Neurology Stroke Research Retreat:

Electronic Medical Records & Biomedical Informatics Resources

Arthur Berg, PhDCTSI Biomedical Informatics Program Leader

Bioinformatics Core Director

Biomedical Informatics Services

• Clinical Research Informatics Core

• EMR data

• i2b2

• Health Facts

• Bioinformatics Core

• REDCap

• Profiles

Biomedical InformaticsBiomedical Informatics Services Anna C. Salzberg, Guodong Liu, Ben Tshudy, Robert Aronoff, and Arthur Berg

http://ctsi.psu.edu/

Bioinformatics Core Arthur Berg, PhD Director, Bioinformatics Core

Other Members: Anna Salzberg, Senior Bioinformatician Guodong Liu, Postdoctoral Scholar Rich Rauscher, Director of Research IT

Analytical Services Provided: ! Annotating NGS Data

! Whole genome ! Exome ! ChIP-seq ! TCGA (sequence & GWAS)

! Other Genomewide data structures ! Gene expression array ! SNP array ! Proteomics (iTRAQ) ! Methylation array ! Exon array

! Focused Technologies ! Candidate genes ! Functional SNPs ! Pyrosequencing data ! Focus PCR array

! Analytical Methods ! Genetic association ! Biomarker analysis ! CNV analysis ! Multiple hypothesis correction ! Genetic signatures ! Predictive models ! Pathway/GO analysis ! Haplotype analysis ! Gene-environment interaction ! Gene-gene interaction

! Novel Methodology

How to access these services?

Clinical Informatics Research Core Arthur Berg, PhD

Robert Aronoff, MD

Ben Tshudy, BS

The Bioinformatics Core provides expertise in bioinformatics analysis and computational competency that is required by many areas of clinical and translational research.

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AFRICAYoruba

AFRICAYoruba

AFRICAMandenkaAFRICABantuKenya

AFRICALuhya

AFRICAMaasai

ADMIXEDAfrican American

MIDDLE_EASTMozabite

MIDDLE_EASTBedouin

MIDDLE_EASTPalestinian

MIDDLE_EASTDruze

EUROPEAdygei

EUROPESardinianEUROPETuscan

EUROPEToscans

EUROPEItalian

EUROPEFrench

EUROPEOrcadian

EUROPEEuropean American

EUROPEBasque

EUROPERussian

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CENTRAL_SOUTH_ASIABalochi

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CENTRAL_SOUTH_ASIAKalash

CENTRAL_SOUTH_ASIABurusho

CENTRAL_SOUTH_ASIAPathan

CENTRAL_SOUTH_ASIASindhi

CENTRAL_SOUTH_ASIAHazaraCENTRAL_SOUTH_ASIAUygurEAST_ASIAYakutEAST_ASIAMongolaEAST_ASIATuEAST_ASIAXiboEAST_ASIAOroqenEAST_ASIAHezhenEAST_ASIADaurEAST_ASIAJapanese

EAST_ASIAJapanese

EAST_ASIAYiEAST_ASIANaxiEAST_ASIATujiaEAST_ASIAHan-NChina

EAST_ASIAHan

EAST_ASIAHan

EAST_ASIAChinese American

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ADMIXEDMexican American

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number of cis = 10

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AWTTCAAA (11)

CTGACY (10)

GAGAC (29)

GCCAC (32)

V14/V22/V30/V33/V36

pval_perm: 0/0/0/0/0

pval_norm: 0/0/0/0/0

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AFRICA

Yoruba

AFRICA

Yoruba

AFRICA

Mandenka

AFRICA

BantuKenya

AFRICA

Luhya

AFRICA

Maasai

ADMIXED

African American

MIDDLE_EAST

Mozabite

MIDDLE_EAST

Bedouin

MIDDLE_EAST

Palestinian

MIDDLE_EAST

Druze

EUROPE

Adygei

EUROPE

Sardinian

EUROPE

Tuscan

EUROPE

Toscans

EUROPE

Italian

EUROPE

French

EUROPE

Orcadian

EUROPE

European American

EUROPE

Basque

EUROPE

Russian

CENTRAL_SOUTH_ASIA

Gujarati

CENTRAL_SOUTH_ASIA

Makrani

CENTRAL_SOUTH_ASIA

Balochi

CENTRAL_SOUTH_ASIA

Brahui

CENTRAL_SOUTH_ASIA

Kalash

CENTRAL_SOUTH_ASIA

Burusho

CENTRAL_SOUTH_ASIA

Pathan

CENTRAL_SOUTH_ASIA

Sindhi

CENTRAL_SOUTH_ASIA

Hazara

CENTRAL_SOUTH_ASIA

Uygur

EAST_ASIA

Yakut

EAST_ASIA

MongolaEAST_ASIA

TuEAST_ASIA

XiboEAST_ASIA

OroqenEAST_ASIA

HezhenEAST_ASIA

Daur

EAST_ASIA

Japanese

EAST_ASIA

Japanese

EAST_ASIA

YiEAST_ASIA

NaxiEAST_ASIA

TujiaEAST_ASIA

Han-NChina

EAST_ASIA

Han

EAST_ASIA

Han

EAST_ASIA

Chinese American

EAST_ASIA

SheEAST_ASIA

MiaoEAST_ASIA

DaiEAST_ASIA

LahuEAST_ASIA

CambodianOCEANIA

MelanesianOCEANIA

Papuan

ADMIXED

Mexican American

AMERICA

Maya

AMERICA

PimaAMERICA

ColombianAMERICA

KaritianaAMERICA

Surui

The Clinical Informatics Research Core provides services to perform electronic health record data extraction for research use in a manner that is IRB-compliant and insures the privacy and security of patient data.

Lab values Billing codes Medications Payer data Admission data Diagnosis codes Diagnosis tests Physician provider Consults Patient education

Sample'data'requests'Request' Approach'

Identify)a)cohort)of)smokers)seen)in)specific)clinic.))Cohort)will)be)approached)about)a)smoking)cessation)protocol.))This)is)a)funded)project.)

1) Identify)which)nursing)forms)include)the)proper)smoking)status)

2) The)master)list)of)departmental)physicians)is)not)accurate.))Queries)need)done)by)individual)providers)and)not)department.)

3) Identification)of)appropriate)doctorBpatient)relationship)best)done)through)cross)joining)CPT)data)within)the)HPM)universe.)

Identify)a)cohort)of)patients)with)the)diagnosis)of)acute)renal)failure)that)received)dialysis)and)passed)through)the)HVICU)or)SICU)during)their)hospital)stay.))This)is)for)a)grant)application.)

1) ICD9)diagnoses)and)procedures)are)best)identified)via)HPM)universe.)

2) First)pass)cohort)from)HPM)is)cross)joined)with)Cerner)where)historical)bed)location)list)is)constructed.))HVICU/SICU)cohort)is)identified.)

)

Health Facts Research Database

" Request forms will soon be available on the CTSI Biomedical Informatics website. Before then, you can contact Dr. Berg (berg@psu.edu, x3039).

"  Questions related to the REDCap service should be directed to Terri Sckuda (REDCap@hmc.psu.edu).

Data PharmNet

Lookup PowerChart

Control SurgiNet

profiles.psu.edu

i2b2

i2b2

PSU Data Warehousehttp://infonet/decisionsupport/remedyweb.htm 

Cerner Health FactsMore than 1.3 billion laboratory results

More than 84 million acute admissions, emergency and ambulatory visits

More than nine years of detailed pharmacy, laboratory, billing and registration data

More than 151 million orders for nearly 4,500 drugs by name and brand

Over 100 Cerner clients, including PSH

Fully de-identified

PSU IRB determination

Updated twice annually

Do laboratory test results indicate evidence of adverse drug reactions?What are the demographic and clinical characteristics associated with a given drug treatment?What concomitant drugs did the patient receive?What drugs comprised the empiric regimen and what subsequent changes were made to that regimen?What are the actual doses or treatment regimens for specific patient populations or age groups?How are dosing and treatment regimens changing over time?Were certain dosing patterns linked to different outcomes?Do practice patterns differ by physician specialty or hospital type (size, teaching status, urban/rural)?Did the clinicians adhere to recommended treatment guidelines?Does the timing of this medication affect outcomes?What was the length of stay and what are billed charges?What was the in-hospital mortality for a given condition and what factors were associated with death?

Administrative candidate predictors

•  Admission source, status, service •  Age, gender, race •  Primary/secondary payers •  Primary/secondary diagnoses (names

and condition categories) •  Total length of stay, ICU length of

stay •  Hospital costs and charges •  Discharge status and disposition •  All-cause same-center admission in

preceding year

Clinical candidate predictors

•  Specialty medical services consulted •  Specialty ancillary services consulted •  Blood laboratory values •  Medications name / therapeutic class •  Dosages of medications •  Patient weights during hospitalization •  Transfusions during hospitalization •  Nursing assessments •  Education topics •  Diagnostic tests ordered •  Ordersets utilized

- 1612 consecutive heart failure discharges abstracted - 1280 candidate predictors screened - Target class: Readmission at 30 days ( binary )

CHF ReadmissionCollaboration with Robert Aronoff, MD

High-Dimensional Predictive ModelsAdmissions within prior year ICU Days

Anion Gap Initial Systolic BP

Final BNP BUN-Creatinine Ratio

Ongoing Clinical Trialshttp://www.ninds.nih.gov/disorders/stroke/

detail_stroke.htm#229981105

--Albumin in Acute Ischemic Stroke (ALIAS) Trial-- Antihypertensive Treatment of Acute Cerebral Hemorrhage (ATACH ll)-- A Randomized Trial of Unruptured Brain Arteriovenous Malformations (ARUBA)-- Clot Lysis: Evaluating Accelerated Resolution of Intraventricular Hemorrhage, Phase III (CLEAR III)-- Field Administration of Stroke Therapy Magnesium Trial (FAST-MAG)-- Insulin Resistance Intervention after Stroke Trial (IRIS)-- Interdisciplinary Comprehensive Arm Rehabilitation Evaluation (I-CARE)-- Interventional Management of Stroke Trial (IMS III)-- Platelet-Oriented Inhibition in New TIA and Minor Ischemic Stroke (POINT) Trial-- Stroke Hyperglycemia Insulin Network Effort Trial (SHINE)

Bioinformatics Services• Annotating NGS Data• Whole genome• Exome• RNA-seq• ChIP-seq• TCGA (sequence & GWAS)

• Other Genomewide data structures• Gene expression array• SNP array• Proteomics (iTRAQ)• Methylation array• Exon array

• Focused Technologies• Candidate genes• Functional SNPs

• Pyrosequencing data• Focus PCR array

• Analytical Methods• Genetic association• Biomarker analysis• CNV analysis• Multiple hypothesis

correction• Genetic signatures• Predictive models• Pathway/GO analysis• Haplotype analysis• Gene-environment

interaction• Gene-gene interaction

• Novel Methodology