Citation: Lin LI, Si-Hua QIAN, Tian-Qi LYU, Yu-Hui WANG, Jian-Ping ZHENG. 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

Recent Progress of Library Construction for Next-generation Sequencing

Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China

Corresponding author: Yu-Hui WANG, wangyuhui@nimte.ac.cn Jian-Ping ZHENG, zhengjianping@nimte.ac.cn
Received Date: 25 May 2020
Accepted Date: 10 December 2020

Fund Project: the Natural Science Foundation of Zhejiang Province LY20B050003Ningbo 3315 Innovation Team 2019A-14-Cthe Major Science and Technology Projects in Ningbo 2016C50009

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High-throughput next-generation sequencing (NGS) is a revolutionary technology in gene sequencing. It is widely used in various solutions in biomedical-relevant fields. Library preparation with high quality and low-cost is the key for NGS. With the development of such sequencing platforms, different library preparation technologies have been built. However, these technologies also possess their own strengths and weaknesses. In this review, we first summarized various library preparation methods for NGS, then discussed the complete process of library preparation in single cell sequencing. We hope that this review can help researchers on the optimal selection of library preparation strategies and also offer suggestions for the development of new NGS library preparation technologies, especially in the exploitation of homebred kits.
- Next-generation sequencing,
- Single cell sequencing,
- Library preparation
1. [1]
  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. 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. doi: 10.1146/annurev.bi.57.070188.000245
4. [4]
  METZKER M L. Applications of next-generation sequencing technologies-the next generation[J]. Nat Rev Genet, 2010,11(1):31-46. doi: 10.1038/nrg2626
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. doi: 10.1007/s11906-020-01039-z
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. 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. doi: 10.1080/07357907.2020.1713350
8. [8]
  ZHANG H Y, LIU R J, YAN C. 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. doi: 10.1016/j.tranon.2018.11.015
9. [9]
  CHEN Z, HUANG W, FU G. Current situation and prospects of the human genome project[J]. Chinese J Nat, 2000,22(3):125-133. doi: 10.3969/j.issn.0253-9608.2000.03.001
10. [10]
  STARK R, GRZELAK M, GENETICS J. RNA sequencing: the teenage years[J]. Nat Rew Genet, 2019,20(11):631-656. doi: 10.1038/s41576-019-0150-2
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. Differential gene and transcript expression analysis of RNA-seq experiments with tophat and cufflinks[J]. Nat Protoc, 2012,7(3):562-578. doi: 10.1038/nprot.2012.016
13. [13]
  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. 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]
  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]
  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. 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. doi: 10.1128/AEM.05610-11
19. [19]
  KIA A, GLOECKNER C, OSOTHPRAROP T. Improved genome sequencing using an engineered transposase[J]. BMC Biotechnol, 2017,17(6):1-10.
20. [20]
  JOUALI F, MARCHOUDI N, ANSARI F Z. SARS-CoV-2 genome sequence from Morocco, obtained using ion AmpliSeq technology[J]. Microbiol Resour Announ, 2020,9(31):1-3.
21. [21]
  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. 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. 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. 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. 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. 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. 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. doi: 10.1007/s00775-019-01741-7
31. [31]
  HEAD S R, KOMORI H K, LAMERE S A. 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. Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications[J]. Clin Chem, 2005,51(10):1973-1981. doi: 10.1373/clinchem.2005.053694
33. [33]
  SARANTOPOULOU D, TANG S Y, RICCIOTTI E. 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. Comprehensive comparative analysis of strand-specific RNA sequencing methods[J]. Nat Meth, 2010,7(9):709-715. doi: 10.1038/nmeth.1491
35. [35]
  PARKHOMCHUK D, BORODINA T, AMSTISLAVSKIY V. 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. 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. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing[J]. Methods, 2008,44(1):3-12. doi: 10.1016/j.ymeth.2007.09.009
38. [38]
  VIOLLET S, FUCHS R T, MUNAFO D B. T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis[J]. BMC Biotech, 2011,11(72):1-14.
39. [39]
  MAN L N, YANG J B, DING Y F. Research progress on three generation sequencing technology and its application[J]. China Anim Husb Vet Med, 2019,46(8):2245-2256.
40. [40]
  XU Y K, MA Y, HU X X. 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. Single molecule real-time(SMRT) sequencing comes of age: application and utilities for medical diagnostics[J]. Nucl Acids Res, 2018,46(5):2159-2168. doi: 10.1093/nar/gky066
42. [42]
  JAIN M, OLSEN H E, PATEN B. 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. Zero-mode waveguides for single-molecule analysis at high concentrations[J]. Science, 2003,299(5607):682-686. doi: 10.1126/science.1079700
44. [44]
  TRAVERS K J, CHINE C S, RANK D R. 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. Engineering of protein nanopores for sequencing, chemical or protein sensing and disease diagnosis[J]. Curr Opin Biotechnol, 2018,51:80-89. doi: 10.1016/j.copbio.2017.11.006
46. [46]
  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]
  WEN L, TANG F C. Recent progresses in single-cell transcriptome analysis[J]. Chinese Bull Life Sci, 2014,26(3):228-233.
48. [48]
  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. Landscape of infiltrating T Cells in liver cancer revealed by single-cell sequencing[J]. Cell, 2017,169(7):1342-1356. doi: 10.1016/j.cell.2017.05.035
50. [50]
  GUO X Y, ZHANG Y Y, ZHENG L T. Global characterization of T Cell in non-small-cell lung cancer by single-cell sequencing[J]. Nat Med, 2018,24(7):978-985. doi: 10.1038/s41591-018-0045-3
51. [51]
  LI J C, XU K Q. Single cell RNA sequencing technology and its applications[J]. Chem Life, 2020,40(8):1208-1219.
52. [52]
  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. Quantitative assessment of single-cell RNA-sequencing methods[J]. Nat Meth, 2014,11(1):41-46. doi: 10.1038/nmeth.2694
54. [54]
  MACOSKO E Z, BASU A, SATIJA R. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets[J]. Cell, 2015,161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002
55. [55]
  KLEIN A M, MAZUTIS L, AKARTUNA I. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells[J]. Cell, 2015,161(5):1187-1201. doi: 10.1016/j.cell.2015.04.044
56. [56]
  ZHENG G, TERRY J M, BELGRADER P. 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. Single cell map of diverse immune phenotypes in the breast tumor microenvironment[J]. Cell, 2018,174(5):1293-1308. doi: 10.1016/j.cell.2018.05.060
58. [58]
  HAN X P, WANG R Y, ZHOU Y C. Mapping the mouse cell atlas by microwell-seq[J]. Cell, 2018,22(172):1091-1107.
59. [59]
  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. 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. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification[J]. Proc Natl Acad Sci, 2015,112(38):11923-11928. doi: 10.1073/pnas.1513988112
62. [62]
  CHU W K, EDGE P, LEE H S. Ultraaccurate genome sequencing and haplotyping of single human cells[J]. Proc Natl Acad Sci, 2017,114(47):12512-12517. doi: 10.1073/pnas.1707609114
63. [63]
  CHAPMAN A R, HE Z, LU S J. Single cell transcriptome amplification with MALBAC[J]. PLoS ONE, 2015,10(3):1-12.
64. [64]
  CHEN C Y, XING D, TAN L Z. Single-cell whole-genome analyses by linear amplification via transposon insertion (LIANTI)[J]. Science, 2017,356(6334):189-194. doi: 10.1126/science.aak9787
65. [65]
  ZAHN H, STEIF A, LAKS E. Scalable whole-genome single-cell library preparation without preamplification[J]. Nat Meth, 2017,14(2):167-173. doi: 10.1038/nmeth.4140
66. [66]
  RAMSKOLD D, LUO S, WANG Y C. Full-length mRNA-seq from single cell levels of RNA and individual circulating tumor cells[J]. Nat Biotech, 2012,30(8):777-782. doi: 10.1038/nbt.2282
67. [67]
  POCELLI S, BJORKLUND A K, FARIDANI O R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells[J]. Nat Meth, 2013,10(11):1096-1098. doi: 10.1038/nmeth.2639
68. [68]
  ZIEGENHAIN C, VIETH B, PAREKH S. Comparative analysis of single-cell RNA sequencing methods[J]. Mol Cell, 2017,65(4):631-643. doi: 10.1016/j.molcel.2017.01.023
69. [69]
  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. RNA sequencing by direct tagmentation of RNA/DNA hybrids[J]. Proc Natl Acad Sci, 2020,117(6):2886-2893. doi: 10.1073/pnas.1919800117
71. [71]
  ROSENBERG A B, ROCO C M, MUSCAT R A. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding[J]. Science, 2018,360(6385):176-182. doi: 10.1126/science.aam8999
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