REVIEW

Single-cell genomics: An overview

  • Qichao WANG 1 ,
  • Xianmin ZHU 1,2 ,
  • Yun FENG 1 ,
  • Zhigang XUE 1 ,
  • Guoping FAN , 2,3,4
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  • 1. Stem Cell Research Center, Department of Regenerative Medicine, Tongji University School of Medicine, Tongji University, Shanghai 200092, China
  • 2. Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, China
  • 3. School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
  • 4. Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA

Received date: 26 Aug 2013

Accepted date: 05 Nov 2013

Published date: 01 Dec 2013

Copyright

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg

Abstract

The newly developed next-generation sequencing platforms, in combination with genome-scale amplification methods, provide a powerful tool to study genomics from a single cell. This mini-review summarizes the technologies of single cell genomics and their applications in several areas of biomedical research including stem cells, cancer biology and reproductive medicine. Particularly, it highlights recent advances in single cell exome sequencing, RNA-seq, and genome sequencing. The application of these powerful techniques will shed new light on the fundamental principles of gene transcription and genome organization at single-cell level and improve our understanding of cellular heterogeneity and diversity in multicellular organisms.

Cite this article

Qichao WANG , Xianmin ZHU , Yun FENG , Zhigang XUE , Guoping FAN . Single-cell genomics: An overview[J]. Frontiers in Biology, 2013 , 8(6) : 569 -576 . DOI: 10.1007/s11515-013-1285-8

1
Aird D, Ross M G, Chen W S, Danielsson M, Fennell T, Russ C, Jaffe D B, Nusbaum C, Gnirke A (2011). Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol, 12(2): R18

DOI PMID

2
Allen L Z, Ishoey T, Novotny M A, McLean J S, Lasken R S, Williamson S J (2011). Single virus genomics: a new tool for virus discovery. PLoS ONE, 6(3): e17722

DOI PMID

3
Bhutani N, Burns D M, Blau H M (2011). DNA demethylation dynamics. Cell, 146(6): 866-872

DOI PMID

4
Buganim Y, Faddah D A, Cheng A W, Itskovich E, Markoulaki S, Ganz K, Klemm S L, van Oudenaarden A, Jaenisch R (2012). Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell, 150(6): 1209-1222

DOI PMID

5
Chaffer C L, Weinberg R A (2011). A perspective on cancer cell metastasis. Science, 331(6024): 1559-1564

DOI PMID

6
Clark M J, Homer N, O’Connor B D, Chen Z, Eskin A, Lee H, Merriman B, Nelson S F (2010). U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet, 6(1): e1000832

DOI PMID

7
Corneveaux J J, Kruer M C, Hu-Lince D, Ramsey K E, Zismann V L, Stephan D A, Craig D W, Huentelman M J (2007). SNP-based chromosomal copy number ascertainment following multiple displacement whole-genome amplification. Biotechniques, 42(1): 77-83

DOI PMID

8
Dalerba P, Kalisky T, Sahoo D, Rajendran P S, Rothenberg M E, Leyrat A A, Sim S, Okamoto J, Johnston D M, Qian D, Zabala M, Bueno J, Neff N F, Wang J, Shelton A A, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke M F, Quake S R (2011). Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol, 29(12): 1120-1127

DOI PMID

9
Dean F B, Hosono S, Fang L, Wu X, Faruqi A F, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore S F, Egholm M, Lasken R S (2002). Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA, 99(8): 5261-5266

DOI PMID

10
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009). Real-time DNA sequencing from single polymerase molecules. Science, 323(5910): 133-138

DOI PMID

11
Esteller M (2007). Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet, 8(4): 286-298

DOI PMID

12
Fan H C, Wang J, Potanina A, Quake S R (2011). Whole-genome molecular haplotyping of single cells. Nat Biotechnol, 29(1): 51-57

DOI PMID

13
Farago C, Chester I C (1961). Cancer in the Territory of Papua and New Guinea: a preliminary communication. Med J Aust, 48(2): 1033-1035

PMID

14
Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, Wong W, Schadt E (2013). Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLOS Comput Biol, 9(3): e1002935

DOI PMID

15
Frontera W R, Zayas A R, Rodriguez N (2012). Aging of human muscle: understanding sarcopenia at the single muscle cell level. Phys Med Rehabil Clin N Am, 23(1): 201-207, xiii (xiii.)

DOI PMID

16
Galán A, Montaner D, Póo M E, Valbuena D, Ruiz V, Aguilar C, Dopazo J, Simón C (2010). Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis. PLoS ONE, 5(10): e13615

DOI PMID

17
Geschwind D H, Konopka G (2009). Neuroscience in the era of functional genomics and systems biology. Nature, 461(7266): 908-915

DOI PMID

18
Guo Y, Yang Y, Zhou J, Czajkowsky D M, Liu B, Shao Z (2012). Microdissection of spatially identified single nuclei in a solid tumor for single cell whole genome sequencing. Biotechniques, 0(0): 1-3

PMID

19
Hamburger A W, Salmon S E (1977). Primary bioassay of human tumor stem cells. Science, 197(4302): 461-463

DOI PMID

20
Hanson E K, Ballantyne J (2005). Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA. Anal Biochem, 346(2): 246-257

DOI PMID

21
Hashimshony, T., Wagner, F., Sher, N., and Yanai, I. (2012). CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell reports2, 666-673.

22
He C (2010). Grand challenge commentary: RNA epigenetics? Nat Chem Biol, 6(12): 863-865

DOI PMID

23
Heitzer E, Auer M, Gasch C, Pichler M, Ulz P, Hoffmann E M, Lax S, Waldispuehl-Geigl J, Mauermann O, Lackner C, Höfler G, Eisner F, Sill H, Samonigg H, Pantel K, Riethdorf S, Bauernhofer T, Geigl J B, Speicher M R (2013). Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res, 73(10): 2965-2975

DOI PMID

24
Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Li F, Wu K, Liang J, Shao D, Wu H, Ye X, Ye C, Wu R, Jian M, Chen Y, Xie W, Zhang R, Chen L, Liu X, Yao X, Zheng H, Yu C, Li Q, Gong Z, Mao M, Yang X, Yang L, Li J, Wang W, Lu Z, Gu N, Laurie G, Bolund L, Kristiansen K, Wang J, Yang H, Li Y, Zhang X, Wang J (2012). Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell, 148(5): 873-885

DOI PMID

25
Hughes S, Jones J L (2007). The use of multiple displacement amplified DNA as a control for methylation specific PCR, pyrosequencing, bisulfite sequencing and methylation-sensitive restriction enzyme PCR. BMC Mol Biol, 8(1): 91

DOI PMID

26
Hutchison C A 3rd, Smith H O, Pfannkoch C, Venter J C (2005). Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci USA, 102(48): 17332-17336

DOI PMID

27
Iourov I Y, Vorsanova S G, Yurov Y B (2012). Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases. Curr Genomics, 13(6): 477-488

DOI PMID

28
Islam S, Kjällquist U, Moliner A, Zajac P, Fan J B, Lönnerberg P, Linnarsson S (2011). Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res, 21(7): 1160-1167

DOI PMID

29
Jones P A, Baylin S B (2007). The epigenomics of cancer. Cell, 128(4): 683-692

DOI PMID

30
Kleinsmith L J, Pierce G B Jr (1964). Multipotentiality of Single Embryonal Carcinoma Cells. Cancer Res, 24: 1544-1551

PMID

31
Lecault V, Vaninsberghe M, Sekulovic S, Knapp D J, Wohrer S, Bowden W, Viel F, McLaughlin T, Jarandehei A, Miller M, Falconnet D, White A K, Kent D G, Copley M R, Taghipour F, Eaves C J, Humphries R K, Piret J M, Hansen C L (2011). High-throughput analysis of single hematopoietic stem cell proliferation in microfluidic cell culture arrays. Nat Methods, 8(7): 581-586

DOI PMID

32
Lee, J.Y., Dong, S.M., Kim, S.Y., Yoo, N.J., Lee, S.H., and Park, W.S. (1998). A simple, precise and economical microdissection technique for analysis of genomic DNA from archival tissue sections. Virchows Archiv: an international journal of pathology 433, 305-309.

33
Li L, Clevers H (2010). Coexistence of quiescent and active adult stem cells in mammals. Science, 327(5965): 542-545

DOI PMID

34
Ling J, Deng Y, Long X, Liu J, Du H, Cao B, Xu K (2012). Single-nucleotide polymorphism array coupled with multiple displacement amplification: accuracy and spatial resolution for analysis of chromosome copy numbers in few cells. Biotechnol Appl Biochem, 59(1): 35-44

DOI PMID

35
Lu S, Zong C, Fan W, Yang M, Li J, Chapman A R, Zhu P, Hu X, Xu L, Yan L, Bai F, Qiao J, Tang F, Li R, Xie X S (2012). Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science, 338(6114): 1627-1630

DOI PMID

36
Luthra R, Medeiros L J (2004). Isothermal multiple displacement amplification: a highly reliable approach for generating unlimited high molecular weight genomic DNA from clinical specimens. J Mol Diagn, 6(3): 236-242

DOI PMID

37
Mardis E R (2008). The impact of next-generation sequencing technology on genetics. Trends Genet, 24(3): 133-141

DOI PMID

38
McLean J S, Lombardo M J, Ziegler M G, Novotny M, Yee-Greenbaum J, Badger J H, Tesler G, Nurk S, Lesin V, Brami D, Hall A P, Edlund A, Allen L Z, Durkin S, Reed S, Torriani F, Nealson K H, Pevzner P A, Friedman R, Venter J C, Lasken R S (2013). Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Res, 23(5): 867-877

DOI PMID

39
McVean G A, Myers S R, Hunt S, Deloukas P, Bentley D R, Donnelly P (2004). The fine-scale structure of recombination rate variation in the human genome. Science, 304(5670): 581-584

DOI PMID

40
McWilliam Leitch E C, McLauchlan J (2013). Determining the cellular diversity of hepatitis C virus quasispecies by single-cell viral sequencing. J Virol, 87(23): 12648-12655

DOI PMID

41
Metzker M L (2010). Sequencing technologies- the next generation. Nat Rev Genet, 11(1): 31-46

DOI PMID

42
Morozova O, Marra M A (2008). Applications of next-generation sequencing technologies in functional genomics. Genomics, 92(5): 255-264

DOI PMID

43
Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie W R, Hicks J, Wigler M (2011). Tumour evolution inferred by single-cell sequencing. Nature, 472(7341): 90-94

DOI PMID

44
Niedringhaus T P, Milanova D, Kerby M B, Snyder M P, Barron A E (2011). Landscape of next-generation sequencing technologies. Anal Chem, 83(12): 4327-4341

DOI PMID

45
Paez J G, Lin M, Beroukhim R, Lee J C, Zhao X, Richter D J, Gabriel S, Herman P, Sasaki H, Altshuler D, Li C, Meyerson M, Sellers W R (2004). Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res, 32(9): e71

DOI PMID

46
Pan X, Durrett R E, Zhu H, Tanaka Y, Li Y, Zi X, Marjani S L, Euskirchen G, Ma C, Lamotte R H, Park I H, Snyder M P, Mason C E, Weissman S M (2013). Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci USA, 110(2): 594-599

DOI PMID

47
Pan X, Urban A E, Palejev D, Schulz V, Grubert F, Hu Y, Snyder M, Weissman S M (2008). A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc Natl Acad Sci USA, 105(40): 15499-15504

DOI PMID

48
Park S Y, Gönen M, Kim H J, Michor F, Polyak K (2010). Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J Clin Invest, 120(2): 636-644

DOI PMID

49
Quenneville, S., Turelli, P., Bojkowska, K., Raclot, C., Offner, S., Kapopoulou, A., and Trono, D. (2012). The KRAB-ZFP/KAP1 system contributes to the early embryonic establishment of site-specific DNA methylation patterns maintained during development. Cell reports2, 766-773.

50
Ramsköld D, Luo S, Wang Y C, Li R, Deng Q, Faridani O R, Daniels G A, Khrebtukova I, Loring J F, Laurent L C, Schroth G P, Sandberg R (2012). Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol, 30(8): 777-782

DOI PMID

51
Reya T, Morrison S J, Clarke M F, Weissman I L (2001). Stem cells, cancer, and cancer stem cells. Nature, 414(6859): 105-111

DOI PMID

52
Rothberg J M, Hinz W, Rearick T M, Schultz J, Mileski W, Davey M, Leamon J H, Johnson K, Milgrew M J, Edwards M, Hoon J, Simons J F, Marran D, Myers J W, Davidson J F, Branting A, Nobile J R, Puc B P, Light D, Clark T A, Huber M, Branciforte J T, Stoner I B, Cawley S E, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza J A, Namsaraev E, McKernan K J, Williams A, Roth G T, Bustillo J (2011). An integrated semiconductor device enabling non-optical genome sequencing. Nature, 475(7356): 348-352

DOI PMID

53
Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno K D, Imai T, Ueda H R (2013). Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol, 14(4): R31

DOI PMID

54
Schoenborn L, Yates P S, Grinton B E, Hugenholtz P, Janssen P H (2004). Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Appl Environ Microbiol, 70(7): 4363-4366

DOI PMID

55
Shalek A K, Satija R, Adiconis X, Gertner R S, Gaublomme J T, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta J J, Gennert D, Gnirke A, Goren A, Hacohen N, Levin J Z, Park H, Regev A (2013). Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature, 498(7453): 236-240

DOI PMID

56
Shendure J, Ji H (2008). Next-generation DNA sequencing. Nat Biotechnol, 26(10): 1135-1145

DOI PMID

57
Simone N L, Bonner R F, Gillespie J W, Emmert-Buck M R, Liotta L A (1998). Laser-capture microdissection: opening the microscopic frontier to molecular analysis. Trends Genet, 14(7): 272-276

DOI PMID

58
Song C X, Clark T A, Lu X Y, Kislyuk A, Dai Q, Turner S W, He C, Korlach J (2012). Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods, 9(1): 75-77

DOI PMID

59
Tahiliani M, Koh K P, Shen Y, Pastor W A, Bandukwala H, Brudno Y, Agarwal S, Iyer L M, Liu D R, Aravind L, Rao A (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 324(5929): 930-935

DOI PMID

60
Tan D W, Jensen K B, Trotter M W, Connelly J T, Broad S, Watt F M (2013). Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells. Development, 140(7): 1433-1444

DOI PMID

61
Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch B B, Siddiqui A, Lao K, Surani M A (2009). mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods, 6(5): 377-382

DOI PMID

62
Tang F, Lao K, Surani M A (2011). Development and applications of single-cell transcriptome analysis. Nat Methods, 8(4 Suppl): S6-S11

PMID

63
Torres L, Ribeiro F R, Pandis N, Andersen J A, Heim S, Teixeira M R (2007). Intratumor genomic heterogeneity in breast cancer with clonal divergence between primary carcinomas and lymph node metastases. Breast Cancer Res Treat, 102(2): 143-155

DOI PMID

64
Tzvetkov M V, Becker C, Kulle B, Nürnberg P, Brockmöller J, Wojnowski L (2005). Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification. Electrophoresis, 26(3): 710-715

DOI PMID

65
Unger M A, Chou H P, Thorsen T, Scherer A, Quake S R (2000). Monolithic microfabricated valves and pumps by multilayer soft lithography. Science, 288(5463): 113-116

DOI PMID

66
Voet T, Kumar P, Van Loo P, Cooke S L, Marshall J, Lin M L, Zamani Esteki M, Van der Aa N, Mateiu L, McBride D J, Bignell G R, McLaren S, Teague J, Butler A, Raine K, Stebbings L A, Quail M A, D’Hooghe T, Moreau Y, Futreal P A, Stratton M R, Vermeesch J R, Campbell P J (2013). Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res, 41(12): 6119-6138

DOI PMID

67
Wang J, Fan H C, Behr B, Quake S R (2012). Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell, 150(2): 402-412

DOI PMID

68
Wu A R, Neff N F, Kalisky T, Dalerba P, Treutlein B, Rothenberg M E, Mburu F M, Mantalas G L, Sim S, Clarke M F, Quake S R (2013). Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods,

DOI PMID

69
Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, He W, Zeng L, Xing M, Wu R, Jiang H, Liu X, Cao D, Guo G, Hu X, Gui Y, Li Z, Xie W, Sun X, Shi M, Cai Z, Wang B, Zhong M, Li J, Lu Z, Gu N, Zhang X, Goodman L, Bolund L, Wang J, Yang H, Kristiansen K, Dean M, Li Y, Wang J (2012). Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell, 148(5): 886-895

DOI PMID

70
Xue Z, Huang K, Cai C, Cai L, Jiang C Y, Feng Y, Liu Z, Zeng Q, Cheng L, Sun Y E, Liu J Y, Horvath S, Fan G (2013). Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature, 500(7464): 593-597

DOI PMID

71
Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Li R, Qiao J, Tang F (2013). Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol, 20(9): 1131-1139

DOI PMID

72
Zandi S, Ahsberg J, Tsapogas P, Stjernberg J, Qian H, Sigvardsson M (2012). Single-cell analysis of early B-lymphocyte development suggests independent regulation of lineage specification and commitment in vivo. Proc Natl Acad Sci USA, 109(39): 15871-15876

DOI PMID

73
Zhao Y, Gong X, Chen L, Li L, Liang Y, Chen S, Zhang Y (2013). Site-specific methylation of placental HSD11B2 gene promoter is related to intrauterine growth restriction. Eur J Hum Genet,

DOI PMID

74
Zong C, Lu S, Chapman A R, Xie X S (2012). Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338(6114): 1622-1626

DOI PMID

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