The single-cell lab or how to perform single-cell molecular analysis

Whole Genome Amplification: Methods and Protocols

Volumn , Issue , 2015, Pages 43-55

  Kirchner, Roland ^a   Alunni Fabbroni, Marianna ^b  

^a LEUKOCARE AG   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

Cellular heterogeneity; Gene expression profiling; PCR; Single cell analysis; Whole genome amplification

Indexed keywords

ANIMAL; GENE EXPRESSION PROFILING; GENOME; GENOMICS; HUMAN; NUCLEIC ACID AMPLIFICATION; PROCEDURES; SINGLE CELL ANALYSIS; STANDARDS;

ANIMALS; GENE EXPRESSION PROFILING; GENOME; GENOMICS; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SINGLE-CELL ANALYSIS;

EID: 84955122428     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4939-2990-0_3     Document Type: Chapter

References (71)

1. Fujii H, Marsh C, Cairns P, Sidransky D, Gabrielson E (1996) Genetic divergence in the clonal evolution of breast cancer. Cancer Res 56(7):1493-1497
2. Macintosh CA, Stower M, Reid N, Maitland NJ (1998) Precise microdissection of human prostate cancers reveals genotypic heterogeneity. Cancer Res 58(1):23-28
3. Klein CA, Blankenstein TJ, Schmidt-Kittler O, Petronio M, Polzer B, Stoecklein NH, Riethmuller G (2002) Genetic heterogeneity of single disseminated tumour cells in minimal residual cancer. Lancet 360(9334):683-689. doi: 10.1016/S0140-6736(02)09838-0
4. Tang DG (2012) Understanding cancer stem cell heterogeneity and plasticity. Cell Res 22(3):457-472. doi: 10.1038/cr.2012.13
5. Passegue E, Jamieson CH, Ailles LE, Weissman IL (2003) Normal and leukemic hematopoiesis:are leukemias a stem cell disorder or a reacquisition of stem cell characteristics? Proc Natl Acad Sci U S A 100(Suppl 1):11842-11849. doi: 10.1073/pnas.2034201100
6. Cai L, Friedman N, Xie XS (2006) Stochastic protein expression in individual cells at the single molecule level. Nature 440(7082):358-362. doi: 10.1038/nature04599
7. Ottesen EA, Hong JW, Quake SR, Leadbetter JR (2006) Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314(5804):1464-1467. doi: 10.1126/science.1131370
8. Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6(6):451-464. doi: 10.1038/nrg1615
9. Coumans FA, van Dalum G, Beck M, Terstappen LW (2013) Filter characteristics influencing circulating tumor cell enrichment from whole blood. PLoS One 8(4), e61770. doi: 10.1371/journal.pone.0061770
10. Posel C, Moller K, Frohlich W, Schulz I, Boltze J, Wagner DC (2012) Density gradient centrifugation compromises bone marrow mononuclear cell yield. PLoS One 7(12):e50293. doi: 10.1371/journal.pone.0050293
11. McNiece I, Briddell R, Stoney G, Kern B, Zilm K, Recktenwald D, Miltenyi S (1997) Largescale isolation of CD34+ cells using the Amgen cell selection device results in high levels of purity and recovery. J Hematother 6(1):5-11
12. Johnson KW, Dooner M, Quesenberry PJ (2007) Fluorescence activated cell sorting: a window on the stem cell. Curr Pharm Biotechnol 8(3):133-139
13. Ibrahim SF, van den Engh G (2007) Flow cytometry and cell sorting. Adv Biochem Eng Biotechnol 106:19-39. doi: 10.1007/10_2007_073
14. Frohlich J, Konig H (2000) New techniques for isolation of single prokaryotic cells. FEMS Microbiol Rev 24(5):567-572
15. Barteneva NS, Ketman K, Fasler-Kan E, Potashnikova D, Vorobjev IA (2013) Cell sorting in cancer research-diminishing degree of cell heterogeneity. Biochim Biophys Acta 1836(1):105-122. doi: 10.1016/j.bbcan.2013.02.004
16. Fracasso T, Heinrich M, Hohoff C, Brinkmann B, Pfeiffer H (2009) Ultrasound-accelerated formalin fixation improves the preservation of nucleic acids extraction in histological sections. Int J Legal Med 123(6):521-525. doi: 10.1007/s00414-009-0368-1
17. Cheng L, Zhang S, MacLennan GT, Williamson SR, Davidson DD, Wang M, Jones TD, Lopez-Beltran A, Montironi R (2013) Laser-assisted microdissection in translational research: theory, technical considerations, and future applications. Appl Immunohistochem Mol Morphol 21(1):31-47. doi: 10.1097/PAI.0b013e31824d0519
18. Kim JO, Kim HN, Hwang MH, Shin HI, Kim SY, Park RW, Park EY, Kim IS, van Wijnen AJ, Stein JL, Lian JB, Stein GS, Choi JY (2003) Differential gene expression analysis using paraffin-embedded tissues after laser microdissection. J Cell Biochem 90(5):998-1006. doi: 10.1002/jcb.10680
19. Miura K, Bowman ED, Simon R, Peng AC, Robles AI, Jones RT, Katagiri T, He P, Mizukami H, Charboneau L, Kikuchi T, Liotta LA, Nakamura Y, Harris CC (2002) Laser capture microdissection and microarray expression analysis of lung adenocarcinoma reveals tobacco smoking- and prognosis-related molecular profiles. Cancer Res 62(11):3244-3250
20. Lindeman N, Waltregny D, Signoretti S, Loda M (2002) Gene transcript quantitation by realtime RT-PCR in cells selected by immunohistochemistry-laser capture microdissection. Diagn Mol Pathol 11(4):187-192
21. Andersson H, van den Berg A (2004) Microtechnologies and nanotechnologies for single-cell analysis. Curr Opin Biotechnol 15(1):44-49. doi: 10.1016/j.copbio.2004.01.004
22. Edd JF, Di Carlo D, Humphry KJ, Koster S, Irimia D, Weitz DA, Toner M (2008) Controlled encapsulation of single-cells into monodisperse picolitre drops. Lab Chip 8(8):1262-1264. doi: 10.1039/b805456h
23. Brouzes E, Medkova M, Savenelli N, Marran D, Twardowski M, Hutchison JB, Rothberg JM, Link DR, Perrimon N, Samuels ML (2009) Droplet microfluidic technology for single-cell high-throughput screening. Proc Natl Acad Sci U S A 106(34):14195-14200. doi: 10.1073/pnas.0903542106
24. Saliba AE, Saias L, Psychari E, Minc N, Simon D, Bidard FC, Mathiot C, Pierga JY, Fraisier V, Salamero J, Saada V, Farace F, Vielh P, Malaquin L, Viovy JL (2010) Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays. Proc Natl Acad Sci U S A 107(33):14524-14529. doi: 10.1073/pnas.1001515107
25. Vona G, Sabile A, Louha M, Sitruk V, Romana S, Schutze K, Capron F, Franco D, Pazzagli M, Vekemans M, Lacour B, Brechot C, Paterlini-Brechot P (2000) Isolation by size of epithelial tumor cells: a new method for the immunomorphological and molecular characterization of circulatingtumor cells. Am J Pathol 156(1):57-63. doi: 10.1016/S0002-9440(10)64706-2
26. Shafiee H, Caldwell JL, Sano MB, Davalos RV (2009) Contactless dielectrophoresis: a new technique for cell manipulation. Biomed Microdevices 11(5):997-1006. doi: 10.1007/s10544-009-9317-5
27. Di Carlo D, Wu LY, Lee LP (2006) Dynamic single cell culture array. Lab Chip 6(11):1445-1449. doi: 10.1039/b605937f
28. Champlot S, Berthelot C, Pruvost M, Bennett EA, Grange T, Geigl EM (2010) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PloS One 5 (9). doi: 10.1371/journal.pone.0013042
29. Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng JF (2011) Decontamination of MDA reagents for single cell whole genome amplification. PLoS One 6(10):e26161. doi: 10.1371/journal.pone.0026161
30. Kampke T, Kieninger M, Mecklenburg M (2001) Efficient primer design algorithms. Bioinformatics 17(3):214-225
31. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410. doi: 10.1016/S0022-2836(05)80360-2
32. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13:134. doi: 10.1186/1471-2105-13-134
33. Dennis Lo YM (1998) Setting up a PCR laboratory. Methods Mol Med 16:11-17. doi: 10.1385/0-89603-499-2:11
34. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64(10):3724-3730
35. Qiu X, Wu L, Huang H, McDonel PE, Palumbo AV, Tiedje JM, Zhou J (2001) Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl Environ Microbiol 67(2):880-887. doi: 10.1128/AEM.67.2.880-887.2001
36. Wacker MJ, Godard MP (2005) Analysis of one-step and two-step real-time RT-PCR using SuperScript III. J Biomol Tech 16(3):266-271
37. Wong ML, Medrano JF (2005) Real-time PCR for mRNA quantitation. BioTechniques 39(1):75-85
38. Stahlberg A, Kubista M, Pfaffl M (2004) Comparison of reverse transcriptases in gene expression analysis. Clin Chem 50(9):1678-1680. doi: 10.1373/clinchem.2004.035469
39. Dietmaier W, Hartmann A, Wallinger S, Heinmoller E, Kerner T, Endl E, Jauch KW, Hofstadter F, Ruschoff J (1999) Multiple mutation analyses in single tumor cells with improved whole genome amplification. Am J Pathol 154(1):83-95. doi: 10.1016/S0002-9440(10)65254-6
40. Telenius H, Carter NP, Bebb CE, Nordenskjold M, Ponder BA, Tunnacliffe A (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13(3):718-725
41. Zhang L, Cui X, Schmitt K, Hubert R, Navidi W, Arnheim N (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci U S A 89(13):5847-5851
42. Himmelbauer H, Schalkwyk LC, Lehrach H (2000) Interspersed repetitive sequence (IRS)-PCR for typing of whole genome radiation hybrid panels. Nucleic Acids Res 28(2), e7
43. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407-4414
44. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 99(8):5261-5266. doi: 10.1073/pnas.082089499
45. Blanco L, Bernad A, Lazaro JM, Martin G, Garmendia C, Salas M (1989) Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 264(15):8935-8940
46. Silander K, Saarela J (2008) Whole genome amplification with Phi29 DNA polymerase to enable genetic or genomic analysis of samples of low DNA yield. Methods Mol Biol 439:1-18. doi: 10.1007/978-1-59745-188-8_1
47. Lasken RS (2009) Genomic DNA amplification by the multiple displacement amplification (MDA) method. Biochem Soc Trans 37(Pt 2):450-453. doi: 10.1042/BST0370450
48. Lovmar L, Syvanen AC (2006) Multiple displacement amplification to create a long-lasting source of DNA for genetic studies. Hum Mutat 27(7):603-614. doi: 10.1002/humu.20341
49. Han T, Chang CW, Kwekel JC, Chen Y, Ge Y, Martinez-Murillo F, Roscoe D, Tezak Z, Philip R, Bijwaard K, Fuscoe JC (2012) Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development. BMC Genomics 13:217. doi: 10.1186/1471-2164-13-217
50. Junier P, Kim OS, Hadas O, Imhoff JF, Witzel KP (2008) Evaluation of PCR primer selectivity and phylogenetic specificity by using amplification of 16S rRNA genes from betaproteobacterial ammonia-oxidizing bacteria in environmental samples. Appl Environ Microbiol 74(16):5231-5236. doi: 10.1128/AEM.00288-08
51. Ishii K, Fukui M (2001) Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl Environ Microbiol 67(8):3753-3755. doi: 10.1128/AEM.67.8.3753-3755.2001
52. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71(12):8966-8969. doi: 10.1128/AEM.71.12.8966-8969.2005
53. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62(2):625-630
54. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12(2):R18. doi: 10.1186/gb-2011-12-2-r18
55. von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCRbased rRNA analysis. FEMS Microbiol Rev 21(3):213-229
56. Wagner A, Blackstone N, Cartwright P, Dick M, Misof B, Snow P, Wagner GP, Bartels J, Murtha M, Pendleton J (1994) Surveys of gene families using polymerase chain reaction:PCR selection and PCR drift. Syst Biol 43(2):250-261
57. Suzuki M, Rappe MS, Giovannoni SJ (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl Environ Microbiol 64(11):4522-4529
58. Kroneis T, Geigl JB, El-Heliebi A, Auer M, Ulz P, Schwarzbraun T, Dohr G, Sedlmayr P (2011) Combined molecular genetic and cytogenetic analysis from single cells after isothermal wholegenome amplification. Clin Chem 57(7):1032-1041. doi: 10.1373/clinchem.2011.162131
59. Voet T, Kumar P, Van Loo P, Cooke SL, Marshall J, Lin ML, Zamani Esteki M, Van der Aa N, Mateiu L, McBride DJ, Bignell GR, McLaren S, Teague J, Butler A, Raine K, Stebbings LA, Quail MA, D'Hooghe T, Moreau Y, Futreal PA, Stratton MR, Vermeesch JR, Campbell PJ (2013) Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res 41(12):6119-6138. doi: 10.1093/nar/gkt345
60. Corneveaux JJ, Kruer MC, Hu-Lince D, Ramsey KE, Zismann VL, Stephan DA, Craig DW, Huentelman MJ (2007) SNP-based chromosomal copy number ascertainment following multiple displacement whole-genome amplification. BioTechniques 42(1):77-83
61. Paez JG, Lin M, Beroukhim R, Lee JC, Zhao X, Richter DJ, Gabriel S, Herman P, Sasaki H, Altshuler D, Li C, Meyerson M, Sellers WR (2004) Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res 32(9), e71. doi: 10.1093/nar/gnh069
62. Arriola E, Lambros MB, Jones C, Dexter T, Mackay A, Tan DS, Tamber N, Fenwick K, Ashworth A, Dowsett M, Reis-Filho JS (2007) Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation. Lab Invest 87(1):75-83. doi: 10.1038/labinvest.3700495
63. Lage JM, Leamon JH, Pejovic T, Hamann S, Lacey M, Dillon D, Segraves R, Vossbrinck B, Gonzalez A, Pinkel D, Albertson DG, Costa J, Lizardi PM (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 13(2):294-307. doi: 10.1101/gr.377203
64. Bredel M, Bredel C, Juric D, Kim Y, Vogel H, Harsh GR, Recht LD, Pollack JR, Sikic BI (2005) Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. J Mol Diagn 7(2):171-182. doi: 10.1016/S1525-1578(10)60543-0
65. Mardis ER (2008) The impact of nextgeneration sequencing technology on genetics. Trends Genet 24(3):133-141. doi: 10.1016/j. tig.2007.12.007
66. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES (2009) Highresolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6(1):99-103. doi: 10.1038/nmeth.1276
67. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41(10):1061-1067. doi: 10.1038/ng.437
68. Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, Troge J, Ravi K, Esposito D, Lakshmi B, Wigler M, Navin N, Hicks J (2012) Genome-wide copy number analysis of single cells. Nat Protoc 7(6):1024-1041. doi: 10.1038/nprot.2012.039
69. Mohlendick B, Bartenhagen C, Behrens B, Honisch E, Raba K, Knoefel WT, Stoecklein NH (2013) A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH. PLoS One 8(6):e67031. doi: 10.1371/journal.pone.0067031
70. Zhang C, Zhang C, Chen S, Yin X, Pan X, Lin G, Tan Y, Tan K, Xu Z, Hu P, Li X, Chen F, Xu X, Li Y, Zhang X, Jiang H, Wang W (2013) A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing. PLoS One 8(1):e54236. doi: 10.1371/journal.pone.0054236
71. Dan S, Chen F, Choy KW, Jiang F, Lin J, Xuan Z, Wang W, Chen S, Li X, Jiang H, Leung TY, Lau TK, Su Y, Zhang W, Zhang X (2012) Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing. PLoS One 7(2):e27835. doi: 10.1371/journal.pone.0027835