Abstract:With the advent of the post-genomics era, gene chip and high-throughput sequencing have become two most important technologies in biochemistry and molecular biology. Compared with the traditional genetic methods, these two technologies have made new breakthroughs in the detection efficiency, accuracy and the degree of automation. The gene chip technology is a high-throughput, high-efficiency, and high-automation method. Its core technical protocols have already been widely popularized and used in industrial applications. Although the high-throughput DNA sequencing technology was established after gene chip, its development speed is extremely fast, especially in terms of technical updating and replacement. Continuous improvement makes its application in life sciences an insurmountable advantage. There are marked differences between these two methods by principle. But the application of the two technologies often blend together. This paper briefly discusses and compares the principles of the gene chip and high-throughput sequencing technologies and their utilizations in gene copy number variation, the intestinal microbiology and agriculture.
徐晓丽,林娟,鄢仁祥. 基因芯片与高通量测序技术的原理与应用的比较[J]. 中国生物化学与分子生物学报, 2018, 34(11): 1166-1174.
XU Xiao-Li, LIN Juan, YAN Ren-Xiang. Comparison of Principle and Application of the Gene Chip and High-throughput Sequencing Technologies. Chinese Journal of Biochemistry and Molecular Biol, 2018, 34(11): 1166-1174.
[1] Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome[J]. Nature, 2001, 409(6822): 860-921
[2] Schena M, La Rovere E, Solerio D, et al. Neoadjuvant chemo-radiotherapy for locally advanced esophageal cancer: a monocentric study[J]. Tumori, 2012, 98(4): 451-457
[3] Jung HY, Han HS, Kim HB, et al. Comparison of analytical and clinical performance of HPV 9G DNA Chip, PANArray HPV genotyping chip, and hybrid-capture II assay in cervicovaginal Swabs[J]. J Pathol Transl Med, 2016, 50(2): 138-146
[4] Li Q, Wu C, Song G, et al. Genome-wide analysis of long noncoding RNA expression profiles in human xuanwei lung cancer[J]. Clin Lab, 2015, 61(10): 1515-1523
[5] 孙兵, 闫彩霞, 张廷婷, 等.基因芯片技术在植物基因克隆中的应用研究进展[J]. 基因组学与应用生物学(Sun B, Yan CX, Zhang TT, et al. Advances in Application of Gene Chip Technology in Plant Gene Cloning[J]. Genom Appl Biol, 2009, 28(1): 153-158
[6] Fodor SP, Read JL, Pirrung MC, et al. Light-directed, spatially addressable parallel chemical synthesis[J]. Science, 1991, 251(4995): 767-773
[7] Fodor SP, Rava RP, Huang XC, et al. Multiplexed biochemical assays with biological chips[J]. Nature, 1993, 364(6437): 555-556
[8] Pirrung MC. Spatially addressable combinatorial libraries[J]. Chem Rev, 1997, 97(2): 473-488
[9] 裘敏燕, 李瑶, 谢毅, 等. 基因芯片技术及其应用[J]. 第二军医大学学报(Qiu MY, Li Y, Xie Y, et al. Gene chip technology and its application[J]. Acad J Sec Milit Med Univ), 2001, 22(6): 534-537
[10] 贾文刚. 3种非接触式点样针性能对比[J]. 生命科学仪器(Jia WG. Comparison of the performance of three non-contact needles[J]. Life Sci Instrum), 2010, 8(4): 46-49
[11] 张忠民, 陈建庭, 金大地. 基因芯片原理概述[J]. 现代医院(Zhang ZM, Chen JT, Jin DD. Gene Chip Theory Overview [J]. Mod Hosp), 2002, 2(5): 3-4
[12] Dongsong N, Zhou JY. FISH is more sensitive than Southern analysis at identifying increased levels of cyclin D1 gene amplified in breast cancer cell lines[J]. Mol Biol Rep, 2010, 37(7): 3473-3480
[13] Gu Q, Sivanandam TM, Kim CA. Signal stability of Cy3 and Cy5 on antibody microarrays[J]. Proteome Sci, 2006, 4: 21
[14] 凌寒. 卫生部发布《中国出生缺陷防治报告(2012)》[J]. 中国当代医药(Ling H, The Ministry of Health promulgated the "China Birth Defects Prevention Report (2012)" [J]. Chin Mod Med), 2012, 19(28): 1
[15] 熊惠玲, 马艳, 郑玉建. 出生缺陷的病因学研究进展[J]. 新疆医科大学学报(Xiong HL, Ma Y, Zheng YJ. Progress in Etiology of Birth Defects[J]. J Xinjiang Med Univ), 2006, 29(8): 765-766
[16] Fruscalzo A, Londero AP, Biasizzo J, et al. Second trimester maternal plasma and amniotic fluid adipokines in women who will develop gestational diabetes mellitus[J]. Gynecol Endocrinol, 2015, 31(12): 934-938
[17] 王晨冉, 冯碧波, 翟建军. 微阵列比较基因组杂交应用于产前诊断中的研究进展[J]. 中华妇幼临床医学杂志电子版(Wang CR, Feng BB, Huo JJ. Advances in microarray hybrid genomic hybridization in prenatal diagnosis[J]. Chin J Obstet Gynecol Pediatr Electron Ed), 2014, 10(3):118-121
[18] Brownstein Z, Friedman LM, Shahin H, et al. Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in Middle Eastern families[J]. Genome Biol, 2011, 12(9): R89
[19] Shaffer LG, Lupski JR. Molecular mechanisms for constitutional chromosomal rearrangements in humans[J]. Annu Rev Genet, 2000, 34: 297-329
[20] Simovich MJ, Yatsenko SA, Kang SH, et al. Prenatal diagnosis of a 9q34.3 microdeletion by array-CGH in a fetus with an apparently balanced translocation[J]. Prenat Diagn, 2007, 27(12): 1112-1117
[21] Van den Veyver IB, Patel A, Shaw CA, et al. Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases[J]. Prenat Diagn, 2009, 29(1): 29-39
[22] 高健, 郭文潮, 王方娜,等. 6944名高危孕妇羊水的细胞遗传学分析[J]. 中华医学遗传学杂志(Gao J, Guo WC, Wang FN, et al. A cytogenetic analysis of amniotic fluid in 6944 high-risk pregnant women [J]. Chin J Med Genet), 2014, 31(4): 533-534
[23] Pole JC, Courtay-Cahen C, Garcia MJ, et al. High-resolution analysis of chromosome rearrangements on 8p in breast, colon and pancreatic cancer reveals a complex pattern of loss, gain and translocation[J]. Oncogene, 2006, 25(41): 5693-5706
[24] Kim TM, Yim SH, Lee JS, et al. Genome-wide screening of genomic alterations and their clinicopathologic implications in non-small cell lung cancers[J]. Clin Cancer Res, 2005, 11(23): 8235-8242
[25] Paris PL, Andaya A, Fridlyand J, et al. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors[J]. Hum Mol Genet, 2004, 13(13): 1303-1313
[26] Trost D, Ehrler M, Fimmers R, et al. Identification of genomic aberrations associated with shorter overall survival in patients with oligodendroglial tumors[J]. Int J Cancer, 2007, 120(11): 2368-2376
[27] Yamamoto Y, Chochi Y, Matsuyama H, et al. Gain of 5p15.33 is associated with progression of bladder cancer[J]. Oncology, 2007, 72(1-2): 132-138
[28] 李梅, 刘银坤, 李山. 阵列比较基因组杂交技术在肿瘤研究中的应用进展[J]. 国际检验医学杂志(Li M, Liu YK, Li S. The application of array comparative genomic hybridization in tumor research[J].Int J Lab Med), 2009, 30(10): 979-980
[29] Sanger F, Nicklen S, Coulson AR. DNA Sequencing with chain-terminating inhibitors[J]. Proc Natl Acad Sci U S A, 1977, 74(12): 5463-5467
[30] Smith LM, Sanders JZ, Kaiser RJ, et al. Fluorescence detection in automated DNA sequence analysis[J]. Nature, 1986, 321(6071): 674-679
[31] Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics[J]. Genomics, 2008, 92(5): 255-264
[32] Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing[J]. Hum Mol Genet, 2010, 19(R2): R227-R240
[33] dela Torre R, Larkin J, Singer A, et al. Fabrication and characterization of solid—state nanopore arrays for high-throughput DNA sequencing[J]. Nanotechnology, 2012, 23(38): 385308
[34] Del Savio L, Loi M, Stupka E. Epigenetics and future generations[J]. Bioethics, 2015, 29(8): 580-587
[35] Zannas AS, Provencal N, Binder EB. Epigenetics of posttraumatic stress disorder: current evidence, challenges, and future directions[J]. Biol Psychiatry, 2015, 78(5): 327-335
[36] El Shamieh S, Visvikis-Siest S. Genetic biomarkers of hypertension and future challenges integrating epigenomics[J]. Clin Chim Acta, 2012, 414: 259-265
[37] 贾梅兰,王茂春,徐园,等. 二代测序应用于检测GT1-7细胞中KISS和GnRH启动子的DNA甲基化状态的研究[J]. 现代生物医学进展(Jia ML, Wang MC, Xu Y, et al. Second-generation sequencing for the detection of DNA methylation status of KISS and GnRH promoters in GT1-7 cells [J]. Prog Mod Biomed), 2017, 17(29): 5607-5610
[38] Valverde JR, Alonso J, Palacios I, et al. RB1 gene mutation up-date, a meta-analysis based on 932 reported mutations available in a searchable database[J]. BMC Genet, 2005, 6:53
[39] 何明燕,安宇,李刚,等. 儿童视网膜母细胞瘤患者RB1基因胚系突变的特征分析[J]. 中华医学遗传学杂志(He MY, An Y, Li G, et al. Analysis of RB1 gene germline mutation in children with retinoblastoma[J]. Chin J Med Genet), 2013, 30(5): 509-512
[40] Crawford B, Adams SB, Sittler T, et al. Multi-gene panel testing for hereditary cancer predisposition in unsolved high-risk breast and ovarian cancer patients[J]. Breast Cancer Res Treat, 2017, 163(2): 383-390
[41] Moldovan L, Mitroi A, Petrescu CM, et al. Classification of breast carcinomas according to gene expression profiles[J]. J Med Life, 2013, 6(1): 14-17
[42] Wang J, Yang X, Xiao H, et al. Determination of the mechanism of action of repetitive halothane exposure on rat brain tissues using a combined method of microarray gene expression profiling and bioinformatics analysis[J]. Mol Med Rep, 2015, 12(6): 8071-8076
[43] 王影, 何玺玉, 杨尧. 基因芯片技术在产前诊断中的应用[J]. 国际遗传学杂志(Wang Y, He XY, Yang Y. The application of gene chip technology in prenatal diagnosis [J]. Int J Genet), 2014, 37(1): 37-40.
[44] 戚庆炜, 刘俊涛, 边旭明,等. 基于微阵列芯片的比较基因组杂交技术在产前诊断中应用[J]. 中华妇产科杂志(Qi QW, Liu JT, Bian XM, et al. Application of comparative genomic hybridization based on microarray chip in prenatal diagnosis[J].Chin J Obstet Gynecol), 2013, 48(5): 381-384
[45] 陈欣洁, 宋艳琴, 陈敦金,等. 全基因组扩增技术在产前诊断中的应用[J]. 实用医学杂志(Chen XJ, Song YQ, Chen GJ, et al. Application of whole genome amplification technology in prenatal diagnosis[J]. J Pract Med), 2016, 32(13): 2181-2183
[46] Sahoo T, Cheung SW, Ward P, et al. Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization[J]. Genet Med, 2006, 8(11): 719-727
[47] Turnbaugh PJ, Ridaura VK, Faith JJ, et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice[J]. Sci Transl Med, 2009, 1(6): 6ra14
[48] 肖翔,官春云,尹明智,等.基因芯片技术在农业中应用的研究进展[J]. 中国农学通报(Xiao X, Guan CY, Yin MZ, et al. Advances in Application of Gene Chip Technology in Agriculture [J]. Chin Agric Sci Bull), 2012, 28(33): 187-193