Recent Progress of Library Construction for Next-generation Sequencing
- Corresponding author: Yu-Hui WANG, wangyuhui@nimte.ac.cn Jian-Ping ZHENG, zhengjianping@nimte.ac.cn
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
LIU W. Human genome project[J]. Adv Biochem Biophys, 2001,28(002):135-136.
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.
SANGER F. Sequences, sequences, and sequences[J]. Annu Rev Biochem, 1988,57(1):1-28. doi: 10.1146/annurev.bi.57.070188.000245
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
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
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.
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
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
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
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
QIN D H. Next-generation sequencing and its clinical application[J]. Cancer Biol Med, 2019,16(1):4-10.
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
TIAN L, ZHANG Y, ZHAO Y F. Development and application of new generation sequencing technology[J]. Biotech Bull, 2015,31(11):1-8.
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.
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.
FENG Y Y, CHAI Z, ZHANG H, et al. Increased stability of the sequencing library adaptor: CN 111139533.A[P]. 2020-05-12.
ZHENG J, SHI C, SHEN D. Compositions and methods for preparing sequencing libraries: US, 20160349152.[P]. 2016-12-01.
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
KIA A, GLOECKNER C, OSOTHPRAROP T. Improved genome sequencing using an engineered transposase[J]. BMC Biotechnol, 2017,17(6):1-10.
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.
CUI K, WU W W, DIAO Q Y. Application and research progress on transcriptomics[J]. Biotech Bull, 2019,35(7):1-9.
HAN Y X, GAO S G, MUEGGE K. Advanced applications of RNA sequencing and challenges[J]. Bioinf Biol Insights, 2015,9(S1):29-46.
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.
HRDLICKOVA R, TOLOUE M, TIAN B. RNA-seq methods for transcriptome analysis[J]. WIRES RNA, 2017,8(1):1-24.
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.
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.
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.
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.
SHRMA C M, HAFFMANN S, DARFEUILLE F. The primary transcriptome of the major human pathogen helicobacter pylori[J]. Nature, 2010,464(11):250-255.
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
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.
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
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.
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
PARKHOMCHUK D, BORODINA T, AMSTISLAVSKIY V. Transcriptome analysis by strand-specific sequencing of complementary DNA[J]. Nucl Acids Res, 2009,37(18):1-10.
MAGNOLIA B, NATHALIE B, ALISA L. Strand-specific transcriptome sequencing using SMART technology[J]. Curr Protoc Mol Biol, 2016,116(1):1-18.
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
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.
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.
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.
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
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.
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
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.
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
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.
WEN L, TANG F C. Recent progresses in single-cell transcriptome analysis[J]. Chinese Bull Life Sci, 2014,26(3):228-233.
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.
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
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
LI J C, XU K Q. Single cell RNA sequencing technology and its applications[J]. Chem Life, 2020,40(8):1208-1219.
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.
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
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
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
ZHENG G, TERRY J M, BELGRADER P. Massively parallel digital transcriptional profiling of single cells[J]. Nat Commun, 2017,8(14049):1-12.
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
HAN X P, WANG R Y, ZHOU Y C. Mapping the mouse cell atlas by microwell-seq[J]. Cell, 2018,22(172):1091-1107.
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.
HASHIMSHONY T, SENDEROVICH N, AVITAL G. CEL-Seq2:sensitive highly-multiplexed single-cell RNA-Seq[J]. Genome Biol, 2016,17(77):1-7.
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
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
CHAPMAN A R, HE Z, LU S J. Single cell transcriptome amplification with MALBAC[J]. PLoS ONE, 2015,10(3):1-12.
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
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
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
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
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
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.
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
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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(a) Nextera XT DNA Library Pre Kit (Illumina); (b) Nextera DNA Flex Library Pre Kit (Illumina)