TODO - Manuscript Task: Verify Hypothyroidism Phenotype

[callahantiff]

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

Finalizing the Hypothyroidism Phenotype

Case Criteria:

• Presence of hypothyroidism ICD9 codes OR Abnormal TSH (>5.0) or FT4 (<0.5) lab results (lab code)
• Presence of thyroid replacement medication (medication string)
• Require > 2 instances of either medication or lab (or combination) with > 3 months between the first and last instance of medication or lab
• NOT presence of secondary causes of hypothyroidism (ICD9 code)
• NOT presence of other thyroid diseases by IC9 codes or CPT codes
• NOT presence of certain thyroid diseases (condition or procedure keyword)
• NOT presence of pregnancy ICD9 codes and an abnormal TSH or FT4 (lab code) 6 mon (before)-1 yr (after) birth
• NOT presence of abnormal b-HCG labs and an abnormal TSH or FT4 (lab code) 6 mon (before)-1 year (after) birth
• NOT presence of recent contrast exposure (all abnormal lab or medication instances within 6 weeks of a contrast study) (labs and/or medication keyword)
• NOT presence of ANY radiation therapy code (if it proceeds hypothyroidism) (CPT code)
• NOT presence of ANY Thyroidectomy code (CPT code)
• NOT presence of ANY thyroid-altering medication (medication string)

Control Criteria:

• Have a normal TSH (0.5 – 5) and normal FT4 (0.5-1.2) (lab code)
• Presence of > 2 past medical history sections and medication lists (could substitute two non-acute clinic visits or annual physical)
• NOT presence of ANY billing codes for hypothyroidism (ICD9 code)
• NOT presence of ANY evidence of thyroid replacement medications (medication string)
• NOT presence of ANY cause of hypothyroidism or hyperthyroidism
• NOT presence of ANY radiation therapy code (if it proceeds hypothyroidism) (CPT code)
• NOT presence of ANY thyroidectomy code (CPT code)
• NOT presence of certain thyroid diseases (condition or procedure keyword)
• NOT presence of ANY thyroid-altering medication (medication string)

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Questions:
LABS: Given the description, have I selected the correct LOINC code?

• TSH and FT4 Labs:

Source	LOINC
Both	3016-3: Thyrotropin [Units/volume] in Serum or Plasma
Both	3024-7: Thyroxine (T4) free [Mass/volume] in Serum or Plasma
Both	3026-2: Thyroxine (T4) [Mass/volume] in Serum or Plasma
Both	32215-6: Thyroxine (T4) free index in Serum or Plasma by calculation
DS 1	29575-8: Thyrotropin [Units/volume] in DBS
DS 1	3021-3: Thyroxine binding globulin [Mass/volume] in Serum or Plasma
DS 1	31144-9: Thyroxine (T4) [Mass/volume] in DBS
DS 1	5385-0: Thyrotropin receptor Ab [Units/volume] in Serum
DS 1	6892-4: Thyroxine (T4) free [Mass/volume] in Serum or Plasma by Dialysis
DS 2	3027-0: Thyroxine (T4)/Thyroxine binding globulin [Mass Ratio] in Serum or Plasma

• Anti-thyroglobulin antibodies: H-TGA, ThyrAB, AThyg-positive

Source	LOINC
Both	3013-0: Thyroglobulin [Mass/volume] in Serum or Plasma
DS 1	8098-6: Thyroglobulin Ab [Units/volume] in Serum or Plasma
DS 2	5380-1: Thyroglobulin Ab [Units/volume] in Serum by Radioimmunoassay (RIA)

• Anti-thyroperoxidase: H-TPO, TPO, AThyP-positive

Source	LOINC
Both	8099-4: Thyroperoxidase Ab [Units/volume] in Serum or Plasma
DS 2	32042-4: Thyroperoxidase Ab [Presence] in Serum or Plasma

• Anti-thyroid antibodies: ThyAb-positive (don't think this is the correct lab)

Source	LOINC
DS 1	30567-2: Thyroid stimulating immunoglobulins [Units/volume] in Serum

• Urine or serum b-HCG

Source	LOINC
DS 1	2112-1: Choriogonadotropin.beta subunit (pregnancy test) [Presence] in Urine
DS 2	21198-7: Choriogonadotropin.beta subunit [Units/volume] in Serum or Plasma

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• One of the control criteria mentioned above states, "presence of >2 past medical history sections and medication lists (could substitute two non-acute clinic visits or annual physical)". Does that mean to be eligible, a patient needs to have at least 2 medications and 2 visits or, to be considered a "medical history section" does it need to be a visit where a diagnosis occurs?

• Another control criteria states, "NOT presence of ANY cause of hypothyroidism or hyperthyroidism". This seems more involved than just looking for occurrences of "hyperthyroidism" or "hypothyroidism", or am I overthinking it?

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@tdbennett, can you please advise on these questions?

[tdbennett]

1. I like this phenotype because it's complicated and might be a good test of the system.

2. Hypothyroidism is usually diagnosed in the office, not the hospital, which I think is what the control criterion you quoted is going for. A "past medical history section" is part of a clinical note that we won't necessarily have, but is required for clinic billing. Can we identify clinic visits and their types (e.g. not acute, annual physical, etc)? If not, we might not be able to do the control criteria completely.

3. The "NOT presence of ANY cause..." statement isn't that helpful. Was there a list on the phenotype page?

4. The labs all look fine, but I didn't do any additional searching. Several of those were in the validation survey we three did I think.

[callahantiff]

1. Glad you like it!

2. As far as I am aware, this is the only information I can get regarding the visit type:

admitting_source_concept_id	visit_type_concept_id
Other	Visit derived from EHR record
Hospice
Ambulatory visit
Hospitals, General Acute Care Hospital
Skilled Nursing Facility
Emergency Room - Hospital
Home / self care
No information

@mgkahn - do you know if there is a better place to look for visit type information?

3. Unfortunately, there is no additional information provided in the phenotype documentation.

4. I was pretty thorough, so if there is nothing obviously wrong then I am confident moving forward with these labs.

[tdbennett]

"Ambulatory visit" looks like the only "clinic" visit useful for the control group, unless they all end up in Other or No information.

[callahantiff]

"Ambulatory visit" looks like the only "clinic" visit useful for the control group, unless they all end up in Other or No information.

Response:
OK, sounds good.

[callahantiff]

We have addressed all open questions; closing this issue for now.