TODO - Manuscript Task: Verify Non-Alcoholic Fatty Liver Disease Phenotype

[callahantiff]

Creating as a separate issue to break-up issue #2

Finalizing the Non-Alcoholic Fatty Liver Disease Phenotype

Case Criteria:

• CASE TYPE 1
  • Presence of certain chronic liver diseases (ICD9 code)
  • Evidence by text positive for diagnostic phrases of hepatic steatosis, either by imaging or by histology in biopsy report (procedure keyword)
  • NOT presence of ANY exclusionary codes (ICD9 code)
  • NOT presence of ANY medications (preferably exclude when use >3 months) (medication string)

• CASE TYPE 2
  • Presence of certain chronic liver diseases (ICD9 code)
  • Evidence by text positive for hepatic steatosis of in clinical notes (condition, drug, procedure, observation keywords)
  • NOT presence of ANY exclusionary codes (ICD9 code)
  • NOT presence of ANY medications (preferably exclude when use >3 months) (medication string)

Control Criteria:

• NOT presence of ANY exclusionary codes (ICD9 code)

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Questions:

• Can we search for any occurrence of "hepatic steatosis” in the patient record to satisfy this case criteria, "Evidence of hepatic steatosis, either by imaging or by histology in biopsy report”?

• For Case Type 2, can we search for any occurrence of the following terms, in the patient record to satisfy this case criteria, "Evidence of hepatic steatosis in clinical notes”? Or, should the two case types be combined given that we do not have notes (for the pediatric data) as the criteria requires.
  • steatosis
  • steatohepatitis
  • non-alcoholic fatty liver disease
  • non-alcoholic steatohepatitis
  • fatty liver-non-alcoholic
  • NAFL
  • NAFLD
  • NASH
  • NAS
  • fatty liver
  • activity score

For both questions above, we get the following hits:

Data	source_string	standard_code	standard_name	vocabulary_id	domain_id
Both	fatty liver	716379000	Acute fatty liver of pregnancy	SNOMED	Condition
Both	fatty liver	50325005	Alcoholic fatty liver	SNOMED	Condition
Both	fatty liver	371330000	Fatty liver	SNOMED	Condition
Both	fatty liver	197315008	Non-alcoholic fatty liver	SNOMED	Condition
Both	fatty liver	5360002	Nonalcoholic fatty liver	SNOMED	Condition
Both	fatty liver	371329005	Nonalcoholic fatty liver	SNOMED	Condition
DS2	non-alcoholic fatty liver disease	1079451000000100	Assessment using NAFLD (Non-Alcoholic Fatty Liver Disease) fibrosis score	SNOMED	Procedure
DS2	non-alcoholic fatty liver disease	1079441000000100	NAFLD (Non-Alcoholic Fatty Liver Disease) fibrosis score	SNOMED	Observation
DS2	non-alcoholic fatty liver disease	1079461000000100	Non-Alcoholic Fatty Liver Disease (NAFLD) fibrosis score	SNOMED	Observation
Both	steatohepatitis	722866000	Non-alcoholic fatty liver disease without non-alcoholic steatohepatitis	SNOMED	Condition
DS2	steatohepatitis	722866000	Non-alcoholic fatty liver disease without non-alcoholic steatohepatitis	SNOMED	Condition
Both	steatohepatitis	442685003	Nonalcoholic steatohepatitis	SNOMED	Condition
Both	steatohepatitis	442191002	Steatohepatitis	SNOMED	Condition
DS2	steatohepatitis	765482002	Steatohepatitis caused by ingestible alcohol	SNOMED	Condition

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@tdbennett, can you please advise on these questions?

[tdbennett]

I think I'm probably missing a few things here (what is both vs. DS2?). But, that said, I'm not sure that we can do this phenotype at all. Both case types require notes (1 - imaging or pathology reports, 2 - clinical notes), which we don't have.

What am I missing?

[callahantiff]

I think that I should have started by asking that question first. It's what I meant to ask in my second question -- whether or not this phenotype was possible given our data limitations. So, it sounds like we want to exclude this and then close this issue?

[callahantiff]

Phenotype requires data that is not available for peds and adults -- closing this issue and removing this from the list of eligible phenotypes.