Biomedical Discovery through Data Mining and Data Science
Nicholas P. Tatonetti, PhD Columbia University
November 14th, 2016
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
Nicholas P. Tatonetti, PhD Columbia University
November 14th, 2016
between geography and phenotype
between geography and phenotype
thalidamide use and birth defects
microphones
microphones
microphones
throughput sequencing technology
microphones
throughput sequencing technology
Bytes to KB Megabytes to Terabytes
microphones
throughput sequencing technology
Bytes to KB Megabytes to Terabytes
>99% of Hospitals have Electronic Health Records
kilobytes of data
kilobytes of data
petabytes of data
kilobytes of data
petabytes of data
much information
kilobytes of data
petabytes of data
much information
analysis (“hypothesis generation”) catch up to the tools of observation
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
drug interactions
drug interactions
way to detect drug-drug interactions
years
events (pharmacovigilance)
in time)
14
Adverse Events ACUTE RESP. DISTRESS ANEMIA
CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE
15
Adverse Events ACUTE RESP. DISTRESS ANEMIA
CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE
15
Adverse Events ACUTE RESP. DISTRESS ANEMIA
CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE
15
Adverse Events ACUTE RESP. DISTRESS ANEMIA
CARDIAC FAILURE DEHYDRATION Drugs METFORMIN ROSIGLITAZONE PRAVASTATIN TACROLIMUS PREDNISOLONE
15
most of these red lines are false - which are true?
16
data sets (unknown biases)
associated with heart attacks
associated with hyperglycemia
missing variables
describes the patient covariates
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
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
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
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
If there are no observations then no associations can be found.
21
Diabetes
21
Diabetes
level of detection
21
Diabetes
level of detection unmeasured severe effect
21
Diabetes
level of detection unmeasured severe effect measured minor effects
21
Diabetes
level of detection unmeasured severe effect measured minor effects
underlying disease
21
Diabetes
level of detection unmeasured severe effect measured minor effects
underlying disease
21
Severe ADE’s can be identifjed by the presence
Adverse Event
level of detection unmeasured severe effect measured minor effects
22
Severe ADE’s can be identifjed by the presence
Adverse Event
level of detection unmeasured severe effect measured minor effects
underlying severe AE
22
Severe ADE’s can be identifjed by the presence
Adverse Event
level of detection unmeasured severe effect measured minor effects
underlying severe AE
for an adverse event
22
T2DM
Increased Blood Glucose
Pain Numbness
level of detection unmeasured severe effect
Severe ADEs can be identified by the presence
measured minor effects
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
To the electronic health records…
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)
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)
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)
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)
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)
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
Simulating Pre-Diabetics
Simulating Pre-Diabetics
Simulating Pre-Diabetics
C
b i n a t i
C
t r
P a r
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
been replicated
AL George, J. Clin. Invest. (2013)
congenital or drug-induced change in electrical activity of the heart that can lead to potentially fatal arrhythmia: torsades de pointes (TdP)
congenital LQTS
caused by blocking the hERG channel (KCNH2)
From Berger et al., Science Signaling (2010)
LQTS
tachycardia
AFib
bradycardia
level of detection unmeasured severe effect measured minor effects
Lorberbaum, et al. Drug Safety (2016)
commonly taken drugs in the world
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)
antibiotic) and lansoprazole (proton pump inhibitor)
prolongation/ hERG block
antibiotic) and lansoprazole (proton pump inhibitor)
prolongation/ hERG block
(another cephalosporin) – no evidence in FAERS of an interaction
antibiotic) and lansoprazole (proton pump inhibitor)
prolongation/ hERG block
(another cephalosporin) – no evidence in FAERS of an interaction
(another cephalosporin) – no evidence in FAERS of an interaction
antibiotic) and lansoprazole (proton pump inhibitor)
prolongation/ hERG block
(another cephalosporin) – no evidence in FAERS of an interaction
(another cephalosporin) – no evidence in FAERS of an interaction
Ceftriaxone Cefuroxime
Ceftriaxone+ Lansoprazole
Lorberbaum, et al. In Revision
Side Effect Profile
Ceftriaxone+ Lansoprazole
Lorberbaum, et al. In Revision
Side Effect Profile
Ceftriaxone+ Lansoprazole Cefuroxime+ Lansoprazole
Lorberbaum, et al. In Revision
* * * * * * * * * * * *
Ceftriaxone+ Lansoprazole Cefuroxime+ Lansoprazole
* * * *
Lorberbaum, et al. In Revision
* * * * * * * * * * * *
Ceftriaxone+ Lansoprazole Cefuroxime+ Lansoprazole
* * * *
Lorberbaum, et al. In Revision
~10ms longer
neighborhoods: a subset of the interactome surrounding AE “seed” proteins
connectivity to seeds using:
targeting proteins within an AE neighborhood more likely to be involved in mediating that AE
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)
neighborhoods: a subset of the interactome surrounding AE “seed” proteins
connectivity to seeds using:
targeting proteins within an AE neighborhood more likely to be involved in mediating that AE
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
genes as seeds
Lorberbaum, et al. Clin. Pharmacol. Ther. (2015)
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)
Nanion Patchliner
Lorberbaum, et al. JACC (In press)
Voltage protocol: step to +40mV followed by a return to -40mV
Kass (CUMC Pharmacology Dept.)
expressing the hERG channel
clamp experiment
and lansoprazole
Ceftriaxone+Lansoprazole
Lorberbaum, et al. JACC (In press)
Ceftriaxone+Lansoprazole Cefuroxime+Lansoprazole
Lorberbaum, et al. JACC (In press)
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)
0mV 50mV 100ms Wildtype channel 1μM Lansoprazole + 100μM Ceftriaxone (10% block) 10μM Lansoprazole + 100μM Ceftriaxone (55% block) Lorberbaum, et al. JACC (In press)
0mV 50mV 100ms Wildtype channel 1μM Lansoprazole + 100μM Ceftriaxone (10% block) 10μM Lansoprazole + 100μM Ceftriaxone (55% block) Lorberbaum, et al. JACC (In press)
10ms longer most common at CUMC
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
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)