Strategic Management of Anatomic Pathology Laboratory Information Systems for Enhancement of Transla

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Strategic Management of Anatomic Pathology
Laboratory Information Systems for Enhancement of
Translational Research Efforts.

• Ashokkumar A. Patel, MD
• Case Comprehensive Cancer Center
• Case Western Reserve University, Department of
  Pathology
• ashok.patel_at_case.edu
• APIII 2008

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Objectives

• Understand the advantages and limitations of the
  AP LIS and AP LIS data for translational
  research.
• How to provide large, clean, structurally sound
  and de-identified data set from the AP LIS
• Integrate this data set with other data resources
  to support translational research.
• How to take advantage of your APLIS to enhance
  biorepository efforts?
• A case study from Case Western Reserve University

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Overview Example of facilities and locations
that interact with the AP-LIS.
Data sharing with Cancer Center
Paraffin tissue repository
Outcomes studies
Data requirements for new standards (DICOM
supp122, HL7 CDA)
Clinical Research projects
Billing/Finance systems
Need Direct feeds to Cancer Registry
Residency training studies
McPherson Pincus Henry's Clinical Diagnosis
and Management by Laboratory Methods, 21st ed.
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Anatomic Pathology Report
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General Comments

• The AP report is a signed document, not a
  database to database transaction.
• It has been designed for a specific purpose (even
  though it is used for many others)
• It is a communication between physicians
• It is an identified document in the header and
  in the text

LIS
EHR
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Evolution of Pathology LIS

• Anatomic Pathology
• Paper reports
• Text based electronic reports
• Billing/transaction APLIS
• Template synoptic reporting
• Structured synoptic reporting
• Structured meta-data encoded reports

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Structured Data Entry

• Various forms of structured data entry are
  becoming popular in pathology
• Rule based dictations and intelligent
  transcription
• Dictation templates and Macros
• Structured Data Entry Programs
• Low level structured data programs enhance
  parsing and auto coding
• High level programs enforce consistency,
  completeness and can hard code coding

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Structured Data Entry Tools
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PATHOLOGY REPORTSTODAY
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Pathology Reports After Synoptic Reporting
University Hospitals
7/24/2007
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A Partially Structured Document
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Send specimens to pathology lab
Surgery
Accession/ Log specimen
Gross
Order blocks/slides
Pathology Data Flow
AP Lab Info System
Preliminary Dx./ Ancillary testing
Diagnosis
Final Report
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Partially Structure Document

• A partially structured document
• Large Narrative Sections (Fields) such as Final
  Diagnosis, Gross Description represent
  database elements
• If the case involves more than one clinical
  specimen (or Part), the narrative sections
  divided by the author into sub-sections (one sub
  section for each clinical specimen)
• The information model does not match the real
  world situation!

Patient (surgical event)
Left Arm Nevus B
Right Arm Nevus A
Case S07-100 Report Final Diagnosis A Dermal
Nevus. B Compound Nevus
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Large Narrative Fields that are Structured to the
Author
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Suppressed data within AP Lab Info System
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• Suppressed data
• Processing, coding and other data generated by
  the department
• Many not be interesting to the surgeon (but may
  be interesting to others)

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• Pathology descriptions and diagnosis
• histology processing and inventory data at the
  part, block and slide level
• LIS that can act as a massive tissue banking
  system, with data associated directly with
  specimens.

Histology data can be found in discreet data
fields for basic information identifying blocks
and slides.
Individual slide information can be useful for
DICOM whole slide imaging.
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CASE STUDY at
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Information derived from our APLIS For 1995-2007
routine accessions and GYN-cytology. gt 1
million reports processed 1 Facility
UH-CMC Grouped by Sub-specialty pathology
groups/ Organ Systems.
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Data Integration

• Cancer Registry
• Clinical Trails
• Biorepository inventory system
• Family Medicine registry
• Epidemiology/Genetics/Hereditary research
  databases
• Links to whole slide images (in
  process)

TissueBank
Pathology LIS
Cancer Registry
Datawarehouse
Data Mart
Data Mart
Data Mart
Data Mart
Disease Specific Registries (Researchers)
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Links to Frozen Tissue Bank Specimens
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Method

• Identify all variations of specimen and part
  identifiers in the data set (2005 reports)
• Identify all variations in person identifiers in
  the data set
• Parse identifiers from text and text sections
  from each other
• Store in an XML file(s)

Find Problems
Study Dataset
Write/Run Parsers
Find Problems
Write XML Files
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Identification of objects and information
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Identification of objects and information Curren
t limitations with AP-LIS data
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What happens to specimen A?
Dr. I.M. Hacker (surgeon) sends 5 containers from
patient Xs surgery removing tumor from left
lung.
Left upper lobe
A
UPPER DIVISION LEFT UPPER APICAL POSTERIOR
ANTERIOR SEGMENTS
B
C
AP WINDOW 5 POSTERIOR
ANTERIOR AP WINDOW
D
12L
E
8
F
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This is three database lines of text representing
a single paragraph. Full hard returns create new
paragraphs within a single database field.
Free text blob This is a single database field
representing multiple paragraphs. The narrative
text is mixed with the identifier.
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What does Left Upper lobe or 12L
represent? Links to database dictionary must be
specific and accurately linked to narrative
text. (i.e. Part type/specimen received).
Part and Block Identifier are part of the
narrative text.
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Part Labels -Shows up on Final Report -Free
text value -Represents what surgeon wrote on
specimen container -Vocabulary not controlled by
Pathology
Part Types -Suppressed database value -Does not
show up on Final Report -Discreet values and
Vocabulary controlled by Pathology -Avoid using
generic terms to define data dictionary.
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Example Case 2
ltprimary-attribute name"part_id" content"A"
line-nbr"0" auto-create"false"
master-pattern"( A-Za-z(-,.
A-Za-z),. )" preferred-pattern"(A-Z)
"gt
Colon is used
Identifiers are hard to find not consistently
implemented. This makes it very hard to address
information about Specimen A
Dash - is used
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Only Letters used
"( A-Za-z(-,. A-Za-z),. )"
Colon used
Period used
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Large free text fields with no separation
of Identifiers from descriptions
The author is structuring data within a field.
If it is not identified, it not useable!
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Identification of objects and information
allows-Reorganization of AP LIS data for
Researcher friendly views
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Which block has tumor for specimen A?
Research Request Tissue sections on
Adenocarcinoma of the Lung with Adjacent normal
sections.
1
2
3
PartA
Left upper lobe
4
5
6
7
8
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Creation of XML files
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XML

• A file that acts like a database
• Identifies and separates all data elements
• Makes each element addressable
• Allows easy reconfiguration of the file
• Create child files that that contain a subset of
  the parent file in any structure you want
• Coding and Structured Data can be included in any
  XML based report
• One can include links to images or links to lab
  manuals

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Original String
Parse String
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Parse text link part (specimen)
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Embedded Identifiers
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• Identifiers embedded in the body of the report
• Pathologists Names
• Patient Names
• Hospitals
• Clinical History
• Specimens (Slide IDs)
• There are good clinical and legal reasons for
  this
• But requires complex, quirky and high
  maintenance de-id parsing for use in the
  non-clinical space

Imbedded ID
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A subset of available information from your APLIS
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Discreet Data elements
Represents a subset of the useful information in
the LIS
Free Text Sections
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Histology data can be found in discreet data
fields of basic information for identifying
blocks and slides.
Individual slide information can be useful for
DICOM whole slide imaging.
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Discreet data for billing codes, SNOMED codes,
and link to other specimens from same patient.
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A subset of available informationHOWEVER
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Specimen processing information (poorly linked to
narrative data)
Left Upper Lobe Entire Mass
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Coding information (poorly linked to narrative
data)
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Auto coding errors
ltprimary-attribute name"part_id" content"A"
line-nbr"0" auto-create"false"
master-pattern"( A-Za-z(-,.
A-Za-z),. )" preferred-pattern"(
A-Z,. )"gt
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Auto coding errors
Example Case 3
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Who is to be blamed?

• Pathologists
• Transcriptionists
• Residents
• Gross/accessioning techs

• Anatomic Pathology Laboratory Information system
• Auto coder

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Summary

• With a great deal of effort, one can parse a
  pathology report so that the data components are
  addressable
• Such a data set will allow useful things such as
  reports on single part or reports that include
  just gross description and specimen processing
• This will be unique data set - no one else has
  such a data set
• There is no substitute for clear and consistent
  labeling when the data is collected and entered
  into your system
• Limitations to APLIS exists, because we accept
  those limitations

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Best Practice

• Proper training of staff
• Be consistent with transcription of free text
  fields.
• Punctuation
• Labeling key section(s)/part(s)
• Defining data dictionary
• Specific and descriptive as possible
• (Bx, other / Misc. Vs. Bx, prostate)
• Understanding how text data effects other parts
  of the system.
• Clinicians reading report
• Auto coding/Billing
• Future research needs

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Summary

• Structured data will lead to opportunities
• Tissue Banking
• Measure Quality and Efficiency
• Outcomes Research
• Grant Funding
• DICOM/Imaging
• Molecular
• Many others.

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Acknowledgement

• Rajnish Gupta System Architect
• Bob Lanese DBA/webmaster

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Thank You.
If everyone is thinking alike, then someone
isnt thinking. George S. Patton, Jr.

• Ashokkumar A. Patel, MD
• ashok.patel_at_case.edu
• 216-368-5106

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• A LEFT UPPER LOBE, WEDGE RESECTIONCRLF--MOD
  ERATELY DIFFERENTIATED ADENOCARCINOMA, SEE
  NOTE.CRLF--EMPHYSEMATOUS CHANGES.CRLFCR
  LFNote The carcinoma measures 1.2 x 1.1 cm in
  largest dimension. It is subpleural, but does
  not penetrate into the pleura (elastic stain on
  sections A5 and A6). Angiolymphatic invasion is
  not identified. The margins of this wedge
  resection are uninvolved.CRLFCRLFB
  UPPER DIVISION, LEFT UPPER APICAL POSTERIOR AND
  ANTERIOR SEGMENTS, RESECTIONCRLF--EMPHYSEMATO
  US CHANGES.CRLF--RECENT HEMORRHAGE,
  CONSISTENT WITH RESECTION SITE (SPECIMEN
  A).CRLF--BRONCHIAL MARGIN, NO EVIDENCE OF
  MALIGNANCY.CRLF--VASCULAR MARGIN, NO EVIDENCE
  OF MALIGNANCY.CRLF--NO EVIDENCE OF MALIGNANCY
  IN ONE PERIBRONCHIAL LYMPH NODE.CRLFCRLFC
  AP WINDOW 5 POSTERIOR LYMPH NODES,
  BIOPSYCRLF--NO EVIDENCE OF MALIGNANCY IN
  THREE LYMPH NODES.CRLFCRLFD ANTERIOR AP
  WINDOW, LYMPH NODES, BIOPSYCRLF--NO EVIDENCE
  OF MALIGNANCY IN TWO LYMPH NODES.CRLFCRLFE
  12 L LYMPH NODES, BIOPSYCRLF--NO EVIDENCE
  OF MALIGNANCY IN ONE LYMPH NODECRLFCRLFF
  LYMPH NODES DESIGNATED 8, BIOPSYCRLF--NO
  EVIDENCE OF MALIGNANCY IN SEVEN LYMPH
  NODES.CRLFCRLF

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