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以海量数据计算揭示人类疾病发生机制及相关分子标志物

DOI: 10.1360/052011-720, PP. 72-79

Keywords: 组学,数据整合,生物信息学,系统生物学,分子标志物

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Abstract:

高通量芯片和深度测序技术为在全基因组水平上绘制高分辨率的基因组变异、RNA转录、转录因子结合及组蛋白修饰图谱等研究提供了前所未有的机遇.这些技术彻底改变了以往有关转录组学、调控网络以及表观遗传调控的研究方法,产生了海量的多水平组学数据,并开启了高效数据整合研究的先河.然而,如何有效地整合这些数据仍然是一个巨大的挑战.本文总结了高通量组学数据的产生对相关领域研究的主要影响及其与人类疾病的关系,并介绍了多种用于数据整合分析的生物信息学方法.最后,以炎症疾病为例进行说明.

References

[1]  81 Fronza R, Tramonti M, Atchley W R, et al. Joint analysis of transcriptional and post-transcriptional brain tumor data: searching for emergent properties of cellular systems. BMC Bioinformatics, 2011, 12: 86??
[2]  82 Fronza R, Tramonti M, Atchley W R, et al. Brain cancer prognosis: independent validation of a clinical bioinformatics approach. J Clin Bioinforma, 2012, 2: 2??
[3]  83 Wu G, Zhu L, Dent J E, et al. A comprehensive molecular interaction map for rheumatoid arthritis. PLoS One, 2010, 5: e10137??
[4]  1 Lander E S, Linton L M, Bruce B, et al. Initial sequencing and analysis of the human genome. Nature, 2001, 409: 860-921??
[5]  2 Venter J C, Adams M D, Myers E W, et al. The sequence of the human genome. Science, 2001, 291: 1304-1351??
[6]  3 Pennisi E. Breakthrough of the year. Human genetic variation. Science, 2007, 318: 1842-1843??
[7]  4 Nielsen R. Genomics: in search of rare human variants. Nature, 2010, 467: 1050-1051??
[8]  5 Nik-Zainal S, Alexandrov L B, Wedge D C, et al. Mutational processes molding the genomes of 21 breast cancers. Cell, 2012, 149: 979-993??
[9]  6 Pasaniuc B, Rohland N, McLaren P J, et al. Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet, 2012, 44: 631-635??
[10]  7 Collins F. Has the revolution arrived? Nature, 2010, 464: 674-675
[11]  8 Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet, 2007, 3: e114??
[12]  9 Ashley E A, Butte A J, Wheeler M T, et al. Clinical assessment incorporating a personal genome. Lancet, 2010, 375: 1525-1535??
[13]  10 Bird A. Perceptions of epigenetics. Nature, 2007, 447: 396-398??
[14]  11 Greer E L, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet, 2012, 13: 343-357
[15]  12 Chi P, Allis C D, Wang G G. Covalent histone modifications—miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer, 2010, 10: 457-469??
[16]  13 Mann B S, Johnson J R, Cohen M H, et al. FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist, 2007, 12: 1247-1252??
[17]  14 Sekigawa I, Kawasaki M, Ogasawara H, et al. DNA methylation: its contribution to systemic lupus erythematosus. Clin Exp Med, 2006, 6: 99-106??
[18]  15 Maciejewska-Rodrigues H, Karouzakis E, Strietholt S, et al. Epigenetics and rheumatoid arthritis: the role of SENP1 in the regulation of MMP-1 expression. J Autoimmun, 2010, 35: 15-22??
[19]  16 Miao F, Smith D D, Zhang L, et al. Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes. Diabetes, 2008, 57: 3189-3198??
[20]  17 Amir R E, Van den Veyver I B, Wan M, et al. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet, 1999, 23: 185-188
[21]  18 Tsankova N, Renthal W, Kumar A, et al. Epigenetic regulation in psychiatric disorders. Nat Rev Neurosci, 2007, 8: 355-367
[22]  19 Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell, 2007, 129: 823-837??
[23]  20 Eckhardt F, Lewin J, Cortese R, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet, 2006, 38: 1378-1385
[24]  21 Hesselberth J R, Chen X, Zhang Z, et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods, 2009, 6: 283-289??
[25]  22 Yu H, Zhu S, Zhou B, et al. Inferring causal relationships among different histone modifications and gene expression. Genome Res, 2008, 18: 1314-1324??
[26]  23 Xiao S, Xie D, Cao X, et al. Comparative epigenomic annotation of regulatory DNA. Cell, 2012, 149: 1381-1392??
[27]  24 Jin C, Li J, Green C D, et al. Histone demethylase UTX-1 regulates C. elegans life span by targeting the insulin/IGF-1 signaling pathway. Cell Metab, 2011, 14: 161-172
[28]  25 Xue H, Xian B, Dong D, et al. A modular network model of aging. Mol Syst Biol, 2007, 3: 147
[29]  26 Zhou B, Yang L, Li S, et al. Midlife gene expressions identify modulators of aging through dietary interventions. Proc Natl Acad Sci USA, 2012, 109: E1201-E1209??
[30]  27 Wei G, Wei L, Zhu J, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity, 2009, 30: 155-167??
[31]  28 Wei G, Abraham B J, Yaqi R, et al. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity, 2011, 35: 299-311??
[32]  29 Voineagu I, Wang X, Johnston P, et al. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature, 2011, 474: 380-384??
[33]  30 Kang H J, Kawasawa Y I, Cheng F, et al. Spatio-temporal transcriptome of the human brain. Nature, 2011, 478: 483-489??
[34]  31 Yang L, Duff M O, Graveley B R, et al. Genomewide characterization of non-polyadenylated RNAs. Genome Biol, 2011, 12: R16
[35]  32 Yin Q F, Yang L, Zhang Y, et al. Long noncoding RNAs with snoRNA ends. Mol Cell, 2012, 48: 219-230??
[36]  33 Hvistendahl M. My microbiome and me. Science, 2012, 336: 1248-1250??
[37]  34 Snyder M, Du J, Gerstein M. Personal genome sequencing: current approaches and challenges. Genes Dev, 2010, 24: 423-431??
[38]  35 Chen R, Mias G I, Li-Pook-Than J, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell, 2012, 148: 1293-1307??
[39]  36 Davis B D. The isolation of biochemically deficient mutants of bacteria by means of penicillin. Proc Natl Acad Sci USA, 1949, 35: 1-10??
[40]  37 Bedell M A, Jenkins N A, Copeland N G. Mouse models of human disease. Part I: techniques and resources for genetic analysis in mice. Genes Dev, 1997, 11: 1-10??
[41]  38 Bedell M A, Largaespada D A, Jenkins N A, et al. Mouse models of human disease. Part II: recent progress and future directions. Genes Dev, 1997, 11: 11-43??
[42]  39 Hardouin S N, Nagy A. Mouse models for human disease. Clin Genet, 2000, 57: 237-244
[43]  40 Francis-West P H, Robson L, Evans D J. Craniofacial development: the tissue and molecular interactions that control development of the head. Adv Anat Embryol Cell Biol, 2003, 169: III-VI, 1-138??
[44]  41 Wilkie A O, Morriss-Kay G M. Genetics of craniofacial development and malformation. Nat Rev Genet, 2001, 2: 458-468
[45]  42 Allanson J E, O''Hara P, Farkas L G, et al. Anthropometric craniofacial pattern profiles in Down syndrome. Am J Med Genet, 1993, 47: 748-752??
[46]  43 Allanson J E, Hennekam R C. Rubinstein-Taybi syndrome: objective evaluation of craniofacial structure. Am J Med Genet, 1997, 71: 414-419??
[47]  44 Allanson J E, Cole T R. Sotos syndrome: evolution of facial phenotype subjective and objective assessment. Am J Med Genet, 1996, 65: 13-20??
[48]  45 Allanson J E, Hall J G, Hughes H E, et al. Noonan syndrome: the changing phenotype. Am J Med Genet, 1985, 21: 507-514??
[49]  46 Beaty T H, Murray J C, Marazita M L, et al. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet, 2010, 42: 525-529??
[50]  47 Birnbaum S, Ludwig K U, Reutter H, et al. Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat Genet, 2009, 41: 473-477??
[51]  48 Mangold E, Ludwig K U, Birnbaum S, et al. Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. Nat Genet, 2010, 42: 24-26??
[52]  49 Rahimov F, Marazita M L, Visel A, et al. Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet, 2008, 40: 1341-1347??
[53]  50 Boehringer S, van der Lijn F, Liu F, et al. Genetic determination of human facial morphology: links between cleft-lips and normal variation. Eur J Hum Genet, 2011, 19: 1192-1197??
[54]  51 Kayser M, de Knijff P. Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet, 2011, 12: 179-192??
[55]  52 Little A C, Jones B C, DeBruine L M. Facial attractiveness: evolutionary based research. Philos Trans R Soc Lond B Biol Sci, 2011, 366: 1638-1659??
[56]  53 Meyer-Marcotty P, Alpers G W, Gerdes A B, et al. Impact of facial asymmetry in visual perception: a 3-dimensional data analysis. Am J Orthod Dentofacial Orthop, 2010, 137: 168 e1-e8; discussion 168-169??
[57]  54 Albert A M, Ricanek K Jr, Patterson E. A review of the literature on the aging adult skull and face: implications for forensic science research and applications. Forensic Sci Int, 2007, 172: 1-9??
[58]  55 Fu Y, Guo G, Huang T S. Age synthesis and estimation via faces: a survey. Pattern Analysis and Machine Intelligence, IEEE Transactions on, 2010, 32: 1955-1976??
[59]  56 Bowyer K W, Chang K, Flynn P. A survey of approaches and challenges in 3D and multi-modal 3D+ 2D face recognition. Comput Vis Image Und, 2006, 101: 1-15??
[60]  57 Burton A M, Wilson S, Cowan M, et al. Face recognition in poor-quality video: evidence from security surveillance. Psychol Sci, 1999, 10: 243-248??
[61]  58 Poh M Z, McDuff D J, Picard R W. Non-contact, automated cardiac pulse measurements using video imaging and blind source separation. Opt Express, 2010, 18: 10762-10774??
[62]  59 Boehringer S, van der Lijin F, Liu F, et al. Genetic determination of human facial morphology: links between cleft-lips and normal variation. Eur J Hum Genet, 2011, 19: 1192-1197??
[63]  60 Farkas L G, Katic M J, Forrest C R. International anthropometric study of facial morphology in various ethnic groups/races. J Craniofac Surg, 2005, 16: 615??
[64]  61 Weinberg S M, Naidoo S D, Bardi K M, et al. Face shape of unaffected parents with cleft affected offspring: combining three—dimensional surface imaging and geometric morphometrics. Orthod Craniofac Res, 2009, 12: 271-281??
[65]  62 Hammond P, Hutton T J, Allanson J E, et al. 3D analysis of facial morphology. Am J Med Genet A, 2004, 126: 339-348
[66]  63 Maal T J, van Looon B, Plooij J M, et al. Registration of 3-dimensional facial photographs for clinical use. J Oral Maxillofac Surg, 2010, 68: 2391-2401??
[67]  64 Wan J, Shen L, Fang S, et al. A framework for 3D analysis of facial morphology in fetal alcohol syndrome. MIAR''10 Proceedings of the 5th international conference on Medical imaging and augmented reality Pages, 2010, 118-127
[68]  65 Guo J, Mei X, Tang K. Automatic landmark annotation and dense correspondence registration for 3D human face images, arXiv:1212.4920
[69]  66 Bhuiyan Z A, Klein M, Hammond P, et al. Genotype-phenotype correlations of 39 patients with Cornelia De Lange syndrome: the Dutch experience. J Med Genet, 2006, 43: 568-575
[70]  67 Hammond P, Hannes F, Suttie M, et al. Fine-grained facial phenotype-genotype analysis in Wolf-Hirschhorn syndrome. Eur J Hum Genet, 2012, 20: 33-40??
[71]  68 Hammond P, Hutton T J, Allanson J, et al. 3D dense surface models identify the most discriminating facial features in dysmorphic syndromes. 54th Annual Meeting of the American Society for Human Genetics, Toronto, Canada, 2004, 1
[72]  69 Hutton T J, Buxton B F, Hammond P, et al. Estimating average growth trajectories in shape-space using kernel smoothing. Medical Imaging, IEEE Transactions on, 2003, 22: 747-753??
[73]  70 Hammond P, Hutton T J, Allanson J E, et al. Discriminating power of localized three-dimensional facial morphology. Am J Hum Genet, 2005, 77: 999-1010??
[74]  71 Hammond P, Forster-Gibson C, Chudley A E, et al. Face-brain asymmetry in autism spectrum disorders. Mol psychiatry, 2008, 13: 614-623??
[75]  72 Kasperavi?iūtè D, Catarino C B, Chinthapalli K, et al. Uncovering genomic causes of co-morbidity in epilepsy: gene-driven phenotypic characterization of rare microdeletions. PLoS ONE, 2011, 6: e23182??
[76]  73 Han J D. Understanding biological functions through molecular networks. Cell Res, 2008, 18: 224-237??
[77]  74 Yeger-Lotem E, Riva L, Su L J, et al. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet, 2009, 41: 316-323??
[78]  75 Chen F, Zhang W, Liang Y, et al. Transcriptome and network changes in climbers at extreme altitudes. PLoS One, 2012, 7: e31645??
[79]  76 Huang J, Liu Y, Zhang W, et al. eResponseNet: a package prioritizing candidate disease genes through cellular pathways. Bioinformatics, 2011, 27: 2319-2320??
[80]  77 Scher J U, Abramson S B. The microbiome and rheumatoid arthritis. Nat Rev Rheumatol, 2011, 7: 569-578
[81]  78 Stahl E A, Raychaudhuri S, Remmers E F, et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet, 2010, 42: 508-514??
[82]  79 Kochi Y, Okada Y, Suzuki A, et al. A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility. Nat Genet, 2010, 42: 515-519??
[83]  80 Liu Y, Zhang C, Zhao L, et al. Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity. Brief Funct Genomics, 2010, 9: 355-361??

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