新一代测序技术的文库制备方法研究进展

李琳 钱四化 吕天琦 王宇辉 郑建萍

引用本文: 李琳, 钱四化, 吕天琦, 王宇辉, 郑建萍. 新一代测序技术的文库制备方法研究进展[J]. 应用化学, 2021, 38(1): 11-23. doi: 10.19894/j.issn.1000-0518.200158 shu
Citation:  LI Lin,  QIAN Si-Hua,  LYU Tian-Qi,  WANG Yu-Hui,  ZHENG Jian-Ping. Recent Progress of Library Construction for Next-generation Sequencing[J]. Chinese Journal of Applied Chemistry, 2021, 38(1): 11-23. doi: 10.19894/j.issn.1000-0518.200158 shu

新一代测序技术的文库制备方法研究进展

    通讯作者: 王宇辉,E-mail:wangyuhui@nimte.ac.cn; 郑建萍,E-mail:zhengjianping@nimte.ac.cn
  • 基金项目:

    浙江省自然科学基金(No.LY20B050003)、宁波市3315创新团队(No.2019A-14-C)和宁波市科技重大专项(No.2016C50009)项目资助

摘要: 具有高通量优势的新一代测序技术(Next Generation Sequencing,NGS)是基因测序领域的一场技术革命,为生物医学领域向纵深发展提供了越发全面的解决方案。文库制备作为基因测序的上游技术,其高质量与低成本的制备技术是测序的关键。随着各大测序平台的兴起,NGS的文库制备技术方案也呈现多样化发展,但是各具优缺点。本文在已有研究基础上,综述了新一代测序的最新文库制备方法,以及单细胞测序文库制备的全流程最新进展。我们希望本综述能为研究人员在文库制备方案的选择,新的NGS文库制备技术尤其是国内文库制备试剂盒的开发提供指导。

English


    1. [1] 刘威.人类基因组计划大事件[J]. 生物化学与生物物理进展, 2001, 28(002):135-136.LIU W. Human genome project[J]. Adv Biochem Biophys, 2001, 28(002):135-136.

    2. [2] SHAHEENUZZAMN M D, LIU T X, SHI S D, et al. Development of sequencing technology and role of next generation sequencing technology in wheat research:a review[J]. Pak J Bot, 2020,52(5):1867-1878.

    3. [3] SANGER F. Sequences, sequences, and sequences[J]. Annu Rev Biochem, 1988, 57(1):1-28.

    4. [4] METZKER M L. Applications of next-generation sequencing technologies-the next generation[J]. Nat Rev Genet, 2010, 11(1):31-46.

    5. [5] LAISSUE P,VAIMAN D. Exploring the molecular aetiology of preeclampsia by massive parallel sequencing of DNA[J]. Curr Hypertens Rep, 2020, 22(4):1-10.

    6. [6] GOODWIN S, MCPHERSON J D, MCCOMBIE W R. Coming of age:ten years of next-generation sequencing technologies[J]. Nat Rew Genet, 2016, 17(6):333-351.

    7. [7] NGUYEN H T, TRAN D H, NGO Q D, et al. Evaluation of a liquid biopsy protocol using ultra-deep massive parallel sequencing for detecting and quantifying circulation tumor DNA in colorectal cancer patients[J]. Cancer Invest, 2020, 38(2):85-93.

    8. [8] ZHANG H Y, LIU R J, YAN C, et al. Advantage of next-generation sequencing in dynamic monitoring of circulating tumor DNA over droplet digital PCR in cetuximab treated colorectal cancer patients[J]. Trasl Oncol, 2019, 12(3):426-431.

    9. [9] 陈竺,黄薇,傅刚,等.人类基因组计划现状与展望[J].自然杂志, 2000, 22(3):125-133.CHEN Z,HUANG W,FU G, et al. Current situation and prospects of the human genome project[J]. Chinese J Nat, 2000, 22(3):125-133.

    10. [10] STARK R, GRZELAK M, GENETICS J. RNA sequencing:the teenage years[J]. Nat Rew Genet, 2019, 20(11):631-656.

    11. [11] QIN D H. Next-generation sequencing and its clinical application[J].Cancer Biol Med, 2019, 16(1):4-10.

    12. [12] TRAPNELL C, ROBERTS A, GOFF L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with tophat and cufflinks[J]. Nat Protoc, 2012, 7(3):562-578.

    13. [13] 田李,张颖,赵云峰. 新一代测序技术的发展和应用[J]. 生物技术通报,2015:31(11):1-8.TIAN L, ZHANG Y, ZHAO Y F. Development and application of new generation sequencing technology[J]. Biotech Bull, 2015, 31(11):1-8.

    14. [14] KNIERIM E, LUCKE B, SCHWARZ J M, et al. Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing[J]. Plos Ones, 2011, 6(11):1-6.

    15. [15] 孙子奎,王峰,丁方美,等. 一种采用一步法进行DNA末端修复/加dA的方法及应用:中国,201610040334.O[P]. 2016-05-11.SUN Z K,WANG F,DING F M,et al. A one-step approach and application to DNA terminal repair/additon of dA:CN, 201610040334.O[P]. 2016-05-11.

    16. [16] 冯延叶,柴智,张会,等.稳定性增加的测序文库接头:中国,111139533.A[P].2020-05-12.FENG Y Y,CHAI Z,ZHANG H,et al. Increased stability of the sequencing library adaptor:CN 111139533.A[P]. 2020-05-12.

    17. [17] ZHENG J,SHI C,SHEN D. Compositions and methods for preparing sequencing libraries:US,20160349152.[P]. 2016-12-01.

    18. [18] MARINE R, POLSON S W, RAVEL J,et al. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA[J]. Appl Environ Microbiol, 2011, 77(22):8071-8079.

    19. [19] KIA A, GLOECKNER C, OSOTHPRAROP T, et al. Improved genome sequencing using an engineered transposase[J]. BMC Biotechnol, 2017, 17(6):1-10.

    20. [20] JOUALI F, MARCHOUDI N, ANSARI F Z, et al. SARS-CoV-2 genome sequence from Morocco, obtained using ion AmpliSeq technology[J]. Microbiol Resour Announ, 2020, 9(31):1-3.

    21. [21] 崔凯,吴伟伟,刁其玉. 转录组测序技术的研究和应用进展[J]. 生物技术通报,2019,35(7):1-9.CUI K, WU W W, DIAO Q Y. Application and research progress on transcriptomics[J]. Biotech Bull, 2019, 35(7):1-9.

    22. [22] HAN Y X, GAO S G, MUEGGE K, et al. Advanced applications of RNA sequencing and challenges[J]. Bioinf Biol Insights, 2015, 9(S1):29-46.

    23. [23] PISANO M P, TABONE O, BODINIER M, et al.RNA-seq transcriptome analysis reveals LTR-retrotransposons modulation in human perpheral blood monouclear cells(PBMCs) after in vivo lipopolysaccharides(LPS) injection[J]. J Virol, 2020:94(19):1-25.

    24. [24] HRDLICKOVA R, TOLOUE M,TIAN B. RNA-seq methods for transcriptome analysis[J]. WIRES RNA, 2017, 8(1):1-24.

    25. [25] HERBERT Z T, KERSHNER J P, BUTTY V L, et al. Cross-site comparison of ribosomal depletion kits for illumina RNAseq library construction[J]. BMC Genomics, 2018, 19(199):1-10.

    26. [26] BUSH S J, MCCULLOCH M E B, SUMMERS K M, et al. Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries[J]. BMC Bioinf, 2017, 18(18):301-315.

    27. [27] CULVINER P H, GUEGLER C K, LAUB M T. A Simple, Cost-effective, and robust method for rRNA depletion in RNA-sequencing studies[J]. mBio, 2020, 11(2):10-20.

    28. [28] ZHULIDOW P A, BOGDANOVA E A, SHCHEGLOV A S, et al. Simple cDNA normalization using kamchatka crab duplex-specific nuclease[J]. Nucl Acids Res, 2004, 32(3):1-8.

    29. [29] SHRMA C M, HAFFMANN S, DARFEUILLE F, et al. The primary transcriptome of the major human pathogen helicobacter pylori[J]. Nature, 2010, 464(11):250-255.

    30. [30] DRUSIN S I,RASIA R M, ORENO D M. Study of the role of Mg2+ in dsRNA processing mechanism by bacterial RNAse III through QM/MM simulations[J]. J Biol Inorg Chem, 2020, 25(1):89-98.

    31. [31] HEAD S R, KOMORI H K, LAMERE S A, et al. Library construction for next-generation sequencing:overviews and challenges[J]. Biotechniques, 2014, 56(2):61-64.

    32. [32] KURN N, CHEN P C,HEATH J D, et al. Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications[J]. Clin Chem, 2005, 51(10):1973-1981.

    33. [33] SARANTOPOULOU D, TANG S Y, RICCIOTTI E, et al. Comparative evaluation of RNA-Seq library preparation methods for strand-specifcity and low input[J]. Sci Rep, 2019, 9(7091):1-10.

    34. [34] LEVIN J Z, YASSOUR M, ADICONIS X A, et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods[J]. Nat Meth, 2010, 7(9):709-715.

    35. [35] PARKHOMCHUK D, BORODINA T, AMSTISLAVSKIY V, et al. Transcriptome analysis by strand-specific sequencing of complementary DNA[J]. Nucl Acids Res, 2009, 37(18):1-10.

    36. [36] MAGNOLIA B, NATHALIE B, ALISA L, et al. Strand-specific transcriptome sequencing using SMART technology[J]. Curr Protoc Mol Biol, 2016, 116(1):1-18.

    37. [37] HAFNER M, LANDFRAF P, LUDWIG J, et al. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing[J]. Methods, 2008, 44(1):3-12.

    38. [38] VIOLLET S, FUCHS R T, MUNAFO D B, et al. T4 RNA ligase 2 truncated active site mutants:improved tools for RNA analysis[J]. BMC Biotech, 2011, 11(72):1-14:.

    39. [39] 马丽娜,杨进波,丁逸菲,等. 三代测序技术及其应用研究进展[J].中国畜牧兽医,2019,46(8):2245-2256.MAN L N, YANG J B, DING Y F, et al. Research progress on three generation sequencing technology and its application[J]. China Anim Husb Vet Med, 2019,46(8):2245-2256.

    40. [40] 许亚昆,马越,胡小茜,等. 基于三代测序技术的微生物组学研究进展[J].生物多样性,2019,27(5):534-542.XU Y K, MA Y, HU X X, et al. Analysis of prospective microbiology research using third-generation sequencing technology[J]. Biodivers Sci, 2019, 27(5):534-542.

    41. [41] ARDUI S, ADAM A, VERMEESCH J R, et al. Single molecule real-time(SMRT) sequencing comes of age:application and utilities for medical diagnostics[J]. Nucl Acids Res, 2018, 46(5):2159-2168.

    42. [42] JAIN M,OLSEN H E, PATEN B, et al. The oxford nanopore minion:delivery of nanopore sequencing to the genomics community[J]. Genome Biol, 2016, 17(239):1-12.

    43. [43] LEVENE M J, KORLACH J,TURNER S W, et al. Zero-mode waveguides for single-molecule analysis at high concentrations[J]. Science, 2003, 299(5607):682-686.

    44. [44] TRAVERS K J, CHINE C S, RANK D R, et al. A flexible and efficient template format for circular consensus sequencing and SNP detection[J]. Nucl Acids Res, 2010, 38(15):1-8.

    45. [45] WANG S Y, ZHAO Z Y, HAQUE F Z, et al. Engineering of protein nanopores for sequencing, chemical or protein sensing and disease diagnosis[J]. Curr Opin Biotechnol, 2018, 51:80-89.

    46. [46] 耿佳, 郭培宣. 噬菌体phi29 DNA包装马达磷脂嵌合体在单分子检测及纳米医学领域的应用[J]. 生命科学, 2011, 23(11):1114-1129.GENG J, GUO P X. Membrane-embedded channel of bacteriophage phi29 DNA-packaging motor for single molecule sensing and nanomedicine[J].Chin Bull Life Sci, 2011,23(11):1114-1129.

    47. [47] 文路, 汤富酬. 单细胞转录组分析研究进展[J]. 生命科学, 2014, 26(3):228-233.WEN L, TANG F C. Recent progresses in single-cell transcriptome analysis[J]. Chinese Bull Life Sci, 2014, 26(3):228-233.

    48. [48] 赵丽娜,赵晓航.循环肿瘤细胞单细胞测序-液体活检的新视角[J]. 生命科学, 2018,3(1):63-72.ZHAO L N,ZHAO X H.Single cell sequencing analysis of circulating tumor cells:a new horizon of liquid biopsy[J]. Chinese Bull Life Sci, 2018, 30(1):63-72.

    49. [49] ZHENG C H, ZHENG L T, YOO J, et al. Landscape of infiltrating T Cells in liver cancer revealed by single-cell sequencing[J]. Cell, 2017, 169(7):1342-1356.

    50. [50] GUO X Y, ZHANG Y Y, ZHENG L T, et al. Global characterization of T Cell in non-small-cell lung cancer by single-cell sequencing[J]. Nat Med, 2018, 24(7):978-985.

    51. [51] 李贱成,徐克前,单细胞转录组测序技术及应用[J]. 生命的化学, 2020, 40(8):1208-1219.LI J C, XU K Q. Single cell RNA sequencing technology and its applications[J]. Chem Life, 2020,40(8):1208-1219.

    52. [52] 吴春卉, 姜有为, 程鑫. 微流控芯片在单细胞捕获中的应用[J]. 科技先导, 2018, 36(16):39-45.WU C H, WANG Y W, CHENG X. Application of microfluidic chip in single cell capture[J].Sci Tech Leader, 2018, 36(16):39-45.

    53. [53] WU A R, NEFF N F, KALISKY T, et al. Quantitative assessment of single-cell RNA-sequencing methods[J]. Nat Meth, 2014, 11(1):41-46.

    54. [54] MACOSKO E Z, BASU A, SATIJA R, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets[J]. Cell, 2015, 161(5):1202-1214.

    55. [55] KLEIN A M, MAZUTIS L, AKARTUNA I, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells[J]. Cell, 2015, 161(5):1187-1201.

    56. [56] ZHENG G, TERRY J M, BELGRADER P, et al. Massively parallel digital transcriptional profiling of single cells[J]. Nat Commun, 2017, 8(14049):1-12.

    57. [57] AZIZI E, CARR A J, PLITAS G, et al. Single cell map of diverse immune phenotypes in the breast tumor microenvironment[J]. Cell, 2018, 174(5):1293-1308.

    58. [58] HAN X P, WANG R Y, ZHOU Y C, et al. Mapping the mouse cell atlas by microwell-seq[J].Cell, 2018, 22(172):1091-1107.

    59. [59] 杨子宁, 郝莎, 程涛. 单细胞转录组测序技术新进展及其在造血系统研究中的应用[J]. 中国科学:生命科学, 2020, 50(3):287-295.YANG Z N,HAO S, CHENG T. New Advances in single cell transcriptomic sequencing technology and its application in hematopoietic system[J].Sci Chinese Life Sci, 2020, 50(3):287-295.

    60. [60] HASHIMSHONY T, SENDEROVICH N, AVITAL G, et al. CEL-Seq2:sensitive highly-multiplexed single-cell RNA-Seq[J]. Genome Biol, 2016, 17(77):1-7.

    61. [61] FU Y S, LI C M, LU S J, et al. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification[J]. Proc Natl Acad Sci, 2015,112(38):11923-11928.

    62. [62] CHU W K, EDGE P, LEE H S, et al. Ultraaccurate genome sequencing and haplotyping of single human cells[J]. Proc Natl Acad Sci, 2017, 114(47):12512-12517.

    63. [63] CHAPMAN A R, HE Z, LU S J, et al. Single cell transcriptome amplification with MALBAC[J]. PLoS ONE, 2015, 10(3):1-12.

    64. [64] CHEN C Y, XING D, TAN L Z, et al. Single-cell whole-genome analyses by linear amplification via transposon insertion (LIANTI)[J]. Science, 2017, 356(6334):189-194.

    65. [65] ZAHN H, STEIF A, LAKS E, et al. Scalable whole-genome single-cell library preparation without preamplification[J].Nat Meth, 2017, 14(2):167-173.

    66. [66] RAMSKOLD D, LUO S, WANG Y C, et al. Full-length mRNA-seq from single cell levels of RNA and individual circulating tumor cells[J]. Nat Biotech, 2012, 30(8):777-782.

    67. [67] POCELLI S, BJORKLUND A K, FARIDANI O R, et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells[J], Nat Meth, 2013, 10(11):1096-1098.

    68. [68] ZIEGENHAIN C, VIETH B, PAREKH S, et al. Comparative analysis of single-cell RNA sequencing methods[J]. Mol Cell, 2017, 65(4):631-643.

    69. [69] 阎海,王思振,焦宇辰,等. 一种快速构建扩增子文库的方法:中国107012139.A[P]. 2017-08-04.YAN H,WANG S Z, JIAO Y C,et al. A Fast method for constructing an amplicon library:CN,107012139.A[P]. 2017-08-04.

    70. [70] DI L, SUN Y, LI J, et al. RNA sequencing by direct tagmentation of RNA/DNA hybrids[J]. Proc Natl Acad Sci, 2020, 117(6):2886-2893.

    71. [71] ROSENBERG A B, ROCO C M, MUSCAT R A, et al. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding[J]. Science, 2018, 360(6385):176-182.

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