Molecular tools for companion diagnostics

New Biotechnology

Volumn 29, Issue 6, 2012, Pages 634-640

  Zieba, Agata ^a   Grannas, Karin ^a   Söderberg, Ola ^a   Gullberg, Mats ^b   Nilsson, Mats ^a   Landegren, Ulf ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b OLINK BIOSCIENCE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANTICANCER DRUG; CANCER THERAPY; CLINICAL CARE; CLINICAL TRIAL; DIAGNOSTIC TOOLS; DRUG DEVELOPMENT; GUIDE SELECTION; HERCEPTIN; MOLECULAR FEATURE; MOLECULAR TOOLS; PERSONALISED MEDICINES; TRASTUZUMAB;

DRUG THERAPY; MONOCLONAL ANTIBODIES; RNA;

MEDICINE;

DNA; RNA;

ARTICLE; CANCER THERAPY; CIRCULATING TUMOR CELL; CLINICAL TRIAL (TOPIC); CROSS REACTION; DISEASE MARKER; GENE AMPLIFICATION; GENE MUTATION; GENE SEQUENCE; GENOTYPE; HUMAN; MOLECULAR DIAGNOSIS; MOLECULAR RECOGNITION; PERSONALIZED MEDICINE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; TREATMENT RESPONSE;

GENOTYPING TECHNIQUES; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; NEOPLASM PROTEINS; NEOPLASMS; NEOPLASTIC CELLS, CIRCULATING; SEQUENCE ANALYSIS, DNA;

EID: 84865431528     PISSN: 18716784     EISSN: 18764347     Source Type: Journal    
DOI: 10.1016/j.nbt.2012.05.004     Document Type: Article

References (46)

1. What happened to personalized medicine? Nat. Biotechnol. (2012) 30, 1.
2. Druker B.J., et al. Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N. Engl. J. Med. 2001, 344:1031-1037.
3. Joensuu H. Treatment of inoperable gastrointestinal stromal tumor (GIST) with Imatinib (Glivec, Gleevec). Med. Klin. (Munich) 2002, 97(Suppl. 1):28-30.
4. Sonneveld D.J., et al. Improved long term survival of patients with metastatic nonseminomatous testicular germ cell carcinoma in relation to prognostic classification systems during the cisplatin era. Cancer 2001, 91:1304-1315.
5. Warrell R.P., et al. Differentiation therapy of acute promyelocytic leukemia with tretinoin (all-trans-retinoic acid). N. Engl. J. Med. 1991, 324:1385-1393.
6. Saltz L.B., et al. Phase II trial of cetuximab in patients with refractory colorectal cancer that expresses the epidermal growth factor receptor. J. Clin. Oncol. 2004, 22:1201-1208.
7. Capper D., et al. Immunohistochemical testing of BRAF V600E status in 1,120 tumor tissue samples of patients with brain metastases. Acta Neuropathol. (Berl.) 2011, 123:223-233.
8. Parsons D.W., et al. An integrated genomic analysis of human glioblastoma multiforme. Science 2008, 321:1807-1812.
9. Greenman C., et al. Patterns of somatic mutation in human cancer genomes. Nature 2007, 446:153-158.
10. Ha K., et al. Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. BMC Med. Genomics 2011, 4:75.
11. Nagalakshmi U., et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349.
12. Wang Z., et al. RNA-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
13. Ohtsuki S., et al. Quantitative targeted absolute proteomics-based ADME research as a new path to drug discovery and development: methodology, advantages, strategy, and prospects. J. Pharm. Sci. 2011, 100:3547-3559.
14. Caprioli R.M., et al. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal. Chem. 1997, 69:4751-4760.
15. Chaurand P., Caprioli R.M. Direct profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry. Electrophoresis 2002, 23:3125-3135.
16. Gold L., et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One 2010, 5:e15004.
17. Yanagisawa K., et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 2003, 362:433-439.
18. Gnirke A., et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 2009, 27:182-189.
19. Hodges E., et al. Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 2007, 39:1522-1527.
20. Dahl F., et al. Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:9387-9392.
21. Tewhey R., et al. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat. Biotechnol. 2009, 27:1025-1031.
22. Casazza A., et al. Systemic and targeted delivery of semaphorin 3A inhibits tumor angiogenesis and progression in mouse tumor models. Arterioscler. Thromb. Vasc. Biol. 2011, 31:741-749.
23. Weinstein J.A., et al. High-throughput sequencing of the zebrafish antibody repertoire. Science 2009, 324:807-810.
24. Brose M.S., et al. BRAF and RAS mutations in human lung cancer and melanoma. Cancer Res. 2002, 62:6997-7000.
25. Nilsson M., et al. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 1994, 265:2085-2088.
26. Larsson C., et al. In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat. Methods 2004, 1:227-232.
27. Lizardi P.M., et al. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 1998, 19:225-232.
28. Larsson C., et al. In situ detection and genotyping of individual mRNA molecules. Nat. Methods 2010, 7:395-397.
29. Grizzle W.E., et al. Evaluation of biomarkers in breast and prostate cancer. J. Cell. Biochem. Suppl. 1994, 19:259-266.
30. Magdelenat H. Tumour markers in oncology: past, present and future. J. Immunol. Methods 1992, 150:133-143.
31. Lequin R.M. Enzyme immunoassay (EIA)/enzyme-linked immunosorbent assay (ELISA). Clin. Chem. 2005, 51:2415-2418.
32. Fredriksson S., et al. Protein detection using proximity-dependent DNA ligation assays. Nat. Biotechnol. 2002, 20:473-477.
33. Gullberg M., et al. Cytokine detection by antibody-based proximity ligation. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:8420-8424.
34. Darmanis S., et al. ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing. PLoS One 2011, 6:e25583.
35. Andersen J.N., et al. Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci. Transl. Med. 2010, 2:43-55.
36. Vogel S.S., et al. Fanciful FRET. Sci. STKE 2006, 18:re2.
37. Shi Y., et al. A novel proximity assay for the detection of proteins and protein complexes: quantitation of HER1 and HER2 total protein expression and homodimerization in formalin-fixed, paraffin-embedded cell lines and breast cancer tissue. Diagn. Mol. Pathol. 2009, 18:11-21.
38. Truong K., Ikura M. The use of FRET imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo. Curr. Opin. Struct. Biol. 2001, 11:573-578.
39. Huang B., et al. Super-resolution fluorescence microscopy. Annu. Rev. Biochem 2009, 78:993-1016.
40. Soderberg O., et al. Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat. Methods 2006, 3:995-1000.
41. Zieba A., et al. Bright-field microscopy visualization of proteins and protein complexes by in situ proximity ligation with peroxidase detection. Clin. Chem. 2010, 56:99-110.
42. Leuchowius K.J., et al. High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation. Mol. Cell. Proteomics 2010, 9:178-183.
43. Gajadhar A.S., et al. In situ analysis of mutant EGFRs prevalent in glioblastoma multiforme reveals aberrant dimerization, activation and differential response to anti-EGFR targeted therapy. Mol. Cancer Res. 2012, 10:428-440.
44. Weibrecht I., et al. Simultaneous visualization of both signaling cascade activity and end-point gene expression in single cells. PLoS One 2011, 6:e20148.
45. de Bono J.S., et al. Circulating tumor cells predict survival benefit from treatment in metastatic castration-resistant prostate cancer. Clin. Cancer Res. 2008, 14:6302-6309.
46. Somlo G., et al. Multiple biomarker expression on circulating tumor cells in comparison to tumor tissues from primary and metastatic sites in patients with locally advanced/inflammatory, and stage IV breast cancer, using a novel detection technology. Breast Cancer Res. Treat. 2011, 128:155-163.