SLE (Systemic Lupus Erythematosus) using SLICC (Systemic Lupus Internation Collaborating Clinics) Criteria

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Systemic Lupus Erythematosus (SLE) is a chronic, systemic autoimmune disease that can affect many parts of the body including skin, lungs, brain, heart, kidneys, joints, and blood vessels. SLE presentation can vary significantly between patients. Because of this, it can be challenging to identify a patient as having SLE. Between 300,000 and 2,000,000 people in the US are estimated to have SLE. Determination of an exact number of people affected is challenging as the disease is difficult to identify given the diverse presentations and the length of time it may take for symptoms to appear. Electronic Health Records (EHR) are widely used in healthcare setting and are a rich source of information about the patients that can be mined for classification of SLE and earlier identification. 

For the eMERGE network*, we are using the SLICC (Systemic Lupus International Collaborating Clinics) Criteria to determine if patients have SLE. A group of rheumatologists came up with SLICC criteria in 2012 to improve clinical relevance, and to incorporate the new knowledge of SLE immunology.

non-NLP:  Version 4.6 of the pseudocode uses structured EHR data only - NOTE: the SQL pseudocode document is the definitive list of codes and cutoff values and logic to use, if that doc contradicts other files here, please let us know and use the SQL pseudocode doc (https://phekb.org/sites/phenotype/files/FINAL_SLE_SLICC_SQL_code_w_vocab...)

w/ NLP:  Version 5.x and later of the pseudocode uses the output of version 4.x, adding NLP (natural language processing) for some of the SLICC criteria that are more accurate with NLP.  3 files have been added for the NLP, namely:

  1. pseudocode with NLP portions in red in a Word doc;
  2. the types of text documents needed highlighted in an Excel file;
  3. and a zip file w/ a README Word doc w/ NLP instructions, the Python & R code in Jupyter notebooks, & the format of the input to the NLP, which is 2 inputs:
    1. ​output from version 4.x of the algorithm, i.e. this input DD matches the output DD for version 4.x
    2. text from notes from in- & out-patient encounters with any primary care, rheumatology, or nephrology departments, & from kidney biopsy pathology reports

* for other studies/projects/networks we have also used the ACR/EULAR criteria, which has some overlapping classification attributes with SLICC.  Thus we have also posted 2 additional files with information on all the classification criteria as follows:

  1. Supplementary tables with :
    1. Data Definitions which includes correctioions to a few typos in the ICD9/10 codes
    2. Sensitivity and Specificity of each of the Classification Attributes
  2. more information about the specific codes in an Excel file
Unstructured Data: 
NLP
Structured data: 
CPT
ICD10
ICD9
Data Source/clinical domain: 
observations
medications
Files: 
Algorithm v. 5.4 (with NLP) summary & appendices (input is text + output from v. 4.x)
Types of documents highlighted in green that are needed for NLP
NLP code v3, in- & out-put DDs & ex. files, & README.doc for implementation, v. 2.4
Algorithm v.4.64 (w/o NLP) with most changes marked from V4.5 (some codes corrected /added & minor logic updates)
codes in SQL fmt. for inclusion & exclusion by criteria with logic: ICD for diagnoses, ICD & CPT for procs, LOINC for labs
Detailed LOINC codes with expected results by LOINC code for labs
Supplementary Tables w/ Data Definitions and Accuracy Statistics
Detailed information on specific codes used
Information
Phenotype ID: 
1091
Date Created: 
Friday, September 14, 2018
Status: 
Final
Do Not List on the Collaboration Phenotypes List
Contact information
Contact Author: 
Jen Pacheco
Authors: 
Anika Ghosh, Jennifer Pacheco, Theresa Walunas, Rosalind Ramsey-Goldman
Institution: 
Northwestern University
Network Associations: 
eMERGE
View Phenotyping Groups: 
eMERGE Mayo Group
eMERGE Phenotype WG
Owner Phenotyping Groups: 
eMERGE Northwestern Group
Demographics
Gender: 
Female
Male
Age: 
Pediatric
Adult
Geriatric
Race: 
Arctic (Siberian, Eskimo, etc.)
Black (African American, West African, Ethiopian, etc.)
Caucasian (European)
Caucasian (North African, Middle East, Other)
East Asian (Mongol, Tibetan, Korean, Japanese, Thai, etc.)
Indigenous Australian
Mixed Race
Native American
Other Race
Pacific Islander (Polynesian, Micronesian, Hawaiian, etc.)
 

Suggested Citation

Anika Ghosh, Jennifer Pacheco, Theresa Walunas, Rosalind Ramsey-Goldman. Northwestern University. SLE (Systemic Lupus Erythematosus) using SLICC (Systemic Lupus Internation Collaborating Clinics) Criteria. PheKB; 2018 Available from: https://phekb.org/phenotype/1091

PubMed References

33903204

    Comments

    Can you provide LOINC codes and or OMOP concept_id codes for the labs requested in the algorithm?

    due to issues with not only our OMOP instance but also the source data that feeds into it, we are still evaluating our OMOP version.  our data warehouse team has been meeting with us weekly to solve the major issues.  by the end of May we hope to have the most important issues resolved so we can do a better (but still won't be perfect) test of the OMOP version.  Jen

    Noted one possible code discrepency in the SLE_SLICC_LOINC_codes.docx documentation.

    For Hemolytic Anemia Inclusion lab test, should LOINC code 2532-0 Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma be included and LOINC code 2085-9 Cholesterol in HDL [Mass/Volume] in Serum or Plasma be excluded?

    For Hemolytic Anemia Inclusion lab test LDH:

    Yes, exclude LOINC code 2085-9 Cholesterol in HDL [Mass/Volume] in Serum or Plasma.

    Include LOINC code 2532-0 Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma https://uts.nlm.nih.gov/metathesaurus.html#2532-0;0;1;CODE;2019AA;EXACT_...

    We will update the pseudocode & code list (SLE_SLICC_LOINC_codes.docx) posted on PheKB to reflect and clarify these changes this week. 

    Thanks,  Jen

    emerge_lupus_pseudocode_V1.docx requires controls to currently be between the ages of 18 and 45 years. We only have 5 individuals under the age of 45 in the entire Marshfield eMERGE cohort. With age restriction only on controls we will end up with something like 500 or more cases with a median age of 78 and 2 controls with a median age of 44. If we remove the age restriction on the controls we end up with approximately 3200 controls with a median age of 73. Does it make sense to include the age restriction on the controls?

    we found some discrepancies in the ICD codes we had listed in our pseudocode vs. the query we used to test our algorithm.  we're checking those out and if there any ICD codes to add/subtract there should be only a few and we'll let you know within the next few weeks.  Jen

    Submitted by Xinnan Niu on

    Have you figured out the discrepancy problem for ICD codes in the pseudocode ? If yes, when are you going to correct/revise them ? I was told the deadline to implement the pseudocode is May 16 (next Wednesday ).

    Thanks

    I was out of the country on vacation May 1-15, and in the meantime others have been working on correcting the ICD and LOINC codes, thanks for asking and pointing these out.  We have a meeting tomorrow with the clinician expert for this, after which we should have updated / corrected ICD and LOINC codes.  I don't see a deadline of May 16, so no worries about that.  Thanks for your patience, Jennifer 

    Submitted by Dustin Key on

    Hi, for the hemolytic anemia inclusion critieria and the  LDH lab, I would like to confirm that the upper limit cutoff is indeed > 2 u /L?   Thank you,  Dustin

    For hemolytic anemia inclusion criteria LDH lab, the upper limit cutoff should actually be 2 times the upper limit of normal (and the unit of measure should be u/L).  In other words, the upper limit cutoff is NOT simply > 2 u/L, we were trying to say that whatever the upper limit of normal is at your site, only include those with a number that is greater than twice your upper limit of normal.

      We will update the pseudocode & code list (SLE_SLICC_LOINC_codes.docx) posted on PheKB to reflect and clarify these changes this week. 

    Thanks,  Jen

     

    Yes, for exclusion codes marked with "*", exclude those patients whose exclusion codes are found within = +/- (before or after) 7 days of inclusion code.

      We will update the pseudocode & code list (SLE_SLICC_LOINC_codes.docx) posted on PheKB to reflect and clarify these changes this week. 

    Thanks,  Jen

    Submitted by Xinnan Niu on

    These two loinc are used to code WBC casts, how are we able to use them to include patients whose Red cell cout: >0/HPF under micrscope ? How about the LOINC 51790-4 which is used to do RBC casts [#/area] in Urine sediment by Microscopy high power field?

    Yes LOINC lab codes '5820-6','33825-1' (red cell value >0/hpf), are actually used to code White Blood Cell (WBC) casts, so do NOT use them use to include patients whose Red Blood Cell (RBC) count: >0/HPF under microscope.  

    Yes, Add the LOINC 51790-4 which is used to do RBC casts [#/area] in Urine sediment by Microscopy high power field.  

     We will update the pseudocode & code list (SLE_SLICC_LOINC_codes.docx) posted on PheKB to reflect and clarify these changes this week.   

    Thanks,  Jen

    Submitted by Xinnan Niu on

    LOINC: ‘731-0’, ‘26474-7’,’26478-8’,’736-9’,’737-7’,‘26464-8’,‘6690-2’ (value <4)

    I think the value <4 should be for LOINC "26464-8" which is the Whole WBC and the value <1.5k for the rest of LOINC, which Leukocytes [#/volume] in Blood, correct ?

    For the Leukopenia criteria, there are actually 2 separate labs :
    1) Leukocytes, the overall WBC of all white blood cell types 
    2) Lymphocytes, a subtype of leukocytes/WBCs 
     
    Thus:
     
    1) For LOINC lab codes ‘26464-8’ & ,‘6690-2’, are counts of
    LEUKocytes, the value should be < 4 .  

    2) the rest of the LOINC lab codes,
    ‘731-0’,‘26474-7’,’26478-8’,’736-9’,’737-7’,
    are counts of LYMPHocytes,
    the value for all should be < 1.5k . 

    Thank you for helping us to figure this out.

      We will update the pseudocode & code list (SLE_SLICC_LOINC_codes.docx) posted on PheKB to reflect and clarify these changes this week. 

    Thanks,  Jen

    We have now posted our Algorithm V4.63 (no NLP) with most changes marked from Algorithm V4.5:  there are a few codes corrected per the comments posted here and also from the clinician expert, & also 1 minor logic update (excluding hemolytic anemia labs that occured within 7 days of preeclampsia diagnosis). Since the changes are minor, it is OK to just make these changes in your re-implementation of this phenotype algorithm when NLP is added in "year 5" of eMERGE phase III.  Please note the codes and logic in the SQL code format are the most accurate as this is the document we reviewed multiple times with our clinician expert.  

    Thank you for your patience, Jen

    For the 1st 2 LOINC codes below, '14646-4','18263-4', these are NOT For LDH, they are for HDL.  

    Similarly,  
    Yes, '2085-9' is NOT for LDH, it's HDL, as pointed out by at least 1 other person in the comments here.  

    Thank you for helping us to figure this out.  

      We will update the pseudocode & code list (SLE_SLICC_LOINC_codes.docx) posted on PheKB to reflect and clarify these changes this week. 

    Thanks,  Jen

    Hi,

    Are there pediatric values that you have for Lymphocytes and other labs for the lab-based subphenotypes?

     

    Hi Todd, 

    Is there a clinician you know who can help us determine the ranges we should look for in children for the blood counts?  

    Our SLE clinician expert here doesn't treat children.  She did state that the antibody and urine lab ranges should be the same for children & adults.  

    Thanks,  

    Jen

    SLE (lupus) alg. & pseudocode docs updated today again (for the non-NLP version) - I hope by now we have caught all the typos.  I highlighted &/or tracked the differences in most places in the algorithm & (SQL) pseudocode docs.  Please NOTE: the (SQL) pseudocode doc is our de-facto definitive list of codes and logic as that is the document many people reviewed many times with our clinician expert.  Please let us know if you find any more discrepancies in our documentation. Thank you! Jen 

    just uploaded files with the corrections/additions to codes/logic for SLE (lupus) non-NLP alg.  

    Jen

    Columbia discovered an error in the NLP code for oral ulcers, we are working on correcting the issue & will post updated code as soon as possible.  We will also post the data dictionaries for the 4 output files from the NLP on the DD tab soon as well.  Thank you for your patience. Jen