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*DISEASE* presence of chronic neurological condition #5

Open sebbacon opened 4 years ago

sebbacon commented 4 years ago

Code for identifying binary variable "presence of chronic neurological condition"

to include:

CarolineMorton commented 4 years ago

Helen McD to share codelist when available. It does exist but wasn't updated last year like the others so may not be as good.

LSHTM definition:

A diagnosis ever of stroke, TIA or conditions in which respiratory function may be compromised due to neurological disease

CarolineMorton commented 4 years ago

Code list v2 read:

neuro_expanded_Jan18.xlsx

CarolineMorton commented 4 years ago

DEFINITION: Patients who have a diagnosis ever of stroke, TIA or conditions in which respiratory function may be compromised due to neurological disease.

CODE LISTS: Read 3 code list (when available). Created using this method by TPP:

  1. Read 2 LSHTM code list https://github.com/ebmdatalab/tpp-sql-notebook/files/4409932/neuro_expanded_Jan18.xlsx

  2. Adding in key clusters from QOF and mapping to CTV3 (read code 3) - added by Caroline Morton (@CarolineMorton) qof-neuro.xlsx

    • No inclusion of epilepsy as does not compromise respiratory function
    • No inclusion of QOF neuropathy as this relates to foot checks in diabetes patients in the most common incidence.

  3. Adding in high level snowmed codes and mapping to CTV3. Key Terms searched for in CT SNOWMED BROWSER: snowmed-neuro.xlsx Added by Caroline Morton (@CarolineMorton)

    NOTE: Could have gone further to by adding all eponymous rare conditions but these are included within the original Read 2 list and should map across

  4. Final list sense checked by clinician

    • List sense checked by Brian Nicholson. List includes many conditions but not stroke or tia.
    • Discussed at meeting on 8-4-20 with @hmcd @alexwalkercebm @amirmehrkar: neurological conditions to be included stroke, parkinsons, MS, MND, cerebral palsy, quadriplegia, progressive cerebellar disease, huntington's, polio, dementia and mysathenia. Decision to exclude TIA, encephalitis and meningitis.
    • Reviewed again by @CarolineMorton and sorted into conditions:
      • Stroke (TIA excluded, carotid artery stenosis/occlusion excluded, arterial syndromes included such as lacunar syndrome)
      • Parkinson's Disease (parkinsonism due to other causes such as drugs excluded)
      • Motor Neuron Disease (disease such as primary lateral sclerosis which fall under MND included)
      • Multiple Sclerosis (demylination where condition unspecified excluded)
      • Cerebral Palsy
      • Creutzfeldt–Jakob disease (CJD)
      • Quadraplegia
      • Progressive Cerebellar Disease (Cerebellar ataxia excluded)
      • Huntington's Disease
      • Polio
      • Dementia
      • Mysathenia
      • Progressive degeneration syndromes post viral infection such as PML included

NEURO-CM.xlsx

POTENTIAL BIASES:

CLINICAL SIGN OFF & DATE:

EPIDEMIOLOGY SIGN OFF & DATE:

SHARED WITH WIDER TEAM: Yes/No

FINAL SIGN OFF DATE (and apply label)

laurietomlinson commented 4 years ago

@CarolineMorton @brianmackenna I have been through the list and highlighted a few areas to discuss. Basically to be specific if we are looking for vascualr pathology in adults. Discuss on a call tomorrow?

CarolineMorton commented 4 years ago

Perfect. I can ring you in the afternoon if that's ok. Clinic in the morning. Is there a good time for you?

laurietomlinson commented 4 years ago

Just ring/zoom when you are free

laurietomlinson commented 4 years ago

Really sorry @CarolineMorton but this NEURO-CM.xlsx looks like just the stroke list? Can't see any other neuro codes

CarolineMorton commented 4 years ago

If you download it, you should be able to see the other diseases. The filter may still be on, if it is, then you can click the drop down for filter at the top of the reason column and press select all.

Thanks

Sent: Wednesday, April 15, 2020 at 11:20 PM From: "laurietomlinson" notifications@github.com To: "ebmdatalab/tpp-sql-notebook" tpp-sql-notebook@noreply.github.com Cc: "CarolineMorton" carolinemorton@gmx.com, "Mention" mention@noreply.github.com Subject: Re: [ebmdatalab/tpp-sql-notebook] DISEASE presence of chronic neurological condition (#14)

Really sorry @CarolineMorton but this NEURO-CM.xlsx looks like just the stroke list? Can't see any other neuro codes

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ebmdatalab/tpp-sql-notebook/issues/14#issuecomment-614286197

CarolineMorton commented 4 years ago

@laurietomlinson i have reuploaded the codelist today. it is NEURO-CM.xlsx as before and you should be able to see all the diseases now.

thank you

CarolineMorton commented 4 years ago

To summarise our conversation this morning with @alexwalkercebm @hmcd @laurietomlinson (with input from @LiamSmeeth). Our aim is now to try to find common neurological conditions and those patients with conditions such as stroke or dementia. This is because: (from Liam via Helen)

Chronic risk being dominated by stroke/dementia, for most of whom there won’t be a particularly increased risk of respiratory infection. Cardiovascular risk is looking particularly relevant to COVID, and stroke/dementia may be important as indicating vascular risk. His suggestion is to have one variable for stroke/dementia, and another for the other neurological conditions.

I have therefore split the larger dataset into 3:

Other neuro is defined as:

We have agreed to remove Polio, Myopathy, Deficiency related disorders, metabolic disorders and Hemiplegia.

@hjforbes has spent a lot of time reviewing stroke codes for ebmdatalab/tpp-sql-notebook#63 and I have asked her to review our stroke list to see if any that need to be added to or moved around. see final list. Notes on this:

FINAL DEMENTIA CODEliST compiled by @CarolineMorton: dementia.xlsx FINAL STROKE CODELIST, compiled by @hjforbes stroke_final.xlsx

LiamSmeeth commented 4 years ago

Thanks Caroline yes looks great BW

From: CarolineMorton notifications@github.com Reply to: ebmdatalab/tpp-sql-notebook reply@reply.github.com Date: Monday, 20 April 2020 at 14:45 To: ebmdatalab/tpp-sql-notebook tpp-sql-notebook@noreply.github.com Cc: Liam Smeeth Liam.Smeeth@lshtm.ac.uk, Mention mention@noreply.github.com Subject: Re: [ebmdatalab/tpp-sql-notebook] DISEASE presence of chronic neurological condition (#14)

To summarise our conversation this morning with @alexwalkercebmhttps://github.com/alexwalkercebm @hmcdhttps://github.com/hmcd @laurietomlinsonhttps://github.com/laurietomlinson (with input from @LiamSmeethhttps://github.com/LiamSmeeth). Our aim is now to try to find common neurological conditions and those patients with conditions such as stroke or dementia. This is because: (from Liam via Helen)

Chronic risk being dominated by stroke/dementia, for most of whom there won’t be a particularly increased risk of respiratory infection. Cardiovascular risk is looking particularly relevant to COVID, and stroke/dementia may be important as indicating vascular risk. His suggestion is to have one variable for stroke/dementia, and another for the other neurological conditions.

I have therefore split the larger dataset into 3:

Other neuro is defined as:

We have agreed to remove Polio, Myopathy, Deficiency related disorders, metabolic disorders and Hemiplegia.

@hjforbeshttps://github.com/hjforbes has spent a lot of time reviewing stroke codes for ebmdatalab/tpp-sql-notebook#63https://github.com/ebmdatalab/tpp-sql-notebook/issues/63 and I have asked her to review our stroke list to see if any that need to be added to or moved around.

FINAL DEMENTIA CODEliST compiled by @CarolineMortonhttps://github.com/CarolineMorton: dementia.xlsxhttps://github.com/ebmdatalab/tpp-sql-notebook/files/4503811/dementia.xlsx

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ebmdatalab/tpp-sql-notebook/issues/14#issuecomment-616563742, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APDUVH4CAXMAAOAHZULGJWTRNRGXLANCNFSM4LXKHJIQ.

hmcd commented 4 years ago

Three separate exposure groups under this issue (1) Stroke/TIA (2) Dementia (3) Other chronic neurological conditions (as risk factors for respiratory infection)

DEFINITIONS: (1) Stroke/TIA: Patients who have ever had a diagnosis of a stroke or TIA. (2) Dementia: Patients who have ever had a diagnosis of dementia (of any aetiology or unspecified) (2) Other chronic neurological conditions (as risk factors for respiratory infection): Patients who have ever had a diagnosis of the specified chronic neurological conditions in which respiratory function may be compromised, comprising: motor neurone disease, myasthenia gravis, Creutzfeld-Jakob Disease, muscular dystrophy, multiple sclerosis, Parkinson's disease (not parkinsonism), cerebral palsy, Huntington's disease, quadriplegia or hemiplegia, post-viral progressive degeneration syndromes (such as PML, SSPE but not post-polio), malignant primary brain tumour, and progressive cerebellar disease (not cerebellar ataxia only).

Output 3 columns for each of the three exposure groups: 1) a binary variable denoting the presence of one of the codes at any point in the patient record (2) a string variable with the Read term for the earliest recorded code (3) the earliest date of this code

CODE LISTS: Read 3 code lists.

Created using this method by TPP:

Read 2 LSHTM code list https://github.com/ebmdatalab/tpp-sql-notebook/files/4409932/neuro_expanded_Jan18.xlsx

Adding in key clusters from QOF and mapping to CTV3 (read code 3) - added by Caroline Morton (@CarolineMorton) qof-neuro.xlsx

No inclusion of epilepsy as does not compromise respiratory function No inclusion of QOF neuropathy as this relates to foot checks in diabetes patients in the most common incidence. Adding in high level snowmed codes and mapping to CTV3. Key Terms searched for in CT SNOWMED BROWSER: snowmed-neuro.xlsx Added by Caroline Morton (@CarolineMorton)

NOTE: Could have gone further to by adding all eponymous rare conditions but these are included within the original Read 2 list and should map across

Final list sense checked by clinician

List sense checked by Brian Nicholson. List includes many conditions but not stroke or tia. Discussed at meeting on 8-4-20 with @hmcd @alexwalkercebm @amirmehrkar: neurological conditions to be included stroke, parkinsons, MS, MND, cerebral palsy, quadriplegia, progressive cerebellar disease, huntington's, polio, dementia and mysathenia. Decision to exclude TIA, encephalitis and meningitis. Reviewed again by @CarolineMorton and sorted into conditions: Stroke (TIA excluded, carotid artery stenosis/occlusion excluded, arterial syndromes included such as lacunar syndrome) Parkinson's Disease (parkinsonism due to other causes such as drugs excluded) Motor Neuron Disease (disease such as primary lateral sclerosis which fall under MND included) Multiple Sclerosis (demylination where condition unspecified excluded) Cerebral Palsy Creutzfeldt–Jakob disease (CJD) Quadraplegia Progressive Cerebellar Disease (Cerebellar ataxia excluded) Huntington's Disease Polio Dementia Mysathenia Progressive degeneration syndromes post viral infection such as PML included NEURO-CM.xlsx

Discussion with @LiamSmeeth - Chronic risk being dominated by stroke/dementia, for most of whom there won’t be a particularly increased risk of respiratory infection. Cardiovascular risk is looking particularly relevant to COVID, and stroke/dementia may be important as indicating vascular risk. plan to separate into three separate groups of interest (1) Stroke/TIA (2) dementia and (3) other chronic neurological conditions. List separated by @CarolineMorton

(1) Stroke/TIA list reviewed by @hjforbes 310 codes in total, 261 from @CarolineMorton list and 49 additional ones from @hjforbes (issue ebmdatalab/tpp-sql-notebook#63) Removal of all TIAs Inclusion of haemorrhagic strokes Removal of codes where there was uncertainty about diagnosis. for example TIA/Stroke annual review Removal of exception codes

(2) Final Dementia codelist compiled by @CarolineMorton

(3) Final Chronic neurological codelist compiled by @laurietomlinson (@hmcd checked reconciliation and uploaded. Notes on changes by @laurietomlinson - removed reversible myasthenic syndromes, included back muscular dystrophy as discussed, noted that malignant primary brain tumours and hemiplegia also included and agreed with these, noted that polio was still included and checked re earlier decision - @hmcd checked - decision had been to remove polio, removed by @hmcd for final list. List with LT comments other_neuro_only_LT_comments.xlsx

** FINAL CODELISTS **

(1) FINAL STROKE CODELIST, compiled by @hjforbes stroke_final.xlsx

(2) FINAL DEMENTIA CODELIST compiled by @CarolineMorton dementia_final.xlsx

(3) FINAL OTHER NEUROLOGICAL CONDITIONS CODELIST compiled by @laurietomlinson other_neuro_final.xlsx

FLEXIBILITY NEEDED BETWEEN STUDIES: None 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:

CLINICAL SIGN OFF & DATE: Stroke/TIA by Caroline Morton @CarolineMorton 21 April 2020 Dementia by Caroline Morton @CarolineMorton 21 April 2020 Other chronic neurological conditions by Laurie Tomlinson @laurietomlinson 21 April 2020

EPIDEMIOLOGY SIGN OFF & DATE: Stroke/TIA Harriet Forbes (@hjforbes) 21 April 2020 Dementia and other chronic neurological conditions @hmcd 22 April 2020

SHARED WITH WIDER TEAM: Not final versions as needed urgently for analysis

FINAL SIGN OFF DATE 22 April 2020 03:00