Medical data and text mining: Linking diseases, drugs, and adverse reactions

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Lars Juhl Jensen

Science

Jensen et al., Nature Reviews Genetics, 2012

Jensen et al., Nature Communications, 2014

Clozapine
clozapi
n
clossapi
n
klozapin
e
chlosapi
n
chlosapi
ne
chlozapi
n
chlozapi
ne
klossapi
n
closapin
e
klozapi
nklosapi
n

Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuationAdverse event
Adverse eventNegative modifier Indication Pre-existing
condition
Adverse drug reaction Possible
adverse drug reaction
ADR of
additional drug

Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuationAdverse eventIdentification start
Adverse eventNegative modifier Indication Pre-existing
condition
Adverse drug reaction Possible
adverse drug reaction
ADR of
additional drug

Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuation
Adverse eventNegative modifier Indication Pre-existing
condition
Adverse drug reaction Possible
adverse drug reaction
Adverse event
ADR of
additional drug
Identification start

Drug substance ADE p-value
Chlordiazepoxide Nystagmus 4.0e-8
Simvastatin Personality
changes
8.4e-8
Dipyridamole Visual impairment 4.4e-4
Citalopram Psychosis 8.8e-4
Bendroflumethiazi
de
Apoplexy 8.5e-3
Eriksson et al., Drug Safety, 2014

Acknowledgments
Disease trajectories
Anders Bøck Jensen
Tudor Oprea
Pope Moseley
Søren Brunak
Adverse drug reactions
Robert Eriksson
Thomas Werge
Søren Brunak
EHR text mining
Peter Bjødstrup
Jensen
Robert Eriksson
Henriette Schmock
Francisco S. Roque
Anders Juul
Marlene Dalgaard
Massimo Andreatta
Sune Frankild
Eva Roitmann
Thomas Hansen
Karen Søeby
Søren Bredkjær
Thomas Werge
Søren Brunak

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INTRODUCTION Overutilization of Proton pump inhibitors (PPI) in hospitalized patients is a well-recognized problem. In our previous study at St. Luke’s Hospital, we found that the lack of published guidelines for PPI use in non-critically ill patients results in overutilization of PPI in hospitalized patients. We conducted an educational intervention program to address this problem. DISCUSSION Overutilization of PPI in non-critically ill hospitalized patients is a known problem in medical practice. Use of PPI has been implicated in number of adverse consequences including but not limited to Clostridium difficile infection, pneumonia, and osteoporosis. In recent studies, PPI was found to be associated with increased in-hospital mortality, increased risk of cardiovascular events, dementia and chronic renal failure (CRF). We studied the magnitude of the problem in our hospital and employed an educational intervention program, which resulted in a significant reduction of inappropriate use of PPI in the hospital. There were several limitations to our study. This was a retrospective study where we noted a lack of proper documentation for outpatient use of PPI. We also were unable to precisely determine for how long the patients were taking PPI as outpatients. Our intervention included only medical residents (a total of 41), so we excluded data from NPs, hospitalists or PCPs after intervention. As a result, we are unable to determine the effect of the educational intervention on their practice. CONCLUSION PPIs have long been considered as relatively harmless drugs. In recent years, it has been implicated in several adverse effects that increases patient morbidity and mortality along with increased healthcare expenditure. Our data shows that proper education and ongoing surveillance, especially during admission and discharge can significantly reduce overutilization of PPI.

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Medical data and text mining: Linking diseases, drugs, and adverse reactions

1. Medical data and text mining Linking diseases, drugs, and adverse reactions Lars Juhl Jensen

2. structured data

3. Jensen et al., Nature Reviews Genetics, 2012

4. unstructured data

6. central registries

7. individual hospitals

9. opt-out

10. opt-in

11. Danish registries

12. civil registration system

13. CPR number

14. established in 1968

15. Jensen et al., Nature Reviews Genetics, 2012

16. national discharge registry

17. 14 years

18. 6.2 million patients

19. 45 million admissions

20. 68 million records

21. 119 million diagnosis

22. ICD-10

23. Jensen et al., Nature Reviews Genetics, 2012

24. not research

25. reimbursement

26. diagnosis trajectories

27. naïve approach

28. comorbidity

29. Jensen et al., Nature Reviews Genetics, 2012

30. confounding factors

31. “known knowns”

32. gender

33. age

34. type of hospital encounter

35. Jensen et al., Nature Communications, 2014

36. “known unknowns”

37. smoking

38. diet

39. “unknown unknowns”

40. reporting biases

41. matched controls

42. temporal correlations

43. multiple testing

44. trajectories

45. Jensen et al., Nature Communications, 2014

46. trajectory networks

47. Jensen et al., Nature Communications, 2014

48. key diagnoses

49. Jensen et al., Nature Communications, 2014

50. direct medical implications

51. electronic health records

52. structured data

53. Jensen et al., Nature Reviews Genetics, 2012

54. unstructured data

55.

56. free text

57. Danish

58. busy doctors

59. typos

60. psychiatric patients

61. text mining

62. comprehensive dictionary

63. drugs

64. adverse drug reactions

65. expansion rules

66. Clozapine

67. Clozapine clozapi n clossapi n klozapin e chlosapi n chlosapi ne chlozapi n chlozapi ne klossapi n closapin e klozapi nklosapi n

68. post-coordination rules

69. failure of kidney

70. renal failure

71. pharmacovigilance

72. clinical trials

73. spontaneous reports

74.

75. underreporting

76. data mining

77. structured data

78. medication

79. semi-structured data

80. drug indications

81. known ADRs

82. unstructured data

83. adverse drug reactions

84. temporal correlations

85. hand-crafted rules

86. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuationAdverse event Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction ADR of additional drug

87. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuationAdverse eventIdentification start Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction ADR of additional drug

88. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuation Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction Adverse event ADR of additional drug Identification start

89. Eriksson et al., Drug Safety, 2014 Drug introduction Drug discontinuation Adverse eventNegative modifier Indication Pre-existing condition Adverse drug reaction Possible adverse drug reaction Adverse event ADR of additional drug Identification start

90. recall known ADRs

91. estimate ADR frequencies

92. Eriksson et al., Drug Safety, 2014

93. discover new ADRs

94. Drug substance ADE p-value Chlordiazepoxide Nystagmus 4.0e-8 Simvastatin Personality changes 8.4e-8 Dipyridamole Visual impairment 4.4e-4 Citalopram Psychosis 8.8e-4 Bendroflumethiazi de Apoplexy 8.5e-3 Eriksson et al., Drug Safety, 2014

95. Acknowledgments Disease trajectories Anders Bøck Jensen Tudor Oprea Pope Moseley Søren Brunak Adverse drug reactions Robert Eriksson Thomas Werge Søren Brunak EHR text mining Peter Bjødstrup Jensen Robert Eriksson Henriette Schmock Francisco S. Roque Anders Juul Marlene Dalgaard Massimo Andreatta Sune Frankild Eva Roitmann Thomas Hansen Karen Søeby Søren Bredkjær Thomas Werge Søren Brunak

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