Accessing Genetic Information with Liquid Biopsies

Trends in Genetics

Volumn 31, Issue 10, 2015, Pages 564-575

  Cai, Xuyu ^a   Janku, Filip ^b   Zhan, Qimin ^c   Fan, Jian Bing ^a,d  

^a ILLUMINA INC   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c PEKING UNION MEDICAL COLLEGE   (China)

^d AnchorDx Corporation   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPSY TECHNIQUE; CANCER SCREENING; CIRCULATING TUMOR CELL; DEGENERATIVE DISEASE; EPIGENETICS; EXOSOME; GENE EXPRESSION; GENETIC ANALYSIS; HUMAN; NEXT GENERATION SEQUENCING; NON INVASIVE PROCEDURE; PRENATAL DIAGNOSIS; PRIORITY JOURNAL; REVIEW; SENSITIVITY AND SPECIFICITY; SOMATIC MUTATION; BIOPSY; BLOOD; GENE THERAPY; GENETICS; HIGH THROUGHPUT SEQUENCING; NEOPLASM; PATHOLOGY; PROCEDURES; TUMOR EMBOLISM;

DNA; RNA;

BIOPSY; DNA; GENETIC THERAPY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; NEOPLASTIC CELLS, CIRCULATING; RNA;

EID: 84943383544     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2015.06.001     Document Type: Review

References (70)

1. Diaz L.A., Bardelli A. Liquid biopsies: genotyping circulating tumor DNA. J. Clin. Oncol. 2014, 32:579-586.
2. Haber D.A., Velculescu V.E. Blood-based analyses of cancer: circulating tumor cells and circulating tumor DNA. Cancer Discov. 2014, 4:650-661.
3. Heitzer E., et al. Circulating tumor cells and DNA as liquid biopsies. Genome Med. 2013, 5:73.
4. Bidard F-C., et al. Going with the flow: from circulating tumor cells to DNA. Sci. Transl. Med. 2013, 5:207ps14.
5. Schwarzenbach H., et al. Cell-free nucleic acids as biomarkers in cancer patients. Nat. Rev. Cancer 2011, 11:426-437.
6. Collins F.S., Varmus H. A new initiative on precision medicine. N. Engl. J. Med. 2015, 372:793-795.
7. Lander E.S. Cutting the Gordian helix - regulating genomic testing in the era of precision medicine. N. Engl. J. Med. 2015, 372:1185-1186.
8. Riethdorf S., et al. Detection of circulating tumor cells in peripheral blood of patients with metastatic breast cancer: a validation study of the CellSearch system. Clin. Cancer Res. 2007, 13:920-928.
9. Rack B., et al. Circulating tumor cells predict survival in early average-to-high risk breast cancer patients. J. Natl. Cancer Inst. 2014, Published online May 15, 2014. 10.1093/jnci/dju066.
10. Bidard F-C., et al. Clinical validity of circulating tumour cells in patients with metastatic breast cancer: a pooled analysis of individual patient data. Lancet Oncol. 2015, 15:406-414.
11. Scher H.I., et al. Circulating tumor cell biomarker panel as an individual-level surrogate for survival in metastatic castration-resistant prostate cancer. J. Clin. Oncol. 2015, 33. 1348-1255.
12. Hodgkinson C.L., et al. Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer. Nat. Med. 2014, 20:897-903.
13. Yu M., et al. Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition. Science 2013, 339:580-584.
14. Aceto N., et al. Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell 2015, 158:1110-1122.
15. Yu M., et al. Ex vivo culture of circulating breast tumor cells for individualized testing of drug susceptibility. Science 2014, 345:216-220.
16. Baccelli I., et al. Identification of a population of blood circulating tumor cells from breast cancer patients that initiates metastasis in a xenograft assay. Nat. Biotechnol. 2013, 31:539-544.
17. Sarioglu A.F., et al. A microfluidic device for label-free, physical capture of circulating tumor cell clusters. Nat. Methods 2015, 12:685-691.
18. Benn P., et al. Non-invasive prenatal testing for aneuploidy: current status and future prospects. Ultrasound Obstet. Gynecol. 2013, 42:15-33.
19. Newman A.M., et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat. Med. 2014, 20:548-554.
20. Murtaza M., et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013, 497:108-112.
21. Dawson S-J., et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N. Engl. J. Med. 2013, 368:1199-1209.
22. Forshew T., et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci. Transl. Med. 2012, 4:136ra68.
23. Hyman D.M., et al. Prospective blinded study of BRAFV600E mutation detection in cell-free DNA of patients with systemic histiocytic disorders. Cancer Discov. 2015, 5:64-71.
24. Board R., et al. Detection of PIK3CA mutations in circulating free DNA in patients with breast cancer. Breast Cancer Res. Treat. 2010, 120:461-467.
25. Bettegowda C., et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci. Transl. Med. 2014, 6:224ra24.
26. Chan K.C.A., et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:18761-18768.
27. Skog J., et al. Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat. Cell Biol. 2008, 10:1470-1476.
28. Properzi F., et al. Exosomes: the future of biomarkers in medicine. Biomark. Med. 2013, 7:769-778.
29. Cheng L., et al. Prognostic serum miRNA biomarkers associated with Alzheimer. Mol. Psychiatry 2014, Published online October 28, 2014. 10.1038/mp.2014.127.
30. Koh W., et al. Noninvasive in vivo monitoring of tissue-specific global gene expression in humans. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:7361-7366.
31. Katoh, M. (2014) Cardio-miRNAs and onco-miRNAs: circulating miRNA-based diagnostics for non-cancerous and cancerous diseases. Published online October 16, 1014 http://dx.doi.org/10.3389/fcell.2014.00061.
32. Vogelstein B., et al. Cancer genome landscapes. Science 2013, 339:1546-1558.
33. Diehl F., et al. BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nat. Methods 2006, 3:551-559.
34. Thierry A.R., et al. Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA. Nat. Med. 2014, 20:430-435.
35. Kinde I., et al. Detection and quantification of rare mutations with massively parallel sequencing. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:9530-9535.
36. Schmitt M.W., et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:14508-14513.
37. Kennedy S.R., et al. Detecting ultralow-frequency mutations by duplex sequencing. Nat. Protoc. 2014, 9:2586-2606.
38. Lou D.I., et al. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:19872-19877.
39. Quail M., et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13:341.
40. Lv W., et al. Noninvasive prenatal testing for Wilson disease by use of circulating single-molecule amplification and resequencing technology (cSMART). Clin. Chem. 2014, 61:172-181.
41. Leary R.J., et al. Development of personalized tumor biomarkers using massively parallel sequencing. Scie. Transl. Med. 2010, 2:20ra14.
42. Leary R.J., et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci. Transl. Med. 2012, 4:162ra154.
43. Chan K.C.A., et al. Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin. Chem. 2013, 59:211-224.
44. Lohr J.G., et al. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat. Biotechnol. 2014, 32:479-484.
45. Shen H., Laird P.W. Interplay between the cancer genome and epigenome. Cell 2013, 153:38-55.
46. Lange C.P., Laird P.W. Clinical applications of DNA methylation biomarkers in colorectal cancer. Epigenomics 2013, 5:105-108.
47. Beggs A.D., et al. Whole-genome methylation analysis of benign and malignant colorectal tumours. J. Pathol. 2013, 229:697-704.
48. You J.S., Jones P.A. Cancer genetics and epigenetics: two sides of the same coin?. Cancer Cell 2012, 22:9-20.
49. Shah R., et al. Biomarkers for early detection of colorectal cancer and polyps: systematic review. Cancer Epidemiol. Biomarkers Prev. 2014, 23:1712-1728.
50. Lange C.P.E., et al. Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancer. PLoS ONE 2012, 7:e50266.
51. Fackler M.J., et al. Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. Cancer Res. 2014, 74:2160-2170.
52. Imperiale T.F., et al. Multitarget stool DNA testing for colorectal-cancer screening. N. Engl. J. Med. 2014, 370:1287-1297.
53. Bibikova M., et al. High density DNA methylation array with single CpG site resolution. Genomics 2011, 98:288-295.
54. Campan M., et al. Methylight. Methods in Molecular Biology 2009, Vol. 507:325-337. Humana Press.
55. Witwer K.W. Circulating microRNA biomarker studies: pitfalls and potential solutions. Clin. Chem. 2014, 61:56-63.
56. Lo Y.M.D. Transplantation monitoring by plasma DNA sequencing. Clin. Chem. 2011, 57:941-942.
57. Snyder T.M., et al. Universal noninvasive detection of solid organ transplant rejection. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:6229-6234.
58. Tsimberidou A.M., et al. Personalized medicine in a phase I clinical trials program: the MD Anderson cancer center initiative. Clin. Cancer Res. 2012, 18:6373-6383.
59. Gerlinger M., et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 2012, 366:883-892.
60. Sequist L.V., et al. Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. Sci. Transl. Med. 2011, 3:75ra26.
61. Higgins M.J., et al. Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood. Clin. Cancer Res. 2012, 18:3462-3469.
62. Diaz L.A., et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 2012, 486:537-540.
63. Misale S., et al. Blockade of EGFR and MEK intercepts heterogeneous mechanisms of acquired resistance to anti-EGFR therapies in colorectal cancer. Sci. Transl. Med. 2014, 6:224ra26.
64. Diehl F., et al. Circulating mutant DNA to assess tumor dynamics. Nat. Med. 2007, 14:985-990.
65. Spindler K.L.G., et al. Quantitative cell-free DNA, KRAS, and BRAF mutations in plasma from patients with metastatic colorectal cancer during treatment with cetuximab and irinotecan. Clin. Cancer Res. 2012, 18:1177-1185.
66. Nygaard A.D., et al. The prognostic value of KRAS mutated plasma DNA in advanced non-small cell lung cancer. Lung Cancer 2015, 79:312-317.
67. Laird P.W. Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 2010, 11:191-203.
68. van Dijk E.L., et al. Ten years of next-generation sequencing technology. Trends Genet. 2014, 30:418-426.
69. Diep D., et al. Library-free methylation sequencing with bisulfite padlock probes. Nat. Methods 2012, 9:270-272.
70. Warton K., et al. Methylation-capture and next-generation sequencing of free circulating DNA from human plasma. BMC Genomics 2014, 15:476.