# Presentation: 151431

## Regenstrief SPIN Query Tool

- Clem McDonald, M.D.
- September 15, 2003

- © 2003 Regenstrief Institute, Inc.

## Overview of what we have in SPIN today

- Five (5) hospital systems
- Clarian
- IU/Riley
- Methodist
- Community
- St. Francis
- St. Vincent
- Wishard
- Total of thirteen (13) hospitals
- Tumor registry data for some

- © 2003 Regenstrief Institute, Inc.

## © 2003 Regenstrief Institute, Inc.

- State Board of Health

- County Health Department

- Quest

- LabCorp

## Pathology data in hand

- Confidential data – not for distribution

| Institution | Years | Comment |  |  |
| --- | --- | --- | --- | --- |
| Hosp A | 1989-2003 | Waiting for 200-300K more |  |  |
| Ameripath hosp B | 1980-2003 |  |  |  |
| Hosp C | 2003 (now) | 15 year archive coming |  |  |
| Ameripath Hosp D | 1990-2003 |  |  |  |
| Hosp E | 1975-2003 |  |  |  |

- © 2003 Regenstrief Institute, Inc.

## Surg Path Report Parsing / Coding

- Estimated from sample
- Sure we can get  to 82% (naked DX and Successful)- prob better

- © 2003 Regenstrief Institute, Inc.

## NAACCR Tumor registry data

- From Indiana State for:
- Tumor DX
- Survival
- Organ site of primary
- Etc.
- State query restricted to same 5 hospital systems
- Date range 1997 - 2003
- # records = 136 K/up from 129 K
- # patients = 128 K/up from 112 K
- Based on current 850K surg path reports, we find path reports in 50% of tumor registry patients. With the additional 400K path reports we have been promised, we could expect path reports  in 75% of them

- © 2003 Regenstrief Institute, Inc.

## Table 2  Distribution of NAACCR Tumor registry case by Institution

| Institution | # Tumor Registry
Records | # of Patients |
| --- | --- | --- |
| Hosp A | 68,528 | 64,710 |
| Pub Health Hosp B | 20,418 | 18,991 |
| Pub Health Hosp D | 12,520 | 11,821 |
| Pub Health Hosp C | 28,697 | 26,685 |
| Hosp E | 6,563 | 6,256 |
| TOTAL | 136,726 | 128,463 |

- © 2003 Regenstrief Institute, Inc.

## Lab data included in database

- So for have included tumor related labs ONLY for patients with either a surg path report OR a tumor registry record and included only 2 hospitals
- This represents 320K patients (about 1/3 of patients with TR or Surg Path reports. Time frames differ from hospital to hospital:
- Wishard		1975-2003
- Clarian IU		1989-2003
- Clarian Methodist	1995-2003

- © 2003 Regenstrief Institute, Inc.

## Patient linking

- We have HIPAA business associate agreements and IRB approval to link within the Indianapolis consortium
- We have software that does the linking within our city wide project
- Have not implemented any linking yet
- So, patient numbers are not de-duplicated – YET

- © 2003 Regenstrief Institute, Inc.

## The data hierarchy

- Each patient has
- Many distinct different observations
- Each observation can be repeated on different dates/times
- Some observations have many results, e.g. one pathology report can have many specimens – a specimen can have more than one finding
- Currently
- Query tool returns cohorts by patient
- Returns only one result per data and one finding per result

- © 2003 Regenstrief Institute, Inc.

## © 2003 Regenstrief Institute, Inc.

## Variable selection tree collapsed 

- You can expand and collapse nodes one at a time or enmass. Or enmass by pressing the Expand / collapse button at the bottom of the screen)

- © 2003 Regenstrief Institute, Inc.

## Variable selection tree (expanded)

- © 2003 Regenstrief Institute, Inc.

## Search for variable by word in variable name

- © 2003 Regenstrief Institute, Inc.

## Tab for  selecting auto coded surg path findings is clicking on explicit threshold produces next pop up d

- Click to open tab that allows setting of  date constraints

- Click to open tab to set search criteria on  specimen type, site and procedure.

- © 2003 Regenstrief Institute, Inc.

## Pop up showing Auto coded surg path findings Click on #obs or #patients to sort by counts

- © 2003 Regenstrief Institute, Inc.

## User clicked on Specimen tab.  Note three tabs: Tissue Type, Body Site, Collection Method.  Screen offers same options for search by word and sorting. 

- User clicked on Specimen tab.  Note three tabs: Tissue Type, Body Site, Collection Method.  Screen offers same options for search by word and sorting.

- © 2003 Regenstrief Institute, Inc.

## User clicked Body Site tab.                                                              Same options for searching, sorting and selecting.

- © 2003 Regenstrief Institute, Inc.

## User clicked on collection method tab.                                       Same options for searching, sorting and selecting.

- Reports  total number of available codes

- © 2003 Regenstrief Institute, Inc.

## © 2003 Regenstrief Institute, Inc.

## Data Types

- Variables can have values that are
- Numeric
- Text
- Codes
- Dates (rare – other values also have dates)

- © 2003 Regenstrief Institute, Inc.

## Variable with numeric values

- Some tumor registry variables (e.g., # years of survival)
- Laboratory results (e.g., %blasts, PSA)
- Eventually, variables such as Gleason score parsed out of the pathology text

- © 2003 Regenstrief Institute, Inc.

## Select PSA variable.  Note the count of number of observations available to help the searching process.

- © 2003 Regenstrief Institute, Inc.

## Search options when variable is numeric – e.g., PSA

- © 2003 Regenstrief Institute, Inc.

## Variables with text “values”

- Surg path reports (en toto) (the only one that is operational now)
- Other kinds of reports
- Clinical variables that have text as values

- © 2003 Regenstrief Institute, Inc.

## Select a variable on which to define a search criteria (text data type)

- © 2003 Regenstrief Institute, Inc.

## Variables with coded values

- Auto coded surg path findings
- Most tumor registry variables
- Many laboratory reports (e.g., Hep  B Surface Ag)
- DRG and diagnoses

- © 2003 Regenstrief Institute, Inc.

## Selecting Inpatient DRG codes 

- Selecting Inpatient DRG codes

- © 2003 Regenstrief Institute, Inc.

## Inpatient DRG choices (only have Wishard and some Clarian values stored so far.

- © 2003 Regenstrief Institute, Inc.

## Select Hepatitis H surface ab – click on explicit,                                                get list of answers that may be of interest.

- © 2003 Regenstrief Institute, Inc.

## Pop-up for entering search criteria

- © 2003 Regenstrief Institute, Inc.

##  Choice of tumor registry ICD0-3 codes on which to search for (tumor registry primary site). User search and sort-like other screens

-  Choice of tumor registry ICD0-3 codes on which to search for (tumor registry primary site). User search and sort-like other screens

- Note that the ICD0-3 codes have a hierarchical structure that is represented by a tree.

- © 2003 Regenstrief Institute, Inc.

## © 2003 Regenstrief Institute, Inc.

## Setting cut points on numeric data in breakdown screen

- Users enter the range and the increment and computer generates the cut points.

- © 2003 Regenstrief Institute, Inc.

## Review of query response for breakdown of cancer primary site, Hep B surf AB results, gender and tumor survival.

- © 2003 Regenstrief Institute, Inc.

## Drag the gender dimension to the holding pen                and change the cross tab look

- © 2003 Regenstrief Institute, Inc.

## Re-arrange the display options

- © 2003 Regenstrief Institute, Inc.

## Results of turning off some of the display options

- © 2003 Regenstrief Institute, Inc.

## Put another dimension in the holding pin                        and sort the bins by total number of cases

- © 2003 Regenstrief Institute, Inc.