OHSU

Joe Gray

Gray, Joe-Profile Photo

Email:
Phone: 503 418-9302
Fax: 503 418-9311

Current Appointments
Gordon Moore Endowed Chair
Chair, Department of Biomedical Engineering
Director, OHSU Center for Spatial Systems Biomedicine
Associate Director for Translational Research, OHSU Knight Cancer Institute

Office
Center for Health & Healing
Mail Code: CH13B
3303 SW Bond Ave., Room #13000
Portland, OR 97239


Professional Associations
Dr. Gray is involved in several projects and collaborations with organizations outside of Oregon Health & Science University. View list


Research Interests
The Gray Laboratory explores mechanisms by which genomic, transcriptional and proteomic abnormalities occur in selected cancers, elucidates how these abnormalities contribute to cancer pathophysiologies and assesses the ways in which these abnormalities influence responses to gene targeted therapies. Current studies focus on developing: (a) integrated analyses of the spectrum of recurrent abnormalities that influence cancer behavior (b) mathematical models that describe how cancer-associated molecular abnormalities influence individual responses to therapeutic inhibitors (c) novel therapeutic approaches to treat breast or ovarian cancer subpopulations that do not respond well to current aggressive chemotherapeutic strategies (d) proteomic strategies for early detection of breast cancer related proteins in blood (e) automated functional assessment of genes deregulated by genomic abnormalities in cancers, and (f) molecular imaging for early detection of metastasis prone breast cancer.

Integrated analysis
We are assessing abnormalities associated with clinical outcome in breast cancers using a combination of comparative genomic hybridization (CGH), massively parallel sequencing (whole exome sequencing and RNA sequencing) and reverse phase protein lysate arrays to assess allele specific genome copy number, RNA expression, and protein and phosphoprotein levels in cancer related genes. These studies are supported by the NCI Bay Area Breast Cancer SPORE and The Cancer Genome Altas project.

Mathematical models
We are developing mathematical methods to predict individual responses to therapeutic agents using information on responses to these agents in a collection of cell lines grown in vitro. Major emphasis in this project is on breast cancer. Current emphasis is on development of statistical, Bayesian and ODE models of Her-family signaling. Work in this area is supported by an NCI Center for Cancer Systems Biology award.

Novel therapeutic approaches
We are using advanced genomic analysis and high content, high throughput imaging to assess responses to NCI and private sector compounds for our collection of ~100 breast, ovary, prostate and pancreas cancer cell lines. Our goal is to identify therapeutic agents that will be highly effective against tumor subtypes that do poorly on aggressive therapy. In addition, we are developing siRNA therapeutic approaches to treat tumors that amplify and over express transcripts to which the tumors become addicted. Current emphasis is on development of strategies to identify and inhibit functionally important genes in regions of amplification associated with poor outcome. This work is supported by an NCI Ovarian Cancer SPORE, the NCI Bay Area Breast Cancer SPORE, the NIH Foundation and an AACR Stand Up to Cancer Award.

Early detection
We are using information about genomic and transcriptional abnormalities in breast cancer to guide the development of mass spectrometric strategies that can detect breast cancer subtype specific proteins in order to enable early detection of metastasis prone breast cancers. We are giving special attention to detection of aberrant proteins that result from cancer specific alternative splicing, glycosylation or phosphorylation. Mass spectrometry and capillary isoelectric focusing approaches are being developed to detect these proteins in the blood, MRI and PET imaging approaches are being developed for anatomic detection and scanned ion beam mass spectrometry is being developed for improved histopathological analysis. These studies are supported by grants from the NCI Clinical Proteomic Technologies for Cancer (CPTAC) program and a DOD Innovator award.


Journal Publications (selected from over 300)

  1. Gray, J.W., Carrano, A.V., Steinmetz, L.L., Van Dilla, M.A., Moore, D.H. II, Mayall, B.H., and Mendelsohn, M.L. (1975) Chromosome measurement and sorting by flow systems. Proc. Natl. Acad. Sci. USA, 72(4):231-4.

  2. Latt, S.A., George, Y.S., and Gray, J.W. (1977) Flow cytometric analysis of bromodeoxyuridine-substituted cells stained with 33258 Hoechst. J. Histochem. Cytochem., 25(7):927-34.

  3. Carrano, A.V., Gray, J.W., Langlois, R.G., Burkhart-Schultz, K.J., and Van Dilla, M.A. (1979) Measurement and purification of human chromosomes by flow cytometry and sorting. Proc. Nat. Acad. Sci. USA, 76(3):1382-4.

  4. Gray, J.W., Langlois, R.G., Carrano, A.V., and Van Dilla, M.A. (1979) High resolution chromosome analysis: One and two parameter flow cytometry. Chromosoma, 73(1):9-27.

  5. Norgren, R.M., Gray, J.W., and Young, I.T. (1982) Restoration of profiles from slit-scan flow cytometry. IEEE Trans. Biomed. Eng., 29(2):101-6.

  6. Dolbeare, F., Gratzner, H., Pallavicini, M.G., and Gray, J.W. (1983) Flow cytometric measurement of total DNA content and incorporated bromodeoxyuridine. Proc. Natl. Acad. Sci. USA, 80(18):5573-7.

  7. Pinkel, D., Straume, T., and Gray, J.W. (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc. Natl. Acad. Sci. USA, 83(9):2934-8.

  8. Van Dilla, M.A., Deaven, L.L., Albright, K.L., Allen, N.A., Aubuchon, M.R., Bartholdi, M.F., Browne, N.C., Campbell, E.W., Carrano, A.V., Clark, L.M., Cram, L.S., Fuscoe, J.C., Gray, J.W., Hildebrand, C.E., Jackson, P.J., Jett, J.H., Longmire, J.L., Lozes, C.R., Luedemann, M.L., Martin, J.C., McNinch, J.S., Meincke, L.J., Mendelsohn, M.L., Meyne, J., Moyzis, R.K., Munk, A.C., Perlman, J., Peters, D.C., Silva, A.J., and Trask, B.J. (1986) Human chromosome-specific DNA libraries: Construction and availability. Nat. Biotech., 4(6):537-52.

  9. Gray, J.W., Dean, P.N., Fuscoe, J.C., Peters, D.C., Trask, B.J., van den Engh, G.J., and Van Dilla, M.A. (1987) High-speed chromosome sorting. Science, 238(4825):323-9.

  10. Mullikin, J., Norgren, R., Lucas, J., and Gray, J.W. (1988) Fringe-scan flow cytometry. Cytometry, 9(2):111-20.

  11. Trask, B., van den Engh, G., Pinkel, D., Mullikin, J., van Dekken, H., and Gray, J.W. (1988) Fluorescence in situ hybridization to interphase cell nuclei in suspension allows flow cytometric analysis of chromosome content and microscopic analysis of nuclear organization. Hum. Genet., 78(3):251-9.

  12. Pinkel, D., Landegent, J., Collins, C., Fuscoe, J., Seagraves, R., Lucas, J., and Gray, J.W. (1988) Fluorescence in situ hybridization with human chromosome specific libraries: detection of trisomy 21 and translocations of chromosome 4. Proc. Natl. Acad. Sci. USA, 85(23):9138-42.

  13. Tkachuk, D.C., Westbrook, C.A., Andreeff, M., Donlon, T.A., Cleary, M.L., Suryanarayan, K., Homge, M., Redner, A., Gray, J.W., and Pinkel, D. (1990) Detection of bcr-abl fusion in chronic myleogeneous leukemia by in situ hybridization. Science, 250(4980):559-62.

  14. Kallioniemi, O.-P., Kallioniemi, A., Kurisu, W., Thor, A., Chen, L.-C., Smith, H.S., Waldman, F.M., Pinkel, D., and Gray, J.W. (1992) ERBB2 amplification in breast cancer analyzed by fluorescence in situ hybridization. Proc. Natl. Acad. Sci. USA, 89(12):5321-5.

  15. Kallioniemi, A., Kallioniemi, O.-P., Waldman, F.M., Chen, L.-C., Yu, L.-C., Fung, Y.K., Smith, H.S., Pinkel, D., and Gray, J.W. (1992) Detection of retinoblastoma gene copy number in metaphase chromosomes and interphase nuclei by fluorescence in situ hybridization. Cytogenet. Cell Genet., 60(3-4):190-3.

  16. Kallioniemi, A., Kallioniemi, O.-P., Sudar, D., Rutovitz, D., Gray, J.W., Waldman, F., and Pinkel, D. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science, 258(5083):818-21.

  17. Vooijs, M., Yu, L.-C., Tkachuk, D., Pinkel, D., Johnson, D., and Gray, J.W. (1993) Libraries for each human chromosome, constructed from sorter-enriched chromosomes by using linker-adaptor PCR. Am. J. Hum. Genet., 52(3):586-97.

  18. Kallioniemi, A., Kallioniemi, O.-P., Piper, J., Tanner, M., Stokke, T., Chen, L., Smith, H.S., Pinkel, D., Gray, J.W., and Waldman, F.M. (1994) Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proc. Natl. Acad. Sci. USA, 91(6):2156-60.

  19. Lucito, R., Nakimura, M., West, J.A., Han, Y., Chin, K., Jensen, K., McCombie, R., Gray, J.W., and Wigler, M. (1998) Genetic analysis using genomic representations. Proc. Natl. Acad. Sci. USA, 95(8):4487-92.

  20. Collins, C., Rommens, J.M., Kowbel, D., Godfrey, T., Tanner, M., Hwang, S.I., Polikoff, D., Nonet, G., Cochran, J., Myambo, K., Jay, K.E., Froula, J., Cloutier, T., Kuo, W.-L., Yaswen, P., Dairkee, S., Giovanola, J., Hutchinson, G.B., Isola, J., Kallioniemi, O.-P., Palazzolo, M., Martin, C., Ericsson, C., Pinkel, D., Alberston, D., Li, W.-B., and Gray, J.W. (1998) Positional cloning of ZNF217 and NABC1: Genes amplified at 20q13.2 and overexpressed in breast carcinoma. Proc. Natl. Acad. Sci. USA, 95(15):8703-8.

  21. Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.-L., Chen, C., Zhai, Y., Dairkee, S.H., Ljung, B.M., Gray, J.W., and Albertson, D.G. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20(2):207-11.

  22. Shayesteh, L., Lu, Y., Kuo, W.-L., Baldocchi, R., Godfrey, T., Collins, C., Pinkel, D., Powell, B., Mills, G.B., and Gray, J.W. (1999) PIK3CA is implicated as an oncogene in ovarian cancer. Nat. Genet., 21(1):99-102.

  23. Sternlicht, M.D, Lochter, A., Sympson, C.J., Huey, B., Rougier, J.P., Gray, J.W., Pinkel, D., Bissell, M.J., and Werb, Z. (1999) The stromal proteinase MMP3/stromelysin-1 promotes mammary carcinogenesis. Cell, 98(2):137-46.

  24. Albertson, D.G., Ylstra, B., Segraves, R., Collins, C., Dairkee, S.H., Kowbel, D., Kuo, W.-L., Gray, J.W., and Pinkel, D. (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat. Genet., 25(2):144-6.

  25. Collins, C., Volik, S., Kowbel, D., Ginzinger, D., Ylstra, B., Cloutier, T., Hawkins, T., Predki, P., Martin, C., Wernick, M., Kuo, W.-L., Alberts, A., and Gray, J.W. (2001) Comprehensive genome sequence analysis of a breast cancer amplicon. Genome Res., 11(6):1034-42.

  26. Snijders, A.M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A.K., Huey, B., Kimura, K., Law, S., Myambo, K., Palmer, J., Ylstra, B., Yue, J.P., Gray, J.W., Jain, A.N., Pinkel, D., and Albertson, D.G. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet., 29(3):263-4.

  27. Hodgson, G., Hager, J.H., Volik, S., Hariono, S., Wernick, M., Moore, D., Nowak, N., Albertson, D.G., Pinkel, D., Collins, C., Hanahan, D., and Gray, J.W. (2001) Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat. Genet., 29(4):459-64.

  28. Volik, S., Zhao, S., Chin, K., Brebner, J.H., Herndon, D.R., Tao, Q., Kowbel, D., Huang, G., Lapuk, A., Kuo, W.-L., Magrane, G., de Jong, P., Gray, J.W., and Collins, C. (2003) End-sequence profiling: Sequence-based analysis of aberrant genomes. Proc. Natl. Acad. Sci. USA, 100(13):7696-701.

  29. Albertson, D.G., Collins, C., McCormick, F., and Gray, J.W. (2003) Chromosome aberrations in solid tumors. Nat. Genet., 34(4):369-76.

  30. Kuperwasser, C., Chavarria, T., Wu, M., Magrane, G., Gray, J.W., Carey, L., Richardson, A., and Weinberg, R.A. (2004) Reconstruction of functionally normal and malignant human breast tissues in mice. Proc. Natl. Acad. Sci. USA, 101(14):4966-71.

  31. Chin, K., de Solorzano, C.O., Knowles, D., Jones, A., Chou, W., Rodriguez, E.G., Kuo, W.-L., Ljung, B.M., Chew, K., Myambo, K., Miranda, M., Krig, S., Garbe, J., Stampfer, M., Yaswen, P., Gray, J.W., and Lockett, S.J. (2004) In situ analyses of genome instability in breast cancer. Nat. Genet., 36(9):984-8.

  32. Macrae, M., Neve, R.M., Rodriguez-Viciana, P., Haqq, C., Yeh, J., Chen, C., Gray, J.W., and McCormick, F. (2005) A conditional feedback loop regulates Ras activity through EphA2. Cancer Cell, 8(2):111-8.

  33. Zhang, T., Stilwell, J.L., Gerion, D., Ding, L., Elboudwarej, O., Cooke, P.A., Gray, J.W., Alivisatos, A.P., and Chen, F.F. (2006) Cellular effect of high doses of silica-coated quantum dot profiled with high throughput gene expression analysis and high content cellomics measurements. Nano Lett., 6(4):800-8.

  34. Chin, K., DeVries, S., Fridlyand, J., Spellman, P.T., Roydasgupta, R., Kuo, W.-L., Lapuk, A., Neve, R.M., Qian, Z., Ryder, T., Chen, F., Feiler, H., Tokuyasu, T., Kingsley, C., Dairkee, S., Meng, Z., Chew, K., Pinkel, D., Jain, A., Ljung, B.M., Esserman, L., Albertson, D.G., Waldman, F.M., and Gray, J.W. (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell, 10(6):529-41.

  35. Neve, R.M., Chin, K., Fridlyand, J., Yeh, J., Baehner, F., Fevr, T., Clark, L., Bayani, N., Copp￩, J.P., Tong, F., Speed, T. Spellman, P.T., DeVries, S., Lapuk, A., Wang, N.J., Kuo, W.-L., Stilwell, J.L., Pinkel, D., Albertson, D.G., Waldman, F.M., McCormick, F., Dickson, R.B., Johnson, M.D., Lippman, M., Ethier, S., Gazdar, A., and Gray, J.W. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell, 10(6):515-27.

  36. Nanjundan, M., Nakayama, Y., Cheng, K.W., Lahad, J., Liu, J., Lu, K., Kuo, W.-L., Smith-McCune, K., Fishman, D., Gray, J.W., and Mills, G.B. (2007) Amplification of MDS1/EVI1 and EVI1, located in the 3q26.2 amplicon, is associated with favorable patient prognosis in ovarian cancer. Cancer Res., 67(7):3074-84.

  37. Parvin, B., Ghosh, N., Heiser, L., Knapp, M., Talcott, C., Laderoute, K., Gray, J., and Spellman, P. (2007) Spectral decomposition of signaling networks. IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, 2007 (CIBCB 07), 76-81.

  38. Mao, J.H., Wu, D., Perez-Losada, J., Jiang, T., Li, Q., Neve, R.M., Gray, J.W., Cai, W.W., and Balmain, A. (2007) Crosstalk between Aurora-A and p53: Frequent deletion or downregulation of Aurora-A in tumors from p53 null mice. Cancer Cell, 11(2):161-73.

  39. Kenny, P.A., Lee, G.Y., Myers, C.A., Neve, R.M., Semeiks, J.R., Spellman, P.T., Lorenz, K., Lee, E.H., Barcellos-Hoff, M.H., Petersen, O.W., Gray, J.W., and Bissell, M.J. (2007) The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression. Mol. Oncol., 1(1):84-96.

  40. Guan, Y., Kuo, W.-L., Stilwell, J.L., Takano, H., Lapuk, A.V., Fridlyand, J., Mao, J.-H., Yu, M., Miller, M.A., Santos, J.L., Kalloger, S.E., Carlson, J.W., Ginzinger, D.G., Celniker, S.E., Mills, G.B., Huntsman, D.G, and Gray, J.W. (2007) Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer. Clin. Cancer Res., 13(19):5745-55.

  41. Raphael, B.J., Volik, S., Yu, P., Wu, C., Huang, G., Linardopoulou, E.V., Trask, B.J., Waldman, F., Costello, J., Pienta, K.J., Mills, G.B., Bajsarowicz, K., Kobayashi, Y., Sridharan, S., Paris, P.L., Tao, Q., Aerni, S.J., Brown, R.P., Bashir, A., Gray, J.W., Cheng, J.-F., de Jong, P., Nefedov, M., Ried, T., Padilla-Nash, H.M., and Collins, C.C. (2008) A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol., 9(3):R59. PMC2397511

  42. Chin, L. and Gray, J.W. (2008) Translating insights from the cancer genome into clinical practice. Nature, 452(7187):553-63. PMC2730524

  43. Stemke-Hale, K., Gonzalez-Angulo, A.M., Lluch, A., Neve, R.M., Kuo, W.-L., Davies, M. Carey, M., Hu, Z., Guan, Y., Sahin, A., Symmans, W.F., Pusztai, L., Nolden, L.K., Horlings, H., Berns, K., Hung, M.-C., van de Vijver, M.J., Valero, V., Gray, J.W., Bernards, R., Mills, G.B., and Hennessy, B.T. (2008) An integrative genomic and proteomic analysis of PIK3CA, PTEN and AKT mutations in breast cancer. Cancer Res., 68(15):6084-91. PMC2680495

  44. Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216):1061-8. PMC2671642

  45. Mirzoeva, O.K., Das, D., Heiser, L.M., Bhattacharya, S., Siwak, D., Gendelman, R., Bayani, N., Wang, N.J., Neve, R.M., Guan, Y., Hu, Z., Knight, Z., Feiler, H.S., Gascard, P., Parvin, B., Spellman, P.T., Shokat, K.M., Wyrobek, A.J., Bissell, M.J., McCormick, F., Kuo, W.L,, Mills, G.B., Gray, J.W., and Korn, W.M. (2009) Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition. Cancer Res., 69(2):565-72. PMC2737189

  46. Hennessy, B.T., Gonzalez-Angulo, A.M., Stemke-Hale, K.A., Gilcrease, M.Z., Krishnamurthy, S., Lee, J.-S., Fridlyand, J., Sahin, A., Agarwal, R., Joy, C., Liu, W., Stivers, D., Baggerly, K., Carey, M., Lluch, A., Monteagudo, C., He, X., Weigman, V., Fan, C., Palazzo, J., Hortobagyi, G.N., Nolden, L.K., Wang, N.J., Valero, V., Gray, J.W., Perou, C.M., and Mills, G.B. (2009) Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res., 69(10):4116-24. PMC2737191

  47. Ong, D.C., Ho, Y.M., Rudduck, C., Chin, K., Kuo, W.-L., Lie, D.K., Chua, C.L., Tan, P.H., Eu, K.W., Seow-Choen, F., Wong, C.Y., Hong, G.S., Gray, J.W., and Lee, A.S. (2009) LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast and colorectal cancer. Oncogene, 28(47):4189-200. PMC2844776

  48. Weigelt, B., Lo, A.T., Park, C.C., Gray, J.W., and Bissell, M.J. (2009) HER2 signaling pathway activation and response of breast cancer cells to HER2-targeting agents is dependent strongly on the 3D microenvironment. Breast Cancer Res. Treat., [Epub ahead of print]. PMID: 19701706 NIHMSID: 156204

  49. Kuo, W.-L., Das, D., Ziyad, S., Bhattacharya, S., Gibb, W.J., Heiser, L.M., Sadanandam, A., Fontenay, G.V., Hu, Z., Wang, N.J., Bayani, N., Feiler, H.S., Neve, R.M., Wyrobek, A.J., Spellman, P.T., Marton, L.J. and Gray, J.W. (2009) A systems analysis of chemosensitivity of breast cancer cells to the polyamine analogue PG-11047. BMC Med., 7:77. PMC2803786

  50. Salaita, K., Nair, P.M., Petit, R.S., Neve, R.M., Debo, D., Gray, J.W., and Groves, J.T. (2010) Restriction of receptor movement alters cellular response: physical force sensing by EphA2. Science, 12;327(5971):1380-85. PMC2895569

  51. Lapuk, A., Marr, H., Jakkula, L., Pedro, H., Bhattacharya, S., Purdom, E., Hu, Z., Simpson, K., Pachter, L., Durinck, S., Wang, N., Parvin, B., Fontenay, G., Speed, T., Garbe, J., Stampfer, M., Bayandorian, H., Dorton, S., Clark, T.A., Schweitzer, A., Wyrobek, A., Feiler, H., Spellman, P., Conboy, J., and Gray, J.W. (2010) Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol. Cancer Res., 8(7): 961-74. PMC2911965

  52. Nautiyal, S., Carlton, V.E., Lu, Y., Ireland, J.S., Flaucher, D., Moorhead, M., Gray, J.W., Spellman, P., Mindrinos, M., Berg, P., and Faham, M. . (2010) A high throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc. Natl. Acad. Sci. USA, 107(28):12587-92. PMID: 20616066

  53. Prathapam, T., Aleshin, A., Guan, Y., Gray, J.W., and Martin, G.S. (2010) p27KIP1 mediates addiction of ovarian cancer cells to MYCC (C-MYC) and their dependence on MYC paralogs. J. Biol. Chem., [Epub ahead of print]. PMID: 20647308

Issued United States Patents

Finding leaks in a tandem Van de Graff accelerator
  • Gray, J.W., Hartnell, G.W., and Legg, J.C. Method of locating defects in a high-voltage insulating tube. U.S. Patent #3,76l,720 (1974)
Flow cytometry and sorting
  • Gray, J.W., Alger, T.W., and Lord, D. Fluidic assembly for an ultra-high-speed chromosome flow sorter. U.S. Patent #4,361,400 (1982)
  • Gray, J.W., Hirschfeld, T.B., and Norgren, R.M. Method and apparatus for fringe-scanning chromosome analysis. U.S. Patent #4,596,036 (1986)
BrdUrd/DNA analysis
  • Dolbeare, F. and Gray, J.W. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine. U.S. Patents #4,585,736 (1986); #4,780,406 (1988); #4,812,394 (1989)
Fluorescence in situ hybridization (FISH)
  • Gray, J.W. and Pinkel, D. Methods of preparing and applying single stranded DNA probes to double stranded target DNAs in situ. U.S. Patent #5,028,525 (1991)
  • Gray, J.W. and Pinkel, D. Methods for chromosome-specific staining. U.S. Patents #5,447,841 (1995); #6,596,479 (1995); #6,607,877 (2003); #6,872,817 (2005)
  • Gray, J.W., Pinkel, D., and Tkachuk, D. Method of detecting genetic translocations identified with chromosomal abnormalities (BCR/ABL translocation). U.S. Patent #6,280,929 (2001)
  • Gray, J.W. and Pinkel, D. Methods of biological dosimetry employing chromosome-specific staining. U.S. Patent #6,132,961 (2000)
  • Gray, J.W., Pinkel, D., Kallioniemi, O.-P., Kallioniemi, A., and Sakamoto, M. Methods of staining target chromosomal DNA employing high complexity nucleic acid probes. U.S. Patent #7,115,709 (2006)
  • Pinkel, D., Kallioniemi, O.-P., Kallioniemi, A., Waldman, F., Gray, J.W., and Sakamoto, M. Genomic probing. U.S. Patent #5,856,097 (1995)
  • Weier, H.-U. and Gray, J.W. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using. U.S. Patent #5,427,932 (1995)
  • Gray, J.W., Stokke, T., and Pinkel, D. Detection of amplified or deleted chromosomal regions. U.S. Patents #5,472,842 (1995); #5,633,365 (1997).
  • Gray, J.W. and Weier, H.-U. Y-Chromosome specific nucleic acid probe and method for determining the y-chromosome in situ. U.S. Patents #5,840,482 (1998); #5,888,730 (1999); #6,300,066 (2001)
  • Gray, J. and Weier, H.-U. Quantitative DNA fiber mapping. U.S. Patent #5,851,769 (1998)
Comparative genomic hybridization (CGH)
  • Pinkel, D., Gray, J.W., Kallioniemi, A., Kallioniemi, O.-P., and Waldman, F. Comparative genomic hybridization (CGH). U.S. Patent #5,665,549 (1997); #5,721,098 (1998); #5,965,362 (1999); #5,976,790 (1999); #6,159,685 (2000); #6,335,167 (2002); #7,238,484 (2007), #7,537,895 (2009)
  • Pinkel, D., Albertson, D., and Gray, J.W. Comparative fluorescence hybridization to nucleic acid arrays. U.S. Patents #5,830,645 (1998); #6,562,565 (2003)
  • Pinkel, D. and Gray, J.W. High density array fabrication and readout method for a fiber optic biosensor. U.S. Patents #5,690,894 (1997); #6,146,593 (2000); #6,417,506 (2002)
  • Pinkel, D., Albertson, D.G., and Gray, J.W. Array-based detection of genetic alterations associated with disease. U.S. Patents #6,210,878 (2001); #7,267,947 (2007)
  • Gray, J.W., Pinkel, D., Albertson, D., Collins, C.C., and Baldocchi, R. Comparative fluorescence hybridization to oligonucleotide microarrays. U.S. Patent #6,465,182 (2002)
  • Pinkel, D., Albertson, D.G., Gray, J.W., Hamilton, G., Brown, N.W., and Clark, S.M. High-efficiency microarray printing device. U.S. Patent #6,855,538 (2005)
  • Albertson, D., Pinkel, D., Fridyland, J., Huey, B., Snijders, A., Gray, J.W., Kallioniemi, A., Kallioniemi, O., Waldman, F. Detection of nucleic acid differences by comparative genomic hybridization. U.S. Patent #7,534,567 (2009)
Diagnostic markers
  • Christman, M.F., Gray, J.W., Levin, N.A., Brzoska, P., and Nakamura, H. Genetic alterations that correlate with lung carcinomas. U.S. Patent #5,670,314 (1997)
  • Gray, J.W., Pinkel, D. Collins, C., Kallioniemi, O.-P., and Tanner, M. Amplification of chromosomal region 20q13 as prognostic indicator in breast cancer. U.S. Patents #5,801,021 (1998); #6,268,184 (2001)
  • Gray, J., Collins, C., Godfrey, T., Kowbel, D., Hwang, S., and Rommens, J. Genes from the 20Q13 amplicon and their uses. U.S. Patents #5,892,010 (1999); # 6,808,878 (2005); # 7,049,424 (2006); # 7,413,899 (2008)
  • Shayesteh, L. and Gray, J.W. Genetic aberrations associated with cancer (PIK3CA). U.S. Patents #6,110,673 (2000); #6,277,563 (2001); #6,475,732 (2002); #6,537,761 (2003); # 7,670,767 (2010)
  • Gray, J.W., Pinkel, D., Kallioniemi, O.-P., Kallioniemi, A., and Sakamoto, M. Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17. U.S. Patents #6,475,720 (2002); #6,344,315 (2002); #RE40,929 (2009)
  • Gray, J.W., Pinkel, D., Tkachuk, D., and Westbrook, C. Chromosome specific staining to detect genetic rearrangements. U.S. Patent Application #09/765,291 (2001, amendment filed 2007)
  • Gray, J.W. and Pinkel, D. Methods and compositions for chromosome 21-specific staining. U.S. Patent #6,500,612 (2002)
  • Albertson, D.G., Pinkel, D., Collins, C., and Gray, J.W. Amplicon in the 20q13 region of human chromosome 20 and uses thereof. U.S. Patent #6,664,057 (2003)
  • Giacomini, K.M., Gray, J.W., Lapuk, A.V., and Zhang, S. Use of organic cation transporters for cancer diagnosis and therapy. U.S. Provisional Patent Application #60/793,803 (2006)
  • Albertson, D., Pinkel, D., Collins, C., Gray, J.W., Ystra, B. Detecting CYP24 expression level as a marker for predisposition to cancer. U.S. Patent #7,648,826 (2010)
End sequence profiling (ESP)
  • Collins, C., Volik, S., and Gray, J.W. End sequence profiling. U.S. Patent #6,785,614 (2004)
Mass spectrometric imaging of mass tag labeled specimens
  • Felton, James S., Wu, Kuang Jen J., Knize, Mark G., Kulp, Kristen S., Gray, Joe W. Imaging mass spectrometer with mass tags. US Patent #7,728,287 (2010)
Others
  • Ginzinger, D., Godfrey, T., Jensen, R., and Gray, J.W. Quantitative PCR method to enumerate DNA copy number. U.S. Patent #6,180,349 (2001)
  • Fulwyler, M.J. and Gray, J.W. Capillary array and related methods. US Patents #6,610,499 (2003); #6,818,184 (2005); #6,898,237 (2006); #7,741,104 (2010)