Current and Emerging Technology Approaches in Genomics

Journal of Nursing Scholarship

Volumn 45, Issue 1, 2013, Pages 5-14

  Conley, Yvette P ^a   Biesecker, Leslie G ^b   Gonsalves, Stephen ^b   Merkle, Carrie J ^c   Kirk, Maggie ^d   Aouizerat, Bradley E ^e  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

^d UNIVERSITY OF GLAMORGAN   (United Kingdom)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Epigenomics; Gene expression; Genetics; Genome wide association studies; Genomics; Next generation sequencing; Nursing

Indexed keywords

ARTICLE; EPIGENETICS; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; GENOMICS; HUMAN; NURSING CARE; SEQUENCE ANALYSIS;

EPIGENOMICS; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; NURSING CARE; SEQUENCE ANALYSIS;

EID: 84874522540     PISSN: 15276546     EISSN: 15475069     Source Type: Journal    
DOI: 10.1111/jnu.12001     Document Type: Article

References (43)

1. Arao, T., Matsumoto, K., Maegawa, M., & Nishio, K. (2011). What can and cannot be done using a microarray analysis? Treatment stratification and clinical applications in oncology. Biological and Pharmaceutical Bulletin, 34(12), 1789-1793. doi:JST.JSTAGE/bpb/34.1789.
2. Baden, J., Adams, S., Astacio, T., Jones, J., Markiewicz, J., Painter, J., Green, G. (2011). Predicting prostate biopsy result in men with prostate specific antigen 2.0 to 10.0 ng/ml using an investigational prostate cancer methylation assay. Journal of Urology, 186(5), 2101-2106. doi:10.1016/j.juro.2011.06.052.
3. Balwierz, P. J., Carninci, P., Daub, C. O., Kawai, J., Hayashizahi, Y., Van Belle, W., & van Nimwegen, E. (2009). Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biology, 10. Retrieved from http://genomebiology.com/content/10/7/r73 doi:10.1186/gb-2009-10-7-r7.
4. Baumgartel, K., Zelazny, J., Timcheck, T., Snyder, C., Bell, M., & Conley, Y. P. (2011). Molecular genomic research designs. Annual Review of Nursing Research, 29, 1-26.
5. Bick, D., & Dimmock, D. (2011). Whole exome and whole genome sequencing. Current Opinions in Pediatrics, 23(6), 594-600. doi:10.1097/MOP.0b013e32834b20ec.
6. Biesecker, L. G. (2012). Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: Lessons from the ClinSeq project. Genetic Medicine, 14(4), 393-398. doi:10.1038/gim.2011.78.
7. Biesecker, L. G., Mullikin, J. C., Facio, F. M., Turner, C., Cherukuri, P. F., Blakesley, R. W., Green, E. D. (2009). The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine. Genome Research, 19(9), 1665-1674. doi:10.1101/gr.092841.109.
8. Botstein, D., & Risch, N. (2003). Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease. Nature Genetics, 33(Suppl.), 228-237. doi:10.1038/ng1090.
9. Calzone, K. A., Cashion, A., Feetham, S., Jenkins, J., Prows, C. A., Williams, J. K., & Wung, S. R. (2010). Nurses transforming health care using genetics and genomics. Nursing Outlook, 58(1), 26-35. doi:10.1016/j.outlook.2009.05.001.
10. Capriotti, E., Nehrt, N. L., Kann, M. G., & Bromberg, Y. (2012). Bioinformatics for personal genome interpretation. Brief Bioinformatics, 13(4), 495-512. doi:10.1093/bib/bbr070.
11. Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Lifton, R. P. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Science U S A, 106(45), 19096-19101. doi:10.1073/pnas.0910672106.
12. The Clinical Laboratory Improvement Amendments of 1988 (1989). Health Care Financial Review, 10(4), 141-146.
13. Diamandis, E. P., Sidransky, D., Laird, P. W., Cairns, P., & Bapat, B. (2010). Epigenomics-based diagnostics. Clinical Chemistry, 56(8), 1216-1219. doi:10.1373/clinchem.2010.148007.
14. Emes, R. D., & Farrell, W. E. (2012). Make way for the "next generation": Application and prospects for genome-wide, epigenome-specific, technologies in endocrine research. Journal of Molecular Endocrinology. Retrieved from http://jme.endocrinology-journals.org/content/49/1/R19 doi:10.1530/JME-12-0045.
15. Feinberg, A. P., & Tycko, B. (2004). The history of cancer epigenetics. Nature Reviews. Cancer, 4(2), 143-153. doi:10.1038/nrc1279.
16. Fernandez, A. F., Assenov, Y., Martin-Subero, J. I., Balint, B., Siebert, R., Taniguchi, H., Esteller, M. et al. (2012). A DNA methylation fingerprint of 1628 human samples. Genome Research, 22(2), 407-419. doi:10.1101/gr.119867.110.
17. Fraga, M. F., Herranz, M., Espada, J., Ballestar, E., Paz, M. F., Ropero, S., Esteller, M. et al. (2004). A mouse skin multistage carcinogenesis model reflects the aberrant DNA methylation patterns of human tumors. Cancer Research, 64(16), 5527-5534. doi:10.1158/0008-5472.CAN-03-4061.
18. Gibson, G. (2011). Rare and common variants: Twenty arguments. Nature Reviews Genetics, 13(2), 135-145. doi:10.1038/nrg3118.
19. Hakonarson, H., & Grant, S. F. (2011). Planning a genome-wide association study: Points to consider. Annals of Medicine, 43(6), 451-460. doi:10.3109/07853890.2011.573803.
20. Hill, V. K., Ricketts, C., Bieche, I., Vacher, S., Gentle, D., Lewis, C., & Latif, F. (2011). Genome-wide DNA methylation profiling of CpG islands in breast cancer identifies novel genes associated with tumorigenicity. Cancer Research, 71(8), 2988-2999. doi:10.1158/0008-5472.CAN-10-4026.
21. Human Genetics Strategy Group. (2012). Building on our inheritance. Genomic Technology in Healthcare. Retrieved from http://www.dh.gov.uk/prod_consum_dh/groups/dh_digitalassets/dh/en/documents/digitalasset/dh_132382.pdf.
22. Jenkins, J. F., & Calzone, K. A. (2012). Are nursing faculty ready to integrate genomic content into curricula Nurse Education, 37(1), 25-29. doi:10.1097/NNE.0b013e31823836ec.
23. Kingsmore, S. F., & Saunders, C. J. (2011). Deep sequencing of patient genomes for disease diagnosis: When will it become routine Science Translational Medicine, 3(87), 1-4. 87ps23. doi:10.1126/scitranslmed.3002695.
24. Lujambio, A., Calin, G. A., Villanueva, A., Ropero, S., Sanchez-Cespedes, M., Blanco, D., Esteller, M. et al. (2008). A microRNA DNA methylation signature for human cancer metastasis. Proceedings of the National Academy of Science U S A, 105(36), 13556-13561. doi:10.1073/pnas.0803055105.
25. Majewski, J., Schwartzentruber, J., Lalonde, E., Montpetit, A., & Jabado, N. (2011). What can exome sequencing do for you Journal of Medical Genetics, 48(9), 580-589. doi:10.1136/jmedgenet-2011-100223.
26. Marian, A. J. (2012). Molecular genetic studies of complex phenotypes. Translational Research, 159(2), 64-79. doi:10.1016/j.trsl.2011.08.001.
27. Ned, R. M., Melillo, S., & Marrone, M. (2011). Fecal DNA testing for colorectal cancer screening: The ColoSure test. PLoS Currents, 3. Retrieved from http://currents.plos.org/genomictests/article/fecal-dna-testing-for-colorectal-cancer-od1hzthyodr3-1/, doi:10.1371/currents.RRN1220.
28. Reis-Filho, J. S., & Pusztai, L. (2011). Gene expression profiling in breast cancer: classification, prostication, and prediction. The Lancet, 378, 1812-1828. doi:10.1016/S0140-6736(11)61539-0.
29. Rizzo, J. M., & Buck, M. J. (2012). Key principles and clinical applications of "next-generation" DNA sequencing. Cancer Prevention Research, 7, 887-900. doi:10.1158/1940-6207.CAPR-11-0432.
30. Ryu, S., Joshi, N., McDonnell, K., Woo, J., Choi, H., Gao, D., McCombie, W. R., & Mittal, V. (2011). Discovery of novel human breast cancer microRNAs from deep sequencing data by analysis of pri-microRNA secondary structures. PLoS ONE, 6, e16403. Retrieved from http://www.plosone.org/search/simpleSearch.action?from=globalSimpleSearch&filterJournals=PLoSONE&query=doi%3A10.1371%2Fjournal.pone.0016403 doi:10.1371/journal.pone.0016403.
31. Sastre, L. (2011). New DNA sequencing technologies open a promising era for cancer research and treatment. Clinical Translational Oncology, 13(5), 301-306.
32. Su, P. H., Lin, Y. W., Huang, R. L., Liao, Y. P., Lee, H. Y., Wang, H. C., Lai, H. C. (2012). Epigenetic silencing of PTPRR activates MAPK signaling, promotes metastasis and serves as a biomarker of invasive cervical cancer. Oncogene. Retrieved from http://www.nature.com/onc/journal/vaop/ncurrent/full/onc201229a.html doi:10.1038/onc.2012.29.
33. Su, Z., Ning, B., Fang, H., Hong, H., Perkins, R., Tong, W., & Shi, L. (2011). Next-generation sequencing and its applications in molecular diagnostics. Expert Review of Molecular Diagnostics, 11(3), 333-343. doi:10.1586/erm.11.3.
34. Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N. Surani, M. A. (2009). mRNA-Seq whole-transcriptome analysis of a single cell. Nature Methods, 6, 377-382. doi:10.1038/nmeth.1315.
35. Tucker, T., Marra, M., & Friedman, J. M. (2009). Massively parallel sequencing: the next big thing in genetic medicine. American Journal of Human Genetics, 85(2), 142-154. doi:10.1016/j.ajhg.2009.06.022.
36. van 't Veer, L. J., Dai H., van de Vijver, M. J., He, Y. D., Hart, A. A. M., Mao, M., Friend, S. H. (2002). Gene expression profiling of breast cancer predicts clinical outcome of disease. Nature, 615, 530-536.
37. Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995). Serial analysis of gene expression. Science, 270, 484-487. doi:10.1126/science.270.5235.484.
38. Ware, J. S., Roberts, A. M., & Cook, S. A. (2012). Next generation sequencing for clinical diagnostics and personalised medicine: Implications for the next generation cardiologist. Heart, 98(4), 276-281. doi:10.1136/heartjnl-2011-300742.
39. Warren, J. D., Xiong, W., Bunker, A. M., Vaughn, C. P., Furtado, L. V., Roberts, W. L., Heichman, K. A. (2011). Septin 9 methylated DNA is a sensitive and specific blood test for colorectal cancer. BMC Medicine, 9. Retrieved from http://www.biomedcentral.com/1741-7015/9/133/. doi:10.1186/1741-7015-9-133.
40. Weeraratna, A. T., Nagel, J. E., de Mello-Coelho, V., & Taub, D. D. (2004). Gene expression profiling: From microarrays to medicine. Journal of Clinical Immunology, 24, 213-224. doi:10.1023/B:JOCI.0000025443.44833.1d.
41. Williams, J. K., Prows, C. A., Conley, Y. P., Eggert, J., Kirk, M., & Nichols, F. (2011). Strategies to prepare faculty to integrate genomics into nursing education programs. Journal of Nursing Scholarship, 43(3), 231-238. doi:10.1111/j.1547-5069.2011.01401.
42. Wright, C., Burton, H., Hall, A., Moorthie, S., Pokorska-Bocci, A., Sagoo, G., Skinner, R. (2011). Next steps in the sequence. The implications of whole genome sequencing for health in the UK. Cambridge, UK: PHG Foundation.
43. Yeon, E.-J., Ross, M. E., Shurtleff, S. A., Williams, W. K., Patel, D., Mahfouz, R. Downing, J. R. (2002). Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell, 1, 133-143. doi: 10.1016/S1535-6108(02)00032-6.