Non-alcoholic fatty liver disease (NALFD) & Alcoholic Fatty Liver Disease (ALD)

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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:

Unstructured Data: 
NLP
Structured data: 
CPT
ICD10
ICD9
Data Source/clinical domain: 
observations
medications
Files: 
Pathology Scoring Sheet
Component Scoring of NAS Histology
NAFLD-inclusion-exclusion_final_06182018.docx
Information
Phenotype ID: 
588
Date Created: 
Monday, August 29, 2016
Status: 
Final
Do Not List on the Collaboration Phenotypes List
Contact information
Contact Author: 
Todd Lingren
Institution: 
CCHMC
View Phenotyping Groups: 
Denny’s Group at Vandy
eMERGE CCHMC Group
eMERGE CCHMC/BCH Group
eMERGE CHOP Group
eMERGE Columbia Group
eMERGE Geisinger Group
eMERGE GHC/University of Washington Group
eMERGE Harvard Group
eMERGE Marshfield Group
eMERGE Mayo Group
eMERGE Mount Sinai Group
eMERGE Northwestern Group
eMERGE Phenotype WG
eMERGE Vanderbilt Group
PCORI CDRN/PPRN
Owner Phenotyping Groups: 
eMERGE CCHMC Group
Demographics
Age: 
Pediatric
Adult
 

Suggested Citation

CCHMC. Non-alcoholic fatty liver disease (NALFD) & Alcoholic Fatty Liver Disease (ALD). PheKB; 2016 Available from: https://phekb.org/phenotype/588

Comments

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?

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?

It's in the exclusion diagnoses table. 

V58.69 Z76.0, Z79.891, Z79.899 parenteral nutrition

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?

Are there certain medications that you want us to send? The medication data dictionary does not specify?

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.

 

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]

Submitted by Zi Ye on

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

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?

Submitted by Zi Ye on

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)

is this the phenotype mentioned on 03jan2018 workgroup call, and is it ready for all sites to implement?  thanks.

Submitted by Xinnan Niu on

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. 

Submitted by Xinnan Niu on

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. 

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. 

 

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 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

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

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

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

 

Submitted by Zi Ye on

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 not indicate additional terms needed for the clinical notes processing.

Sections can be variable by location, so we have not provided that information. 

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.

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?

One is for the Disease/Phenotype codes and the other is for covariate codes, from the covariate table in the description doc (Table 4) 

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.

 

Submitted by Xinnan Niu on

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 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,

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

Submitted by Xinnan Niu on

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?

Once added, I can't figure out a way to delete a DD from the tab. 

Submitted by Xinnan Niu on

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

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