Biomedical Discovery through Data Mining and Data Science November - - PowerPoint PPT Presentation

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Biomedical Discovery through Data Mining and Data Science November - - PowerPoint PPT Presentation

Biomedical Discovery through Data Mining and Data Science November 14th, 2016 Nicholas P. Tatonetti, PhD Columbia University Observation is the starting point of biological discovery Observation is the starting point of biological discovery


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SLIDE 1

Biomedical Discovery through Data Mining and Data Science

Nicholas P. Tatonetti, PhD Columbia University

November 14th, 2016

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SLIDE 2

Observation is the starting point

  • f biological discovery
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SLIDE 3

Observation is the starting point

  • f biological discovery
  • Charles Darwin observed relationship

between geography and phenotype

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SLIDE 4

Observation is the starting point

  • f biological discovery
  • Charles Darwin observed relationship

between geography and phenotype

  • William McBride & Widukind Lenz
  • bserved association between

thalidamide use and birth defects

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SLIDE 5

The tools of observation are advancing

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SLIDE 6

The tools of observation are advancing

  • Human senses
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SLIDE 7

The tools of observation are advancing

  • Human senses
  • sight, touch, hearing, smell, taste
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SLIDE 8

The tools of observation are advancing

  • Human senses
  • sight, touch, hearing, smell, taste
  • Mechanical augmentation
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SLIDE 9

The tools of observation are advancing

  • Human senses
  • sight, touch, hearing, smell, taste
  • Mechanical augmentation
  • binoculars, telescopes, microscopes,

microphones

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SLIDE 10

The tools of observation are advancing

  • Human senses
  • sight, touch, hearing, smell, taste
  • Mechanical augmentation
  • binoculars, telescopes, microscopes,

microphones

  • Chemical and Biological augmentations
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SLIDE 11

The tools of observation are advancing

  • Human senses
  • sight, touch, hearing, smell, taste
  • Mechanical augmentation
  • binoculars, telescopes, microscopes,

microphones

  • Chemical and Biological augmentations
  • chemical screening, microarrays, high

throughput sequencing technology

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SLIDE 12

The tools of observation are advancing

  • Human senses
  • sight, touch, hearing, smell, taste
  • Mechanical augmentation
  • binoculars, telescopes, microscopes,

microphones

  • Chemical and Biological augmentations
  • chemical screening, microarrays, high

throughput sequencing technology

  • What’s next?

Bytes to KB Megabytes to Terabytes

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SLIDE 13

The tools of observation are advancing

  • Human senses
  • sight, touch, hearing, smell, taste
  • Mechanical augmentation
  • binoculars, telescopes, microscopes,

microphones

  • Chemical and Biological augmentations
  • chemical screening, microarrays, high

throughput sequencing technology

  • What’s next?

Bytes to KB Megabytes to Terabytes

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SLIDE 14

Your doctor is observing you like never before

>99% of Hospitals have Electronic Health Records

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SLIDE 15

Every drug order is an experiment.

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SLIDE 16

Observation analysis in a petabyte world

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SLIDE 17

Observation analysis in a petabyte world

  • Darwin, McBride, and Lenz were working with

kilobytes of data

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SLIDE 18

Observation analysis in a petabyte world

  • Darwin, McBride, and Lenz were working with

kilobytes of data

  • Today’s scientists are observing terabytes and

petabytes of data

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SLIDE 19

Observation analysis in a petabyte world

  • Darwin, McBride, and Lenz were working with

kilobytes of data

  • Today’s scientists are observing terabytes and

petabytes of data

  • The human mind simply cannot make sense of that

much information

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SLIDE 20

Observation analysis in a petabyte world

  • Darwin, McBride, and Lenz were working with

kilobytes of data

  • Today’s scientists are observing terabytes and

petabytes of data

  • The human mind simply cannot make sense of that

much information

  • Data mining is about making the tools of data

analysis (“hypothesis generation”) catch up to the tools of observation

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SLIDE 21

But, there’s a problem…

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SLIDE 22

Bias confounds observations

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SLIDE 23

Let’s focus on just one example...

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SLIDE 24

Let’s focus on just one example...

Drug-Drug Interactions

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SLIDE 25

Drug-drug interactions (DDIs)

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SLIDE 26

Drug-drug interactions (DDIs)

  • DDIs can occur when a patient takes 2 or more drugs
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SLIDE 27

Drug-drug interactions (DDIs)

  • DDIs can occur when a patient takes 2 or more drugs
  • DDIs cause unexpected side effects
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SLIDE 28

Drug-drug interactions (DDIs)

  • DDIs can occur when a patient takes 2 or more drugs
  • DDIs cause unexpected side effects
  • 10-30% of adverse drug events are attributed to DDIs
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SLIDE 29

Drug-drug interactions (DDIs)

  • DDIs can occur when a patient takes 2 or more drugs
  • DDIs cause unexpected side effects
  • 10-30% of adverse drug events are attributed to DDIs
  • Understanding of DDIs may lead to better outcomes
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SLIDE 30

Drug-drug interactions (DDIs)

  • DDIs can occur when a patient takes 2 or more drugs
  • DDIs cause unexpected side effects
  • 10-30% of adverse drug events are attributed to DDIs
  • Understanding of DDIs may lead to better outcomes
  • precaution in prescription
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SLIDE 31

Drug-drug interactions (DDIs)

  • DDIs can occur when a patient takes 2 or more drugs
  • DDIs cause unexpected side effects
  • 10-30% of adverse drug events are attributed to DDIs
  • Understanding of DDIs may lead to better outcomes
  • precaution in prescription
  • synergistic therapies
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SLIDE 32

Polypharmacy increases with age

76% of older Americans used two or more prescription drugs

0-11 12-19 20-59 60 and over

Age in years

10 20 30 40 50 60 70

Percent

Percent of people on two or more drugs by age United States 2007-2008

SOURCE: CDC/NCHS, National Health and Nutrition Examination Survey

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SLIDE 33

More needs to be done to understand and identify drug-drug interactions

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SLIDE 34

More needs to be done to understand and identify drug-drug interactions

  • Clinical trials do not typically investigate drug-

drug interactions

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SLIDE 35

More needs to be done to understand and identify drug-drug interactions

  • Clinical trials do not typically investigate drug-

drug interactions

  • Observational studies are the only systematic

way to detect drug-drug interactions

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SLIDE 36

Large population databases enable DDI discovery

  • Contain clinical data on millions of patients over many

years

  • Currently being used to establish single drug adverse

events (pharmacovigilance)

  • Eg. Spontaneous Adverse Event Reporting Systems
  • Collect adverse event reports for a patient (a snapshot

in time)

  • Maintained by WHO > FDA > Health Canada

14

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SLIDE 37

Observational data are messy

Adverse Events ACUTE RESP. DISTRESS ANEMIA

  • DECR. BLOOD PRESSURE

CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE

15

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SLIDE 38

Observational data are messy

  • Many drugs, many adverse events

Adverse Events ACUTE RESP. DISTRESS ANEMIA

  • DECR. BLOOD PRESSURE

CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE

15

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SLIDE 39

Observational data are messy

  • Many drugs, many adverse events
  • what causes what?

Adverse Events ACUTE RESP. DISTRESS ANEMIA

  • DECR. BLOOD PRESSURE

CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE

15

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SLIDE 40

Observational data are messy

  • Many drugs, many adverse events
  • what causes what?

Adverse Events ACUTE RESP. DISTRESS ANEMIA

  • DECR. BLOOD PRESSURE

CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE

15

most of these red lines are false - which are true?

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SLIDE 41

Observational data are confounded

16

  • Spontaneous reporting systems are observational

data sets (unknown biases)

  • noise from concomitant drug use (co-Rx effect)
  • drugs co-prescribed with Vioxx more likely to be

associated with heart attacks

  • noise from indications (indication-effect)
  • drugs given to diabetics more likely to be

associated with hyperglycemia

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SLIDE 42

SCRUB

Statistical CorRection of Uncharacterized Bias

  • Implicitly corrects for confounding of both observed and

missing variables

  • Assumes some combination of the drugs and indications

describes the patient covariates

  • Only works on very large data sets
  • N. Tatonetti et al., Science Translational Medicine (2012)
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SLIDE 43

5 10 15 20

Proportional Reporting Ratio

disopyramide dofetilide sotalol flecainide propafenone amiodarone diltiazem mexiletine verapamil quinidine lidocaine tirofiban hydroxyzine

Anti-arrhythmics and Arrhythmia

Method corrects for indication biases

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SLIDE 44

5 10 15 20

Proportional Reporting Ratio

disopyramide dofetilide sotalol flecainide propafenone amiodarone diltiazem mexiletine verapamil quinidine lidocaine tirofiban hydroxyzine

Anti-arrhythmics and Arrhythmia

5 10 15 20

Proportional Reporting Ratio

disopyramide dofetilide sotalol flecainide propafenone amiodarone diltiazem mexiletine verapamil quinidine lidocaine tirofiban hydroxyzine Original PRR Corrected PRR

Anti-arrhythmics and Arrhythmia

Method corrects for indication biases

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SLIDE 45

5 10 15 20

Proportional Reporting Ratio

disopyramide dofetilide sotalol flecainide propafenone amiodarone diltiazem mexiletine verapamil quinidine lidocaine tirofiban hydroxyzine

Anti-arrhythmics and Arrhythmia

5 10 15 20

Proportional Reporting Ratio

disopyramide dofetilide sotalol flecainide propafenone amiodarone diltiazem mexiletine verapamil quinidine lidocaine tirofiban hydroxyzine Original PRR Corrected PRR

Anti-arrhythmics and Arrhythmia

Method corrects for indication biases

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SLIDE 46

Implicit correction of age differences in exposed vs non-exposed

  • 40
  • 20

20 40

(Average Age of Cases) - (Average Age of Controls)

zanamivir memantine atomoxetine rivastigmine actinomycin D galantamine ethosuximide donepezil 6-thioguanine bicalutamide retinoic acid flutamide methylphenidate verteporfin thiotepa acenocoumarol PGE2 darifenacin N-butyldeoxynojirimycin amiodarone Original Corrected

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SLIDE 47

Bias, corrected. Missing data?

If there are no observations then no associations can be found.

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SLIDE 48

Diseases can be identifjed by the side effects they elicit

21

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SLIDE 49

Diseases can be identifjed by the side effects they elicit

Diabetes

21

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SLIDE 50

Diseases can be identifjed by the side effects they elicit

Diabetes

level of detection

21

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SLIDE 51

Diseases can be identifjed by the side effects they elicit

Diabetes

level of detection unmeasured severe effect

21

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SLIDE 52

Diseases can be identifjed by the side effects they elicit

Diabetes

level of detection unmeasured severe effect measured minor effects

21

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SLIDE 53

Diseases can be identifjed by the side effects they elicit

Diabetes

level of detection unmeasured severe effect measured minor effects

  • physicians use observable side effects to form hypothesis about the

underlying disease

21

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SLIDE 54

Diseases can be identifjed by the side effects they elicit

Diabetes

level of detection unmeasured severe effect measured minor effects

  • physicians use observable side effects to form hypothesis about the

underlying disease

  • e.g. you can’t see diabetes, but you can measure blood glucose

21

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SLIDE 55

Severe ADE’s can be identifjed by the presence

  • f more minor (and more common) side effects

Adverse Event

level of detection unmeasured severe effect measured minor effects

22

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SLIDE 56

Severe ADE’s can be identifjed by the presence

  • f more minor (and more common) side effects

Adverse Event

level of detection unmeasured severe effect measured minor effects

  • First, identify the common side effects that are harbingers for the

underlying severe AE

22

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SLIDE 57

Severe ADE’s can be identifjed by the presence

  • f more minor (and more common) side effects

Adverse Event

level of detection unmeasured severe effect measured minor effects

  • First, identify the common side effects that are harbingers for the

underlying severe AE

  • Then, combine these side effects together to form an “effect profjle”

for an adverse event

22

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SLIDE 58

T2DM

Increased Blood Glucose

Pain Numbness

level of detection unmeasured severe effect

Severe ADEs can be identified by the presence

  • f more minor (and more common) side effects

measured minor effects

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SLIDE 59

DDI prediction validation

Table S3 Novel drug-drug interaction predictions for diabetes related adverse events. Rank Drug A Drug B Score Minimum Randomization Rank Known DDI exists 38 PAROXETINE HCL PRAVASTATIN SODIUM 11.351896014962 72 DIOVAN HCT HYDROCHLOROTHIAZIDE 7.1786599539 89 94 CRESTOR PREVACID 4.7923771645 148 107 DESFERAL EXJADE 3.97220625 129 159 COUMADIN VESICARE 0.8928376683 169 160 DEXAMETHASONETHALIDOMIDE 0.8928376683 168 CRITICAL 170 FOSAMAX VOLTAREN 0.5033125 1138 175 ALIMTA DEXAMETHASONE 0.2442375 197

  • Focus on top hit from diabetes classifier
  • paroxetine = depression drug, pravastatin = cholesterol drug
  • Popular drugs, est. ~1,000,000 patients on this combination!
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SLIDE 60

Analyzed blood glucose values for patients on either or both of these drugs

To the electronic health records…

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SLIDE 61

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063)

Baseline After Treatment

Tatonetti, et al. Clinical Pharmacology & Therapeutics (2011)

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SLIDE 62

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063)

Baseline After Treatment

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063) Paroxetine (N = 1,603)

Baseline After Treatment

Tatonetti, et al. Clinical Pharmacology & Therapeutics (2011)

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SLIDE 63

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063)

Baseline After Treatment

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063) Paroxetine (N = 1,603)

Baseline After Treatment

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063) Paroxetine (N = 1,603) Combination (N = 135)

Baseline After Treatment

+18 mg/dl incr. p < 0.001

Tatonetti, et al. Clinical Pharmacology & Therapeutics (2011)

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SLIDE 64

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063) Paroxetine (N = 1,603) Combination (N = 135)

Baseline After Treatment

no diabetics

Tatonetti, et al. Clinical Pharmacology & Therapeutics (2011)

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SLIDE 65

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063) Paroxetine (N = 1,603) Combination (N = 135)

Baseline After Treatment

no diabetics

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

Pravastatin Paroxetine Combination (N=177)

Baseline After Treatment

including diabetics

Tatonetti, et al. Clinical Pharmacology & Therapeutics (2011)

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SLIDE 66

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

5 6 7 8 9 10 11

Blood Glucose Concentration (mmol/L)

Pravastatin (N = 2,063) Paroxetine (N = 1,603) Combination (N = 135)

Baseline After Treatment

no diabetics

80 100 120 140 160 180 200

Blood Glucose Concentration (mg/dl)

Pravastatin Paroxetine Combination (N=177)

Baseline After Treatment

including diabetics

Tatonetti, et al. Clinical Pharmacology & Therapeutics (2011)

~60mg/dl increase

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SLIDE 67

Informatics methods have taken us far, skeptics remain

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SLIDE 68

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
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SLIDE 69

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
  • 10 control mice on normal diet (Ctl Ctl)
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SLIDE 70

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
  • 10 control mice on normal diet (Ctl Ctl)
  • 10 control mice on high fat diet (HFD)
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SLIDE 71

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
  • 10 control mice on normal diet (Ctl Ctl)
  • 10 control mice on high fat diet (HFD)
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SLIDE 72

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
  • 10 control mice on normal diet (Ctl Ctl)
  • 10 control mice on high fat diet (HFD)

Simulating Pre-Diabetics

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SLIDE 73

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
  • 10 control mice on normal diet (Ctl Ctl)
  • 10 control mice on high fat diet (HFD)

Simulating Pre-Diabetics

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SLIDE 74

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
  • 10 control mice on normal diet (Ctl Ctl)
  • 10 control mice on high fat diet (HFD)

Simulating Pre-Diabetics

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SLIDE 75
  • 10 mice on pravastatin + HFD
  • 10 mice on paroxetine + HFD
  • 10 mice on combination + HFD

Informatics methods have taken us far, skeptics remain

  • Insulin Resistant Mouse Model
  • 10 control mice on normal diet (Ctl Ctl)
  • 10 control mice on high fat diet (HFD)
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SLIDE 76

Summary of fasting glucose levels

C

  • m

b i n a t i

  • n

C

  • n

t r

  • l

P a r

  • x

e t i n e P r a v a s t a t i n C t l C t l 60 80 100 120 140 160 180

Average ITT Fasting Glucose (mg/dl)

~60mg/dl increase

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SLIDE 77

Replication is vital to science

  • In biology we would never trust a result that hasn’t

been replicated

  • Why should algorithms be any different?
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SLIDE 78

AL George, J. Clin. Invest. (2013)

Drug-drug interactions and acquired Long QT Syndrome (LQTS)

  • Long QT syndrome (LQTS):

congenital or drug-induced change in electrical activity of the heart that can lead to potentially fatal arrhythmia: torsades de pointes (TdP)

  • 13 genes associated with

congenital LQTS

  • Drug-induced LQTS usually

caused by blocking the hERG channel (KCNH2)

From Berger et al., Science Signaling (2010)

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SLIDE 79

Identify acquired LQTS drug-drug interactions using Latent Signal Detection

LQTS

tachycardia

AFib

bradycardia

level of detection unmeasured severe effect measured minor effects

Lorberbaum, et al. Drug Safety (2016)

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SLIDE 80

Latent Signal Detection of acquired LQTS

  • Ceftriaxone — common in-patient cephalosporin antibiotic
  • Lansoprazole — proton-pump inhibitor used to treat GERD, one of the most

commonly taken drugs in the world

  • In the EHR: Patients on the combination have QT intervals 11ms longer, on

average and are 1.5X as likely to have a QT interval > 500ms

Top Prediction: Ceftriaxone + Lansoprazole

Lorberbaum, et al. Drug Safety (2016)
 Lorberbaum, et al. JACC (In press)

slide-81
SLIDE 81
  • Predicted QT-DDI: ceftriaxone (cephalosporin

antibiotic) and lansoprazole (proton pump inhibitor)

  • Neither drug alone has any evidence of QT

prolongation/ hERG block

  • Negative control: lansoprazole + cefuroxime
slide-82
SLIDE 82
  • Predicted QT-DDI: ceftriaxone (cephalosporin

antibiotic) and lansoprazole (proton pump inhibitor)

  • Neither drug alone has any evidence of QT

prolongation/ hERG block

  • Negative control: lansoprazole + cefuroxime

(another cephalosporin) – no evidence in FAERS of an interaction

slide-83
SLIDE 83
  • Predicted QT-DDI: ceftriaxone (cephalosporin

antibiotic) and lansoprazole (proton pump inhibitor)

  • Neither drug alone has any evidence of QT

prolongation/ hERG block

  • Negative control: lansoprazole + cefuroxime

(another cephalosporin) – no evidence in FAERS of an interaction

  • Negative control: lansoprazole + cefuroxime

(another cephalosporin) – no evidence in FAERS of an interaction

slide-84
SLIDE 84
  • Predicted QT-DDI: ceftriaxone (cephalosporin

antibiotic) and lansoprazole (proton pump inhibitor)

  • Neither drug alone has any evidence of QT

prolongation/ hERG block

  • Negative control: lansoprazole + cefuroxime

(another cephalosporin) – no evidence in FAERS of an interaction

  • Negative control: lansoprazole + cefuroxime

(another cephalosporin) – no evidence in FAERS of an interaction

Ceftriaxone Cefuroxime

slide-85
SLIDE 85

FAERS

Ceftriaxone+ Lansoprazole

Lorberbaum, et al. In Revision

Side Effect Profile

slide-86
SLIDE 86

FAERS

Ceftriaxone+ Lansoprazole

Lorberbaum, et al. In Revision

Side Effect Profile

slide-87
SLIDE 87

FAERS

Ceftriaxone+ Lansoprazole Cefuroxime+ Lansoprazole

Lorberbaum, et al. In Revision

slide-88
SLIDE 88

Electronic Health Records

* * * * * * * * * * * *

Ceftriaxone+ Lansoprazole Cefuroxime+ Lansoprazole

* * * *

Lorberbaum, et al. In Revision

slide-89
SLIDE 89

Electronic Health Records

* * * * * * * * * * * *

Ceftriaxone+ Lansoprazole Cefuroxime+ Lansoprazole

* * * *

Lorberbaum, et al. In Revision

~10ms longer

  • n average
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SLIDE 90

What is the mechanism?

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SLIDE 91

MADSS

  • Use network analysis to build AE

neighborhoods: a subset of the interactome surrounding AE “seed” proteins

  • Score each protein on

connectivity to seeds using:

  • Mean first passage time
  • Betweenness centrality
  • Shared neighbors
  • Inverse shortest path
  • Overarching hypothesis: drugs

targeting proteins within an AE neighborhood more likely to be involved in mediating that AE

  • Ran MADSS using 13 LQTS

genes as seeds

Modular Assembly of Drug Safety Subnetworks

Protein Interaction Seed protein Adverse event (AE) Drug known to cause AE Drug predicted to cause AE

Lorberbaum, et al. Clin. Pharmacol. Ther. (2015)

slide-92
SLIDE 92

MADSS

  • Use network analysis to build AE

neighborhoods: a subset of the interactome surrounding AE “seed” proteins

  • Score each protein on

connectivity to seeds using:

  • Mean first passage time
  • Betweenness centrality
  • Shared neighbors
  • Inverse shortest path
  • Overarching hypothesis: drugs

targeting proteins within an AE neighborhood more likely to be involved in mediating that AE

  • Ran MADSS using 13 LQTS

genes as seeds

Modular Assembly of Drug Safety Subnetworks

Protein Interaction Seed protein Adverse event (AE) Drug known to cause AE Drug predicted to cause AE

  • Ran MADSS using 13 LQTS

genes as seeds

Lorberbaum, et al. Clin. Pharmacol. Ther. (2015)

slide-93
SLIDE 93

Putative mechanisms of QT-DDIs

KCNH2

LQTS

Lansoprazole

SCN5A

Ceftriaxone Diltiazem Phenytoin Fosphenytoin Metoprolol

Cluster 7 Cluster 1 Cluster 3

CACNA1C

CACNG1

CAV3

ATP4A

ADRB1

Known drug-target binding (DrugBank) Predicted drug-hERG binding (Random Forest classifier)

slide-94
SLIDE 94

Nanion Patchliner

Lorberbaum, et al. JACC (In press)

Voltage protocol: step to +40mV followed by a return to -40mV

Automated Patch Clamp

  • Collaboration with Rocky

Kass (CUMC Pharmacology Dept.)

  • Take HEK293 cells over-

expressing the hERG channel

  • Perform a single-cell patch

clamp experiment

  • control
  • ceftriaxone alone
  • lansoprazole alone
  • combination of ceftriaxone

and lansoprazole

slide-95
SLIDE 95

Ceftriaxone+Lansoprazole

Lorberbaum, et al. JACC (In press)

slide-96
SLIDE 96

Ceftriaxone+Lansoprazole Cefuroxime+Lansoprazole

Lorberbaum, et al. JACC (In press)

slide-97
SLIDE 97

Ceftriaxone+Lansoprazole Cefuroxime+Lansoprazole

Cefuroxime + 1μM Lansoprazole Cefuroxime alone 0μM 0.1μM 1μM 10μM 50μM 100μM

Cefuroxime Concentration (μM)

0.0 0.2 0.4 0.6 0.8 1.0 1.2

Change from Control

Cefu+Lanso effect on hERG current 0μM 0.1μM 1μM 10μM 50μM 100μM

Ceftriaxone Concentration (μM)

0.0 0.2 0.4 0.6 0.8 1.0 1.2

Change from Control

Ceftriaxone + 10μM Lansoprazole Ceftriaxone + 1μM Lansoprazole Ceftriaxone alone Ceft+Lanso effect on hERG current Lorberbaum, et al. JACC (In press)

slide-98
SLIDE 98
slide-99
SLIDE 99

0mV 50mV 100ms Wildtype channel 1μM Lansoprazole + 100μM Ceftriaxone (10% block) 10μM Lansoprazole + 100μM Ceftriaxone (55% block) Lorberbaum, et al. JACC (In press)

Computational model of human ventricular myocyte

slide-100
SLIDE 100

0mV 50mV 100ms Wildtype channel 1μM Lansoprazole + 100μM Ceftriaxone (10% block) 10μM Lansoprazole + 100μM Ceftriaxone (55% block) Lorberbaum, et al. JACC (In press)

Computational model of human ventricular myocyte

10ms longer most common at CUMC

slide-101
SLIDE 101

Data mining clinical information

  • Drug-drug interactions can be discovered using
  • bservational data
  • paroxetine/pravastatin
  • ceftriaxone/lansoprazole
  • EHR data accurately predict prospective experiments
slide-102
SLIDE 102

tatonettilab.org nick.tatonetti@columbia.edu @nicktatonetti

Current Lab Members

Rami Vanguri, PhD Kayla Quinnies, PhD Alexandra Jacunski Tal Lorberbaum Mary Boland Joseph Romano Yun Hao Phyllis Thangaraj Alexandre Yahi Fernanda Polubriaginof, MD

Collaborators Funding

NIGMS R01GM107145 Herbert Irving Fellowship PhRMA Research Starter Grant NCI P30CA013696 NIMH R03MH103957

Thank you

David Goldstein, PhD Krzysztof Kiryluk, MD, MS David Vawdrey, PhD Robert Kass, PhD Kevin Sampson, PhD Brent Stockwell, PhD George Hripcsak, MD, MS Ziad Ali, MD, DPhil Ray Woosley, MD, PhD (Credible Meds) Konrad Karczewski, PhD (Broad/MGH) Joel Dudley, PhD (Mount Sinai) Li Li, PhD (Mount Sinai) Patrick Ryan, PhD (OHDSI) Russ Altman (Stanford) Issac Kohane (HMS) Shawn Murphy (HMS)