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:

Information
Phenotype ID: 
588
Date Created: 
Monday, August 29, 2016
Status: 
Final
Do Not List on the Collaboration Phenotypes List
Contact information
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
Unstructured Data: 
NLP
Structured data: 
CPT
ICD10
ICD9
Data Source/clinical domain: 
observations
medications
Demographics
Age: 
Pediatric
Adult
Files: 
Image icon Pathology Scoring Sheet
File Component Scoring of NAS Histology
File NAFLD-inclusion-exclusion_final_06182018.docx

Suggested Citation

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

Jim Linneman

Tue, 2017-02-07 10:54

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?

Todd Lingren

Mon, 2017-03-13 15:02

Please exclude if patient has TPN dx  in a one year before first NAFLD dx.

Thank you.

Rajiv Nadukuru

Thu, 2017-08-10 13:34

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?

Todd Lingren

Thu, 2017-08-10 15:09

It's in the exclusion diagnoses table. 

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

Jim Linneman

Thu, 2017-08-10 08:49

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?

Jim Linneman

Thu, 2017-08-10 14:35

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

Rajiv Nadukuru

Fri, 2017-08-11 11:23

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.

 

Todd Lingren

Mon, 2017-08-14 13:45

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]

Zi Ye

Thu, 2017-11-30 19:15

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

Todd Lingren

Tue, 2018-01-09 10:26

Data Dictionary represents the data we need. Sorry for the confusion. 

the LOINC code for SGOT is 27344-1

Ken Borthwick

Thu, 2018-02-01 09:52

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?

Zi Ye

Fri, 2017-12-01 10:32

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)

Jane Grafton

Fri, 2018-01-05 14:49

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

Xinnan Niu

Mon, 2018-01-08 15:26

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. 

Xinnan Niu

Mon, 2018-01-08 15:27

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. 

Todd Lingren

Tue, 2018-01-09 07:59

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. 

 

Barbara Benoit

Tue, 2018-01-09 10:20

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.

Ning Sunny Shang

Tue, 2018-01-09 10:34

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

Ning Sunny Shang

Tue, 2018-01-09 10:43

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

Ning Sunny Shang

Tue, 2018-01-09 10:43

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

Ning Sunny Shang

Tue, 2018-01-09 10:45

In NAFLD_DataDictionary_HxVisitsDx_v2.csv, do you only want the encounters (LOS) that only have height or weight?

Thank you, 

Sunny

Ning Sunny Shang

Tue, 2018-01-09 11:01

So there will be lots of LOS that have no height or weight?

Todd Lingren

Tue, 2018-01-09 11:04

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

 

Zi Ye

Thu, 2018-01-18 18:51

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)

Todd Lingren

Mon, 2018-01-22 09:19

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. 

Frank Mentch

Fri, 2018-01-19 16:13

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.

Todd Lingren

Mon, 2018-01-22 09:18

Thank you. All other implementations can use days.

Sarah Bland

Mon, 2018-01-22 15:00

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?

Todd Lingren

Mon, 2018-01-22 15:13

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

Todd Lingren

Mon, 2018-01-22 15:25

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.

 

Xinnan Niu

Tue, 2018-01-23 10:07

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?

Todd Lingren

Thu, 2018-01-25 11:46

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.

Kathryn Jackson

Thu, 2018-01-25 11:33

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

Todd Lingren

Thu, 2018-01-25 11:43

Those critera are "AND"

Xinnan Niu

Fri, 2018-01-26 10:30

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?

Todd Lingren

Fri, 2018-01-26 10:38

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

Todd Lingren

Fri, 2018-01-26 13:23

latest version of the dd only, please.

Xinnan Niu

Mon, 2018-01-29 09:48

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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