VIReC Database and Metho

Cyber Seminar Series

RESEARCHERS’ GUIDE TO VA DATA
VIReC Database and Methods Cyber Seminar S

Measuring Laboratory Use a

Results using VA Decision Sup

System National Extract Da

April 4, 2011

Elizabeth Tarlov, RN, PhD

VA Information Resource Center

RESEARCHERS’ GUIDE TO VA DATA
Session Outline

O i f VA DSS ti l l b d Overview of VA DSS national lab dFinding information in VA DSS natl bd a ataMeasurement of laboratory use anresults in VA studiesExample of VA studies that have uDSS national lab dataWhere to g p o for more help

RESEARCHERS’ GUIDE TO VA DATA
Session Outline

O i f VA DSS ti l l b d Overview of VA DSS national lab dFinding information in VA DSS natl bd a ataMeasurement of laboratory use anresults in VA studies Example of VA studies that have uDSS national lab dataWhere to g p o for more help

RESEARCHERS’ GUIDE TO VA DATA
Audience Poll

Are you currently conducting researi i DSS LAB d/ LAR N i is using DSS LAB and/or LAR NationExtracts (NDE)?

– Yes– No

RESEARCHERS’ GUIDE TO VA DATA
Audience Poll

How would you rate your overall knoof h DSS LAB d LAR NDE ? f the DSS LAB and LAR NDEs?

– 1 (No knowledge)– 2– 3– 4– 5 (Expert-level knowledge)

RESEARCHERS’ GUIDE TO VA DATA
DSS Overview

What is DSS?– VA’s managerial cost accounting and 

executive information system

What is its primary purpose?– Provide managerially-useful informat

(e g productivity measures costs p(e.g., productivity measures, costs pof work, quality assessment) to

• Managers

• Undersecretary for Health• Secretary• Congress

RESEARCHERS’ GUIDE TO VA DATA
DSS Overview

Health Care Production Proc

Raw Intermediate 

Health Care Production Production Proc

Proc

Materials:

Labor

Products:

Labs

P

Pa

(E 

Supplies

Equipment

X-Rays

Nursing hours

(E

RESEARCHERS’ GUIDE TO VA DATA
DSS Source Data

Financial Systems

• Payroll• Building Depreciation

Workload

• VistA Packages

• Laborator

y

Pa

• VistA 

• Building Depreciation • NPCD• etc.

y

• Pharmacy• Nursing• etc.

NPCD

• PTF• etc.

DSS Processes

DSS 

Data

RESEARCHERS’ GUIDE TO VA DATA
Where to Find DSS Lab Da

VISN S t S i C t (VVISN Support Services Cen

ter (V

– Reports– Data C bu

bes

VINCIAustin Information Technology Center 

() p AITC

) Mainframe Com

pu

– National Data Extracts

RESEARCHERS’ GUIDE TO VA DATA
Where to Find DSS Lab Da

––Austin Information Technology Cent(AITC) Mainframe Computer– National Data Extracts

tod ’ f ay

s focus

RESEARCHERS’ GUIDE TO VA DATA
Where to Find DSS Lab Da

Austin Information Technology Center (AITC) Mainframe Compu

– National Data Extracts

– SAS Files

– Monthly or quarterly ‘updates’– Files are cumulative year

-to

-

date

RESEARCHERS’ GUIDE TO VA DATA
National Data Extracts (ND

Clinical NDEs

LAB

– Workload and costs– Test-level records

LAR

– Laboratory results for a def

of tests (currently, 89)

– Test-level records

PHARADECS/ECQ

RESEARCHERS’ GUIDE TO VA DATA
National Data Extracts

Other NDE Classific

“Core” Extracts

– Inpatient an

d

outpatient encountlevel data 

Program Activity

– e.g., No-Show, RA

Financial

RESEARCHERS’ GUIDE TO VA DATA
LAB & LAR NDE SAS Files

D t il bl f D

a

t

a avail

abl

e from

– FY 2002 (LAB)– FY 2000 (LAR)

NDE File organization

– FY 2004 f d FY 2004 forwar

d

• 21 different files for each fiscal year, ea• By VISN (includes inpatient and outpatie

RESEARCHERS’ GUIDE TO VA DATA
LAB & LAR NDE SAS Files

Data available from 

– FY 2002 (LAB)– FY 2000 (LAR)

NDE File organization

– FY 2004 forward

• 21 different files for each fiscal year, ea• B

y( p p 

 VISN 

(includes in

patient and out

patie

– FY 2000 (LAR) – FY 2003

• 8 different files for each fiscal year, each • G f VISN (4 ) Groups

of VISN

s (4 groups

)

• Inpatient and outpatient data in separat

RESEARCHERS’ GUIDE TO VA DATA
LAB & LAR NDE SAS Files

File Naming Convention / Mainframe 

For example,

RMTPRD.MED.DSS.SAS.FYxx.VISNyy.nde

For example,

• RMTPRD.MED.DSS.SAS.FY09.VISN01

• Contains FY 2009 inpatient and 

outpatient data from facilities in V

* Naming for FY2000 – FY2003 reflects different file organization – s

website.

RESEARCHERS’ GUIDE TO VA DATA
LAB & LAR NDE SAS Files

File Naming Convention / Mainframe 

For example,

RMTPRD.MED.DSS.SAS.FYxx.VISNyy.nde

For example,

• RMTPRD.MED.DSS.SAS.FY09.VISN01

• Contains FY 2009 inpatient and 

outpatient data from facilities in V

• RMTPRD MED DSS SAS FY RMTPRD.MED.DSS.SAS.FY05.VISN12

• Contains FY 2005 inpatient and 

out

patient data from facilities in V

* Naming for FY2000 – FY2003 reflects different file organization – 

website.

RESEARCHERS’ GUIDE TO VA DATA
Session Outline

O i f VA DSS ti l l b d Overview of VA DSS national lab dFinding information in VA DSS natl bd a ataMeasurement of laboratory use anresults in VA studies Example of VA studies that have uDSS national lab dataWhere to g p o for more help

RESEARCHERS’ GUIDE TO VA DATA
What information can I find in 

LAB and LAR NDEs?

LAB LAR

Tests performed

– One record for each 

completed billable test

Test results

– Patient-specific 

completed billable test tests

– Includes those performed at 

point-of-care and some 

research records

tests

– For those 76, all 

entered into Vist

research records LAB)

– Identifies where and when 

performed

LAB)

Patient informa

Costs and other information pertinent to accountin

g

Patient information

RESEARCHERS’ GUIDE TO VA DATA
What information can I find in 

LAB and LAR NDEs?

LAB LAR

Tests performed

– One record for each 

completed billable test

Test results

– Patient-specific 

completed billable test tests

– Includes those performed at 

point-of-care and some 

research records

tests

– Extraction proce

records for those 

research records from VistA Labo

– Where and when performed

Costs

a

n

d ot

h

er 

from VistA Labo

package

Patient informa

Costs a d ot einformation pertinent to accountingPatient information

RESEARCHERS’ GUIDE TO VA DATA
in the 

LAB and LAR NDEs

Diagnoses, procedures, and other clinicinformationGender, race/ethnicityTests that are not patient-specific

– e.g., tests done as lab controls or other 

standardization procedures

Research records, unless considered VA patient and an encounter is generated iVistA PCE file

RESEARCHERS’ GUIDE TO VA DATA
Selected Key Variables

LAB LAR

Test identifier Test identifier

Where performed Result

Referral flag Units reported

Clinic Stop Code Dates

Dates

RESEARCHERS’ GUIDE TO VA DATA
Test Identifiers:

How do I find records containing the 

interested in?

VA_LMIP: Laboratory Management InProgram– National list (aka NLT code)– Entered by lab staff– Assigned locally– N t t d di d Not standardized

FEED_KEY

– 5-digit character variable– Usually an LMIP code

RESEARCHERS’ GUIDE TO VA DATA

y
Test Identifiers

IPNUM: Intermediate Product Number– Assigned by DSS based on LMIP– One IPNUM ma

y g be assi

gned to >1 LMIP

TESTNAME– DSS

-d i d IP d i ti derived IP description

– Free-form text field

– File maintained by individual site teams– Name assigned to same test can vary acro

t ti

RESEARCHERS’ GUIDE TO VA DATA

s

t

ations
Test Identifiers

VA

_

LMIP

FEED_KEY

IPNUM

TESTNAME

RESEARCHERS’ GUIDE TO VA DATA
Test Identifiers

DSSLARNO – Result ID

– Assigned by DSS, 1 – 89– List of available tests on VIReC and DS

websites (at end)

Logical Observation Identifier NamCodes (LOINC)

RESEARCHERS’ GUIDE TO VA DATA
LOINC Codes

http://www loinc org http://www.loinc.org

Logical Observation Identifier Names aCodes (LOINC) - universal identifierHighly specific - Identifies test, methoanalysis, specimen sourceLab results records pulled based on LOImplemented nationwide for FY 2009Should result in better match between and LAR records than previous method (based on test names)Currently, VistA LOINC file contains olversion of LOINC code set

RESEARCHERS’ GUIDE TO VA DATA
FY11 LAR TESTS

(abridged)

LAR 

Test # 

DSS Test Name Reporting Units LOINC

Code 

0001 Hemoglobin G/DL 718-7 0002 Potassium (Serum) Potassium (Serum) MEQ/L or MMOL/L MEQ/L or MMOL/L 2823-30003 Sodium (Serum) MEQ/L or MMOL/L 2951-2, 290004 Lithium (Serum) MMOL/L 14334-0005 BUN (Blood Urea Nitrogen) MG/DL 3094-0 0006 WBC (Total WBC Count) K/UL or K/MM3 26464-8,66

804-5 

0007 Digoxin NG/ML 10535-0008 Theophylline UG/ML 4049-3 0009 AST (Aspartate Transferase) U/L 1920-8, 3020010 Glucose (Serum) MG/DL 2345-7, 150011 Creatinine Clearance ML/MIN 2164-2 0013 GGTP (Gamma GT) IU/L 2324-2 0014 Dilantin ( y) Phen toin) MCG/ML 3968-50015 Valproic Acid MCG/ML 4086-5 0016 Carbamazepine (Tegretol) MCG/ML 3432-2 0017 Hemoglobin A1C (Glycohemoglobin) % 17855-8, 178

4548-4, 45

0018 Alpha 1 Antitrypsin MG/DL 1825-9 0019 PSA (Prostatic Specific AG) NG/ML 2857-1 0020 CD-4 (Absolute T Cell Count) CELLS/CMM, 

CELLS/MM3, CELLS/UL 

8127-3, 244

0021 Prothrombin Time SEC 5902-2, 590022 Total Thyroxine (T-4) MCG/DL 3026-2 0023 Total Triiodothyronine (T-3) NG/DL 3053-6 0024 Thyroid Stimulating Hormone (TSH) Thyroid Stimulating Hormone (TSH) MCU/ML 11579-0 11

0, 11

3016-3 

0025 Folic Acid/Folate NG/ML 2284-8 0026 Vitamin B12 Level PG/ML 2132-9 

... ... ... ... 

0087 Hepatitis B Virus DNA NEG-POS or NON-REACTIVE-REACTIVE 5007-0, 13126-

2, 29610

RESEARCHERS’ GUIDE TO VA DATA

, 96 0

0088 Hepatitis C Genotype text 32286-7, 480089 Hepatitis C (RIBA) NEG-POS or NON-REACTIVE-REACTIVE 24011-9, 334

34162-8, 51
How do I find test results

RESULT –

Test Result

– Result of the test identified by DSSLARN– V lid l V

alid values

-10000 t 10000 10000 t

o 10000 

– Up to 4 decimal digits– Some results are text/non

-numeric

TESTUNIT – Units in which the test is reported

DSSLARNO RESULT + TESTUNIT 

=

RESEARCHERS’ GUIDE TO VA DATA
Example: Total Thyroxine (

DSSLARNO = 0022RESULT = 4.2TESTUNIT = mcg/dl

DSSLARNO 0022

4.2 + mcg/dl= 

RESEARCHERS’ GUIDE TO VA DATA
What about Non-numeric Re

For example: HIV Antibody

Translation T t R lt Value

Tes

t

Result

0 Negative, Non-Reactive1 Positive, Reactive2 Borderline, Indeterminate3 Test not performed, Quantity not sufficient or other reason5 Result cannot be translated translated

RESEARCHERS’ GUIDE TO VA DATA
Should I find a one-to-on

correspondence between LAB a

records?

Not for

– Tests whose values are calculated from 

t t l ( ti i l ) test values (e.g., creati

nine

clearance

)

• Only the tests from which the calculated 

are derived 

(, ) i.e., serum creatinine

) are c

and have an associated record in the LA

– “Send outs”: Two records generated

1. In-house labor cost of specimen collect

preparation and shipping 

2. Cost of 

p g ( 

erformin

g the test 

(or cost cha

non-VA source)

REF_FLG = “Y”, if sent to another VA sourc

RESEARCHERS’ GUIDE TO VA DATA
Session Outline

O i f VA DSS ti l l b d Overview of VA DSS national lab dFinding information in VA DSS NaLab dataMeasurement of laboratory use anresults in VA studies Example of VA studies that have uDSS national lab dataWhere to g p o for more help

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #1

Diabetes Quality of Care: Hgb A1c Freq

Question:We re conducting a retrospective cohort study 

’re conducting a retrospective cohort study 

quality among patients with Diabetes. We’d lmeasure frequency of Hemoglobin A1c testing our cohort in FY 2010. Sh ld h 

hould we use the LA

obtain this information?

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #1

Diabetes Quality of Care: Hgb A1c Freq

Answer:No!LAB NDE is the best source of information folab”.

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #1

Goal:

Diabetes Quality of Care: Hgb A1c Freq

Measure frequency of Hemoglobin A1c testing amcohort in FY 2010.Procedure:Use the LAB file.

1. Obtain feeder key(s) or IPNUM for Hgb A1c te

• DSS Intermediate Products table (URL at e

• Search on name (“Description” field) and a

e.g., Glycohemoglobin, Glycosylated Hem

Glycated Hemoglobin, Hb A1c

• Can double check by searching on IP num

found. 

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #1

Diabetes Quality of Care: Hgb A1c Freq

di d bl

FdrS

ys IP Num FdrKe

y

CPT/HCPC/LMIP/ECS NatlCode Descri

ption

DSS Intermediate Pro

duct Tabl

e

y

y

p

ASC 22273 83036 CPT GLYCOSYLATED HEMOGLOBASC 77318 83037 CPT GLYCOSYLATED HB, HOME DLAB 1148 85027 LMIP Glycosylated HGB, totalLAB 1149 85051 LMIP Glycohemogl...t FractionLAB 1150 85052 LMIP GLYCOHEMOGLOBIN A(1) CLAB 68820 82890 LMIP GLYCOHEMOGLOBIN A1C POLAB 81947 82117 LMIP GLYCOHEMOGLOBIN HBA 1C LAB 91238 85053 LMIP GLYCOHEMOGLOBIN HBA 1C

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #1

Procedure (cont’d):

Diabetes Quality of Care: Hgb A1c Fre

Procedure (cont d):

2. In LAB NDE: Identify study patients NDE: Identify study patients records 

’ records 

SCRSSN, and

3. Keep only FY 2010 records: 

• Several date variables• SVC_DTE (service date)• YYYYMMDD• Default = Year and month that VistA extra

p, y erformed, concatenated with ‘01’ for day

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #1

Procedure (cont’d):

Diabetes Quality of Care: Hgb A1c Freq

4. Pull records with Feed_Key = values identified 

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #1

Procedure (cont’d):

Diabetes Quality of Care: Hgb A1c Freq

Procedure (cont d):

5. Wait! Eliminate ‘duplicates’ resulting from send

referral labs.

• Drop if REF_FLG (referral flag) = ‘Y’

Yield: All study cohort records for Hemoglobin A1

performed in FY 2010

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #2

Preventing Kidney Disease: Change in Serum 

Question (from the historical files):“We’re pg y lanning a study of the effectiveness attendance in preventing chronic kidney disepatients with hypertension and diabetes. We 2500 participants receiving care in 10 facilitieVISNs. One of our outcome measures is chanserum creatinine over the study period, JuneSeptember, 2010. Can we use the DSS LAR this? What other advice can you give us?”

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #2

Preventing Kidney Disease: Change in Serum 

Goal:Measure change in serum creatinine between JunSeptember, 2010. Measurement Issues:1. Switch in method used by DSS to extract resu

VistA, implemented October 1, 2008

2. Specimen source not ind d icate

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #2

Measurement Issues:

Preventing Kidney Disease: Change in Serum 

1. Switch in method used by DSS to extract resu

VistA, implemented October 1, 2008

• Pre- FY09: VistA record extract using test n

(remember the test-name linking issue?)

• FY09 forward, LOINC codes• What challenges does this present?

• Discontinuity in ‘measurement’ of the ou

presents potential threat to validity in th

longitudinal study

• Little is known yet about LOINC code 

implementation and resulting data quali

RESEARCHERS’ GUIDE TO VA DATA
Case Scenario #2

Measurement Issues:

Preventing Kidney Disease: Change in Serum 

2. Specimen source not indicated

• TESTNAME = “Serum Creatinine” but some 

out-of-range and suggest urine, rather than creatinines

• No DSS field indicating source of lab specim• Solution going forward: LOINC!

• LOINC codes are specific to the specime• When it says “Serum Creatinine”, it real

RESEARCHERS’ GUIDE TO VA DATA
Measurement Issues 

Take Home Messages

DSS Lab Data: Fabulous resource, complex databaseC f l i ti i t d Care

f

ul examination i

s warran

t

e

d

Clinical advice is critical

RESEARCHERS’ GUIDE TO VA DATA
Session Outline

O i f VA DSS ti l l b d Overview of VA DSS national lab dFinding information in VA DSS natl bd a ataMeasurement of laboratory use anresults in VA studies Examp g le of VA studies using VA Dnational lab dataWhere to g p o for more help

RESEARCHERS’ GUIDE TO VA DATA
How has outpatient healthcare utilizat

measured in VA studies?

L i axm san, t l 2

et 

al., 2

Repeated HemoglobOrdering in the VA HSystemAmerican Journal of 

RESEARCHERS’ GUIDE TO VA DATA
How have laboratory use and results b

measured in VA studies?:

L i axm san, t l 2011 et 

al., 2011

R t ti h t t d f ti t R

e

trospective co

hort 

s

t

u

d

y

of patien

t

s new

diagnosed with diabetes in FY2006 (n=1,0Evaluation of healthcare quality/efficiency: appropriateness/timing of Hemoglobin A1C Identified cohort usin

g p out

patient encounte

DSS LAR NDEOutcome measures: 

– Proportion of patients receiving repeat Hb

testing within 30 and 90 days

– Distribution and frequency of repeated Hb

tests in 365 days

RESEARCHERS’ GUIDE TO VA DATA
How have laboratory use and results b

measured in VA studies?:

L i axm san, t l 2011 et 

al., 2011

R t ti h t t d f ti t R

e

trospective co

hort 

s

t

u

d

y

of patien

t

s new

diagnosed with diabetes in FY2006 (n=1,0Evaluation of healthcare quality/efficiency: appropriateness/timing of Hemoglobin A1C Identified cohort usin

g p out

patient encounte

DSS LAR NDEOutcome measures: 

– Proportion of patients receiving repeat Hb

testing within 30 and 90 days

– Distribution and frequency of repeated Hb

tests in 365 days

RESEARCHERS’ GUIDE TO VA DATA
How have laboratory use and results b

measured in VA studies?:

L i axm san, t l 2011 et 

al., 2011

Measurement issues

– Presence of lab result used as proxy 

ordered

• 17% had no HbA1c test• C id i LAB NDE t if Consider using LAB NDE t

o verify

• Accounting for non-VA labs

RESEARCHERS’ GUIDE TO VA DATA
How have laboratory use and results b

measured in VA studies?:

L i axm san, t l 2011 et 

al., 2011

M t i easurement issues

– Out-of-range values

• 0.1% >50%

– Time-to-repeat testing

• Order date (ORD_DATE)• Result date (RES_DATE)• T t d t (SVC DTE) Test d

a

t

e (SVC

_DTE)

RESEARCHERS’ GUIDE TO VA DATA
Session Outline

O i f VA DSS ti l l b d Overview of VA DSS national lab dFinding information in VA DSS natl bd a ataMeasurement of laboratory use anresults in VA studies Examples of VA studies that have VA DSS national lab dataWhere to g p o for more help

RESEARCHERS’ GUIDE TO VA DATA
Data Access

DSS National Data Extract

Access Information:

See VIReC website

http://vaww.virec.research.va.gov/

t/TrainingNewUsersToolkit/DataAccess.htm 

RESEARCHERS’ GUIDE TO VA DATA
VIReC Website

– http://www.virec.research.va.gov

http://vaww.virec.research.va.gov

– Information on VA data sources and h

access data

– DSS NDEs

• Research User Guide (RUG)• S l t i bl f i S

elect variabl

e frequencies

• Select person-level frequencies• Periodic u

p qy dates and data 

qualit

y inform

RESEARCHERS’ GUIDE TO VA DATA
VIReC Help

HSRData Listserv

– Join at the VIReC website– Discussion among >400 data stewards Discussion among >400 data stewards

managers, and users

– Past messages in archive (on intranet)

VIReC Help Desk

– VIReC staff will answer your question a

direct you to available resources on to

– VIReC@va.gov – (708) 202-2413

RESEARCHERS’ GUIDE TO VA DATA
Decision Support Offic

Website

Intranet only

http://vaww dss med va gov/indehttp://vaww.dss.med.va.gov/inde

–Multiple resources–Left navigation panel:

•National Reporting•P D t rogram Documen

t

s

RESEARCHERS’ GUIDE TO VA DATA
Selected Recent References o

VA DSS National Laboratory D

Please view the attachment located ihandout section of the Live Meeting presentation

RESEARCHERS’ GUIDE TO VA DATA
Questions?

RESEARCHERS’ GUIDE TO VA DATA
Upcoming Seminars

May 2, 2011“Improving Mortality Ascertainment 

th VA Vit l St t D t t” th

e VA Vit

al St

a

tus D

a

taset”

Noreen ArnoldJune 6, 2011“O i f f i S “Overview o

f VA Data, In VA Data, In

formation 

S

National Databases and Research Us

D i H PhD MPH RN Denise Hynes, PhD, MPH, RN

RESEARCHERS’ GUIDE TO VA DATA