The genome revolution and its role in understanding complex diseases

Biochimica et Biophysica Acta - Molecular Basis of Disease

Volumn 1842, Issue 10, 2014, Pages 1889-1895

  Hofker, Marten H ^a   Fu, Jingyuan ^a   Wijmenga, Cisca ^a  

^a UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

Complex disease; Disease etiology; Functional analysis; Genetic variation; Genome

Indexed keywords

ACYL COENZYME A DESATURASE 1; DNA FRAGMENT; TRANSCRIPTION FACTOR 7 LIKE 2;

ACYL COENZYME A DESATURASE 1 GENE; ALGORITHM; ALZHEIMER DISEASE; CAENORHABDITIS ELEGANS; CELIAC DISEASE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPLEX DISEASE; CRISPR CAS SYSTEM; CYSTIC FIBROSIS; DNA MICROARRAY; DNA REPLICATION; DNA SEQUENCE; DROSOPHILA; DUCHENNE MUSCULAR DYSTROPHY; DYSLIPIDEMIA; GENE; GENE EXPRESSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC COUNSELING; GENETIC DISORDER; GENETIC DRIFT; GENETIC LINKAGE; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HAPLOTYPE MAP; HERITABILITY; HUMAN; HUMAN GENOME; HUNTINGTON CHOREA; IRX3 GENE; LINKAGE ANALYSIS; MATHEMATICAL MODEL; NATURAL SELECTION; NEXT GENERATION SEQUENCING; NON INSULIN DEPENDENT DIABETES MELLITUS; NONHUMAN; PERSONALIZED MEDICINE; PHENOTYPE; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; PYROSEQUENCING; REVIEW; SANGER SEQUENCING; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION FACTOR 7 LIKE 2 GENE;

EID: 84908501679     PISSN: 09254439     EISSN: 1879260X     Source Type: Journal    
DOI: 10.1016/j.bbadis.2014.05.002     Document Type: Review

References (83)

1. Libby P., Ridker P.M., Hansson G.K. Progress and challenges in translating the biology of atherosclerosis. Nature 2011, 473:317-325.
2. Hood L. A personal journey of discovery: developing technology and changing biology. Annu. Rev. Anal. Chem. 2008, 1:1-43.
3. Altmüller J., Palmer L.J., Fischer G., Scherb H., Wjst M. Genomewide scans of complex human diseases: true linkage is hard to find. Am. J. Hum. Genet. 2001, 69:936-950.
4. Jeffreys A.J. DNA sequence variants in the G gamma-, A gamma-, delta- and beta-globin genes of man. Cell 1979, 18:1-10.
5. Botstein D., White R.L., Skolnick M., Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 1980, 32:314-331.
6. Rich S.S., Norris J.M., Rotter J.I. Genes associated with risk of type 2 diabetes identified by a candidate-wide association scan: as a trickle becomes a flood. Diabetes 2008, 57:2915-2917.
7. de Knijff P., Havekes L.M. Apolipoprotein E as a risk factor for coronary heart disease: a genetic and molecular biology approach. Curr. Opin. Lipidol. 1996, 7:59-63.
8. Corder E.H., Saunders A.M., Strittmatter W.J., Schmechel D.E., Gaskell P.C., Small G.W., et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. Science 1993, 261:921-923.
9. Altshuler D.M., Gibbs R.A., Peltonen L., Dermitzakis E., Schaffner S.F., Yu F., et al. Integrating common and rare genetic variation in diverse human populations. Nature 2010, 467:52-58.
10. Donis-Keller H., Green P., Helms C., Cartinhour S., Weiffenbach B., Stephens K., et al. A genetic linkage map of the human genome. Cell 1987, 51:319-337.
11. Osoegawa K., Mammoser A.G., Wu C., Frengen E., Zeng C., Catanese J.J., et al. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 2001, 11:483-496.
12. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
13. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., et al. The sequence of the human genome. Science 2001, 291:1304-1351.
14. Schuster S. Next-generation sequencing transforms today's biology. Nature 2007, 5:16-18.
15. Buermans H.P.J., den Dunnen J.T. Next generation sequencing technology: Advances and applications. Biochim. Biophys. Acta 2014, 1932-1941. (in this issue).
16. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.a, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
17. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.
18. Nachman M.W., Crowell S.L. Estimate of the mutation rate per nucleotide in humans. Genetics 2000, 156:297-304.
19. Roach J.C., Glusman G., Smit A.F.A., Huff C.D., Hubley R., Shannon P.T., et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 2010, 328:636-639.
20. Conrad D.F., Keebler J.E.M., DePristo M.A., Lindsay S.J., Zhang Y., Casals F., et al. Variation in genome-wide mutation rates within and between human families. Nat. Genet. 2011, 43:712-714.
21. Gibbs R.A., Belmont J.W., Hardenbol P., Willis T.D., Yu F., Yang H., et al. The International HapMap Project. Nature 2003, 426:789-796.
22. Abecasis G.R., Auton A., Brooks L.D., DePristo M.A., Durbin R.M., Handsaker R.E., et al. An integrated map of genetic variation from 1092 human genomes. Nature 2012, 491:56-65.
23. Boomsma D.I.D.I., Wijmenga C., Slagboom E.P., Swertz M.A., Karssen L.C., Abdellaoui A., et al. The Genome of the Netherlands: design, and project goals. Eur. J. Hum. Genet. 2014, 22:221-227.
24. Hinds D.A., Stuve L.L., Nilsen G.B., Halperin E., Eskin E., Ballinger D.G., et al. Whole-genome patterns of common DNA variation in three human populations. Science 2005, 307:1072-1079.
25. Pritchard J.K., Cox N.J. The allelic architecture of human disease genes: common disease-common variant. . .or not?. Hum. Mol. Genet. 2002, 11:2417-2423.
26. Gibson G. Rare and common variants: twenty arguments. Nat. Rev. Genet. 2011, 13:135-145.
27. Wellcome T., Case T., Consortium C. Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature 2007, 447:661-678.
28. Herbert A., Gerry N.P., McQueen M.B., Heid I.M., Pfeufer A., Illig T., et al. A common genetic variant is associated with adult and childhood obesity. Science 2006, 312:279-283.
29. Loos R.J.F., Barroso I., O'rahilly S., Wareham N.J. Comment on "A common genetic variant is associated with adult and childhood obesity". Science 2007, 315:187.
30. Trynka G., Hunt K.A., Bockett N.A., Romanos J., Mistry V., Szperl A., et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat. Genet. 2011, 43:1193-1201.
31. Zhernakova A., van Diemen C.C., Wijmenga C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat. Rev. Genet. 2009, 10:43-55.
32. Parkes M., Cortes A., van Heel D.A., Brown M.A. Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat. Rev. Genet. 2013, 14:661-673.
33. Eichler E.E., Flint J., Gibson G., Kong A., Leal S.M., Moore J.H., et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet. 2010, 11:446-450.
34. Hunt K.A., Mistry V., Bockett N.A., Ahmad T., Ban M., Barker J.N., et al. Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 2013, 498:232-235.
35. Westra H.-J., Franke L. From genome to function by studying eQTLs. Biochim. Biophys. Acta 2014, 1896-1902. (in this issue).
36. Westra H.J., Peters M.J., Esko T., Yaghootkar H., Schurmann C., Kettunen J., et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 2013, 45:1238-1243.
37. Kumar V., Westra H.J., Karjalainen J., Zhernakova D.V., Esko T., Hrdlickova B., et al. Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet. 2013, 9:e1003201.
38. Hrdlickova B., de Almeida R.C., Borek Z., Withoff S. Genetic variation in the non-coding genome: Involvement ofmicro-RNAs and long non-coding RNAs in disease. Biochim. Biophys. Acta 2014, 1910-1922. (in this issue).
39. Nicolae D.L., Gamazon E., Zhang W., Duan S., Dolan M.E., Cox N.J. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 2010, 6:e1000888.
40. Zhong H., Beaulaurier J., Lum P.Y., Molony C., Yang X., Macneil D.J., et al. Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet. 2010, 6:e1000932.
41. Fehrmann R.S.N., Jansen R.C., Veldink J.H., Westra H.J., Arends D., Bonder M.J., et al. 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. 2011, 7:e1002197.
42. Cookson W., Liang L., Abecasis G., Moffatt M., Lathrop M. Mapping complex disease traits with global gene expression. Nat. Rev. Genet. 2009, 10:184-194.
43. Fu J., Wolfs M.G.M., Deelen P., Westra H.J., Fehrmann R.S.N., Te Meerman G.J., et al. Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet. 2012, 8:e1002431.
44. Grundberg E., Small K.S., Hedman Å.K., Nica A.C., Buil A., Keildson S., et al. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat. Genet. 2012, 44:1084-1089.
45. Gregersen P.K. Cell type-specific eQTLs in the human immune system. Nat. Genet. 2012, 44:478-480.
46. Musunuru K., Strong A., Frank-Kamenetsky M., Lee N.E., Ahfeldt T., Sachs K.V., et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 2010, 466:714-719.
47. Smemo S., Tena J.J., Kim K.H., Gamazon E.R., Sakabe N.J., Gómez-Marín C., et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 2014, 507:371-375.
48. Dina C., Meyre D., Gallina S., Durand E., Körner A., Jacobson P., et al. Variation in FTO contributes to childhood obesity and severe adult obesity. Nat. Genet. 2007, 39:724-726.
49. Hess M.E., Brüning J.C. The fat mass and obesity-associated (FTO) gene: obesity and beyond?. Biochim. Biophys. Acta 2014, 2039-2047. (in this issue).
50. Aitman T.J., Boone C., Churchill G.A., Hengartner M.O., Mackay T.F.C., Stemple D.L. The future of model organisms in human disease research. Nat. Rev. Genet. 2011, 12:575-582.
51. Sin O., Michels H., Nollen E.A.A. Genetic screens in Caenorhabditis elegans models for neurodegenerative diseases. Biochim. Biophys. Acta 2014, 1951-1959. (in this issue).
52. Smeets C.J.L.M., Verbeek D.S. Cerebellar ataxia and functional genomics: Identifying the routes to cerebellar neurodegeneration. Biochim. Biophys. Acta 2014, 2030-2038. (in this issue).
53. Bakkers J. Zebrafish as a model to study cardiac development and human cardiac disease. Cardiovasc. Res. 2011, 91:279-288.
54. Davis E.E., Frangakis S., Katsanis N. Interpreting human genetic variation with in vivo zebrafish assay. Biochim. Biophys. Acta 2014, 1960-1970. (in this issue).
55. Shu L., Zien K., Gutjahr G., Oberholzer J., Pattou F., Kerr-Conte J., et al. TCF7L2 promotes beta cell regeneration in human and mouse pancreas. Diabetologia 2012, 55:3296-3307.
56. Le Bacquer O., Shu L., Marchand M., Neve B., Paroni F., Kerr Conte J., et al. TCF7L2 splice variants have distinct effects on beta-cell turnover and function. Hum. Mol. Genet. 2011, 20:1906-1915.
57. Boj S.F., van Es J.H., Huch M., Li V.S.W., José A., Hatzis P., et al. Diabetes risk gene and Wnt effector Tcf7l2/TCF4 controls hepatic response to perinatal and adult metabolic demand. Cell 2012, 151:1595-1607.
58. Mansour S.L., Thomas K.R., Capecchi M.R. Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes. Nature 1988, 336:348-352.
59. Wouters K., Shiri-Sverdlov R., van Gorp P.J., van Bilsen M., Hofker M.H. Understanding hyperlipidemia and atherosclerosis: lessons from genetically modified APOE and LDLR mice. Clin. Chem. Lab. Med. 2005, 43:470-479.
60. Smith A.J., De Sousa M.A., Kwabi-Addo B., Heppell-Parton A., Impey H., Rabbitts P. A site-directed chromosomal translocation induced in embryonic stem cells by Cre-loxP recombination. Nat. Genet. 1995, 9:376-385.
61. Wang H., Yang H., Shivalila C.S., Dawlaty M.M., Cheng A.W., Zhang F., et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 2013, 153:910-918.
62. Wijshake T., Baker D.J., van de Sluis B. Endonucleases: new tools to edit the mouse genome. Biochim. Biophys. Acta 2014, 1942-1950. (in this issue).
63. Wang T., Wei J.J., Sabatini D.M., Lander E.S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014, 343:80-84.
64. Nadeau J.H., Dudley A.M. Genetics. Systems genetics. Science 2011, 331:1015-1016.
65. Civelek M., Lusis A.J. Systems genetics approaches to understand complex traits. Nat. Rev. Genet. 2014, 15:34-48.
66. Cénit M.C., Matzaraki V., Tigchelaar E.F., Zhernakova A. Rapidly expanding knowledge on the role of the gut microbiome in health and disease. Biochim. Biophys. Acta 2014, 1981-1992. (in this issue).
67. van der Sijde M.R., Ng A., Fu J. Systems genetics: From GWAS to disease pathways. Biochim. Biophys. Acta 2014, 1903-1909. (in this issue).
68. Fu J., Keurentjes J.J.B., Bouwmeester H., America T., Verstappen F.W.A., Ward J.L., et al. System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat. Genet. 2009, 41:166-167.
69. Kuivenhoven J.A., Hegele R.A. Mining the genome for lipid genes. Biochim. Biophys. Acta 2014, 1993-2009. (in this issue).
70. Touw C.M.L., Derks T.G.J., Bakker B.M., Groen A.K., Smit G.P.A., Reijngoud D.J. From genome to phenome-Simple inborn errors of metabolism as complex traits. Biochim. Biophys. Acta 2014, 2021-2029. (in this issue).
71. Suhre K., Shin S.Y., Petersen A.K., Mohney R.P., Meredith D., Wägele B., et al. Human metabolic individuality in biomedical and pharmaceutical research. Nature 2011, 477:54-60.
72. Dharuri H., Demirkan A., van Klinken J.B., Mook-Kanamori D.O., van Duijn C.M., 't Hoen P.A.C., et al. Genetics of the human metabolome, what is next?. Biochim. Biophys. Acta 2014, 1923-1931. (in this issue).
73. Bernstein B.E., Birney E., Dunham I., Green E.D., Gunter C., Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
74. Schaub M.A., Boyle A.P., Kundaje A., Batzoglou S., Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012, 22:1748-1759.
75. Khetarpal S.A., Rader D.J. Genetics of lipid traits: Genome-wide approaches yield new biology and clues to causality in coronary artery disease. Biochim. Biophys. Acta 2014, 2010-2020. (in this issue).
76. Lage K. Protein-protein interactions and genetic diseases: The interactome. Biochim. Biophys. Acta 2014, 1971-1980. (in this issue).
77. GTEx Consortium The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 2013, 45:580-585.
78. Schadt E.E., Lamb J., Yang X., Zhu J., Edwards S., Guhathakurta D., et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet. 2005, 37:710-717.
79. Marbach D., Costello J.C., Küffner R., Vega N.M., Prill R.J., Camacho D.M., et al. Wisdom of crowds for robust gene network inference. Nat. Methods 2012, 9:796-804.
80. Neto E.C., Broman A.T., Keller M.P., Attie A.D., Zhang B., Zhu J., et al. Modeling causality for pairs of phenotypes in system genetics. Genetics 2013, 193:1003-1013.
81. Bordbar A., Mo M.L., Nakayasu E.S., Schrimpe-Rutledge A.C., Kim Y.M., Metz T.O., et al. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol. Syst. Biol. 2012, 8:558.
82. Sanseau P., Agarwal P., Barnes M.R., Pastinen T., Richards J.B., Cardon L.R., et al. Use of genome-wide association studies for drug repositioning. Nat. Biotechnol. 2012, 30:317-320.
83. Zhou K., Pearson E.R. Insights from genome-wide association studies of drug response. Annu. Rev. Pharmacol. Toxicol. 2013, 53:299-310.