Next-generation sequencing in aging research: Emerging applications, problems, pitfalls and possible solutions

Ageing Research Reviews

Volumn 9, Issue 3, 2010, Pages 315-323

  de Magalhães, João Pedro ^a   Finch, Caleb E ^b   Janssens, Georges ^c  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Bioinformatics; Epigenetics; Functional genomics; Senescence; Systems biology

Indexed keywords

DNA; RNA; TRANSCRIPTION FACTOR FKHRL1;

AGING; BIOINFORMATICS; CHROMATIN IMMUNOPRECIPITATION; COMPUTER PROGRAM; DEVELOPMENTAL GENETICS; DNA SEQUENCE; EPIGENETICS; FUNCTIONAL GENOMICS; GENE MUTATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; INTERMETHOD COMPARISON; INTESTINE FLORA; LONGEVITY; NONHUMAN; PROTEIN DNA INTERACTION; REVIEW; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION;

AGING; ANIMALS; COMPUTATIONAL BIOLOGY; GENOMICS; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 77952553604     PISSN: 15681637     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.arr.2009.10.006     Document Type: Review

References (69)

1. Adler A.S., Sinha S., Kawahara T.L., Zhang J.Y., Segal E., and Chang H.Y. Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes Dev. 21 (2007) 3244-3257
2. Ansorge W.J. Next-generation DNA sequencing techniques. Nat. Biotechnol. 25 (2009) 195-203
3. Austad S.N. Comparative biology of aging. J. Gerontol. A: Biol. Sci. Med. Sci. 64 (2009) 199-201
4. Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., Wei G., Chepelev I., et al. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837
5. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., Hall K.P., Evers D.J., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456 (2008) 53-59
6. Berezikov E., Thuemmler F., van Laake L.W., Kondova I., Bontrop R., Cuppen E., and Plasterk R.H. Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 38 (2006) 1375-1377
7. Busuttil R.A., Garcia A.M., Reddick R.L., Dolle M.E., Calder R.B., Nelson J.F., and Vijg J. Intra-organ variation in age-related mutation accumulation in the mouse. PLoS One 2 (2007) e876
8. Christensen K., Johnson T.E., and Vaupel J.W. The quest for genetic determinants of human longevity: challenges and insights. Nat. Rev. Genet. 7 (2006) 436-448
9. Church G.M. Genomes for all. Sci. Am. 294 (2006) 46-54
10. Cloonan N., Forrest A.R., Kolle G., Gardiner B.B., Faulkner G.J., Brown M.K., Taylor D.F., Steptoe A.L., et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5 (2008) 613-619
11. Cox-Foster D.L., Conlan S., Holmes E.C., Palacios G., Evans J.D., Moran N.A., Quan P.L., Briese T., et al. A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318 (2007) 283-287
12. de Magalhaes J.P. Aging research in the post-genome era: new technologies for an old problem. In: Foyer C.H., Faragher R., and Thornalley P.J. (Eds). Redox Metabolism and Longevity Relationships in Animals and Plants (2009), Taylor and Francis, New York and Abingdon 99-115
13. de Magalhaes J.P., Budovsky A., Lehmann G., Costa J., Li Y., Fraifeld V., and Church G.M. The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell 8 (2009) 65-72
14. de Magalhaes J.P., and Church G.M. Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging. Mech. Ageing Dev. 128 (2007) 355-364
15. de Magalhaes J.P., Curado J., and Church G.M. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 25 (2009) 875-881
16. Down T.A., Rakyan V.K., Turner D.J., Flicek P., Li H., Kulesha E., Graf S., Johnson N., et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26 (2008) 779-785
17. Finch C.E. The Biology of Human Longevity: Inflammation, Nutrition, and Aging in the Evolution of Lifespans (2007), Academic Press, Burlington, MA
18. Finch C.E., and Tanzi R.E. Genetics of aging. Science 278 (1997) 407-411
19. Flachsbart F., Caliebe A., Kleindorp R., Blanche H., von Eller-Eberstein H., Nikolaus S., Schreiber S., and Nebel A. Association of FOXO3A variation with human longevity confirmed in German centenarians. Proc. Natl. Acad. Sci. U.S.A. 106 (2009) 2700-2705
20. Fraga M.F., and Esteller M. Epigenetics and aging: the targets and the marks. Trends Genet. 23 (2007) 413-418
21. Giallourakis C., Henson C., Reich M., Xie X., and Mootha V.K. Disease gene discovery through integrative genomics. Annu. Rev. Genomics Hum. Genet. 6 (2005) 381-406
22. Gupta P.K. Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol. 26 (2008) 602-611
23. Hamady M., Walker J.J., Harris J.K., Gold N.J., and Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 5 (2008) 235-237
24. Harold D., Abraham R., Hollingworth P., Sims R., Gerrish A., Hamshere M.L., Pahwa J.S., Moskvina V., et al. Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat. Genet. 41 (2009) 1088-1093
25. He L., and Hannon G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5 (2004) 522-531
26. Heijmans B.T., Tobi E.W., Stein A.D., Putter H., Blauw G.J., Susser E.S., Slagboom P.E., and Lumey L.H. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 17046-17049
27. Kim H.D., Shay T., O'Shea E.K., and Regev A. Transcriptional regulatory circuits: predicting numbers from alphabets. Science 325 (2009) 429-432
28. Kim J.B., Porreca G.J., Song L., Greenway S.C., Gorham J.M., Church G.M., Seidman C.E., and Seidman J.G. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316 (2007) 1481-1484
29. Klein R.J., Zeiss C., Chew E.Y., Tsai J.Y., Sackler R.S., Haynes C., Henning A.K., SanGiovanni J.P., et al. Complement factor H polymorphism in age-related macular degeneration. Science 308 (2005) 385-389
30. Korbel J.O., Urban A.E., Affourtit J.P., Godwin B., Grubert F., Simons J.F., Kim P.M., Palejev D., et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318 (2007) 420-426
31. Korshunova Y., Maloney R.K., Lakey N., Citek R.W., Bacher B., Budiman A., Ordway J.M., McCombie W.R., et al. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res. 18 (2008) 19-29
32. Lee C.K., Weindruch R., and Prolla T.A. Gene-expression profile of the ageing brain in mice. Nat. Genet. 25 (2000) 294-297
33. Li B., and Leal S.M. Discovery of rare variants via sequencing: implications for the design of complex trait association studies. PLoS Genet. 5 (2009) e1000481
34. Mardis E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24 (2008) 133-141
35. Marioni J.C., Mason C.E., Mane S.M., Stephens M., and Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18 (2008) 1509-1517
36. McKernan K.J., Peckham H.E., Costa G.L., McLaughlin S.F., Fu Y., Tsung E.F., Clouser C.R., Duncan C., et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19 (2009) 1527-1541
37. Meier A., Fiegler H., Munoz P., Ellis P., Rigler D., Langford C., Blasco M.A., Carter N., et al. Spreading of mammalian DNA-damage response factors studied by ChIP-chip at damaged telomeres. EMBO J. 26 (2007) 2707-2718
38. Mortazavi A., Williams B.A., McCue K., Schaeffer L., and Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5 (2008) 621-628
39. Ng S.B., Turner E.H., Robertson P.D., Flygare S.D., Bigham A.W., Lee C., Shaffer T., Wong M., et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461 (2009) 272-276
40. Pan F., Chiu C.H., Pulapura S., Mehan M.R., Nunez-Iglesias J., Zhang K., Kamath K., Waterman M.S., et al. Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res. 35 (2007) D756-759
41. Pomraning K.R., Smith K.M., and Freitag M. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47 (2009) 142-150
42. Pop M., and Salzberg S.L. Bioinformatics challenges of new sequencing technology. Trends Genet. 24 (2008) 142-149
43. Prabhu S., and Pe'er I. Overlapping pools for high-throughput targeted resequencing. Genome Res. 19 (2009) 1254-1261
44. Pushkarev D., Neff N.F., and Quake S.R. Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 27 (2009) 847-852
45. Richardson B. Impact of aging on DNA methylation. Ageing Res. Rev. 2 (2003) 245-261
46. Robertson G., Hirst M., Bainbridge M., Bilenky M., Zhao Y., Zeng T., Euskirchen G., Bernier B., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4 (2007) 651-657
47. Salipante S.J., and Horwitz M.S. A phylogenetic approach to mapping cell fate. Curr. Top. Dev. Biol. 79 (2007) 157-184
48. Shendure J., and Ji H. Next-generation DNA sequencing. Nat. Biotechnol. 26 (2008) 1135-1145
49. Singleton A.B., Farrer M., Johnson J., Singleton A., Hague S., Kachergus J., Hulihan M., Peuralinna T., et al. Alpha-Synuclein locus triplication causes Parkinson's disease. Science 302 (2003) 841
50. Sladek R., Rocheleau G., Rung J., Dina C., Shen L., Serre D., Boutin P., Vincent D., et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445 (2007) 881-885
51. Slonim D.K. From patterns to pathways: gene expression data analysis comes of age. Nat. Genet. 32 Suppl (2002) 502-508
52. Solomon M.J., Larsen P.L., and Varshavsky A. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53 (1988) 937-947
53. Storey J.D., and Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 9440-9445
54. Sugarbaker D.J., Richards W.G., Gordon G.J., Dong L., De Rienzo A., Maulik G., Glickman J.N., Chirieac L.R., et al. Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 3521-3526
55. Sultan M., Schulz M.H., Richard H., Magen A., Klingenhoff A., Scherf M., Seifert M., Borodina T., et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321 (2008) 956-960
56. Tan Q., Kruse T.A., and Christensen K. Design and analysis in genetic studies of human ageing and longevity. Ageing Res. Rev. 5 (2006) 371-387
57. Trapnell C., and Salzberg S.L. How to map billions of short reads onto genomes. Nat. Biotechnol. 27 (2009) 455-457
58. Turnbaugh P.J., and Gordon J.I. The core gut microbiome, energy balance and obesity. J. Physiol. 587 (2009) 4153-4158
59. Valouev A., Johnson D.S., Sundquist A., Medina C., Anton E., Batzoglou S., Myers R.M., and Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5 (2008) 829-834
60. Vera J.C., Wheat C.W., Fescemyer H.W., Frilander M.J., Crawford D.L., Hanski I., and Marden J.H. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol. Ecol. 17 (2008) 1636-1647
61. Vijg J., and Suh Y. Genetics of longevity and aging. Annu. Rev. Med. 56 (2005) 193-212
62. Wang Y., Lawler D., Larson B., Ramadan Z., Kochhar S., Holmes E., and Nicholson J.K. Metabonomic investigations of aging and caloric restriction in a life-long dog study. J. Proteome Res. 6 (2007) 1846-1854
63. Wang Z., Gerstein M., and Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10 (2009) 57-63
64. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447 (2007) 661-678
65. Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., He W., Chen Y.J., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452 (2008) 872-876
66. Willcox B.J., Donlon T.A., He Q., Chen R., Grove J.S., Yano K., Masaki K.H., Willcox D.C., et al. FOXO3A genotype is strongly associated with human longevity. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 13987-13992
67. Xu X., Zhan M., Duan W., Prabhu V., Brenneman R., Wood W., Firman J., Li H., et al. Gene expression atlas of the mouse central nervous system: impact and interactions of age, energy intake and gender. Genome Biol. 8 (2007) R234
68. Zahn J.M., Poosala S., Owen A.B., Ingram D.K., Lustig A., Carter A., Weeraratna A.T., Taub D.D., et al. AGEMAP: a gene expression database for aging in mice. PLoS Genet. 3 (2007) e201
69. Zhang B., and Horvath S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4 (2005) Article17