Genomic sequencing: Assessing the health care system, policy, and big-data implications

Health Affairs

Volumn 33, Issue 7, 2014, Pages 1246-1253

  Phillips, Kathryn A ^a   Trosman, Julia R ^b   Kelley, Robin K ^c   Pletcher, Mark J ^c   Douglas, Michael P ^c   Weldon, Christine B ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Center for Business Models in Healthcare   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; ERLOTINIB;

ARTICLE; BIG DATA; BIOINFORMATICS; BREAST CANCER; CANCER RISK; CLINICAL RESEARCH; CLINICAL TRIAL (TOPIC); COST EFFECTIVENESS ANALYSIS; DATA ANALYSIS; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; GENOME; GENOMICS; HEALTH CARE COST; HEALTH CARE POLICY; HEALTH CARE SYSTEM; HUMAN; INFORMATION TECHNOLOGY; LUNG CANCER; MOLECULARLY TARGETED THERAPY; OVARY CANCER; PATIENT CARE; PATIENT CODING; PERSONALIZED MEDICINE; REIMBURSEMENT; DATA MINING; DNA SEQUENCE; ECONOMIC MODEL; ECONOMICS; HEALTH CARE DELIVERY; INFORMATION PROCESSING; INSURANCE; PROCEDURES;

DATA MINING; DATASETS AS TOPIC; DELIVERY OF HEALTH CARE; GENETIC TESTING; GENOMICS; HEALTH CARE COSTS; HEALTH POLICY; HUMANS; INSURANCE COVERAGE; MODELS, ECONOMIC; SEQUENCE ANALYSIS, DNA;

EID: 84905979411     PISSN: 02782715     EISSN: 15445208     Source Type: Journal    
DOI: 10.1377/hlthaff.2014.0020     Document Type: Article

References (39)

1. Berg JS, Khoury MJ, Evans JP. Deploying whole genome sequencing in clinical practice and public health: meeting the challenge one bin at a time. Genet Med. 2011;13(6):499- 504.
2. Evans JP, Berg JS. Next-generation DNA sequencing, regulation, and the limits of paternalism: the next challenge. JAMA. 2011;306(21): 2376-7.
3. National Institutes of Health. Genetics home reference: handbook: genetic testing [Internet]. Bethesda (MD): NIH; 2014 May 26 [cited 2014 May 28]. Available from: http:// ghr.nlm.nih.gov/handbook/testing
4. Ferrusi IL, Marshall DA, Kulin NA, Leighl NB, Phillips KA. Looking back at 10 years of trastuzumab therapy: what is the role of HER2 testing? A systematic review of health economic analyses. Per Med. 2009; 6(2):193-215.
5. Goodwin PJ, Phillips K-A, West DW. Prognosis of breast cancer in carriers of BRCA1 and BRCA2 mutations. New Engl J Med. 2007;357(15):1555; author's reply 1556.
6. Phillips GD, Fields CT, Li G, Dowbenko D, Schaefer G, Miller K, et al. Dual targeting of HER2-positive cancer with trastuzumab emtansine and pertuzumab: critical role for neuregulin blockade in antitumor response to combination therapy. Clin Cancer Res. 2014; 20(2):456-68.
7. Berliner JL, Fay AM, Cummings SA, Burnett B, Tillmanns T. NSGC practice guideline: risk assessment and genetic counseling for hereditary breast and ovarian cancer. J Genet Couns. 2013;22(2):155-63.
8. Perkel J. Finding the true $1000 genome. Biotechniques. 2013; 54(2):71-4.
9. DeFrancesco L. Life Technologies promises $1,000 genome. Nat Biotechnol. 2012;30(2):126.
10. Chen J, Qian F, Yan W, Shen B. Translational biomedical informatics in the cloud: present and future. Biomed Res Int. 2013;2013:658925.
11. Caulfield T, Evans J, McGuire A, McCabe C, Bubela T, Cook-Deegan R, et al. Reflections on the cost of "low-cost" whole genome sequencing: framing the health policy debate. PLoS Biol. 2013;11(11): e1001699.
12. Faruki H. Genomic testing: the clinical laboratory perspective. Clin Pharmacol Ther. 2013;94(2):190-2.
13. Johansen Taber KA, Dickinson BD, Wilson M. The promise and challenges of next-generation genome sequencing for clinical care. JAMA Intern Med. 2014;174(2):275-80.
14. Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA. 2011; 305(15):1577-84.
15. Pasche B, Absher D.Whole-genome sequencing: a step closer to personalized medicine. JAMA. 2011; 305(15):1596-7.
16. Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, et al. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA. 2011;305(15):1568-76.
17. Green RC, Berg JS, Berry GT, Biesecker LG, Dimmock DP, Evans JP, et al. Exploring concordance and discordance for return of incidental findings from clinical sequencing. Genet Med. 2012;14(4):405-10.
18. Vassy JL, Lautenbach DM, McLaughlin HM, Kong SW, Christensen KD, Krier J, et al. The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine. Trials. 2014;15(1):85.
19. Feldman B, Martin EM, Skotnes T. Genomics and the role of big data in rience. O'Reilly Data [blog on the Internet]. 2013 Aug 23 [cited 2014 May 20]. Available from: http:// strata.oreilly.com/2013/08/ genomics-and-the-role-of-big-datain-personalizing-the-healthcareexperience. html
20. O'Driscoll A, Daugelaite J, Sleator RD. "Big data," Hadoop, and cloud computing in genomics. J Biomed Inform. 2013;46(5):774-81.
21. Schatz MC, Langmead B. The DNA data deluge. IEEE Spectrum [serial on the Internet]. 2013 Jun 27 [cited 2014 May 20]. Available from: http://spectrum.ieee.org/bio medical/devices/the-dna-datadeluge
22. Groves P, Kayyali B, Knott D, Van Kuiken S. The "big data" revolution in healthcare: accelerating value and innovation [Internet]. Summit (NJ): McKinsey and Company, Center for US Health System Reform, Business Technology Office; 2013 Jan [cited 2014 May 20]. Available from: http://www.mckinsey.com/ insights/health_systems/~/media/ 7764A72F70184C8EA88D805092 D72D58.ashx
23. Lindeman NI, Cagle PT, Beasley MB, Chitale DA, Dacic S, Giaccone G, et al. Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology. J Mol Diagn. 2013;15(4):415-53.
24. Mardis ER. Next-generation sequencing platforms. Ann Rev Anal Chem (Palo Alto Calif.). 2013;6: 287-303.
25. Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, et al. Clinical interpretation and implications of whole-genome sequencing. JAMA. 2014;311(10): 1035-45.
26. Feero WG. Clinical application of whole-genome sequencing: proceed with care. JAMA. 2014;311(10): 1017-9.
27. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, et al. Assuring the quality of nextgeneration sequencing in clinical laboratory practice. Nat Biotechnol. 2012;30(11):1033-6.
28. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, 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.
29. Ambry Genetics. BRCA1 and BRCA2 test offerings for clinical trials and research [Internet]. Aliso Viejo (CA): Ambry Genetics; [cited 2014 May 28]. Available from: http:// www.ambrygen.com/genomicservices/ brca1-and-brca2-testofferings-clinical-trials-and-research
30. Invitae. Our test catalog [Internet]. San Francisco (CA): Invitae; [cited 2014 May 28]. Available from: https://www.invitae.com/en/testcatalog/
31. Burke W, Matheny Antommaria AH, Bennett R, Botkin J, Clayton EW, Henderson GE, et al. Recommendations for returning genomic incidental findings? We need to talk! Genet Med. 2013;15(11):854-9.
32. Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15(7):565-74.
33. Evans BJ. Minimizing liability risks under the ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15(12): 915-20.
34. Townsend A, Adam S, Birch PH, Friedman JM. Paternalism and the ACMG recommendations on genomic incidental findings: patients seen but not heard. Genet Med. 2013;15(9):751-2.
35. Berg JS, Amendola LM, Eng C, Allen EV, Gray SW, Wagle N, et al. Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium. Genet Med. 2013; 15(11):860-7.
36. Stanton MW. Expanding patientcentered care to empower patients and assist providers [Internet]. Rockville (MD): Agency for Healthcare Research and Quality; 2002 May [cited 2014 May 20]. (Research in Action, Issue 5). Available from: http://www.ahrq.gov/qual/ ptcareria.htm
37. Chawla NV, Davis DA. Bringing big data to personalized healthcare: a patient-centered framework. J Gen Intern Med. 2013;28(Suppl 3): S660-5.
38. Sclafani F, Gullo G, Sheahan K, Crown J. BRAF mutations in melanoma and colorectal cancer: a single oncogenic mutation with different tumour phenotypes and clinical implications. Crit Rev Oncol Hematol. 2013;87(1):55-68.
39. Mao M, Tian F, Mariadason JM, Tsao CC, Lemos R Jr, Dayyani F, et al. Resistance to BRAF inhibition in BRAF-mutant colon cancer can be overcome with PI3K inhibition or demethylating agents. Clin Cancer Res. 2013;19(3):657-67. July