E., et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet. 2010, 11:446-450.
3. Rockman M.V. The QTN program and the alleles that matter for evolution: all that's gold does not glitter. Evolution 2012, 66:1-17.
4. Giudicessi J.R., Ackerman M.J. Determinants of incomplete penetrance and variable expressivity in heritable cardiac arrhythmia syndromes. Transl. Res. 2013, 161:1-14.
5. Furniss D., et al. A variant in the sonic hedgehog regulatory sequence (ZRS) is associated with triphalangeal thumb and deregulates expression in the developing limb. Hum. Mol. Genet. 2008, 17:2417-2423.
6. Garber J.E., Offit K. Hereditary cancer predisposition syndromes. J. Clin. Oncol. 2005, 23:276-292.
7. + T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat. Med. 1999, 5:512-517.
8. Weinberger L.S., et al. Transient-mediated fate determination in a transcriptional circuit of HIV. Nat. Genet. 2008, 40:466-470.
9. Balaban N.Q., et al. Bacterial persistence as a phenotypic switch. Science 2004, 305:1622-1625.
10. McAdams H.H., Arkin A. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:814-819.
11. Hornung G., et al. Noise-mean relationship in mutated promoters. Genome Res. 2012, 22:2409-2417.
12. Lu H.P., et al. Single-molecule enzymatic dynamics. Science 1998, 282:1877-1882.
13. Spencer S.L., et al. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature 2009, 459:428-432.
14. Tay S., et al. Single-cell NF-κB dynamics reveal digital activation and analogue information processing. Nature 2010, 466:267-271.
15. Albeck J.G., et al. Frequency-modulated pulses of ERK Activity transmit quantitative proliferation signals. Mol. Cell 2013, 49:249-261.
16. Snijder B., et al. Population context determines cell-to-cell variability in endocytosis and virus infection. Nature 2009, 461:520-523.
17. Werfel J., et al. How changes in extracellular matrix mechanics and gene expression variability might combine to drive cancer progression. PLoS ONE 2013, 8:e76122.
18. Baserga R. The Biology of Cell Reproduction 1985, Harvard University Press.
19. Alberts B., et al. Molecular Biology of the Cell 2007, Garland Publishing. 5th revised edn.
20. Berg R.D. The indigenous gastrointestinal microflora. Trends Microbiol. 1996, 4:430-435.
21. Shalek A.K., et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 2013, 498:236-240.
22. Araten D.J., et al. A quantitative measurement of the human somatic mutation rate. Cancer Res. 2005, 65:8111-8117.
23. Clamp M., et al. Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:19428-19433.
24. Perrat P.N., et al. Transposition-driven genomic heterogeneity in the Drosophila brain. Science 2013, 340:91-95.
25. Drummond D.A., Wilke C.O. The evolutionary consequences of erroneous protein synthesis. Nat. Rev. Genet. 2009, 10:715-724.
26. Pelechano V., et al. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 2013, 497:127-131.
27. Ferrell J.E., Machleder E.M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 1998, 280:895-898.
28. Suel G.M., et al. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 2006, 440:545-550.
29. Raj A., et al. Variability in gene expression underlies incomplete penetrance. Nature 2010, 463:913-918.
30. Barkoulas M., et al. Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation. Dev. Cell 2013, 24:64-75.
31. Blair D.R., et al. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell 2013, 155:70-80.
32. Carter A.J., Houle D. Artificial selection reveals heritable variation for developmental instability. Evolution 2011, 65:3558-3564.
33. Yvert G., et al. Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast. BMC Syst. Biol. 2013, 7:54.
34. Ziv N., et al. Genetic and nongenetic determinants of cell growth variation assessed by high-throughput microscopy. Mol. Biol. Evol. 2013, 10.1093/molbev/mst138.
35. Beaumont H.J., et al. Experimental evolution of bet hedging. Nature 2009, 462:90-93.
36. Ansel J., et al. Cell-to-cell stochastic variation in gene expression is a complex genetic trait. PLoS Genet. 2008, 4:e1000049.
37. Fehrmann S., et al. Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability. Mol. Syst. Biol. 2013, 9:695.
38. Jimenez-Gomez J.M., et al. Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genet. 2011, 7:e1002295.
39. Yang J., et al. FTO genotype is associated with phenotypic variability of body mass index. Nature 2012, 490:267-272.
40. Fraser H.B., Schadt E.E. The quantitative genetics of phenotypic robustness. PLoS ONE 2010, 5:e8635.
41. Visscher P.M., Posthuma D. Statistical power to detect genetic loci affecting environmental sensitivity. Behav. Genet. 2010, 40:728-733.
42. Brouzes E., et al. Droplet microfluidic technology for single-cell high-throughput screening. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:14195-14200.
43. Leung C.T., Brugge J.S. Outgrowth of single oncogene-expressing cells from suppressive epithelial environments. Nature 2012, 482:410-413.
44. Lynch M., Walsch B. Genetics and Analysis of Quantitative Traits 1998, Sinauer.
45. Geldermann H. Investigations on inheritance of quantitative characters in animals by gene markers I. Methods. Theor. Appl. Genet. 1975, 46:319-330.
46. Brems H., et al. Mechanisms in the pathogenesis of malignant tumours in neurofibromatosis type 1. Lancet Oncol. 2009, 10:508-515.
47. Veitia R.A. Stochasticity or the fatal 'imperfection' of cloning. J. Biosci. 2005, 30:21-30.
48. Cook D.L., et al. Modeling stochastic gene expression: implications for haploinsufficiency. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:15641-15646.
49. Bosl W.J., Li R. The role of noise and positive feedback in the onset of autosomal dominant diseases. BMC Syst. Biol. 2010, 4:93.
50. Kemkemer R., et al. Increased noise as an effect of haploinsufficiency of the tumor-suppressor gene neurofibromatosis type 1 in vitro. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:13783-13788.