Normalization of Phenotypic Data from a Clinical Data Warehouse: - PowerPoint PPT Presentation

Normalization of Phenotypic Data from a Clinical Data Warehouse: Case Study of Heterogeneous Blood Type Data with Surprising Results James J. Cimino, MD Formerly: Chief of the Laboratory for Informatics Development NIH Clinical Center, National Institutes of Health Bethesda, Maryland, USA Now: Director, Informatics Institute University of Alabama at Birmingham Birmingham, Alabama, USA E INF ORMAT ICS INST IT UT

Lecture Overview  Started out trying to normalize laboratory data  Mapped different tests to common findings  Identified need to “atomize” data  Real data set found some surprises  Speculation on causes  Take-home messages E INF ORMAT ICS INST IT UT

Biomedical Translational Research Information System (BTRIS) Institute System Old EHR Personal System Lab Curent EHR System BTRIS E INF ORMAT ICS INST IT UT

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ABO Blood Typing - from Wikipedia E INF ORMAT ICS INST IT UT

ABO and Rh Blood Typing Rh Negative - - - - Anti- Anti- Anti- Anti- Rh Rh Rh Rh - from Wikipedia E INF ORMAT ICS INST IT UT

ABO and Rh Blood Typing Rh Positive + + + + R R R R h h h h Rh antigen Rh antigen Rh antigen Rh antigen R R R R h h h h - from Wikipedia E INF ORMAT ICS INST IT UT

Panels Reporting Multiple Antigens and Interpretations Panel Tests Result ABO GRP-RH TYPE ABO GRP-RH TYPE O POSITIVE ABO GRP-RH TYPE ABO GRP-RH TYPE A POSITIVE ABO GRP-RH TYPE ABO GRP-RH TYPE A NEGATIVE ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 0 B ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - B 4+ positive ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - Rh POS O ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 0 negative ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - B 0 ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - Rh NEG E INF ORMAT ICS INST IT UT

What are the Underlying Atomic Findings? Rh Positive + + + + R R R R h h h h Rh antigen Rh antigen Rh antigen Rh antigen R R R R h h h h Absence of A ag Absence of B ag Absence of B ag Absence of A ag - from Wikipedia E INF ORMAT ICS INST IT UT

Variants and Typographical Errors Panel Tests Result ABO GRP-RH TYPE ABO GRP-RH TYPE O POSITIVE ABO GRP-RH TYPE ABO GRP-RH TYPE 0 POS ABO GRP-RH TYPE ABO GRP-RH TYPE A POSITIVE ABO GRP-RH TYPE ABO GRP-RH TYPE A NEG ABO GRP-RH TYPE ABO GRP-RH TYPE A NEGATIVE ABO GRP-RH TYPE ABO GRP-RH TYPE AB NEG ABO GRP-RH TYPE ABO GRP-RH TYPE B POS ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 0 ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 1+ ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 2+ ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 3+ ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 4+ ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A M4 ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - B 0 ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - B 4+ ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - Rh NEG ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - Rh POS E INF ORMAT ICS INST IT UT

Interpretation of Presence or Absence of Antigens Antigens Summary Panel Tests Result ABO GRP-RH TYPE ABO GRP-RH TYPE O POSITIVE abR ABO GRP-RH TYPE ABO GRP-RH TYPE 0 POS abR ABO GRP-RH TYPE ABO GRP-RH TYPE A POSITIVE AbR ABO GRP-RH TYPE ABO GRP-RH TYPE A NEG Abr ABO GRP-RH TYPE ABO GRP-RH TYPE A NEGATIVE Abr ABO GRP-RH TYPE ABO GRP-RH TYPE AB NEG ABr ABO GRP-RH TYPE ABO GRP-RH TYPE B POS aBR ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 0 a abR ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - B 1+ b ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] – Rh Pos R ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - A 4+ A ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - B 4+ B ABr ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - Rh NEG r ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] – A 0 a abR ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] – B 0 b ABO Group and Rh Type [ABORH] ABO Group and Rh Type [ABORH] - Rh POS R E INF ORMAT ICS INST IT UT

Does the Atomic Approach Support Data Integration? Hypothesis: Different tests of the same blood type should produce the same atomic results. Experiment: Different tests on the same patient should produce the same atomic results. E INF ORMAT ICS INST IT UT

Experimenting with BTRIS  Queried BTRIS for all ABO and Rh test results  Identify unique panel/test combinations  Identify unique results of panel/tests combinations  Create atomic maps for each unique result  Identify each patient’s phenotype (union of atoms)  Examine phenotypes for discrepant results E INF ORMAT ICS INST IT UT

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Summary of Results 66 unique Panels 43,760 Patients Summarization 139 unique Tests 176,676 Panels 334 unique Panel-Test combinations 593,637 Tests 3949 unique results Manual Review to Select Relevant Tests 21 unique Panels 43,486 patients Filtering 32 unique tests 165,981 panels 59 unique Panel-Test combinations 307,884 Tests 1452 unique results 23,903 patients with 19,583 patients multiple panels with single panel 479 discrepant phenotypes (2.00%) E INF ORMAT ICS INST IT UT

Expected Phenotypes Antigenic Evidence Phenotype # Patients abR O+ 17132 AbR A+ 13925 aBR B+ 4710 abr O- 2538 Abr A- 2316 ABR AB+ 1441 aBr B- 645 ABr AB- 214 E INF ORMAT ICS INST IT UT

Incomplete Phenotypes Antigenic Evidence Phenotype # Patients r - 10 R + 8 ab O 7 Ab A 5 AB AB 1 aB B 1 bR + 1 E INF ORMAT ICS INST IT UT

Discrepant Phenotypes Antigenic Evidence Phenotype # Patients AabR (discrepant) 132 abRr (discrepant) 89 AbRr (discrepant) 67 aBbR (discrepant) 51 AaBbR (discrepant) 50 AabRr (discrepant) 28 ABbR (discrepant) 24 aBRr (discrepant) 19 AaBR (discrepant) 17 Aabr (discrepant) 13 aBbr (discrepant) 11 ABRr (discrepant) 7 AaBbRr (discrepant) 6 aBbRr (discrepant) 6 ABbr (discrepant) 6 AaBbr (discrepant) 3 ABbRr (discrepant) 2 E INF ORMAT ICS INST IT UT

Examples of Same-Patient Discrepant Results Subj Date Test Result Ags Interp. 59 1/31/1989 ABO & RH O POSIT. abR abR (O+) 59 1/31/1989 ABO & RH A POSIT. AbR AbR (O-) 724 1/24/1989 ABO & RH O NEG abr abr (O-) 724 2/13/1989 ABO & RH O POS abR abR (O+) 986 1/2/1999 ABO Group and Rh - Rh POS R ABR 986 1/2/1999 ABO Group and Rh - A 4+ A (AB+) 986 1/2/1999 ABO Group and Rh - B 4+ B 986 1/18/2000 ABO Group and Rh - Rh POS R 986 1/18/2000 ABO Group and Rh - A 4+ A AbR (A+) 986 1/18/2000 ABO Group and Rh – B 0 b E INF ORMAT ICS INST IT UT

Examples of Same-Patient Discrepant Results Subj Date Test Result Ags Interp. Phen. 59 1/31/1989 ABO & RH O POSIT. abR abR (O+) AabRr 59 1/31/1989 ABO & RH A POSIT. AbR AbR (O-) 724 1/24/1989 ABO & RH O NEG abr abr (O-) abRr 724 2/13/1989 ABO & RH O POS abR abR (O+) 986 1/2/1999 ABO Group and Rh - Rh POS R ABR 986 1/2/1999 ABO Group and Rh - A 4+ A (AB+) 986 1/2/1999 ABO Group and Rh - B 4+ B AbBR 986 1/18/2000 ABO Group and Rh - Rh POS R 986 1/18/2000 ABO Group and Rh - A 4+ A AbR (A+) 986 1/18/2000 ABO Group and Rh – B 0 b E INF ORMAT ICS INST IT UT

More Examples of Same-Patient Discrepant Results Subj Date Test Result Ags Interp. 1090 1/2/2002 ABO Group and Rh - ABO A Ab AbR 1090 1/2/2002 ABO Group and Rh - Rh POS R (A+) 1090 1/2/2002 ABO Group and Rh - A 4+ A 1090 1/2/2002 ABO Group and Rh - B 0 b 1090 1/28/2003 ABO Group and Rh - ABO B aB aBR 1090 1/28/2003 ABO Group and Rh - Rh POS R (B+) 1090 1/28/2003 ABO Group and Rh - A 0 a 1090 1/28/2003 ABO Group and Rh - B 4+ B E INF ORMAT ICS INST IT UT

More Examples of Same-Patient Discrepant Results Subj Date Test Result Ags Interp. Phen. 1090 1/2/2002 ABO Group and Rh - ABO A Ab AbR 1090 1/2/2002 ABO Group and Rh - Rh POS R (A+) 1090 1/2/2002 ABO Group and Rh - A 4+ A 1090 1/2/2002 ABO Group and Rh - B 0 b AaBbR 1090 1/28/2003 ABO Group and Rh - ABO B aB aBR 1090 1/28/2003 ABO Group and Rh - Rh POS R (B+) 1090 1/28/2003 ABO Group and Rh - A 0 a 1090 1/28/2003 ABO Group and Rh - B 4+ B E INF ORMAT ICS INST IT UT

Possible Explanation: Random Laboratory Error  Doubling the tests for a patient should double the chance of random error  bCorrelation was 0.7127 (P<.00001) but slope was only 0.04 (not 0.5) E INF ORMAT ICS INST IT UT

Summary of Results: Discrepancies within a single panel 66 unique Panels 43,760 Patients Summarization 334 unique Panel-Test combinations 176,676 Panels 139 unique Tests 593,637 Tests 3949 unique results Manual Review to Select Relevant Tests 21 unique Panels 43,486 patients Filtering 59 unique Panel-Test combinations 165,981 panels 32 unique tests 307,884 Tests 1452 unique results 23,903 patients with 19,583 patients multiple panels with single panel 479 discrepant 7 discrepant phenotypes (2.00%) phenotypes (0.04%) E INF ORMAT ICS INST IT UT