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-  2018 

功能基因组学在非综合征型唇腭裂遗传结果功能研究中的应用
Implementation of Functional Genome in the Functional Study of Non-coding Variants Associated with Non-syndromic Cleft Lip with or without Cleft Palate.

DOI: 10.13701/j.cnki.kqyxyj.2018.12.001

Keywords: 非综合征型唇腭裂,功能基因组,机器学习,
Non-syndromic cleft lip with or without cleft palate
,Functional genome,Machine learning

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Abstract:

摘要 唇腭裂是口腔常见的先天性颅颌面缺损,部分患儿的发病与遗传背景有关。全基因组关联分析(genome-wide association study,GWAS)等研究揭示了多个与该疾病相关的易感基因位点在基因组非编码DNA区域,由于我们对于这些非编码DNA在人唇腭发育过程中的功能缺乏了解,因此对有效的易感基因位点进行系统化生物学验证成为唇腭裂遗传学结果向临床转化中的难点。本文通过对人及小鼠颅颌面发育组织特异性功能基因组结果及机器学习可能的应用方式进行系统阐述,初步建立唇腭裂相关非编码DNA突变功能研究的完整体系

References

[1]  Birnbaum S,Ludwig KU,Reutter H,et al. Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24 [J]. Nat Genet,2009,41(4)∶473-477
[2]  Leslie EJ, Carlson JC, Shaffer JR,et al. Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with or without cleft palate [J]. Hum Genet,2017,136(3)∶275-286
[3]  Mangold E,Ludwig KU,Birnbaum S,et al. Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate [J]. Nat Genet,2010,42(1)∶24-26
[4]  Roadmap Epigenomics Consortium, Kundaje A, Meuleman W,et al. Integrative analysis of 111 reference human epigenomes [J]. Nature,2015,518(7539)∶317-330
[5]  Beer MA. Predicting enhancer activity and variant impact using gkm-SVM [J]. Hum Mutat, 2017, 38(9)∶1251-1258
[6]  Lee D, Gorkin DU, Baker M, et al. A method to predict the impact of regulatory variants from DNA sequence [J]. Nat Genet, 2015, 47(8)∶955-961
[7]  Brinkley JF, Fisher S, Harris MP, et al. The FaceBase Consortium: a comprehensive resource for craniofacial researchers [J]. Development,2016,143(14)∶2677-2688
[8]  Attanasio C, Nord AS, Zhu Y, et al. Fine tuning of craniofacial morphology by distant-acting enhancers [J]. Science, 2013, 342(6157)∶1241006
[9]  Ghandi M, Mohammad-Noori M, Ghareghani N, et al. gkmSVM: an R package for gapped-kmer SVM [J]. Bioinformatics, 2016, 32(14)∶2205-2207
[10]  Shen Z, Bao W, Huang DS. Recurrent neural network for predicting transcription factor binding sites [J]. Sci Rep, 2018, 8(1)∶15270
[11]  Camargo M,Rivera D,Moreno L,et al. GWAS reveals new recessive loci associated with non-syndromic facial clefting [J]. Eur J Med Genet,2012,55(10)∶510-514
[12]  Ludwig KU, Mangold E, Herms S, et al. Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci [J]. Nat Genet, 2012, 44(9)∶968-971
[13]  Moreno LM, Mansilla MA, Bullard SA, et al. FOXE1 association with both isolated cleft lip with or without cleft palate, and isolated cleft palate [J]. Hum Mol Genet, 2009, 18(24)∶4879-4896
[14]  Wilderman A, VanOudenhove J, Kron J,et al. High-resolution epigenomic atlas of human embryonic craniofacial development [J]. Cell Rep, 2018, 23(5)∶1581-1597
[15]  Leslie EJ,Liu H,Carlson JC,et al. A genome-wide association study of nonsyndromic cleft palate identifies an etiologic missense variant in GRHL3 [J]. Am J Hum Genet,2016,98(4)∶744-754
[16]  Leslie EJ, Taub MA, Liu H, et al. Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci [J]. Am J Hum Genet, 2015, 96(3)∶397-411
[17]  Beaty TH, Taub MA, Scott AF, et al. Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study [J]. Hum Genet, 2013, 132(7)∶771-781
[18]  Mangold E, Bohmer AC, Ishorst N, et al. Sequencing the GRHL3 coding region reveals rare truncating mutations and a common susceptibility variant for nonsyndromic cleft palate [J]. Am J Hum Genet, 2016, 98(4)∶755-762
[19]  Consortium EP. An integrated encyclopedia of DNA elements in the human genome [J]. Nature, 2012, 489(7414)∶57-74
[20]  Rada-Iglesias A, Bajpai R, Prescott S, et al. Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest [J]. Cell Stem Cell, 2012,11(5)∶633-648
[21]  Beaty TH,Murray JC,Marazita ML,et al.A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4 [J]. Nat Genet,2010,42(6)∶525-529
[22]  Grant SF,Wang K,Zhang H,et al. A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24[J].J Pediatr,2009,155(6)∶909-913
[23]  Wolf ZT, Brand HA, Shaffer JR, et al. Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate [J]. PLoS Genet, 2015, 11(3)∶e1005059
[24]  Yu Y, Zuo X, He M, et al. Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity [J]. Nat Commun,2017,8∶14364
[25]  Eshete MA, Liu H, Li M, et al. Loss-of-function GRHL3 variants detected in African patients with isolated cleft palate [J]. J Dent Res, 2018, 97(1)∶41-48
[26]  Maurano MT, Humbert R, Rynes E, et al. Systematic iocalization of common disease-associated variation in regulatory DNA [J]. Science,2012,337(6099)∶1190-1195
[27]  Liu H, Leslie EJ, Carlson JC, et al. Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting [J]. Nat Commun, 2017, 8∶14759
[28]  Soldner F, Stelzer Y, Shivalila CS, et al. Parkinson-associated risk variant in distal enhancer of alpha-synuclein modulates target gene expression [J]. Nature, 2016, 533(7601)∶95-99
[29]  Ye J, Tucker NR, Weng LC, et al. A functional variant associated with atrial fibrillation regulates PITX2c expression through TFAP2a [J]. Am J Hum Genet, 2016, 99(6)∶1281-1291
[30]  Chai Y, Jiang X, Ito Y, et al. Fate of the mammalian cranial neural crest during tooth and mandibular morphogenesis [J]. Development, 2000, 127(8)∶1671-1679
[31]  Prescott SL, Srinivasan R, Marchetto MC, Grishina I, et al. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest [J]. Cell, 2015, 163(1)∶68-83
[32]  Smith EM, Lajoie BR, Jain G, et al. Invariant TAD boundaries constrain cell-type-specific looping interactions between promoters and distal elements around the CFTR locus [J]. Am J Hum Genet, 2016, 98(1)∶185-201

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