Non-alcoholic fatty liver disease (NAFLD)
Nonalcoholic fatty liver disease (NAFLD) is becoming the most common cause of chronic liver disease in the developing world, found in 17-30% of the population in Western countries and 2-4% worldwide. NAFLD is diagnosed predominantly in the fourth through sixth decades of life, although the childhood obesity epidemic has caused an increase in the rate of pediatric NAFLD. The prevalence of NAFLD varies by ethnicity, affecting ~45% of Hispanics, 33% of Whites, and 24% of Blacks. Among Whites, NAFLD is more common in men than in women but not in other racial background (Angulo, P. (2007)).
Alcoholic Fatty Liver Disease (ALD):
In order to compare the genetic or clinical results between non-alcoholic and alcoholic fatty liver disease, we will also collect individuals with alcoholic fatty liver condition using available ICD-9 code:
Comments
NAFLD - Table 1 Case Exclusion Diagnosis
In starting to look at your algorithm I noted that the majority of our potential cases have either V58.69 or Z79.899 diagnoses "Long Term Use of medications". These diagnoses are listed in Table 1 of your NAFLD algorithm as case exclusion diagnosis. Are you certain you wish to use these codes as exclusion diagnoses?
Time-based Exclusion
Please exclude if patient has TPN dx in a one year before first NAFLD dx.
Thank you.
Does it mean if any of the
Does it mean if any of the exclusion codes is before1 yr of 1st NAFLD code, exclude the patient?
Ex : If 1st NAFLD dx date is today, then exlcude patients who have any exclusion dx code between 08/10/2016 and 08/10/2017?
The time based exclusions
The time based exclusions only apply to the TPN/feeding orders.
may i know what you mean by
may i know what you mean by TPN or feeding orders ?
TPN
It's in the exclusion diagnoses table.
V58.69 Z76.0, Z79.891, Z79.899 parenteral nutrition
NAFLD - Lab LOINC codes
Can you please add the lab LOINC codes for the covariate labs of interest to your algorithm or to the data dictionary documentation?
Bilirubin, AST, ALT, SGOT, LDH, ALP?
Ok, I will update the
Ok, I will update the algorithm description.
NAFLD - Medications
Are there certain medications that you want us to send? The medication data dictionary does not specify?
No medication covariates are
No medication covariates are needed.
Medications
I see that exclusion list has systemic corticosteroids but no meds..Are these the drugs : prednisone, prednisolone, methylprednisolone, beclomethasone, betamethasone, dexamethasone, hydrocortisone and triamcinolone. Fludrocortisone
Please update the algorithm in case these are the drugs.
cdiff steroids
Please use the cdiff corticosteroids descritpion here. Most sites probably have already implemented this.
Corticosteroid Meds
Corticosteroid Medications: Cortisone (Cortisone and Cortisone Acetate), Hydrocortisone (Hydrocortisone, Hydrocortisone Sodium Phosphate, Hydrocortisone Sodium Succinate, Hydrocortisone Acetate, Hydrocortisone Cypionate), Prednisone, Prednisolone (Prednisolone and Prednisolone Sodium Phosphate), Methylprednisolone (Methylprednisolone, Methylprednisolone Sodium Succinate, Methylprednisolone Acetate), Triamcinolone (Triamcinolone, Triamcinolone Acetonide, Triamcinolone Diacetate, Triamcinolone Hexacetonide), Dexamethasone (Dexamethasone, Dexamethasone Acetate, Dexamethasone Sodium Phosphate), Betamethasone (Betamethasone, Betamethasone Sodium Phosphate, Betamethasone Acetate)
Exclude if strength/dose includes a “%”
{[Route must be (IV, IM, or PO)] OR [have a dose/strength (“MG|milligram|miligram”)]} AND[Route not like intranasal|topical|inhaled]
NAFLD - Lab LOINC codes
Hello,
Tests listed in the Table 5 are different from what are listed in the DD. SGOT is listed in the DD, but not in the Table 5. ALP and GGT are listed in the Tabel 5, but not in the DD. Shall we use what listed in the Table 5 only?
Thank you
Data Dictionary represents
Data Dictionary represents the data we need. Sorry for the confusion.
the LOINC code for SGOT is 27344-1
SGOT mapped to AST
We have SGOT labs mapped to 30239-8 (Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma by With P-5'-P) aka AST. The would mean both types of labs would be reported in the AST column. Is this correct, or should I separate?
imaging test for hepatic steatosis
Hello,
we did not find CPT codes relevant to imaging tests for hepatic steatosis. Will you prefer us using relevant CPT codes commonly used in our site or you may add that to the DD?
Thank you,
Zi (Carol)
Please send me a list of the
Please send me a list of the codes you use. Thank you.
11. The ‘HxDiseaseDx_v1’ Data Dictionary requests ICD9/CPT codes
Hello,
For the ICD9 and CPT codes listed in the "HxDiseaseDx_v1" DD, do you need that for CASE 1,2,3,4 or CASE 1 and CASE 2 only?
Thank you,
Zi (Carol)
If relevant, please include
If relevant, please include for all cases.
ready to implement
is this the phenotype mentioned on 03jan2018 workgroup call, and is it ready for all sites to implement? thanks.
Yes, it is ready to implement
Yes, it is ready to implement.
NAFLD phenotype definition
1. How can we define a case who satifiies the criteria defined for both case 1 and case 2 ?
2. What is the value for case 4 ? the data dictionary does not specify/assign a value to it.
NAFLD phenotype definition
1. How can we define a case who satifiies the criteria defined for both case 1 and case 2 ?
2. What is the value for case 4 ? the data dictionary does not specify/assign a value to it.
Case clasification
1. Case 1 is more specific (requires a biopsy report and judgment), and therefore primary. If a patient matches both case 1 and case 2, identify as case 1.
2. Case Classification is listed in a string field in demographics DD sheet.
Labs - LOINC codes
Was the LOINC lab question above answered?
The lab test listed in table 5 are different from the DD. SGOT listed in the DD is not listed in Table 5.
NAFLD_DataDictionary_HxNAS_v2
NAFLD_DataDictionary_HxNAS_v2 is to extract NAFLD activity score and fibrosis stage. Is the data source for this extraction pathology report (liver sample)? In our text, the relevant information is documented as, for example, "NAFLD activity score (NAS) is 2 (1+1+0)". Does this meant that the NAS_Total is 2, NAS_Steatosis is 1, NAS_lobular is 1, NAS_Baloon is 0?
Are there other text patterns for NAS score or fibrosis stage?
Thank you,
Sunny
NAFLD_DataDictionary_CovDx_v1.csv
Does NAFLD_DataDictionary_CovDx_v1.csv refer to Table 4 in the algorithm documentation? If so, some codes from Table 4 might not be listed in VALUES of NAFLD_DataDictionary_CovDx_v1.csv, for example 278.0.
If it is possible, could you please list corresponding tables from the algorithm documentation in the data dictionary COMMENT part?
Thank you,
Sunny
NAFLD_DataDictionary_CovDx_v1.csv
Does NAFLD_DataDictionary_CovDx_v1.csv refer to Table 4 in the algorithm documentation? If so, some codes from Table 4 might not be listed in VALUES of NAFLD_DataDictionary_CovDx_v1.csv, for example 278.0.
If it is possible, could you please list corresponding tables from the algorithm documentation in the data dictionary COMMENT part?
Thank you,
Sunny
NAFLD_DataDictionary_HxVisitsDx_v2.csv
In NAFLD_DataDictionary_HxVisitsDx_v2.csv, do you only want the encounters (LOS) that only have height or weight?
Thank you,
Sunny
all encounters with a LOS. HW is just most recent measurment
all encounters with a LOS. HW is just most recent measurment
more question
So there will be lots of LOS that have no height or weight?
'most recent' measurement needed
The dd says : Height/Weight at Encounter date; or most recent height/weight
So if there was an encounter with HW at 1400 days
and on with only W on 1500 days, then the line with 1500 days would include most recent H, and current W
activity score
Hello,
To identify activity score in the clinical notes, are the key words provided in the DD enough: that will be: total component score, steatosis, lobular inflammation, balooned hepatocytes, firobsis ONLY? If not, can you provide a list of key words including all the variations? Also, can you provide a list of note section that we shall look for to get required information?
Thank you,
Zi (Carol)
In CHOP's validation they did
In CHOP's validation they did not indicate additional terms needed for the clinical notes processing.
Sections can be variable by location, so we have not provided that information.
covariate labs
We've uploaded this file with age in days (DD description has days, DD units has years) and units of mg/dL for bilirubin - all other lab values in U/L per DD.
Thank you. All other
Thank you. All other implementations can use days.
Datasets
Hi,
There are two DDs for NAFLD
One is "NAFLD_DataDictionary_HxDisease_CovDx_v1", which has the following fields -.SUBJID
-.ICD_Code: icd9,10 and cpt code
-.Age
The other one is "NAFLD_DataDictionary_HxDisease_Dx_v1" which has the following fields
-.SUBJID
-.ICD_Code
-.CPT_code
-.Age
This data prepared using this two DDs, which give us redundant dataset. My questions why should we prepare two same identical datasets, instead of one?
Covariate and Disease
One is for the Disease/Phenotype codes and the other is for covariate codes, from the covariate table in the description doc (Table 4)
Corrections made to DD
Please note, The following DDs have been corrected/changed.
History of Visits is now, any encounter with a Ht/Wt. If patient has an encounter, without WEIGHT recorded, you can leave it blank.
Lab age units are corrected to days.
DD
1. The "Data Dictionary", NAFLD_DataDictionary_HxDisease_Dx_v1, has the field CPT_code which is not mentioned/used in the NAFLD Phenotype definition.
Question: Do you have an additional supplement sheet for NALFD definition, which applies CPT codes ?
2. The "Data Dictionary", NAFLD_DataDictionary_CovLab_v3, has a list of fields for clinc lab measurements (see below) as covariates in conditional analysies.
-.Bilirubin
-.AST
-.ALT
-.SGOT
-.LDH
Question: What lab data we should collect for each defined patient, latest/most recent measument?, max?, median?, mean?,min?
1. You can ignore the CPT
1. You can ignore the CPT line. Earlier versions of the algorithms used a CPT for confimation of liver biopsy. That's not necessary because it's built into the case 1/2 definition.
2. All recorded lab variable measurements please.
Hi,
Hi,
I wanted to confirm for case 1 and case 2 generation - the criteria 1-3 are "and" - as in a patient must have a dx, diagnostic report, AND exclude if they are on medication.
Thanks!
-Katie
Correct "AND"
Those critera are "AND"
Data dictionary sheets
There are two DDs, one is NAFLD_DataDictionary_HxNAS_v2.csv and the 2nd one is NAFLD_DataDictionary_HxNAS_v3.csv. Both of them define the same data without difference. I am thinking v2 is old version and v3 is latest. So, we should use v3 and ignore v2, right?
Correct.
Once added, I can't figure out a way to delete a DD from the tab.
So, we should only use v3 for
So, we should only use v3 for that data instead of preparing two data sets, right?
correct
latest version of the dd only, please.
cov_labs had been accidentally replaced
Please find cov_labs (v4) also in the DD list.
DD for NAFLD_DataDictionary_CovLab_v3.csv
The DD of NAFLD_DataDictionary_CovLab_v3.csv defines the following variables
SUBJID Deidentified Subject/eMERGE ID
Age_at_lab Age (days) at lipid lab/at the same age, but multiple test data ?
1.Bilirubin A value measured which captures the amount of Bilirubin
2.AST A value measured which captures the amount of AST or Aspartate Aminotransferase
3.ALT A value measured which captures the amount of Serum Glutamic Pyruvic Transaminase (SGPT-ALT)
4.SGOT A value measured which captures the amount of Serum Glutamic Oxaloacetic Transferase
5. LDH A value measured which captures the amount of Lactate Dehydrogenase (LDH)
Question.
a). For Bilirubin, do we need to collect total bilirubin, conjuated, unconjuated, or all.
b). AST and SGOT refers to the same thing, Aspartate Aminotransferase/serum glutamic-oxaloacetic transaminase. why should we put the two in the same data sheet ?
c). The unit of AST and ALT is u/dl not mg/dl but were defined as mg/dl in DD sheet
all units in the Labs v4 DD shoudl be u/dl
all units in the Labs v4 DD shoudl be u/dl
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