*DISEASE* RA / SLE / Psoriasis

[CarolineMorton]

SLE: From LSHTM: https://datacompass.lshtm.ac.uk/356/

Need to write a definition. @hmcd do you have this easily accessible and could you write below if you do. It is a definition in plain english of what the codes are.

[CarolineMorton]

Psoriasis: https://datacompass.lshtm.ac.uk/1255/

[hjforbes]

@CarolineMorton

Just to confirm, I assume autoimmune disorders are being assessed as a risk factor for severe COVID19?

As there are many autoimmune disorders, I wondered if a decision had been made to only include SLE and psoriasis? Is there a rationale for choosing these? What about others, such as Coeliac disease, Inflammatory bowel disease, MS, ulcerative colitis, Guillain-Barre syndrome, Addison’s etc?

[CarolineMorton]

These are the code lists that @hmcd has provided. If possible, we would want more autoimmune diseases, although not IBD, Addisons, GBS or MS (as they are included elsewhere) in IBD, Endocrine, and Neurological code lists. Coeliac would be good to include.

[hjforbes]

Here's a broad list of autoimmune conditions. There's possibly too many, I suppose it depends how broad we want to go and if we really think they'll be at greater risk of severe Covid?

As mentioned above, some fall into other code lists. I have made a column for those to include (Y-Yes, N-No), with an explanation for the No's. @CarolineMorton and @hmcd

• could you go through and say whether you think they should be in the autoimmune conditions list
• confirm they are not covered by other code lists

Autoimmune conditions.xlsx

[CarolineMorton]

Hi @hjforbes

I will defer to @hmcd for her opinion on this. I suspect we could have a never ending list of auto immune conditions and we probably only want to catch the big ones, otherwise where do you stop?

What do you suggest @hmcd?

[CarolineMorton]

@hjforbes Just having a chat with @hmcd

We are going to initially go for a common autoimmune group that includes:

• Rheumatoid Arthritis
• Psoriasis
• SLE

I have done RA already as included with OA. Would you be able to look at Psoriasis / SLE code lists? We may come back to the longer code lists (for example, vasculitis) at a later date.

[hjforbes]

Sure, on it

[hjforbes]

DEFINITION: Current, or any history of, autoimmune disorders (specifically SLE and psoriasis). As mentioned above this can get expanded to other autoimmune conditions in the future if required.

STEP 1: Read codes version 2 autoimmune_v1.xlsx

STEP 2: QOF (only lupus features in QOF) qof-autoimmune.xlsx

STEP 3: SNOMED cluster snomed-autoimmune.xlsx

[hjforbes]

Further thought @CarolineMorton, should we identify patients with autoimmune conditions currently taking immunosupressants (say a prescription for an immune suppressant within the last three months), and patients with autoimmune conditions not on immunosuppressants? We could look at prescription dose, but that may be a step too far at this stage.

This will help us with the questions:

• who should be on the shielded patients lists? Individuals with SLE or psoriasis not on immunosuppressant therapy are currently not on the shielded patients list.
• what predicts bad outcomes?

[CarolineMorton]

Summary of discussion on phone call from 8-4-2020 with Liam, Ben, Krishnan, @hmcd, Laurie, @alexwalkercebm, @SJWEvans, @StatsFizz, @annaschultze

Plan not to include all autoimmune conditions but to choose large patient populations of patients with autoimmune disease who are not currently in shielding criteria. If positive association found, then may want to do a further study just looking at autoimmunity.

I have renamed this to reflect this.

[CarolineMorton]

DRAFT SIGN OFF

DEFINITION: Patients who have any Read 3 code for Rheumatoid Arthritis or SLE or Psoriasis ever on their medical records held by TPP. Absence of a code on the record is taken as no presence of disease.

Example output:	patient_id	condition	date
123	Rheumatoid Arthritis	1/2/2009
332	SLE	2/4/2016

CODE LISTS: Read 3 code list - FINAL code list: ra-sle-psoriasis-final.xlsx

Created using this method by TPP:

1. Read 2 LSHTM validated code list:

   • SLE or Psoriasis: sle_psoriasis
   • RA: Rheumatoid_arthritis.xlsx

2. Adding in key clusters from QOF and mapping to CTV3

   • SLE QOF qof-autoimmune.xlsx - added by Harriet Forbes (@hjforbes)
     • Psoriasis not in QOF - checked by Harriet Forbes
     • RA QOF - added by Caroline Morton (@CarolineMorton) qof-ra.xlsx
       • searched for rheumatoid arthritis and RA
       • manually checked for extra codes

3. Adding in high level snowmed codes and mapping to CTV3. Key Terms searched for in CT SNOWMED BROWSER:

   • SLE & Psoriasis - snomed-autoimmune.xlsx added by Harriet Forbes
   • RA added by Caroline Morton (@CarolineMorton). Key Terms searched for in CT SNOWMED BROWSER: snowmed-ra.xlsx
     • rheumatoid arthritis
     • caplan's syndrome
     • Juvenile seropositive polyarthritis
     • NOTE: I have included childhood RA which was not originally included in the LSHTM list

4. _Final list sense checked

   • SLE & Psoriasis - sense checked by Laurie Tomlinson. Copy of Autoimmune_CTV3_LT.xlsx
   • RA - checked by Harriet Forbes. Note added a variable, "Include", when 1=Yes and 0=No. RA_CTV3_Raw_HF_checked.xlsx

(see discussion from ebmdatalab/tpp-sql-notebook#19 on RA codes)

Caroline and I discussed over slack we should include RA monitoring invite codes, as patients must have RA to be on a monitoring list, and may help capture the less compliant of the RA patients.

• FLEXIBILITY NEEDED BETWEEN STUDIES: We may want to restrict to patients with certain medications.
• EFFECTS ON COHORT SELECTION: Patients must have been registered for at least 12 months before the index date, in order to allow for recording of disease codes.

POTENTIAL BIASES: We may be missing people who are solely managed in secondary care, perhaps the most severe cases or newly diagnosed.

CLINICAL SIGN OFF & DATE:

EPIDEMIOLOGY SIGN OFF & DATE:

SHARED WITH WIDER TEAM: Yes

FINAL SIGN OFF DATE (and apply label)

[hjforbes]

@laurietomlinson @CarolineMorton

Few queries from this code list

“Localised pustular psoriasis” was excluded from original Read lists, on assumption it doesn’t have a systemic effect (non-specific pustular psoriasis and generalised pustular psoriasis were included). Happy for me to therefore exclude it?

I’m also wondering if “Generalised pustular psoriasis of pregnancy” should be in? Isn’t this transient and likely to resolve after pregnancy?

Limited lupus erythematosus – possibly exclude, as again, local rather than generalised?

Neonatal lupus erythematosus – we had excluded these, on the basis it was unlikely to be relevant to the population, but now I suggest including for thoroughness.

[Bullous impetigo] or [impetigo herpetiformis] – exclude, as it could be impetigo?

[CarolineMorton]

Hi Harriet, Yes this all sounds reasonable. thank you for spotting. Woudlyou be able to change and reupload? You should be able to copy the sign off above into a comment below, with the new documents.

thank you!

[laurietomlinson]

@hjforbes Hi Harriet. My view was that even the localised disease showed an underlying autoimmune predisposition. Given the accuracy of coding, and now that I understand the purpose of the code list, my thought was better to capture more patients rather than being specific. Agree re pregnancy, though I think the 'predisposition' argument still holds. Thanks a lot

[CarolineMorton]

Probably either way will be ok. @laurietomlinson you certainly know more about this than me so happy to go with your suggestion.

[hjforbes]

@laurietomlinson @CarolineMorton Thanks! Ah, I thought it was less predisposition to autoimmune disorders, and more an actual autoimmune disorder we were trying to capture.

if that is correct, I think the following makes sense, but feel free to re-jig if I'm wrong

Include

• Neonatal lupus erythematosus

Exclude

• localised PS and SLE
• [Bullous impetigo] or [impetigo herpetiformis]
• “Generalised pustular psoriasis of pregnancy”

[hjforbes]

@laurietomlinson okay so following that call with Ian, I see your point about predisposition! Sorry. So, I think we want to following:

Include Neonatal lupus erythematosus “Generalised pustular psoriasis of pregnancy” localised PS and SLE

Exclude [Bullous impetigo] or [impetigo herpetiformis]

If yes, I will revise the final code list now

[laurietomlinson]

@hjforbes ha funny I was going to say that the point about localised OA capturing generalised OA was what I meant but you'd already got it. Sounds good to me? Glad you are all settled in Bristol, it looks lovely

[hjforbes]

Copy.of.Autoimmune_CTV3_LT_HF.xlsx

Final list! Only 1 change, as described above.

[CarolineMorton]

Hi Harriet,

Do you think you could combine your RA and SLE/Psoriasis code lists into one and upload here?

Then I do the final sign off. thank you

[hjforbes]

FINAL_RA_PSOR_SLE.xlsx

I have removed the codes we don't want included, to avoid any confusion.

[CarolineMorton]

FINAL SIGN OFF

DEFINITION: Patients who have any Read 3 code for Rheumatoid Arthritis or SLE or Psoriasis ever on their medical records held by TPP. Absence of a code on the record is taken as no presence of disease.

Example output:	patient_id	date
123	1/2/2009
332	2/4/2016

CODE LISTS: Read 3 code list - FINAL code list: FINAL_RA_PSOR_SLE.xlsx

Created using this method by TPP:

1. Read 2 LSHTM validated code list:

   • SLE or Psoriasis: sle_psoriasis
   • RA: Rheumatoid_arthritis.xlsx

2. Adding in key clusters from QOF and mapping to CTV3

   • SLE QOF qof-autoimmune.xlsx - added by Harriet Forbes (@hjforbes)
     • Psoriasis not in QOF - checked by Harriet Forbes
     • RA QOF - added by Caroline Morton (@CarolineMorton) qof-ra.xlsx
       • searched for rheumatoid arthritis and RA
       • manually checked for extra codes

3. Adding in high level snowmed codes and mapping to CTV3. Key Terms searched for in CT SNOWMED BROWSER:

   • SLE & Psoriasis - snomed-autoimmune.xlsx added by Harriet Forbes
   • RA added by Caroline Morton (@CarolineMorton). Key Terms searched for in CT SNOWMED BROWSER: snowmed-ra.xlsx
     • rheumatoid arthritis
     • caplan's syndrome
     • Juvenile seropositive polyarthritis
     • NOTE: I have included childhood RA which was not originally included in the LSHTM list

4. _Final list sense checked

   • SLE & Psoriasis - sense checked by @laurietomlinson and @hjforbes . Copy.of.Autoimmune_CTV3_LT_HF.xlsx
   • RA - checked by Harriet Forbes. Note added a variable, "Include", when 1=Yes and 0=No. RA_CTV3_Raw_HF_checked.xlsx

(see discussion from ebmdatalab/tpp-sql-notebook#19 on RA codes)

Caroline and I discussed over slack we should include RA monitoring invite codes, as patients must have RA to be on a monitoring list, and may help capture the less compliant of the RA patients.

• FLEXIBILITY NEEDED BETWEEN STUDIES: We may want to restrict to patients with certain medications.
• EFFECTS ON COHORT SELECTION: Patients must have been registered for at least 12 months before the index date, in order to allow for recording of disease codes.

POTENTIAL BIASES: We may be missing people who are solely managed in secondary care, perhaps the most severe cases or newly diagnosed.

CLINICAL SIGN OFF & DATE: Caroline Morton @CarolineMorton 10-4-2020

EPIDEMIOLOGY SIGN OFF & DATE: Laurie Tomlinson @laurietomlinson 14-4-2020

SHARED WITH WIDER TEAM: Yes

FINAL SIGN OFF DATE (and apply label) 14-4-2020 09:44