The real informatics challenges of personalized medicine: Not just about the number of central processing units

Personalized Medicine

Volumn 10, Issue 7, 2013, Pages 639-645

  Sheldon, Jonathan ^a   Ou, Wanmei ^b  

^a Oracle Health Sciences   (United Kingdom)

^b Oracle Health Sciences   (United States)

Author keywords

Clinical decision support; Data management; Information access; Omics; Personalized medicine; Relational database; Scalable system; Software solution; Translational research

Indexed keywords

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; BIOINFORMATICS; CLINICAL PRACTICE; DATA ANALYSIS SOFTWARE; DATA BASE; DATA STORAGE DEVICE; DECISION SUPPORT SYSTEM; DNA SEQUENCE; ELECTRONIC MEDICAL RECORD; EXON; GENE EXPRESSION; GENE MUTATION; GENETIC VARIABILITY; HEALTH INSURANCE; HUMAN; HUMAN GENOME; HUMAN GENOME PROJECT; INFORMATION PROCESSING; INTRON; LAW; MEDICAL INFORMATICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PATIENT CARE; PERSONALIZED MEDICINE; PHENOTYPE; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; SEQUENCE ALIGNMENT; STANDARDIZATION; TRANSLATIONAL RESEARCH; TREATMENT OUTCOME;

EID: 84884127466     PISSN: 17410541     EISSN: 1744828X     Source Type: Journal    
DOI: 10.2217/pme.13.16     Document Type: Review

References (46)

1. Cooke GS, Hill AVS. Genetics of susceptibitlity to human infectious disease. Nat. Rev. Genet. 2(12), 967-977 (2001).
2. Evans WE, Relling MV. Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286(5439), 487-491 (1999).
3. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216), 1061-1068 (2008).
4. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474(7353), 609-615 (2011).
5. The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407), 330-337 (2012).
6. Mega JL, Close SL, Wiviott SD et al. Cytochrome P-450 polymorphisms and response to clopidogrel. N. Engl. J. Med. 360(4), 354-362 (2009).
7. Bollag G, Hirth P, Tsai J et al. Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature 467(7315), 596-599 (2010).
8. Schadt EE, Turner S, Kasarskis A. A window into third generation sequencing. Hum. Mol. Genet. 20(4), 853-853 (2011).
9. Dunham I, Kundaje A, Aldred SF; ENCODE Project Consortium. An integrated Encyclopedia of DNA Elements in the human genome. Nature 489(7414), 57-74 (2012).
10. Kahn SD. On the future of genomic data. Science 331(6018), 728-729 (2011).
11. Langmead B, Schatz M, Lin J, Pop M, Salzberg S. Searching for SNPs with cloud computing. Genome Biol. 10(11), R134 (2009).
12. Kodama Y, Shumway M, Leinonen R. The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res. 40(D1), D54-D56 (2012).
13. Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E. Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res. 21(5), 734-740 (2011).
14. Bean J, Brennan C, Shih J-Y et al. MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance to gefitinib or erlotinib. Proc. Natl Acad. Sci. USA 104(52), 20932-20937 (2007).
15. Date CJ. An Introduction to Database Systems. Pearson/Addison Wesley, MA, USA (2004).
16. Ou W, Sheldon J. Oracle Health Sciences Translational Research Center: a Translational Medicine Platform to Address the Big Data Challenge. Oracle Corporation, CA, USA (2012).
17. Giardine B, Riemer C, Hardison RC et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15(10), 1451-1455 (2005).
18. Blankenberg D, Von Kuster G, Coraor N et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. Chapter 19, Unit 19.10.1-21 (2010).
19. Goecks J, Nekrutenko A, Taylor J; Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11(8), R86 (2010).
20. Stein L. Creating a bioinformatics nation. Nature 417(6885), 119-120 (2002).
21. Samwald M, Coulet A, Huerga I et al. Semantically enabling pharmacogenomic data for the realization of personalized medicine. Pharmacogenomics 13(2), 201-212 (2012).
22. Micheel CM, Nass SJ, Omenn G.Evolution of Translational Omics: Lessons Learned and The Path Forward. Micheel CM, Nass SJ, Omenn G (Eds). The National Academies Press, DC, USA (2012).
23. US Department of Health and Human Services; US FDA; Center for Drug Evaluation and Research; Center for Biologics Evaluation and Research. Guidance for Industry: E16 Biomarkers Related to Drug or Biotechnology Product Development: Context, Structure, and Format of Qualification Submissions. US Department of Health and Human Services, US FDA, MD, USA (2011).
24. Friend SH, Ideker T. Biomedical technology and the clinic of the future. POINT: are we prepared for the future doctor visit? Nat. Biotech. 29(3), 215-215 (2011).
25. Aronson SJ, Clark EH, Varugheese M, Baxter S, Babb LJ, Rehm HL. Communicating new knowledge on previously reported genetic variants. Genet. Med. 14(8), 713-719 (2012).
26. Johnson JA, Burkley BM, Langaee TY, Clare-Salzler MJ, Klein TE, Altman RB. Implementing personalized medicine: development of a cost-effective customized pharmacogenetics genotyping array. Clin. Pharmacol. Ther. 92(4), 437-439 (2012).
27. Jing X, Kay S, Marley T, Hardiker NR, Cimino JJ. Incorporating personalized gene sequence variants, molecular genetics knowledge, and health knowledge into an EHR prototype based on the Continuity of Care Record standard. J. Biomed. Inform. 45(1), 82-92 (2012).
28. Samwald M, Adlassnig KP. Pharmacogenomics in the pocket of every patient? A prototype based on quick response codes. J. Am. Med. Inform. Assoc. doi:10.1136/amiajnl-2012-001275 (2013) (Epub ahead of print).
29. Worldwide LHC Computing Grid (2012).http://public.web.cern.ch/public/en/ LHC/computing-en.html
30. Ambrose K. DataBase FileSystem (DBFS) at the Wellcome Trust Sanger Institute (2012).www.myexpospace.com/oracle2012/SessionFiles/CON8513-PDF-8513- 0001.pdf
31. CLC Bio (2012).www.clcbio.com
32. Novoalign (2012).www.novocraft.com/main/index.php
33. DNAnexus: cloud-based NGS (2012).https://dnanexus.com/
34. Bioinformatics Training Network (2013).www.biotnet.org
35. The SAM Format Specification Working Group. The SAM Format Specification (v1.4-r985) (2011).http://samtools.sourceforge.net/SAM1.pdf
36. Variant Call Format version 4.1 (2012).www.1000genomes.org/wiki/Analysis/ variant-call-format
37. The Cancer Genome Atlas Data Portal (2012). https://tcga-data.nci.nih. gov/tcga/tcgaDownload.jsp
38. Life Sciences Data Hub From Oracle Health Sciences. Oracle Corporation, CA, USA (2010).www.oracle.com/us/industries/life-sciences/045757.pdf
39. DN Cooper, EV Ball, PD Stenson, AD Phillips, K Shaw, ME Mort. The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff (2012).www.hgmd.cf.ac.uk/ac/index.php
40. Online Mendelian Inheritance in Man, OMIM® (2012).http://omim.org
41. GeneTests (2012). www.ncbi.nlm.nih.gov/sites/GeneTests/
42. PharmGKB. The Pharmacogenomics Knowledgebase (2012).www.pharmgkb.org
43. ClinVar. 2012.www.ncbi.nlm.nih.gov/clinvar
44. Center for Inidividualized Medicine at Mayo Clinic, Clinomics Program (2013).http://mayoresearch.mayo.edu/center-for-individualized-medicine/ clinomics.cfm
45. Ion AmpliSeq™ Cancer Hotspot Panel v2 (2013).http://products. invitrogen.com/ivgn/product/4475346
46. TruSeq Amplicon - Cancer Panel (2013).www.illumina.com/products/truseq- amplicon-cancer-panel.ilmn