Neurology Stroke Research Retreat: Electronic Medical Records & Biomedical Informatics Resources

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1 Neurology Stroke Research Retreat: lectronic Medical Records & Biomedical Informatics Resources rthur Berg, PhD CTSI Biomedical Informatics Program Leader Bioinformatics Core Director

2 Biomedical Informatics Services Clinical Research Informatics Core MR data i2b2 Health Facts Bioinformatics Core RDCap Profiles

3 Biomedical Informatics Biomedical Informatics Services nna C. Salzberg, Guodong Liu, Ben Tshudy, Robert ronoff, d rthur Berg Clinical Informatics Research Core Bioinformatics Core The Bioinformatics Core provides expertise in bioinformatics alysis d computational competency that is required by my areas of clinical d trslational research. rthur Berg, PhD Director, Bioinformatics Core Other Members: nna Salzberg, Senior Bioinformatici Guodong Liu, Postdoctoral Scholar Rich Rauscher, Director of Research IT Mb uti S Py B gm ntu iaka y So Pyg uth my fr ica Ba Yo rthur Berg, PhD F FRIC RIC F R F IC RIC Robert ronoff, MD ru ba F RIC Yo ru ba Ma Ba nden ntu k Ke a ny a Lu hy F RIC F RIC F RIC a F RIC nalytical Services Provided: Ma nnotating NGS Data Whole genome xome ChIP-seq TCG (sequence & GWS) m e Mo Pa ric D MID DL _ uin S T MID DL _ S T tin i MID DL _ S T Dru ze MID DL d yg ei rd inia Tu n sc Sa To sc OP U RO U P RO P s U R Ita lia n Fre nc h Orc ad i U R OP U RO P U RO P ro S MbutiPygmy FRIC FRIC FRIC FRIC Yoruba FRIC Yoruba FRIC Mdenka FRIC BtuKenya FRIC Luhya FRIC Maasai FRIC S T OP u BiakaPygmy BtuSouthfrica _ U R pe m eri ca n U R OP Ba sq Ru ue U R OP ss i U R OP Gu jara ti C R L_ SO UT H_ S C R L_ C SO UT R H_ L S _S C OU TH R _ L_ S C SO UT R H_ L_ S C SO UT R H_ L_ S C SO UT R H_ L_ C S SO UT R H_ L_ C S SO U TH C RL S S RL OUT _S ST H OU _S _S T H _ ST_ S S T S ST S ST S _ S ST _ S Ma kra fric meric Mozabite MIDDL_ST Bedouin MIDDL_ST Palestini MIDDL_ST Druze dygei ni loc hi Bra hu i Ka las h Bu ru sh o Pa tha n Sin dh i Ha za ra Uy gu r Ya Mo kut ng ola T O Xibu Heroqeo zh n Daen ur Ja pa ne se Ba DMIXD MIDDL_ST UROP Sardini UROP Tusc UROP Toscs UROP Itali UROP French UROP Orcadi UROP urope meric UROP Basque UROP Russi UROP Gujarati CRL_SOUTH_S Ja pa Makri CRL_SOUTH_S Balochi CRL_SOUTH_S Brahui CRL_SOUTH_S Kalash CRL_SOUTH_S Burusho CRL_SOUTH_S Path CRL_SOUTH_S Sindhi CRL_SOUTH_S Hazara Mongola Tu Xibo Oroqen Hezhen Daur Japese Japese Yi Naxi Tujia H-NChina H H Chinese meric She Miao Dai Lahu Cambodi Melesi Papu OCN OCN Mexic meric Maya MRIC MRIC MRIC MRIC MRIC Identify)a)cohort)of)patients)with) the)diagnosis)of)acute)renal) failure)that)received)dialysis)d) passed)through)the)hvicu)or) SICU)during)their)hospital)stay.)) This)is)for)a)grt)application.) pproach' 1) Identify)which)nursing)forms)include)the)proper) smoking)status) 2) The)master)list)of)departmental)physicis)is)not) accurate.))queries)need)done)by)individual)providers) d)not)department.) 3) Identification)of)appropriate)doctorBpatient) relationship)best)done)through)cross)joining)cpt) data)within)the)hpm)universe.) 1) ICD9)diagnoses)d)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 S S ST_ ST_S ST S _ S ST _ S Ha n S T_ S Ch in es Data e me ric PharmNet S T_ S S Miahe o Ca Da MemboLahui l dia es n Pa i pu Me xic m eri ca n DMIXD Pima Colombi Karitia Surui Lab values Billing codes Medications Payer data dmission data Diagnosis codes Diagnosis tests Physici provider Consults Patient education Sample'data'requests' T_ ld CRD9 JK2 624 TLR TNFSF ke li n's oh 0.72 U6 mi X10q X5p13.1 PTGR C6orf S100z 510 number of cis = 10 TNFSF15NOD2 severe 0.5 Normalized xpression How to access these services? Time (min) " Request forms will soon be available on the CTSI Biomedical Informatics website. Before then, you c contact Dr. Berg x3039) S MbutiPygmy BiakaPygmy BtuSouthfrica Yoruba YRI Mdenka BtuKenya LWK MKK Mozabite Bedouin Palestini Druze dygei Sardini Tusc TSI Itali French Orcadi CU Basque Russi TG16L SurgiNet Control R M IC MRIC MRIC MRIC R IC Lookup M 559 PowerChart 0.1 Genotype ssociation on IP Complication LF_1015 (0.42) [27] CTCT (11) WTTC (11) CTGCY (10) GGC (29) GCCC (32) V14/V22/V30/V33/V36 pval_perm: 0/0/0/0/0 pval_norm: 0/0/0/0/ /16301/09507/16020/ /6/6/5/4 ST_ ST_S OCST_S S OC N N D MIX D Ma y Co P a lo im Ka mbia a riti n a Su na ru i Cr Genetic association Biomarker alysis CNV alysis Multiple hypothesis correction Genetic signatures Predictive models Pathway/GO alysis Haplotype alysis Gene-environment interaction Gene-gene interaction CRL_SOUTH_S Yakut se N Yi n-n Tuaxi Ch jia ina Ha n Ha CRL_SOUTH_S Uygur ne Request' Identify)a)cohort)of)smokers) seen)in)specific)clinic.))cohort) will)be)approached)about)a) smoking)cessation)protocol.)) This)is)a)funded)project.) D MIX bit e les nalytical Methods Novel Methodology F RIC za do Focused Technologies Cdidate genes Functional SNPs Pyrosequencing data Focus PCR array ai Be Other Genomewide data structures Gene expression array SNP array Proteomics (itrq) Methylation array xon array Ben Tshudy, BS as fr ic The Clinical Informatics Research Core provides services to perform electronic health record data extraction for research use in a mner that is IRB-complit d insures the privacy d security of patient data " Questions related to the RDCap service should be directed to Terri Sckuda

4 profiles.psu.edu

5

6 i2b2

7 i2b2

8 PSU Data Warehouse

9 Cerner Health Facts More th 1.3 billion laboratory results More th 84 million acute admissions, emergency d ambulatory visits More th nine years of detailed pharmacy, laboratory, billing d registration data Over 100 Cerner clients, including PSH Fully de-identified PSU IRB determination Updated twice nually More th 151 million orders for nearly 4,500 drugs by name d brd

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

11 CHF Readmission Collaboration with Robert ronoff, MD consecutive heart failure discharges abstracted cdidate predictors screened - Target class: Readmission at 30 days ( binary ) dministrative cdidate predictors dmission source, status, service ge, gender, race Primary/secondary payers Primary/secondary diagnoses (names d condition categories) Total length of stay, ICU length of stay Hospital costs d charges Discharge status d disposition ll-cause same-center admission in preceding year Clinical cdidate predictors Specialty medical services consulted Specialty cillary services consulted Blood laboratory values Medications name / therapeutic class Dosages of medications Patient weights during hospitalization Trsfusions during hospitalization Nursing assessments ducation topics Diagnostic tests ordered Ordersets utilized

12 High-Dimensional Predictive Models dmissions within prior year ICU Days nion Gap Initial Systolic BP Final BNP BUN-Creatinine Ratio

13 Ongoing Clinical Trials detail_stroke.htm# lbumin in cute Ischemic Stroke (LS) Trial -- ntihypertensive Treatment of cute Cerebral Hemorrhage (TCH ll) -- Rdomized Trial of Unruptured Brain rteriovenous Malformations (RUB) -- Clot Lysis: valuating ccelerated Resolution of Intraventricular Hemorrhage, Phase III (CLR III) -- Field dministration of Stroke Therapy Magnesium Trial (FST-MG) -- Insulin Resistce Intervention after Stroke Trial (IRIS) -- Interdisciplinary Comprehensive rm Rehabilitation valuation (I-CR) -- Interventional Magement of Stroke Trial (IMS III) -- Platelet-Oriented Inhibition in New T d Minor Ischemic Stroke (POI) Trial -- Stroke Hyperglycemia Insulin Network ffort Trial (SHIN)

14 Bioinformatics Services nnotating NGS Data Whole genome xome RN-seq ChIP-seq TCG (sequence & GWS) Other Genomewide data structures Gene expression array SNP array Proteomics (itrq) Methylation array xon array Focused Technologies Cdidate genes Functional SNPs Pyrosequencing data Focus PCR array nalytical Methods Genetic association Biomarker alysis CNV alysis Multiple hypothesis correction Genetic signatures Predictive models Pathway/GO alysis Haplotype alysis Gene-environment interaction Gene-gene interaction Novel Methodology

1.- L a m e j o r o p c ió n e s c l o na r e l d i s co ( s e e x p li c a r á d es p u é s ).

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