Home LiteratureArticle Details
PMID: 21631906 Published · epublish English Journal Article

Future medical applications of single-cell sequencing in cancer.

Genome medicine ·Vol. 3 ·No. 5 ·2011-05-31 ·Pages 31

Navin N, Hicks J

Abstract

Advances in whole genome amplification and next-generation sequencing methods have enabled genomic analyses of single cells, and these techniques are now beginning to be used to detect genomic lesions in individual cancer cells. Previous approaches have been unable to resolve genomic differences in complex mixtures of cells, such as heterogeneous tumors, despite the importance of characterizing such tumors for cancer treatment. Sequencing of single cells is likely to improve several aspects of medicine, including the early detection of rare tumor cells, monitoring of circulating tumor cells (CTCs), measuring intratumor heterogeneity, and guiding chemotherapy. In this review we discuss the challenges and technical aspects of single-cell sequencing, with a strong focus on genomic copy number, and discuss how this information can be used to diagnose and treat cancer patients.

Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Navin Nicholas
Department of Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA. [email protected].
Hicks James
References (93)
93 references, click to expand
  1. Molecular definition of breast tumor heterogeneity.
    Cancer Cell. 2007 Mar;11(3):259-73 PMID: 17349583
  2. Genotypic intratumoral heterogeneity in breast carcinoma with HER2/neu amplification: evaluation according to ASCO/CAP criteria.
    Am J Clin Pathol. 2009 May;131(5):678-82 PMID: 19369627
  3. Interphase cytogenetics reveals a high incidence of aneuploidy and intra-tumour heterogeneity in breast cancer.
    Br J Cancer. 1995 Jul;72(1):51-5 PMID: 7599066
  4. Genomic analysis of genetic heterogeneity and evolution in high-grade serous ovarian carcinoma.
    Oncogene. 2010 Sep 2;29(35):4905-13 PMID: 20581869
  5. Predictive and prognostic value of peripheral blood cytokeratin-19 mRNA-positive cells detected by real-time polymerase chain reaction in node-negative breast cancer patients.
    J Clin Oncol. 2006 Aug 10;24(23):3756-62 PMID: 16769987
  6. High resolution array-CGH analysis of single cells.
    Nucleic Acids Res. 2007;35(3):e15 PMID: 17178751
  7. Prognostic value of the molecular detection of circulating tumor cells using a multimarker reverse transcription-PCR assay for cytokeratin 19, mammaglobin A, and HER2 in early breast cancer.
    Clin Cancer Res. 2008 May 1;14(9):2593-600 PMID: 18451221
  8. Characteristics associated with recurrence among women with ductal carcinoma in situ treated by lumpectomy.
    J Natl Cancer Inst. 2003 Nov 19;95(22):1692-702 PMID: 14625260
  9. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.
    Cell Stem Cell. 2010 May 7;6(5):468-78 PMID: 20452321
  10. Chromosome analysis of 97 primary breast carcinomas: identification of eight karyotypic subgroups.
    Genes Chromosomes Cancer. 1995 Mar;12(3):173-85 PMID: 7536456
  11. Complex landscapes of somatic rearrangement in human breast cancer genomes.
    Nature. 2009 Dec 24;462(7276):1005-10 PMID: 20033038
  12. Aneuploidy of chromosome 8 as detected by interphase fluorescence in situ hybridization is a recurrent finding in primary and metastatic breast cancer.
    Breast Cancer Res Treat. 1998 Mar;48(2):125-33 PMID: 9596484
  13. DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis.
    Genome Res. 2009 Jul;19(7):1243-53 PMID: 19447965
  14. Approaching solid tumor heterogeneity on a cellular basis by tissue proteomics using laser capture microdissection and biological mass spectrometry.
    J Proteome Res. 2009 May;8(5):2310-8 PMID: 19284784
  15. I-SPY 2: an adaptive breast cancer trial design in the setting of neoadjuvant chemotherapy.
    Clin Pharmacol Ther. 2009 Jul;86(1):97-100 PMID: 19440188
  16. Cancer as an evolutionary and ecological process.
    Nat Rev Cancer. 2006 Dec;6(12):924-35 PMID: 17109012
  17. High-resolution mapping of copy-number alterations with massively parallel sequencing.
    Nat Methods. 2009 Jan;6(1):99-103 PMID: 19043412
  18. Hallmarks of cancer: the next generation.
    Cell. 2011 Mar 4;144(5):646-74 PMID: 21376230
  19. Homogeneity and heterogeneity in pancreas cancer: presence of predominant and minor morphological types and implications.
    Int J Pancreatol. 1986 Jul;1(2):91-4 PMID: 3320225
  20. Evaluation and significance of circulating epithelial cells in patients with hormone-refractory prostate cancer.
    BJU Int. 2007 Mar;99(3):519-24 PMID: 17407512
  21. Lumpectomy compared with lumpectomy and radiation therapy for the treatment of intraductal breast cancer.
    N Engl J Med. 1993 Jun 3;328(22):1581-6 PMID: 8292119
  22. Tumor cells circulate in the peripheral blood of all major carcinomas but not in healthy subjects or patients with nonmalignant diseases.
    Clin Cancer Res. 2004 Oct 15;10(20):6897-904 PMID: 15501967
  23. Isolation of rare circulating tumour cells in cancer patients by microchip technology.
    Nature. 2007 Dec 20;450(7173):1235-9 PMID: 18097410
  24. Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer.
    Methods Mol Biol. 2011;700:89-104 PMID: 21204029
  25. Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA).
    Blood. 2009 Feb 5;113(6):1294-303 PMID: 18922857
  26. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.
    Genome Biol. 2007;8(10):R215 PMID: 17925008
  27. Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer.
    Br J Cancer. 2011 Jan 18;104(2):361-8 PMID: 21063398
  28. Genetic clonal diversity predicts progression to esophageal adenocarcinoma.
    Nat Genet. 2006 Apr;38(4):468-73 PMID: 16565718
  29. Whole genome amplification and its impact on CGH array profiles.
    BMC Res Notes. 2008 Jul 29;1:56 PMID: 18710509
  30. Molecular analysis of the immunoglobulin VH gene rearrangement in a primary cutaneous immunoblastic B-cell lymphoma by micromanipulation and single-cell PCR.
    J Invest Dermatol. 1997 Oct;109(4):541-5 PMID: 9326387
  31. Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones.
    Immunity. 1996 Jan;4(1):47-55 PMID: 8574851
  32. Single circulating tumor cell detection and overall survival in nonmetastatic breast cancer.
    Ann Oncol. 2010 Apr;21(4):729-733 PMID: 19850639
  33. Detection and removal of biases in the analysis of next-generation sequencing reads.
    PLoS One. 2011 Jan 31;6(1):e16685 PMID: 21304912
  34. Genome remodelling in a basal-like breast cancer metastasis and xenograft.
    Nature. 2010 Apr 15;464(7291):999-1005 PMID: 20393555
  35. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype.
    J Clin Invest. 2010 Feb;120(2):636-44 PMID: 20101094
  36. Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation.
    Lab Invest. 2007 Jan;87(1):75-83 PMID: 17170740
  37. Sensitive and accurate detection of copy number variants using read depth of coverage.
    Genome Res. 2009 Sep;19(9):1586-92 PMID: 19657104
  38. Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity.
    Clin Cancer Res. 2006 Oct 1;12(19):5632-40 PMID: 17020965
  39. Intratumoral heterogeneity of HER2/neu expression and its consequences for the management of advanced breast cancer.
    Ann Oncol. 2008 Mar;19(3):595-7 PMID: 18272907
  40. Intratumoral nuclear morphologic heterogeneity in prostate cancer.
    Urology. 1997 Apr;49(4):652-7 PMID: 9111646
  41. Heterogeneity of chromosome 17 and erbB-2 gene copy number in primary and metastatic bladder cancer.
    Cytometry. 1995 Sep 1;21(1):40-6 PMID: 8529469
  42. Ductal carcinoma in situ and the emergence of diversity during breast cancer evolution.
    Clin Cancer Res. 2008 Jan 15;14(2):370-8 PMID: 18223211
  43. Direct genetic analysis of single disseminated cancer cells for prediction of outcome and therapy selection in esophageal cancer.
    Cancer Cell. 2008 May;13(5):441-53 PMID: 18455127
  44. Genetic heterogeneity in HER2 testing in breast cancer: panel summary and guidelines.
    Arch Pathol Lab Med. 2009 Apr;133(4):611-2 PMID: 19391661
  45. Molecular analysis of multifocal prostate cancer by comparative genomic hybridization.
    Prostate. 2008 Dec 1;68(16):1715-24 PMID: 18781578
  46. Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens.
    Nucleic Acids Res. 2010 Aug;38(14):e151 PMID: 20525786
  47. Use of whole genome amplification and comparative genomic hybridisation to detect chromosomal copy number alterations in cell line material and tumour tissue.
    Cytogenet Genome Res. 2004;105(1):18-24 PMID: 15218253
  48. Cytogenetic manifestations of multiple myeloma heterogeneity.
    Genes Chromosomes Cancer. 2005 Jan;42(1):44-57 PMID: 15495197
  49. Whole genome amplification from a single cell: implications for genetic analysis.
    Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5847-51 PMID: 1631067
  50. New technologies for the detection of circulating tumour cells.
    Br Med Bull. 2010;94:49-64 PMID: 20418405
  51. Inferring tumor progression from genomic heterogeneity.
    Genome Res. 2010 Jan;20(1):68-80 PMID: 19903760
  52. Detection of CK-19 mRNA-positive cells in the peripheral blood of breast cancer patients with histologically and immunohistochemically negative axillary lymph nodes.
    Ann Oncol. 2005 Feb;16(2):240-6 PMID: 15668277
  53. CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data.
    Bioinformatics. 2010 Dec 15;26(24):3051-8 PMID: 20966003
  54. Mechanism of chimera formation during the Multiple Displacement Amplification reaction.
    BMC Biotechnol. 2007 Apr 12;7:19 PMID: 17430586
  55. Cytogenetic and flow cytometry DNA analysis of regional heterogeneity in a low grade human glioma.
    Cancer Res. 1995 Apr 1;55(7):1569-77 PMID: 7882367
  56. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells.
    Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4494-9 PMID: 10200290
  57. PSA and beyond: the past, present, and future of investigative biomarkers for prostate cancer.
    ScientificWorldJournal. 2010 Oct 01;10:1919-31 PMID: 20890581
  58. Prevention of invasive breast cancer in women with ductal carcinoma in situ: an update of the National Surgical Adjuvant Breast and Bowel Project experience.
    Semin Oncol. 2001 Aug;28(4):400-18 PMID: 11498833
  59. Flow cytometry--principles and feasibility in transfusion medicine. Enumeration of epithelial derived tumor cells in peripheral blood.
    Vox Sang. 1998;74 Suppl 2:269-74 PMID: 9704456
  60. Circulating melanoma cells and survival in metastatic melanoma.
    Int J Oncol. 2011 Mar;38(3):755-60 PMID: 21206975
  61. Intratumoral genetic heterogeneity in pilocytic astrocytomas revealed by CGH-analysis of microdissected tumor cells and FISH on tumor tissue sections.
    Int J Oncol. 2006 Feb;28(2):353-60 PMID: 16391789
  62. Intratumoral heterogeneity of HER2/neu in breast cancer--a rare event.
    Breast J. 2007 Mar-Apr;13(2):122-9 PMID: 17319852
  63. Karyotypic comparisons of multiple tumorous and macroscopically normal surrounding tissue samples from patients with breast cancer.
    Cancer Res. 1996 Feb 15;56(4):855-9 PMID: 8631024
  64. Biomarker expression and risk of subsequent tumors after initial ductal carcinoma in situ diagnosis.
    J Natl Cancer Inst. 2010 May 5;102(9):627-37 PMID: 20427430
  65. Genetic heterogeneity and clonal evolution in neuroblastoma.
    Br J Cancer. 2001 Jul 20;85(2):182-9 PMID: 11461074
  66. Tumour evolution inferred by single-cell sequencing.
    Nature. 2011 Apr 7;472(7341):90-4 PMID: 21399628
  67. Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays.
    Nucleic Acids Res. 2009 Aug;37(15):e105 PMID: 19541849
  68. Prognostic significance of a grading system considering tumor heterogeneity in muscle-invasive urothelial carcinoma of the urinary bladder.
    Int Urol Nephrol. 2003;35(2):169-73 PMID: 15072488
  69. How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine.
    Br J Cancer. 2010 Oct 12;103(8):1139-43 PMID: 20877357
  70. Breast cancer assessment tools and optimizing adjuvant therapy.
    Nat Rev Clin Oncol. 2010 Dec;7(12):725-32 PMID: 20975745
  71. Single-cell PCR analysis of T helper cells in human lymph node germinal centers.
    Am J Pathol. 2000 Mar;156(3):1067-71 PMID: 10702422
  72. Radiotherapy in breast-conserving treatment for ductal carcinoma in situ: first results of the EORTC randomised phase III trial 10853. EORTC Breast Cancer Cooperative Group and EORTC Radiotherapy Group.
    Lancet. 2000 Feb 12;355(9203):528-33 PMID: 10683002
  73. Clonal heterogeneity in breast cancer: karyotypic comparisons of multiple intra- and extra-tumorous samples from 3 patients.
    Int J Cancer. 1995 Sep 27;63(1):63-8 PMID: 7558454
  74. Comprehensive human genome amplification using multiple displacement amplification.
    Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6 PMID: 11959976
  75. HE4: a new potential early biomarker for the recurrence of ovarian cancer.
    Tumour Biol. 2010 Apr;31(2):113-9 PMID: 20358424
  76. Cytogenetic investigation of testicular carcinoma in situ and early seminoma by high-resolution comparative genomic hybridization analysis of subpopulations flow sorted according to DNA content.
    Cancer Genet Cytogenet. 2004 Mar;149(2):89-97 PMID: 15036883
  77. The genetics of cancer--a 3D model.
    Nat Genet. 1999 Jan;21(1 Suppl):38-41 PMID: 9915499
  78. Intratumoral heterogeneity in breast carcinoma revealed by laser-microdissection and comparative genomic hybridization.
    Cancer Genet Cytogenet. 1999 Apr 15;110(2):94-102 PMID: 10214356
  79. Bone marrow micrometastasis in breast cancer: review of detection methods, prognostic impact and biological issues.
    J Clin Pathol. 2008 May;61(5):570-6 PMID: 18037661
  80. High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.
    Nucleic Acids Res. 2008 Apr;36(7):e39 PMID: 18344524
  81. Personalized copy number and segmental duplication maps using next-generation sequencing.
    Nat Genet. 2009 Oct;41(10):1061-7 PMID: 19718026
  82. Whole genome amplification for array comparative genomic hybridization using DNA extracted from formalin-fixed, paraffin-embedded histological sections.
    J Mol Diagn. 2009 Mar;11(2):109-16 PMID: 19197000
  83. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
    Nature. 2009 Oct 8;461(7265):809-13 PMID: 19812674
  84. Tumor heterogeneity in lung cancer based on light microscopic features. A retrospective study of a consecutive series of 200 patients, treated surgically.
    Virchows Arch A Pathol Anat Histopathol. 1983;402(2):147-53 PMID: 6320525
  85. Intratumor genomic heterogeneity in breast cancer with clonal divergence between primary carcinomas and lymph node metastases.
    Breast Cancer Res Treat. 2007 Apr;102(2):143-55 PMID: 16906480
  86. Clone heterogeneity in diploid and aneuploid breast carcinomas as detected by FISH.
    Cytometry. 2001 Feb 15;46(1):50-6 PMID: 11241507
  87. Distant metastasis occurs late during the genetic evolution of pancreatic cancer.
    Nature. 2010 Oct 28;467(7319):1114-7 PMID: 20981102
  88. Chromosomal imbalances in primary and metastatic pancreatic carcinoma as detected by interphase cytogenetics: basic findings and clinical aspects.
    Br J Cancer. 1998 Apr;77(8):1337-42 PMID: 9579843
  89. ERCC5 is a novel biomarker of ovarian cancer prognosis.
    J Clin Oncol. 2008 Jun 20;26(18):2952-8 PMID: 18565881
  90. Novel patterns of genome rearrangement and their association with survival in breast cancer.
    Genome Res. 2006 Dec;16(12):1465-79 PMID: 17142309
  91. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH.
    Genome Res. 2003 Feb;13(2):294-307 PMID: 12566408
  92. mRNA-Seq whole-transcriptome analysis of a single cell.
    Nat Methods. 2009 May;6(5):377-82 PMID: 19349980
  93. Real-time DNA sequencing from single polymerase molecules.
    Science. 2009 Jan 2;323(5910):133-8 PMID: 19023044
Article Info
Journal
Genome medicine
Abbr.
Genome Med
ISSN
1756-994X
DOI
10.1186/gm247
Email
[email protected]
Published
2011-05-31
Epub
2011-00-31
Pages
31
Language
English
Region
England
NLM ID
101475844
PMCID
PMC3219072
External Links
PubMed source DOI: 10.1186/gm247 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2