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ouhft / COPE

Project Repository for Work Package 4 of the COPE Transplant Trial
https://cope.nds.ox.ac.uk
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Investigate S/AEs that occur to organs that don't fit inclusion criteria #184

Open marshalc opened 7 years ago

marshalc commented 7 years ago

There is a hint from discussions between @ij-cope and @VirginiaChiocchia in Issue #170, that there are S/AE data unlinked to randomisation events.

Whilst it is clear that S/AEs can be linked to ANY Organ that is recorded (even in the minimalist sense) from a Procurement form being started, it is not clear what should be done with these S/AE afterwards.

Will investigate how much data has been collected matching this criteria for further discussion.

marshalc commented 7 years ago

Likely to need discussion on 12th Jan

marshalc commented 7 years ago

Currently we have 84 S/AE records that are not linked to a Recipient.

SELECT
  ae.id as 'Event ID',
  co.id as 'Organ ID',
  cr.id as 'Recipient ID'
FROM
  adverse_event_adverseevent as ae,
  compare_organ as co
LEFT OUTER JOIN compare_recipient as cr
  ON cr.organ_id = co.id
WHERE ae.organ_id = co.id
  AND cr.id ISNULL

First example:

Adverse Event 312. Has selected Trial ID WP441901R... P Form for WP441901 shows two randomised Kidneys in March 2015. There is one closed T Form for WP441901L showing as "Not Transplanted. There is no T Form for WP441901R.

This is marked as a SERIOUS Adverse Event (due to hospitalisation), onset of 8th May 2015 (presumably during a followup period).

Query: @mertenssarah what happened to WP441901R?

Second example:

Adverse Event 96. Has selected Trial ID WP457901L... P Form for WP457901L shows two randomised Kidneys in Aug 2015. There is one closed T Form for WP457901R showing as having a recipient. There is no T Form for WP457901L.

This is marked as a SERIOUS Adverse Event (due to 4 of 6 questions being Yes), onset of 9th Aug (day after procurement).

Query: @mertenssarah what happened to WP457901R?

... @AllyBradley, would you like me to continue investigating, or do we accept that there's a problem given 84 of 324 Adverse Events have no recipient, and the first two examples both refer to recipients...?

marshalc commented 7 years ago

For later reference, the Adverse Events in question are:

mertenssarah commented 7 years ago

WP441901R: was transplanted in Belgium: There is no paper transplantation form as TTs arrived too late and no information was noted by the TTs. Therefore no Transplantation form was opened for this case at the moment. The patient who received this kidney did consent for the trial and is being followed post-tx. Data from the transplantation needs to be asked to the local investigator/surgeon and added retrospectively.

WP457901L: the same story as above: no paper forms were completed therefor no data is entered in the database. These data need to be asked to local investigator

marshalc commented 7 years ago

Leaving aside the data that is 22 months late in being collected...

SELECT
  Count(ae.id) as "Event Count",
  co.id as 'Organ ID'
FROM
  adverse_event_adverseevent as ae,
  compare_organ as co
LEFT OUTER JOIN compare_recipient as cr
  ON cr.organ_id = co.id
WHERE ae.organ_id = co.id
  AND cr.id ISNULL
GROUP BY co.id

Query to get a list of non-recipient S/AEs and the Organs they relate to: Event Count - Organ ID 1 - 14 1 - 43 11 - 256 9 - 261 17 - 277 26 - 278 2 - 297 6 - 337 10 - 338 1 - 382

... haven't looked at Organ 278, but I dread to think what 26 Adverse things happened to them...

AllyBradley commented 7 years ago

@mertenssarah please provide the local investigator contact details so I can request the information for WP441901R and WP457901L.

mertenssarah commented 7 years ago

@AllyBradley I have requested the information of WP441901R to the local investigator. He is in Leuven on friday and will request this information again. WP457901L is a kidney transplanted in VU Rotterdam. @aukjebrat should be able to give you contact details

AllyBradley commented 7 years ago

@mertenssarah please provide me with the local investigator contact details for WP441901R?

AllyBradley commented 7 years ago

@aukjebrat Can you please provide me the local investigator contact details for WP457901L from VU Rotterdam?

marshalc commented 7 years ago

Note to self: One good bit of news, none of the 10 organs with S/AEs are unrandomised, so I can add randomisation data for Issue #170.

marshalc commented 7 years ago

From Issue #170:

However, the issue in the datasets I have extracted from the wp4 database is that the randomisation arm/group is given in the organ and transplantation dataset (wp4_report_organ) and I found out that the adverse events dataset (wp4_report_adverseevents) include Trial IDs that are not included in the other dataset. Therefore, the treatment group (as well as other info such as transplant date) is unavailable for several SAEs and it prevents to produce summaries of SAEs by treatment arm.

FYI @ij-cope and @VirginiaChiocchia :

The reason is that the data extracts have a limited amount of filtering on them, specifically:

The 84 S/AE events would fall foul of the filtering in the both the Organ and Allocation Reports, though they should all relate back to records in the Donor report since all of the 84 are randomised kidneys.

ij-cope commented 7 years ago

It would indeed have been good to have picked up on the data not being collected and getting back to the local investigators earlier. This feeds in with the question on reports showing us 'missing data' or trial IDs not having all of the appropriate forms started. I am sure we will get to this tomorrow during our discussion: optimising the flow of following data return adherence.

marshalc commented 7 years ago

If @AllyBradley believes she has the missing data for the Transplant forms above, this one can be closed now.

AllyBradley commented 7 years ago

There is still missing data for WP457901L. @aukjebrat This kidney is recorded as having been transplanted in VU Medisch Centrum, Netherlands. Are you able to request the transplantation data?

marshalc commented 7 years ago

This looks to be just ongoing data clean up now and not a development task. Will remove from milestones and leave with Ally for follow up