Medical data mining

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Lars Juhl Jensen

Technology Health & Medicine

Medical data mining
Linking diseases, drugs, and adverse
reactions

Lars Juhl Jensen

unstructured data

structured data

Jensen et al., Nature Reviews Genetics, 2012

individual hospitals

central registries

opt-out

opt-in

Danish registries

civil registration system

CPR number

established in 1968

Jensen et al., Nature Reviews Genetics, 2012

national discharge registry

14 years

6.2 million patients

45 million admissions

68 million records

119 million diagnosis

ICD-10

Jensen et al., Nature Reviews Genetics, 2012

reimbursement

not research

diagnosis trajectories

naïve approach

comorbidity

Jensen et al., Nature Reviews Genetics, 2012

confounding factors

“known knowns”

gender

age

type of hospital encounter

Male

Emergency room

Out-patient

In-patient

Female

Jensen et al., submitted, 2013

“known unknowns”

smoking

diet

“unknown unknowns”

reporting biases

disease clustering

temporal correlation

Jensen et al., submitted, 2013

diagnosis trajectories

Jensen et al., submitted, 2013

epilepsy

Jensen et al., submitted, 2013

gout

Jensen et al., submitted, 2013

electronic health records

structured data

Jensen et al., Nature Reviews Genetics, 2012

unstructured data

free text

Danish

busy doctors

psychiatric patients

delusions

text mining

named entity recognition

custom dictionaries

diseases

drugs

adverse drug events

expansion rules

orthographic variation

typos

“negative modifiers”

negations

family members

detailed disease profiles

Text mined codes

Assigned codes

4947 3825

32626

Roque et al., PLOS Computational Biology, 2011

comorbidity

Roque et al., PLOS Computational Biology, 2011

patient stratification

Roque et al., PLOS Computational Biology, 2011

cluster characterization

Roque et al., PLOS Computational Biology, 2011

adverse drug reactions

structured data

medication

clinical narrative

possible ADRs

semi-structured data

SPC
Summary of Product Characteristics

drug indications

known ADRs

temporal correlation

link drugs to ADRs

complex filtering

Eriksson et al., submitted, 2013

new ADRs

Drug substance
ADE
Chlordiazepoxide Nystagmus
Simvastatin
Personality
changes
Dipyridamole
Visual impairment
Citalopram
Psychosis
Bendroflumethiazi Apoplexy
de

p-value
4.0e-8
8.4e-8
4.4e-4
8.8e-4
8.5e-3

Eriksson et al., submitted, 2013

ADR frequencies

Eriksson et al., submitted, 2013

heavily medicated

Eriksson et al., submitted, 2013

ADR dose dependency

Eriksson et al., submitted, 2013

ADR similarity

Eriksson et al., submitted, 2013

drug repurposing

Campillos, Kuhn et al., Science, 2008

Acknowledgments
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

Disease trajectories
Anders Bøck Jensen
Tudor Oprea
Pope Moseley
Søren Brunak

Adverse drug reactions
Robert Eriksson
Thomas Werge
Søren Brunak

Thank you!

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Medical data mining

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

2. unstructured data

3.

4. structured data

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

6. individual hospitals

7. central registries

8.

11. Danish registries

12. civil registration system

14. established in 1968

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

16. national discharge registry

18. 6.2 million patients

19. 45 million admissions

20. 68 million records

21. 119 million diagnosis

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

24. reimbursement

25. not research

26. diagnosis trajectories

27. naïve approach

28. comorbidity

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

30. confounding factors

31. “known knowns”

34. type of hospital encounter

35. Male Emergency room Out-patient In-patient Female Jensen et al., submitted, 2013

36. “known unknowns”

39. “unknown unknowns”

40. reporting biases

41. disease clustering

42.

43. temporal correlation

44. Jensen et al., submitted, 2013

45. diagnosis trajectories

46. Jensen et al., submitted, 2013

48. Jensen et al., submitted, 2013

50. Jensen et al., submitted, 2013

51. electronic health records

52. structured data

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

54. unstructured data

55.

58. busy doctors

59. psychiatric patients

61. text mining

62. named entity recognition

63. custom dictionaries

66. adverse drug events

67. expansion rules

68. orthographic variation

70. “negative modifiers”

72. family members

73. detailed disease profiles

74. Text mined codes Assigned codes 4947 3825 32626 Roque et al., PLOS Computational Biology, 2011

75. comorbidity

76. Roque et al., PLOS Computational Biology, 2011

77. patient stratification

78. Roque et al., PLOS Computational Biology, 2011

79. cluster characterization

80. Roque et al., PLOS Computational Biology, 2011

81. adverse drug reactions

82. structured data

84. clinical narrative

85. possible ADRs

86. semi-structured data

87. SPC Summary of Product Characteristics

88. drug indications

90. temporal correlation

91. link drugs to ADRs

92. complex filtering

93. Eriksson et al., submitted, 2013

95. Drug substance ADE Chlordiazepoxide Nystagmus Simvastatin Personality changes Dipyridamole Visual impairment Citalopram Psychosis Bendroflumethiazi Apoplexy de p-value 4.0e-8 8.4e-8 4.4e-4 8.8e-4 8.5e-3 Eriksson et al., submitted, 2013

96. ADR frequencies

97. Eriksson et al., submitted, 2013

98. heavily medicated

99. Eriksson et al., submitted, 2013

100. ADR dose dependency

101. Eriksson et al., submitted, 2013

102. ADR similarity

103. Eriksson et al., submitted, 2013

104. drug repurposing

105. Campillos, Kuhn et al., Science, 2008

106. Acknowledgments 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 Disease trajectories Anders Bøck Jensen Tudor Oprea Pope Moseley Søren Brunak Adverse drug reactions Robert Eriksson Thomas Werge Søren Brunak

107. Thank you!