RESEARCHERS’ GUIDE TO VA DATA

Measuring Laboratory Use and 

Results Using VA Decision Support 

System National Extract Data

March 4, 2013

 

Presented by:

Elizabeth Tarlov, PhD, RN

1 1 

2013 VIReC Database and Methods Cyber Seminar Series 
RESEARCHERS’ GUIDE TO VA DATA

Session Outline

Overview of VA DSS national lab data

Finding information in VA DSS 

national lab data

Measurement of laboratory use and 

results using DSS data

Example: VA study using DSS national 

lab data

Where to go for more help

2 2 
RESEARCHERS’ GUIDE TO VA DATA

Audience Poll

Why was Friday a special day in the 

world of DSS National Data Extracts?

– Use the questions pane to write your 

answer.

Have you used lab data in CDW (other 

than DSS)?

– Yes

– No

3 3 
RESEARCHERS’ GUIDE TO VA DATA

Session Outline

Overview of VA DSS national lab 

data

Finding information in VA DSS 

national lab data

Measurement of laboratory use and 

results using DSS data

Example: VA study using DSS national 

lab data 

Where to go for more help

4 4 
RESEARCHERS’ GUIDE TO VA DATA

DSS Overview

What is DSS?

– VA’s managerial cost accounting and 

executive information system

What is its primary purpose?

– To provide managerially-useful information 

(e.g., productivity measures, costs per unit 

of work, quality assessment) to:

• Managers

• Undersecretary for Health

• Secretary

• Congress

5 
RESEARCHERS’ GUIDE TO VA DATA

DSS Overview

6 

Raw 

Materials:

Labor 

Supplies

Equipment

Intermediate 

Products:

Labs 

X-Rays

Nursing hours

End 

Products:

Patient Care 

(Encounter) 

Health Care Production Process
RESEARCHERS’ GUIDE TO VA DATA

DSS Source Data

7 

DSS Processes

Financial Systems

• Payroll

• Building Depreciation

• etc.

Workload

• VistA Packages

• Laboratory

• Pharmacy

• Nursing

• etc.

Patient Info

• VistA (CPRS)

• NPCD

• PTF

• etc.

DSS 

Data
RESEARCHERS’ GUIDE TO VA DATA

DSS National Data Extracts

(NDE)

8 

DSS Processes

Financial 

Systems Workload Patient 

Info

DSS 

Data

National Data Extracts

DIS LAB

OUT LAR

RAI

PHA
RESEARCHERS’ GUIDE TO VA DATA

National Data Extracts (NDEs)

Clinical NDEs

LAB

– Workload and costs

– Test-level records

LAR

– Laboratory results for a defined list 

of tests (currently 91)

– Test-level records

PHA

RAD

ECS/ECQ

9 
RESEARCHERS’ GUIDE TO VA DATA

National Data Extracts (NDEs)

Other NDE Classifications

“Core” Extracts

– Inpatient and 

outpatient encounterlevel data 

Program Activity

– e.g., No-Show, RAI

Financial

10
RESEARCHERS’ GUIDE TO VA DATA

DSS NDEs

Schedule: Monthly or quarterly

Cumulative year-to-date

Lab data from 2000 (LAR) or 2002 

(LAB)

11
RESEARCHERS’ GUIDE TO VA DATA

DSS NDE Data Formats

Reports, Data Cubes

– VISN Support Services Center (VSSC)

SQL tables

– Corporate Data Warehouse (CDW)

SAS Datasets

– Discontinued after FY 2012

– Austin Information Technology Center 

(AITC) mainframe computer until 3/1/2013

12

No lab data 

here
RESEARCHERS’ GUIDE TO VA DATA

LAB & LAR NDE Data at CDW

SQL Tables

– FY 2005 forward

– One table for each NDE contains

– inpatient and outpatient data

– for all VISNs

– and all available years

– New format, same data

– Some variable names slightly different from 

SAS names

– Same update schedule

13
RESEARCHERS’ GUIDE TO VA DATA

Session Outline

Overview of VA DSS national lab data

Finding information in VA DSS 

national lab data

Measurement of laboratory use and 

results using DSS data

Example: VA study using DSS national 

lab data

Where to go for more help

1414
RESEARCHERS’ GUIDE TO VA DATA

LAB

Tests performed

– One record for each 

completed billable test

– Includes those performed 

at point-of-care and some 

research records

– Identifies where and when 

performed 

Costs and other 

information pertinent 

to accounting

Patient information

LAR

Test results

– Patient-specific results for 

91 tests

– Extraction process selects 

records for those tests 

only, from VistA

Laboratory package

Patient information

1515

What information can I find in the 

LAB and LAR NDEs?
RESEARCHERS’ GUIDE TO VA DATA

Diagnoses, procedures, and other 

clinical information

Gender, race/ethnicity

Tests 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 in VistA PCE file

1616

in the 

LAB and LAR NDEs
RESEARCHERS’ GUIDE TO VA DATA

Selected Key Variables

1717

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 test I’m 

interested in?

18

VA_LMIP: Laboratory Management Index 

Program

– National list (aka NLT code)

– Entered by lab staff

– Assigned locally

– Not standardized

FEED_KEY

– 5-digit character variable

– Usually an LMIP code
RESEARCHERS’ GUIDE TO VA DATA

Test Identifiers – 

19

IPNUM: Intermediate Product Number

– Assigned by DSS based on LMIP

– One IPNUM may be assigned to >1 LMIP

TESTNAME

– DSS-derived IP description

– Free-form text field

– File maintained by individual site teams

– Name assigned to same test can vary 

across stations
RESEARCHERS’ GUIDE TO VA DATA

Test Identifiers – 

20

LOINC: Logical Observation Identifier 

Names and Codes

– Universal identifier

– Highly specific - Identifies test, 

method of analysis, specimen source

– http://www.loinc.org
RESEARCHERS’ GUIDE TO VA DATA

Test Identifiers - 

21

VA_LMIP

FEED_KEY

TESTNAME

IPNUM

LOINC 

Preferred
RESEARCHERS’ GUIDE TO VA DATA

Test Identifiers – 

22

DSSLARNO – Result ID

– Assigned by DSS, 1 – 91

– List of available tests on VIReC and DSS 

websites (at end)

LOINC
RESEARCHERS’ GUIDE TO VA DATA

LOINC Codes

http://www.loinc.org

Lab results records pulled based on LOINC

Implemented nationwide for FY 2009

Results in better match between LAB and 

LAR records than previous method (based 

on test names)

VistA LOINC file and DSS LOINC file have 

not always contained the same version of 

the LOINC code set.

23
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) MEQ/L or MMOL/L 2823-3

0003 Sodium (Serum) MEQ/L or MMOL/L 2951-2, 2947-0

0004 Lithium (Serum) MMOL/L 14334-7

0005 BUN (Blood Urea Nitrogen) MG/DL 3094-0

0006 WBC (Total WBC Count) K/UL or K/MM3 26464-8,6690-2,

804-5

0007 Digoxin NG/ML 10535-3

0008 Theophylline UG/ML 4049-3

0009 AST (Aspartate Transferase) U/L 1920-8, 30239-8

0010 Glucose (Serum) MG/DL 2345-7, 1558-6

0011 Creatinine Clearance ML/MIN 2164-2

0013 GGTP (Gamma GT) IU/L 2324-2

0014 Dilantin (Phenytoin) MCG/ML 3968-5

0015 Valproic Acid MCG/ML 4086-5

0016 Carbamazepine (Tegretol) MCG/ML 3432-2

0017 Hemoglobin A1C (Glycohemoglobin) % 17855-8, 17856-6, 

4548-4, 4549-2

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, 24467-3

0021 Prothrombin Time SEC 5902-2, 5964-2

0022 Total Thyroxine (T-4) MCG/DL 3026-2

0023 Total Triiodothyronine (T-3) NG/DL 3053-6

0024 Thyroid Stimulating Hormone (TSH) MCU/ML 11579-0, 11580-8

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, 13126-8, 16934-

2, 29610-3

0088 Hepatitis C Genotype text 32286-7, 48574-8

0089 Hepatitis C (RIBA) NEG-POS or NON-REACTIVE-REACTIVE 24011-9, 33462-3, 

34162-8, 5199-5

24
RESEARCHERS’ GUIDE TO VA DATA

How do I find test results?

25

RESULT – Test Result

– Result of the test identified by DSSLARNO

– Valid values -10000 to 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 (T-4)

26

DSSLARNO = 0022

RESULT = 4.2

TESTUNIT = mcg/dl

 DSSLARNO 0022

4.2 + mcg/dl= 
RESEARCHERS’ GUIDE TO VA DATA

What about Non-numeric Results?

27

For example: HIV Antibody

Translation 

Value Test Result

0 Negative, Non-Reactive

1 Positive, Reactive

2 Borderline, Indeterminate

3 Test not performed, Quantity not 

sufficient or other reason

5 Result cannot be translated
RESEARCHERS’ GUIDE TO VA DATA

Should I find a one-to-one correspondence 

between LAB and LAR records?

28

Not for

– Tests whose values are calculated from other 

test values (e.g., creatinine clearance)

• Only the tests from which the calculated values 

are derived (i.e., serum creatinine), are costed 

and have an associated record in the LAB NDE. 

– “Send outs”: Two records generated

1) In-house labor cost of specimen collection, 

preparation and shipping 

2) Cost of performing the test (or cost charged 

by non-VA source)

• REF_FLG = “Y”, if sent to another VA source
RESEARCHERS’ GUIDE TO VA DATA

Session Outline

Overview of VA DSS national lab data

Finding information in VA DSS 

National Lab data

Measurement of laboratory use 

and results using DSS data

Example: VA study using DSS national 

lab data

Where to go for more help

2929
RESEARCHERS’ GUIDE TO VA DATA

Case Scenario

3030

Question:

We’re conducting a retrospective cohort study of 

patients with diabetes to study care quality. We’d like 

to measure frequency of Hemoglobin A1c testing among 

our cohort in FY 2010. Can we use the LAR file to 

obtain this information?

Answer:

No! 

LAB NDE is the best source of information for “fact of 

lab.”

Diabetes Quality of Care: Hgb A1c Frequency
RESEARCHERS’ GUIDE TO VA DATA

Case Scenario

3131

Goal:

Measure frequency of Hemoglobin A1c testing among our 

cohort in FY 2010.

Procedure: 

Use the LAB file. 

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

• DSS Intermediate Products table (URL at end)

• Search on name (“Description” field) and all variants. 

e.g., Glycohemoglobin, Glycosylated Hemoglobin, 

Glycated Hemoglobin, Hb A1c

• Can double check by searching on IP numbers already 

found. 

Diabetes Quality of Care: Hgb A1c Frequency
RESEARCHERS’ GUIDE TO VA DATA

Case Scenario

3232

Diabetes Quality of Care: Hgb A1c Frequency

FdrSys IP Num FdrKey

CPT/HCPC/ 

LMIP/ECS Natl 

Code Description

ASC 22273 83036 CPT GLYCOSYLATED HEMOGLOBIN T

ASC 77318 83037 CPT GLYCOSYLATED HB, HOME DEV

LAB 1148 85027 LMIP Glycosylated HGB, total

LAB 1149 85051 LMIP Glycohemogl...t Fraction

LAB 1150 85052 LMIP GLYCOHEMOGLOBIN A(1) C

LAB 68820 82890 LMIP GLYCOHEMOGLOBIN A1C POC

LAB 81947 82117 LMIP GLYCOHEMOGLOBIN HBA 1C CA

LAB 91238 85053 LMIP GLYCOHEMOGLOBIN HBA 1C

DSS Intermediate Product Table
RESEARCHERS’ GUIDE TO VA DATA

Case Scenario

3333

Procedure (cont’d):

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

SCRSSN, and

3. Keep only FY 2010 records: 

• Several date variables

• SVC_DTE (service date)

• YYYYMMDD

• Default = Year and month that VistA extract was 

performed, concatenated with ‘01’ for day

Diabetes Quality of Care: Hgb A1c Frequency
RESEARCHERS’ GUIDE TO VA DATA

Case Scenario

3434

Procedure (cont’d):

4. Pull records with Feed_Key = values identified in Step 1.

Diabetes Quality of Care: Hgb A1c Frequency 
RESEARCHERS’ GUIDE TO VA DATA

Case Scenario

3535

Procedure (cont’d):

5. Wait! Eliminate ‘duplicates’ resulting from send-out or 

referral labs.

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

Yield: All study cohort records for Hemoglobin A1c tests 

performed in FY 2010

Diabetes Quality of Care: Hgb A1c Frequency
RESEARCHERS’ GUIDE TO VA DATA

Case Scenario

3636

Caveat

Non-VA lab results – 

Patients may obtain lab tests from a facility closer 

to home.

Those will not be captured in DSS lab data

Diabetes Quality of Care: Hgb A1c Frequency
RESEARCHERS’ GUIDE TO VA DATA

Measurement Issues 

Take Home Messages

DSS Lab Data: Fabulous resource, 

complex database

Careful examination is warranted

Clinical advice is critical

37
RESEARCHERS’ GUIDE TO VA DATA

Session Outline

Overview of VA DSS national lab data

Finding information in VA DSS 

national lab data

Measurement of laboratory use and 

results using DSS data

Example: VA study using DSS 

national lab data

Where to go for more help

3838
RESEARCHERS’ GUIDE TO VA DATA

Example from the literature: 

Blood glucose levels and surgical outcomes

Jackson, et al., 2012

Hyperglycemia is Associated 

with Increased Risk of 

Morbidity and Mortality after 

Colectomy for Cancer

Journal of the American 

College of Surgeons

Jackson RS, Amdur RL, White JC, Macsata RA. Hyperglycemia is 

associated with increased risk of morbidity and mortality after 

colectomy for cancer. J Am Coll Surg. 2012 Jan;214(1):68-80.
RESEARCHERS’ GUIDE TO VA DATA

Example: 

Blood glucose levels and surgical outcomes*

Objective: examine the association between 

perioperative BG level and 30-day outcomes after 

elective colectomy for colon cancer.

Study design: Retrospective, linked VA Surgical 

Quality Improvement Program (VASQIP) data with 

DSS lab data

Outcomes:

– Primary - death, cardiac arrest, MI, surgical site 

infection (SSI).

– Secondary - respiratory complications, venous 

thromboembolism (VTE), urinary tract infection 

(UTI), sepsis.

40 *Jackson, et al., 2012
RESEARCHERS’ GUIDE TO VA DATA

Example: 

Blood glucose levels and surgical outcomes*

Blood glucose (BG) as 

predictor/independent variable

DSS lab data: 

LAR NDE (SAS datasets), FY 2000-FY2005

41 *Jackson, et al., 2012
RESEARCHERS’ GUIDE TO VA DATA

Example: 

Blood glucose levels and surgical outcomes*

Measurement objective: median BG values 

– Operative day (OD) 

– Postoperative day 1 (POD1)

BG categorized

– hypoglycemic (BG 80 mg/dL) 

– normoglycemic (BG 80 to 120 mg/dL) 

– mildly hyperglycemic (BG 121 to 160 mg/dL),

– moderately hyperglycemic (BG 161 to 200 

mg/dL) 

– severely hyperglycemic(BG 200 mg/dL).

42 *Jackson, et al., 2012
RESEARCHERS’ GUIDE TO VA DATA

Example: 

Blood glucose levels and surgical outcomes*

Measurement issues:

1. Dealing with spurious or out-of-range values

2. Missing results due to broken lab test name link

3. One common problem not an issue in this study:

• Non-VA labs (VA inpatient sample)

43 *Jackson, et al., 2012
RESEARCHERS’ GUIDE TO VA DATA

Session Outline

Overview of VA DSS national lab data

Finding information in VA DSS 

national lab data

Measurement of laboratory use and 

results using DSS data

Example: VA study using DSS national 

lab data

Where to go for more help

4444
RESEARCHERS’ GUIDE TO VA DATA

VIReC Internet Website

DSS Research User Guide

– http://www.virec.research.va.gov/RUGs/RUGsIndex.htm 

Data Transition to the Corporate Data 

Warehouse

– http://www.virec.research.va.gov/CDW/DataTransition.htm

VHA Corporate Data Warehouse (CDW)

– http://www.virec.research.va.gov/CDW/Overvie

w.htm#CDW_Guide 

45
RESEARCHERS’ GUIDE TO VA DATA

4646

VIReC Help

HSRData Listserv

– Join at the VIReC website

– Discussion among >650 data stewards, 

managers, and users

– Past messages in archive (on intranet)

VIReC Help Desk

– VIReC staff will answer your question and/or 

direct you to available resources on topics

– VIReC@va.gov; 708-202-2413 
RESEARCHERS’ GUIDE TO VA DATA

VA Intranet Websites

Decision Support Office

– Intranet only 

• (URL on VIReC Intranet Website; click on “Data 

Sources” in left navigation pane, scroll down to 

“DSS”)

– Multiple resources including

• NDE Technical Guide, NDE Layout Specifications

• Left navigation pane: National Reporting

47
RESEARCHERS’ GUIDE TO VA DATA

VA Intranet Websites

CDW SharePoint Site

– Send va.gov email to VIReC@va.gov for 

URL

VINCI SharePoint Site

– Send va.gov email to VIReC@va.gov for 

URL

48
RESEARCHERS’ GUIDE TO VA DATA

4949

Questions?

VIReC@va.gov 
RESEARCHERS’ GUIDE TO VA DATA

5050

Upcoming Seminar

 April 1, 2013

 Measuring Outpatient Pharmacy Use in the 

VA Using VA Pharmacy Data: 

– Denise M. Hynes, MPH, PhD, RN