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Yearb Med Inform 2013; 22(01): 172-174
DOI: 10.1055/s-0038-1638851
Original Article
Georg Thieme Verlag KG Stuttgart

Bringing Genome Tests into Clinical Practice

I.N. Sarkar
1   Center for Clinical and Translational Science
2   Department of Microbiology and Molecular Genetics
3   Department of Computer Science University of Vermont, Burlington, VT USA
› Author Affiliations
Further Information

Correpsondence to:

Dr. Indra Neil Sarkar
Center for Clinical and Translational Science
University of Vermont
89 Beaumont Avenue, Given Courtyard N309
Burlington, VT 05405 USA
Phone: +1 802 656 8283   
Fax: +1 802 656 4589   

Publication History

Publication Date:
05 March 2018 (online)

Also available at
 
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Summary

Objective: To provide a review of recent progress in the use of genomic data in clinical contexts.

Method: Survey of key articles selected from the previous year (2012).

Result: Two major themes emerged as areas of focus in 2012: (1) integration of genomic data into electronic health records; and (2) determining the clinical utility of genomic tests.

Conclusion: Significant advances are being made towards the integration of genomic data such that they may useful for clinical decision making. While the short term advances will likely still be seen in clinically valid genotype-phenotype research, there have been promising advances towards developing genomic tests that may be of clinical utility in the near future.


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Keywords

Translational Bioinformatics - Electronic Health Records - Genomics - IMIA Yearbook

 


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  • References

  • 1 Masys DR, Jarvik GP, Abernethy NF, Anderson NR, Papanicolaou GJ, Paltoo DN. et al. Technical desiderata for the integration of genomic data into Electronic Health Records. J Biomed Inform 2012; Jun 45 (3) 419-22.
    CrossrefPubMedGoogle Scholar
  • 2 Altman RB. Personal genomic measurements: the opportunity for information integration. Clin Pharmacol Ther 2013; Jan 93 (1) 21-3.
    CrossrefPubMedGoogle Scholar
  • 3 Biesecker LG, Burke W, Kohane I, Plon SE, Zimmern R. Next-generation sequencing in the clinic: are we ready?. Nat Revi Genet 2012; Nov 13 (11) 818-24.
    PubMedGoogle Scholar
  • 4 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 Informa 2012; Feb 45 (1) 82-92.
    PubMedGoogle Scholar
  • 5 Kohane IS. Using electronic health records to drive discovery in disease genomics. Nat Rev Genet 2011; Jun 12 (6) 417-28.
    CrossrefPubMedGoogle Scholar
  • 6 Goddard KA, Knaus WA, Whitlock E, Lyman GH, Feigelson HS, Schully SD. et al. Building the evidence base for decision making in cancer genomic medicine using comparative effectiveness research. Genet Med 2012; Jul 14 (7) 633-42.
    CrossrefPubMedGoogle Scholar
  • 7 Peissig PL, Rasmussen LV, Berg RL, Linneman JG, McCarty CA, Waudby C. et al. Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. J Am Med Inform Assoc 2012; Mar-Apr 19 (2) 225-34.
    CrossrefPubMedGoogle Scholar
  • 8 Rasmussen-Torvik LJ, Pacheco JA, Wilke RA, Thompson WK, Ritchie MD, Kho AN. et al. High density GWAS for LDL cholesterol in African Americans using electronic medical records reveals a strong protective variant in APOE. Clin Transl Sci 2012; Oct 5 (5) 394-9.
    CrossrefPubMedGoogle Scholar
  • 9 Schildcrout JS, Denny JC, Bowton E, Gregg W, Pulley JM, Basford MA. et al. Optimizing drug outcomes through pharmacogenetics: a case for preemptive genotyping. Clin Pharmacol Ther 2012; Aug 92 (2) 235-42.
    CrossrefPubMedGoogle Scholar
  • 10 Hicks JK, Crews KR, Hoffman JM, Kornegay NM, Wilkinson MR, Lorier R. et al. A clinician-driven automated system for integration of pharmacogenetic interpretations into an electronic medical record. Clin Pharmacol Ther 2012; Nov 92 (5) 563-6.
    CrossrefPubMedGoogle Scholar
  • 11 Delaney JT, Ramirez AH, Bowton E, Pulley JM, Basford MA, Schildcrout JS. et al. Predicting clopidogrel response using DNA samples linked to an electronic health record. Clin Pharmacol Ther 2012; Feb 91 (2) 257-63.
    CrossrefPubMedGoogle Scholar
  • 12 Pulley JM, Denny JC, Peterson JF, Bernard GR, Vnencak-Jones CL, Ramirez AH. et al. Operational implementation of prospective genotyping for personalized medicine: the design of the Vander- bilt PREDICT project. Clin Pharmacol Ther 2012; Jul 92 (1) 87-95.
    CrossrefPubMedGoogle Scholar
  • 13 Do CB, Hinds DA, Francke U, Eriksson N. Comparison of family history and SNPs for predicting risk of complex disease. PLoS Genet 2012; Oct 8 (10) e1002973.
    CrossrefPubMedGoogle Scholar
  • 14 Guttmacher AE, Collins FS, Carmona RH. The family history-more important than ever. N Engl J Med 2004; Nov 25 351 (22) 2333-6.
    CrossrefPubMedGoogle Scholar
  • 15 Roberts NJ, Vogelstein JT, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. The predictive capacity of personal genome sequencing. Sci Transl Med. 2012 May 9 4. (133) 133ra58.
    PubMedGoogle Scholar
  • 16 Morgan AA, Chen R, Butte AJ. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. J Am Med Inform Assoc 2012; Jun 19 (1e) e21-7.
    CrossrefPubMedGoogle Scholar
  • 17 Bodurtha J, Strauss 3rd JF. Genomics and perinatal care. New Engl J Med 2012; Jan 5 366 (1) 64-73.
    CrossrefPubMedGoogle Scholar
  • 18 http://www.cdc.gov/genomics/gtesting/ACCE/index.htm
    PubMed

Correpsondence to:

Dr. Indra Neil Sarkar
Center for Clinical and Translational Science
University of Vermont
89 Beaumont Avenue, Given Courtyard N309
Burlington, VT 05405 USA
Phone: +1 802 656 8283   
Fax: +1 802 656 4589   

  • References

  • 1 Masys DR, Jarvik GP, Abernethy NF, Anderson NR, Papanicolaou GJ, Paltoo DN. et al. Technical desiderata for the integration of genomic data into Electronic Health Records. J Biomed Inform 2012; Jun 45 (3) 419-22.
    CrossrefPubMedGoogle Scholar
  • 2 Altman RB. Personal genomic measurements: the opportunity for information integration. Clin Pharmacol Ther 2013; Jan 93 (1) 21-3.
    CrossrefPubMedGoogle Scholar
  • 3 Biesecker LG, Burke W, Kohane I, Plon SE, Zimmern R. Next-generation sequencing in the clinic: are we ready?. Nat Revi Genet 2012; Nov 13 (11) 818-24.
    PubMedGoogle Scholar
  • 4 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 Informa 2012; Feb 45 (1) 82-92.
    PubMedGoogle Scholar
  • 5 Kohane IS. Using electronic health records to drive discovery in disease genomics. Nat Rev Genet 2011; Jun 12 (6) 417-28.
    CrossrefPubMedGoogle Scholar
  • 6 Goddard KA, Knaus WA, Whitlock E, Lyman GH, Feigelson HS, Schully SD. et al. Building the evidence base for decision making in cancer genomic medicine using comparative effectiveness research. Genet Med 2012; Jul 14 (7) 633-42.
    CrossrefPubMedGoogle Scholar
  • 7 Peissig PL, Rasmussen LV, Berg RL, Linneman JG, McCarty CA, Waudby C. et al. Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. J Am Med Inform Assoc 2012; Mar-Apr 19 (2) 225-34.
    CrossrefPubMedGoogle Scholar
  • 8 Rasmussen-Torvik LJ, Pacheco JA, Wilke RA, Thompson WK, Ritchie MD, Kho AN. et al. High density GWAS for LDL cholesterol in African Americans using electronic medical records reveals a strong protective variant in APOE. Clin Transl Sci 2012; Oct 5 (5) 394-9.
    CrossrefPubMedGoogle Scholar
  • 9 Schildcrout JS, Denny JC, Bowton E, Gregg W, Pulley JM, Basford MA. et al. Optimizing drug outcomes through pharmacogenetics: a case for preemptive genotyping. Clin Pharmacol Ther 2012; Aug 92 (2) 235-42.
    CrossrefPubMedGoogle Scholar
  • 10 Hicks JK, Crews KR, Hoffman JM, Kornegay NM, Wilkinson MR, Lorier R. et al. A clinician-driven automated system for integration of pharmacogenetic interpretations into an electronic medical record. Clin Pharmacol Ther 2012; Nov 92 (5) 563-6.
    CrossrefPubMedGoogle Scholar
  • 11 Delaney JT, Ramirez AH, Bowton E, Pulley JM, Basford MA, Schildcrout JS. et al. Predicting clopidogrel response using DNA samples linked to an electronic health record. Clin Pharmacol Ther 2012; Feb 91 (2) 257-63.
    CrossrefPubMedGoogle Scholar
  • 12 Pulley JM, Denny JC, Peterson JF, Bernard GR, Vnencak-Jones CL, Ramirez AH. et al. Operational implementation of prospective genotyping for personalized medicine: the design of the Vander- bilt PREDICT project. Clin Pharmacol Ther 2012; Jul 92 (1) 87-95.
    CrossrefPubMedGoogle Scholar
  • 13 Do CB, Hinds DA, Francke U, Eriksson N. Comparison of family history and SNPs for predicting risk of complex disease. PLoS Genet 2012; Oct 8 (10) e1002973.
    CrossrefPubMedGoogle Scholar
  • 14 Guttmacher AE, Collins FS, Carmona RH. The family history-more important than ever. N Engl J Med 2004; Nov 25 351 (22) 2333-6.
    CrossrefPubMedGoogle Scholar
  • 15 Roberts NJ, Vogelstein JT, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. The predictive capacity of personal genome sequencing. Sci Transl Med. 2012 May 9 4. (133) 133ra58.
    PubMedGoogle Scholar
  • 16 Morgan AA, Chen R, Butte AJ. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. J Am Med Inform Assoc 2012; Jun 19 (1e) e21-7.
    CrossrefPubMedGoogle Scholar
  • 17 Bodurtha J, Strauss 3rd JF. Genomics and perinatal care. New Engl J Med 2012; Jan 5 366 (1) 64-73.
    CrossrefPubMedGoogle Scholar
  • 18 http://www.cdc.gov/genomics/gtesting/ACCE/index.htm
    PubMed

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