Post on 18-Dec-2015
THE DEVELOPMENT OF SYNOPTIC THE DEVELOPMENT OF SYNOPTIC REPORTS FROM FREE TEXT CONTENT REPORTS FROM FREE TEXT CONTENT OF ARCHIVAL PATHOLOGY REPORTS OF ARCHIVAL PATHOLOGY REPORTS
GENERATED IN THE GENERATED IN THE ANATOMIC PATHOLOGY LABORATORY ANATOMIC PATHOLOGY LABORATORY
INFORMATION SYSTEMINFORMATION SYSTEM
Purpose of Synoptic Purpose of Synoptic ReportsReports
Structure the informationStructure the information Structured form facilitates Structured form facilitates
research queriesresearch queries Structured form facilitates better Structured form facilitates better
patient carepatient care Structured form facilitates better Structured form facilitates better
sharing of information between sharing of information between institutionsinstitutions
Example Synoptic Example Synoptic PagePage
Kidney – Genitorurinary CAP Approved Surgical Pathology Cancer Case Summary (Checklist)
Protocol revision date: January 2005 Applies to invasive carcinomas only
Based on AJCC/UICC TNM, 6th edition
KIDNEY: Nephrectomy, Partial or Radical Patient name: Surgical pathology number: Note: Check 1 response nuless otherwise indicated. MACROSCOPIC Speciman Type ___Partial nephrectomy ___Radical nephrectomy ___Other (specifiy): ________________________________ ___Not specified Laterality ___Right ___Left ___Not specified *Tumor Site (check all that apply) *___Upper pole *___Middle *___Lower pole *___Not specified Focality ___Unifocal ___Multifocal Tumor Size (largest tumor if multipled) Greatest dimension:___cm *Additional dimensions:___x___cm ___Cannot be determined (see comment)
Conversion of Archived Conversion of Archived SystemsSystems
An institution that changes from free An institution that changes from free formatted pathology reports to formatted pathology reports to synoptic reporting may wish to synoptic reporting may wish to convert all archived reports to convert all archived reports to synoptic formsynoptic form
Is it better to convert archived data by Is it better to convert archived data by hand or automatically with respect to:hand or automatically with respect to:• AccuracyAccuracy• TimeTime
Computer MethodsComputer Methods
Search for key wordsSearch for key words Use auto-coding vocabularies so Use auto-coding vocabularies so
that all (or most) variations of that all (or most) variations of linguistically equivalent phrases linguistically equivalent phrases are placed in a uniform phrase for are placed in a uniform phrase for proper pattern matching in proper pattern matching in searchessearches
Use negation algorithmsUse negation algorithms
Special ChallengesSpecial Challenges(What is the Tumor Site for this case?)(What is the Tumor Site for this case?)
Part A. RECTOSIGMOID COLON ULCER, BIOPSY:Part A. RECTOSIGMOID COLON ULCER, BIOPSY:--INFILTRATING MODERATELY DIFFERENTIATED --INFILTRATING MODERATELY DIFFERENTIATED
ADENOCARCINOMA, CONSISTENT WITH ADENOCARCINOMA, CONSISTENT WITH COLONICCOLONIC
ORIGIN, SEE NOTE.ORIGIN, SEE NOTE.
Part C. COLON, LEFT, HEMICOLECTOMY:Part C. COLON, LEFT, HEMICOLECTOMY:--INFILTRATING MODERATELY DIFFERENTIATED --INFILTRATING MODERATELY DIFFERENTIATED
ADENOCARCINOMA OF RECTOSIGMOID ADENOCARCINOMA OF RECTOSIGMOID COLON, COLON,
SEE NOTE.SEE NOTE.
Which is “Whipple” and which Which is “Whipple” and which is “Whipple Pylorous Sparing”?is “Whipple Pylorous Sparing”?
Received fresh for intraoperative consultation, labeled Received fresh for intraoperative consultation, labeled with the patient's name, number and "with the patient's name, number and "WhippleWhipple," is a ," is a bloc section of organs from a Whipple procedure. The bloc section of organs from a Whipple procedure. The specimen consists of a 24.0 cm. in length duodenum specimen consists of a 24.0 cm. in length duodenum and a 6.2 x 4.3 x 4.0 cm. remnant of attached and a 6.2 x 4.3 x 4.0 cm. remnant of attached pancreas, and a portion of distal pancreas, and a portion of distal stomachstomach, 6.5 x 2.5 , 6.5 x 2.5 cm.cm.
Received fresh for intraoperative consultation, post-Received fresh for intraoperative consultation, post-fixed in formalin, labeled with the patient's name and fixed in formalin, labeled with the patient's name and number, is an en bloc resection of organs from a number, is an en bloc resection of organs from a WhippleWhipple procedure. The specimen consists of a 21.5 procedure. The specimen consists of a 21.5 cm. length of duodenum, a 1.5 cm. length of distal cm. length of duodenum, a 1.5 cm. length of distal common bile duct, and an 8.8 x 6.8 x 6.7 cm. remnant common bile duct, and an 8.8 x 6.8 x 6.7 cm. remnant of attached pancreas. of attached pancreas.
Design of ExperimentDesign of Experiment
To determine the feasibility of automated To determine the feasibility of automated conversion of archived reports, we collected all conversion of archived reports, we collected all records for the year 2005 and converted them records for the year 2005 and converted them to synoptic form, both manually and by to synoptic form, both manually and by computer text processing. We then compared computer text processing. We then compared the results for accuracy and the time to process. the results for accuracy and the time to process. The organ sites we studied were: The organ sites we studied were:•PancreasPancreas•KidneyKidney•ColonColon•ProstateProstate•BreastBreast
Estimated Accuracy for Estimated Accuracy for PancreasPancreas
SpecimeSpecimen typen type
Tumor Tumor SiteSite
Tumor Tumor sizesize
HistologiHistologic typec type
HistologiHistologic Gradec Grade
23/2523/25
92%92%
18/2518/25
72%72%
19/2519/25
76%76%
24/2524/25
96%96%
24/2524/25
96%96%
Estimated Accuracy for Estimated Accuracy for KidneyKidney
LateralityLaterality Tumor Tumor SiteSite
Tumor Tumor SizeSize
HistologiHistologic Typec Type
27/2727/27
100%100%
21/2721/27
78%78%
7/277/27
26%26%
24/2724/27
89%89%
Estimated Accuracy for Estimated Accuracy for ColonColon
Tumor SiteTumor Site Tumor SizeTumor Size Histologic Histologic TypeType
40/7540/75
53%53%
42/7542/75
56%56%
74/7574/75
99%99%
Estimated Accuracy for Estimated Accuracy for ProstateProstate
HistologiHistologic Typec Type
Gleason Gleason PrimaryPrimary
Gleason Gleason SecondarSecondaryy
Gleason Gleason TotalTotal
49/5049/50
98%98%
48/5048/50
96%96%
48/5048/50
96%96%
48/5048/50
96%96%
Estimated Accuracy for Estimated Accuracy for BreastBreast
Bloom-Bloom-Richardson Richardson gradegrade
Mitotic ScoreMitotic Score AngiolymphatiAngiolymphatic Invasionc Invasion
100%100% 100%100% 100%100%
Estimated Time for Estimated Time for Computer ConversionComputer Conversion
The average time to develop The average time to develop the text processing code was the text processing code was approximately 4-6 hours per approximately 4-6 hours per organ. The first organ took organ. The first organ took the longest time, the others the longest time, the others were re-written from the first.were re-written from the first.
Estimated Time for a Trained Estimated Time for a Trained Pathologist to convert archive Pathologist to convert archive
reports to synoptic reportsreports to synoptic reports
Total Total TimeTime
Number Number of Casesof Cases
Average Average TimeTime
PancreasPancreas N/AN/A N/AN/A N/AN/A
ColonColon 9:27:489:27:48 7272 7:537:53
BreastBreast 4:46:464:46:46 4848 5:585:58
KidneyKidney 3:57:233:57:23 3232 7:257:25
ProstateProstate 3:38:303:38:30 3030 7:177:17
ConclusionConclusion
Less than 40-60 cases, a trained Less than 40-60 cases, a trained pathologist is quicker.pathologist is quicker.
More than 40-60 cases, automated More than 40-60 cases, automated text processing is quicker.text processing is quicker.
Attempts to improve the accuracy will Attempts to improve the accuracy will increase this time.increase this time.
For archived systems with a very long For archived systems with a very long history and a large volume of patients, history and a large volume of patients, automated processing may be automated processing may be preferred.preferred.
AcknowledgementsAcknowledgements
We wish to thank the We wish to thank the following for their following for their participation in this project:participation in this project:•Ashok PatelAshok Patel•Doug HartmanDoug Hartman•John GilbertsonJohn Gilbertson•Robert LaneseRobert Lanese•Rajnish GuptaRajnish Gupta