Using LOINC for Clinical Trials Lab Test Submissions

Transcription

1 Using LOINC for Clinical Trials Lab Test Submissions Armando Oliva, M.D. Associate Director for Informatics CDER Office of Computational Science Ana Szarfman, M.D., Ph.D. Medical Officer, Data Mining Team CDER Office of Translational Sciences

2 The views expressed in this presentation are those of the speakers and not necessarily those of the Food and Drug Administration

3 Agenda Challenges analyzing lab data What is the LOINC? Why use the LOINC for lab tests? How do we move forward?

4 Challenges Analyzing Lab Data Laboratory data are not always poolable by test within an application or across applications e.g serum glucose, urine glucose Specimen (LBSPEC) variable can help distinguish these two But certain automated tools only look at lab test name

5 Challenges (cont d) SDTM includes support for standardized results but the rules for standardization are neither clear nor adequately followed Results for a test are reported in more than one unit in the standardized variable Normal ranges are incomplete and/or incorrect, and submitted without High and Low values Detected multiple High and Low values ranges being zero

6 Challenges (cont d) Units for laboratory values and other measurements need to be consistent Specify standard units by test, specimen source, and other measurements Support an automated inter-unit conversion system Automate validation by reviewing outliers, and comparing the distribution of results

7 Challenges (cont d) CDISC controlled terminology allows multiple value domains for the same test Total Protein value domain depends on specimen and/or method (continuous for blood chemistry, ordinal for urinalysis) Need to use different test names for tests with different value domains or Modify the metadata model to clarify the use of test name within a classification system, including test, specimen, source, method and other differentiating characteristics This will help automate validation and discovery of aberrant results

8 What is the LOINC? Logical Observation Identifiers Names and Codes Widely used standard terminology for identifying and distinguishing clinical observations, including but not limited to laboratory tests International standard: User guide published in multiple languages (English, Chinese, German, Spanish, Turkish, Estonian) Free of charge

9 LOINC History Initiated by Dr. Clem MacDonald, Regenstrief Institute for Healthcare, in 1994 In response to demand for electronic movement of clinical data from laboratories to consumers of clinical data Sponsors: NLM, other government and private organizations Purpose is to facilitate the exchange and pooling of clinical data for clinical care, outcomes management, and research First release (v 1.0) was on 4/24/95

10 LOINC Scope Latest Version is 2.5 (released Dec 2014) 74,600 records Two sections Laboratory portion (49,528 records) Standard test names and codes Includes chemistry, hematology, serology, microbiology (including parasitology and virology), toxicology Drugs and cell counts for blood smears and cerebrospinal fluids Antibiotic susceptibilities Clinical portion (25,072 records) Vitals signs, hemodynamics, intake/output, ECG, obstetric ultrasound, cardio echo, urologic imaging, pulmonary ventilator management, gastroendoscopic procedures, survey instruments, other

11 Current Use of LOINC American Clinical Laboratory Association (ACLA), recommended adopting LOINC by its members LabCorp Quest SmithKline Beecham (now part of Quest) Mayo Medical Labs, University of Colorado, Intermountain Healthcare, Kaiser Permanente, Clarian Health, Partners Healthcare System, Mayo Clinic, Dept. of Defense, VA, CDC, NAACCR, HIPAA, Blue Cross, Aetna HHS has adopted the LOINC for lab tests to support federal regulations governing the meaningful use of EHR technologies China, Switzerland, Spain, Canada, Mexico, Russia

12 How does the LOINC work? Think of a clinical observation as a question/answer pair LOINC provides the question Other terminologies provide the answer UCUM Serum glucose = 105 mg/dl Sputum culture = streptococcus pneumoniae LOINC SNOMED CT

13 LOINC Code Codes are unique and have no meaning Format is nnnnn-n where the last n is a mod 10 check digit Each LOINC record corresponds to a single test (for lab results) or panel (for lab orders) e.g. CBC (Complete Blood Count) is the order Results are hemoglobin, hematocrit, WBC Count, platelet count, etc. Includes long names, short names and synonyms

14 LOINC Lab Tests Each lab test has 6 parts: 1. Component: the name of the analyte, e.g. glucose, sodium 2. Property: e.g. mass concentration; substance concentration; catalytic activity 3. Time: is the measurement taken at a point in time or over a specified time interval? 4. Sample: specimen; e.g. blood, CSF, urine 5. Scale: e.g. quantitative, ordinal, nominal 6. Method: optional

15 Anatomy of a LOINC Code :Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA LOINC Code Hepatitis B virus surface Ab Component ACnc Pt Ser Qn EIA Property Measured Timing System Scale Method There are six major LOINC axes

16 Why consider LOINC for Lab Tests in Clinical Research? Currently, CDER supports CDISC/NCI terminology for lab test names. Two challenges: Immediate challenge: Controlled terms not granular enough, e.g. serum glucose and urine glucose map to the same term (glucose C ), leads to errors in pooling data (this can be fixed) Long-Term challenge: Terminology not aligned with healthcare (EHRs) or clinical laboratories, which use the LOINC. Presents mapping challenges due to different levels of granularity. Problem only increases over time as more and more research is conducted within EHRs

17 Why consider LOINC for Lab Tests? LOINC is a Meaningful use standard Adopted by HHS for use in EHRs Used by EHRs and clinical laboratories Widely used internationally Improve semantic interoperability (easier to pool lab data across studies and distinguish lab tests that are different) LBLOINC variable already exists in SDTM

18 Why is CDER considering the LOINC? Part of larger strategy to align CDER supported data standards with national HIT initiatives Prescription Drug User Fee Act Five (PDUFA V) Information Technology Plan (FY ) at DrugUserFee/ucm htm Section 4, Goal 3, Reduce the burden of regulation through alignment with existing health IT initiatives, laws, regulations, and mandates such as Executive Orders

19 Clinical Research & Healthcare Clinical Research and Healthcare processes and data are largely silo ed There is a an increasing need to integrate clinical research with healthcare to increase knowledge generation and enhance evidence-based medicine as part of a continuously learning health system Clinical research and healthcare should (many think will) integrate Using the same terminologies for clinical data will facilitate the integration Producers of clinical data (labs, hospitals, clinics) are adopting meaningful use standards, such as the LOINC Consumers of clinical data (e.g. FDA, other public health agencies) should support meaningful use standards as much as possible Institute of Medicine: Integrating Research and Practice: Health System Leaders Working Toward High-Value Care. Working-Toward-High-Value-Care.aspx Integrating Research into Health Care Systems: Executives' Views - Executives-Views.aspx

20 LOINC under the hood Let s examine LOINC in more detail How might LOINC fit in the current world of clinical research? How might we get there?

21 LOINC Glucose Example NCI Term: glucose (C ) Code Long Common Name Short Name Component Property Time Specimen Scale Method Glucose [Mass/volume] in Serum or Plasma Glucose SerPl-mCnc Glucose MCnc Pt Ser/Plas Qn Glucose [Mass/volume] in Serum or Plasma --10 hours fasting Glucose [Mass/volume] in Urine hours fasting Glucose p 10h fast SerPlmCnc Glucose^post 10H CFst MCnc Pt Ser/Plas Qn Glucose^post 12H CFst MCnc Pt Urine Qn Glucose p 12h fast Ur-mCnc Glucose [Mass/volume] in Capillary blood Glucose BldC-mCnc Glucose MCnc Pt BldC Qn Glucose [Mass/volume] in Cerebral spinal fluid Glucose CSF-mCnc Glucose MCnc Pt CSF Qn Glucose [Mass/volume] in Body fluid Glucose Fld-mCnc Glucose MCnc Pt Body fld Qn Glucose [Mass/volume] in Serum or Plasma --1 hour post 50 g glucose PO Glucose [Mass/volume] in Serum or Plasma --2 hours post 75 g glucose PO Glucose 1H p 50 g Glc PO SerPl-mCnc Glucose 2H p 75 g Glc PO SerPl-mCnc Glucose^1H post 50 g glucose PO MCnc Pt Ser/Plas Qn Glucose^2H post 75 g glucose PO MCnc Pt Ser/Plas Qn Glucose [Moles/volume] in Serum or Plasma Glucose SerPl-sCnc Glucose SCnc Pt Ser/Plas Qn

22 LOINC and SDTM important differences exist in current representations LOINC Code LOINC SDTM LB Component Property Timing System Scale Method LBTEST LBTESTCD LBSPEC LBANTREG LBMETHOD LBLOINC ALKALINE PHOSPHATASE CCNC PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA ALKALINE PHOSPHATASE.BONE CCNC PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Bone ALKALINE PHOSPHATASE.BONE/ALKALIN CFR PT SER/PLAS QN E PHOSPHATASE.TOTAL Alkaline Phosphatase ALP SERUM, PLASMA Bone ALKALINE PHOSPHATASE.INTESTINAL CCNC PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Intestine ALKALINE PHOSPHATASE.INTESTINAL/AL KALINE PHOSPHATASE.TOTAL CFR PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Intestine ALKALINE.PHOSPHATASE.LIVER CCNC PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Liver ALKALINE PHOSPHATASE.LIVER/ALKALIN E PHOSPHATASE.TOTAL CFR PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Liver

23 Potential Modifications to SDTM LB LOINC Code LOINC SDTM LB Component Property Timing System Scale Method LBTEST LBTESTCD LBSPEC LBANTREG LBMETHOD LBLOINC ALKALINE PHOSPHATASE CCNC PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA ALKALINE PHOSPHATASE.BONE CCNC PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Bone ALKALINE PHOSPHATASE.BONE/ALKALIN E PHOSPHATASE.TOTAL CFR PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Bone ALKALINE PHOSPHATASE.INTESTINAL CCNC PT SER/PLAS QN Alkaline Phosphatase ALP SERUM, PLASMA Intestine LOINC Code maps to LBLOINC Component maps to LBTEST System maps to LBSPEC Method maps to LBMETHOD Property, Timing, and Scale need new SDTM variables (Timing via existing CDISC timing variables(?), new LBPROP(?), new LBSCALE(?)) SDTM adopts LOINC controlled terminology for each LOINC part

24 LOINC - Challenges Extremely granular, e.g. serum glucose represented by many LOINC codes (fasting, random, finger stick, 2hr pp, etc.) Challenging to pick the right one consistently across organizations Some organizations define and implement a subset of LOINC to decrease coding variability Common or Preferred LOINC terms LOINC Top 2000 codes for Lab Results

25 LOINC - Benefits The increased granularity means Labs with the same LOINC codes are poolable Labs with different Properties have different LOINC codes and can be associated with different reporting units (e.g. Property = mass concentration (mg/dl) vs. Substance concentration (mmol/l)) Labs with different LOINC codes can be associated with different value domains (e.g. Total Protein, serum vs. Total Protein, urine)

26 How to move forward? Potential Path: Two Phases Phase 1 Minimal LOINC support: dip toe Encourage submitters to provide lab-generated LOINC code to populate SDTM LBLOINC (increase awareness, assess current coding variability, assess need for a LOINC subset; what would it look like?) Obtain public comment Phase 2 Full LOINC support: plunge Work with CDISC to modify SDTM, adopt LOINC terminology for LOINC parts Identify a LOINC subset of common or preferred terms to facilitate coding

27 Questions?