Fw: LMIC LPS Covid - Steering Group - Minutes & Actions

13 May 2020
Groups audience: 

Begin forwarded message:
This is the discussion we are having about instruments and standards at the Wellcome Trust questionnaire bank initiative as it turns to and pulls in the LMIC initiative alongside the UK HIC initiative. Here LPS stands for Longitudinal Population Studies in the Wellcome Trust world.
From: "Chambers, John (IMPERIAL SPH)" <***@***.***>
Subject: RE: LMIC LPS Covid - Steering Group - Minutes & Actions
Date: May 13, 2020 at 5:40:16 AM EDT
To: Jay Greenfield <***@***.***>
Cc: Chifundo Kanjala <***@***.***>, Emma Slaymaker <***@***.***>, Michele Ramsay <***@***.***>, Kirsty Le Doare <***@***.***>, Jim Todd <***@***.***>, Ian Goon <***@***.***>, "***@***.***" <***@***.***>, Arofan Gregory <***@***.***>, Kobus Herbst <***@***.***>, Mia Crampin <***@***.***>, Eveline Geubbels <***@***.***>, Paulo Andrade Lotufo
<***@***.***>
Jay:
I think your response addresses the point that co-opting us all into the same model as a one-size fits all is unlikely to be workable.
We have a data dictionary that has evolved over time and which is version controlled. The team are working to get it interoperable with FHIR. There has also been some work towards mapping to OMOP. Those decisions are also context specific.
That said, it would be great to ensure that we can map the COVID questions rapidly between cohorts without getting confused, so a simple tool focussed on the UK and COVID question sets would be great and appropriate.
John
From: Jay Greenfield <***@***.***>
Sent: 13 May 2020 17:33
To: Chambers, John (IMPERIAL SPH) <***@***.***>
Cc: Chifundo Kanjala <***@***.***>; Emma Slaymaker <***@***.***>; Michele Ramsay <***@***.***>; Kirsty Le Doare <***@***.***>; Jim Todd <***@***.***>; Ian Goon <***@***.***>; ***@***.***; Arofan Gregory <***@***.***>; Kobus Herbst <***@***.***>; Mia Crampin <***@***.***>; Eveline Geubbels <***@***.***>; Paulo Andrade Lotufo
<***@***.***>
Subject: Re: LMIC LPS Covid - Steering Group - Minutes & Actions
John:
What approach(es) are you used to using to annotate questionnaires so that downstream the data captured is useful first in data management and subsequently in data analysis?
Besides DDI Codebook / Nesstar Publisher there are other candidates.
I am not sure it is necessary that data producers all have to annotate their questionnaires using the same metadata model. In the United States we see many standards in play with questionnaire annotation including CDISC, HL7 CDA, HL7 FHIR and DDI Codebook. In Africa because of the World Bank the Nesstar version of DDI Codebook has been used across a number of HDSSs. In Europe HL7 CDA is often encountered.
I am also a member of the RDA COVID-19 Epidemiology Working Group where we are tracking the LMIC LPS Covid effort to create a question bank along with other efforts under way including the UK one. In order to aggregate questionnaire data across providers, across cohorts and across borders for use cases like a cross border pandemic early warning system, many schemes for annotating questionnaires willy nilly come into play. Early warning systems can’t count on all data producers using the same metadata standard.
Given the approach Chifundo has outlined here, I am not sure this is a problem you have to solve with LMIC LPS Covid you are developing. If it is a problem, I can connect you with other folks who are working on this issue — cross-border, cross-domain interoperability — in a compressed time frame.
Jay
Jay Greenfield, MA, PhD
Data Documentation Initiative
CODATA Representative
UNECE ModernStats Representative
RDA COVID-19 Epidemiology Working Group Contributor
On May 13, 2020, at 5:14 AM, Chambers, John (IMPERIAL SPH) <***@***.***> wrote:
Thanks
If this is intended to document the questionnaire, that makes sense and can be specified.
I still think that the metadata beyond that would benefit from being greatly streamlined, if this is to be deliver meaningful collation of information in near term.
Just a view!
John
From: Chifundo Kanjala <***@***.***>
Sent: 13 May 2020 17:08
To: Chambers, John (IMPERIAL SPH) <***@***.***>; Emma Slaymaker <***@***.***>; Michele Ramsay <***@***.***>; Kirsty Le Doare <***@***.***>; Jay Greenfield <***@***.***>
Cc: Jim Todd <***@***.***>; Ian Goon <***@***.***>; ***@***.***; Arofan Gregory <***@***.***>; Kobus Herbst <***@***.***>; Mia Crampin <***@***.***>; Eveline Geubbels <***@***.***>; Paulo Andrade Lotufo
<***@***.***>
Subject: Re: LMIC LPS Covid - Steering Group - Minutes & Actions
Hi John,
The plan is that once the questionnaire contents (core and recommended questions) have been agreed on, I can create a DDI specification that cohorts can use as base documentation and tweak it to show cohort specific variations. This specification will have enough detail describing each of the metadata fields in the template.
For more details on the DDI codebook fields descriptions, find attached a more detailed template I am working with in Malawi. It is based on some of the customisations that a team led by Kobus Herbst in the iSHARE project used for documenting data from Health and Demographic Surveillance Systems in the past. I was avoiding providing too much detail as people already have a lot to look at.
A template such as the DDI one that I have provided for describing the studies in a standardised way will go a long way in facilitating comparisons of the data collected and in sharing those data for integration of what the LMIC cohorts are doing into a global ecosystem of Covid19 data.
Regards,
Chifundo
________________________________
From: Chambers, John (IMPERIAL SPH) <***@***.***>
Sent: 13 May 2020 10:30
To: Chifundo Kanjala <***@***.***>; Emma Slaymaker <***@***.***>; Michele Ramsay <***@***.***>; Kirsty Le Doare <***@***.***>; Jay Greenfield <***@***.***>
Cc: Jim Todd <***@***.***>; Ian Goon <***@***.***>; ***@***.*** <***@***.***>; Arofan Gregory <***@***.***>; Kobus Herbst <***@***.***>; Mia Crampin <***@***.***>; Eveline Geubbels <***@***.***>; Paulo Andrade Lotufo
<***@***.***>
Subject: RE: LMIC LPS Covid - Steering Group - Minutes & Actions
Late contribution, sorry.
The biosamples and the control measures matrix look largely right.
I’m afraid the DDI codebook looks unworkable to me. This may be OK for a narrow set of studies that have worked to the Nesstar template, and already collated it, but will not be generalisable to studies that don’t use this approach. The ambition of this degree of collation and harmonisation also looks more suited to a programme of work over several years, than our rapid response to a viral pandemic. The questions posed lack enough information for cohorts to be able to contribute meaningful responses, as indicated by some of the queries on it. If I make educated inferences about what they are asking, then I could see taking months to fill in for our cohort. Does anyone else feel similarly?
Email discussion can come across poorly, sorry. The comments are sincerely well intentioned. I also wasn’t on the meta-data WG, so apologies if I have missed something obvious.
Best wishes
John
From: Chifundo Kanjala <***@***.***>
Sent: 13 May 2020 15:33
To: Emma Slaymaker <***@***.***>; Michele Ramsay <***@***.***>; Kirsty Le Doare <***@***.***>; Jay Greenfield <***@***.***>
Cc: Jim Todd <***@***.***>; Ian Goon <***@***.***>; ***@***.***; Arofan Gregory <***@***.***>; Kobus Herbst <***@***.***>; Mia Crampin <***@***.***>; Chambers, John (IMPERIAL SPH) <***@***.***>; Eveline Geubbels <***@***.***>; Paulo Andrade Lotufo
<***@***.***>
Subject: Re: LMIC LPS Covid - Steering Group - Minutes & Actions
Dear all,
I have responded to some of the questions that were posed about some of the Nesstar metadata fields.
I have also put each subgroup in its own spreadsheet and added an extra sheet for other metadata if needed.
For implementation I guess each of the participating cohorts will need to complete a questionnaire/ table on the bio-samples related documentation.
Jay and Arofan - I wanted to hear your thoughts regarding the question bank and protocol metadata. Is it a good plan to aim to extract those metadata from the Nesstar codebooks, questionnaires and protocols? Or do we need to add metadata fields to the attached template? In the template we are requesting questionnaires, ethical clearance documents and protocols and information on their title, authors, date, country, language and format.
Emma - you had other metadata required for capturing context in the individual cohorts not covered in the current content?
Regards,
Chifundo
________________________________
From: Emma Slaymaker <***@***.***>
Sent: 12 May 2020 23:32
To: Michele Ramsay <***@***.***>; Kirsty Le Doare <***@***.***>; Jay Greenfield <***@***.***>
Cc: Chifundo Kanjala <***@***.***>; Jim Todd <***@***.***>; Ian Goon <***@***.***>; ***@***.***<***@***.***>; Arofan Gregory <***@***.***>; Kobus Herbst <***@***.***>; Mia Crampin <***@***.***>; John Chambers (IMPERIAL SPH) <***@***.***>; Eveline Geubbels <***@***.***>; Paulo Andrade Lotufo
<***@***.***>
Subject: RE: LMIC LPS Covid - Steering Group - Minutes & Actions
Sorry, with attachment!
From: Emma Slaymaker
Sent: 12 May 2020 22:31
To: Michele Ramsay <***@***.***>; Kirsty Le Doare <***@***.***>; Jay Greenfield <***@***.***>
Cc: Chifundo Kanjala <***@***.***>; Jim Todd <***@***.***>; Ian Goon <***@***.***>; ***@***.***; Arofan Gregory <***@***.***>; Kobus Herbst <***@***.***>; Mia Crampin <***@***.***>; John Chambers (IMPERIAL SPH) <***@***.***>; Eveline Geubbels <***@***.***>; Paulo Andrade Lotufo
<***@***.***>
Subject: RE: LMIC LPS Covid - Steering Group - Minutes & Actions
I’ve added a few comments as well, in a funny orange colour!
From: Michele Ramsay <***@***.***>
Sent: 12 May 2020 07:28
To: Kirsty Le Doare <***@***.***>; Jay Greenfield <***@***.***>
Cc: Chifundo Kanjala <***@***.***>; Emma Slaymaker <***@***.***>; Jim Todd <***@***.***>; Ian Goon <***@***.***>; ***@***.***; Arofan Gregory <***@***.***>; Kobus Herbst <***@***.***>; Mia Crampin <***@***.***>; John Chambers (IMPERIAL SPH) <***@***.***>; Eveline Geubbels <***@***.***>; Paulo Andrade Lotufo
<***@***.***>
Subject: LMIC LPS Covid - Steering Group - Minutes & Actions
Dear Kirsty and colleagues,
Thank you for the metadata list – I have made some suggestions in green in the attached.
I was wondering if it would help to have sections in the metadata questionnaire for different purposes (i.e. sampling aligned to purpose):
1. Samples collected pre-COVID (could be used for host genetics)
2. Samples collected during COVID (understanding that there may also be multiple samples at different times (longitudinal) for an individual. Somehow we need to ask this question too.)
a. Viral assessment (SARS-CoV-2 – and the different ways this can be done)
i. Presence of virus
ii. Quantitation
iii. Viral genome sequence
b. Immune response assessment (serum anti-bodies; PBMCs; others)
c. Host genome
It is unclear to me how much detail we need? (Jay’s question below)
Can we assume that every study will have their own SOPs for sample collection, processing, transport and storage?
Also that they will seek appropriate consent for data and sample use and sharing (nationally and internationally).
We could then have questions like:
Do you have SOPs for x, y, z?
Do you have ethics approval and consent for x, y, z?
Do we have a link with the other biological samples group (Teri Manolio / NIH)?
Please let me know how I can help going forward.
Michele
From: Kirsty Le Doare <***@***.***>
Date: Sunday, 10 May 2020 at 13:55
To: Jay Greenfield <***@***.***>
Cc: Chifundo Kanjala <***@***.***>, Emma Slaymaker <***@***.***>, Jim Todd <***@***.***>, Ian Goon <***@***.***>, "***@***.***" <***@***.***>, Arofan Gregory <***@***.***>, Kobus Herbst <***@***.***>, Mia Crampin <***@***.***>, "John Chambers (IMPERIAL SPH)" <***@***.***>, Michele Ramsay <***@***.***>, Eveline Geubbels <***@***.***>, Paulo Andrade Lotufo
<***@***.***>
Subject: Re: LMIC LPS Covid - Steering Group - Minutes & Actions
Hi Jay,
Yes to all, we hoped to collect this as part of the sampling details and from the protocols.
BW
Kirsty
Kirsty Mehring-Le Doare
UKRI Future Leaders Fellow,
Reader in Global Child Health
St George’s, University of London
Consultant in Paediatric Infectious Diseases and Immunology
CSAC Training advisor (PIID)
Follow me on Twitter: @kirstyledoare
From: Jay Greenfield <***@***.***>
Date: Sunday, 10 May 2020 at 12:24
To: Kirsty Le Doare <***@***.***>
Cc: Chifundo Kanjala <***@***.***>, Emma Slaymaker <***@***.***>, Jim Todd <***@***.***>, Ian Goon <***@***.***>, "***@***.***" <***@***.***>, Arofan Gregory <***@***.***>, Kobus Herbst <***@***.***>, Mia Crampin <***@***.***>, "John Chambers (IMPERIAL SPH)" <***@***.***>, Michele Ramsay <***@***.***>, Eveline Geubbels <***@***.***>, Paulo Andrade Lotufo
<***@***.***>
Subject: Re: LMIC LPS Covid - Steering Group - Minutes & Actions
Chifundo and Kirsty:
Is there a need to trace biospecimen receipt control in-house before the specimen goes to the biobank (e.g. pickup, spin, receive, store, ship)?
Is there a need to trace the use/history of the biospecimen once it is received at the biobank (e.g thaw, spin, return, freeze)?
Finally, although they are built into the test kits, is there a need to record the type of genomic sequencing that is being performed?
Jay
On May 10, 2020, at 5:11 AM, Kirsty Le Doare <***@***.***> wrote:
Hi Chifundo,
I think we have to propose and refine the metadata part of the form to include biological samples and control measures. I have included the other members of the biological samples group so that you have a complete email list.
In the attached I have added a notes section where we would like to add additional information regarding the samples and a table to understand what samples are biobanked (in red at the end).
There are two questions that we had that I think can now be deleted (highlighted in yellow).
Eveline and I have asked our respective labs about the information and they have provided comments that I have incorporated here.
BW
Kirsty
Kirsty Mehring-Le Doare
UKRI Future Leaders Fellow,
Reader in Global Child Health
St George’s, University of London
Consultant in Paediatric Infectious Diseases and Immunology
CSAC Training advisor (PIID)
Follow me on Twitter: @kirstyledoare
From: Chifundo Kanjala <***@***.***>
Date: Friday, 8 May 2020 at 13:29
To: Emma Slaymaker <***@***.***>, Jim Todd <***@***.***>, Ian Goon <***@***.***>, Kirsty Le Doare <***@***.***>, "***@***.***" <***@***.***>, "Jay Greenfield (***@***.***)" <***@***.***>, "A. G." <***@***.***>, Kobus Herbst <***@***.***>, Mia Crampin <***@***.***>
Subject: Re: LMIC LPS Covid - Steering Group - Minutes & Actions
Dear all,
For those who are not part of the steering group, please find the minutes from the meeting at the end of this email.
The main thing for metadata is as follows:
Actions: New ‘Meta-data’ working group to be formed, including member(s) of the ‘control measures’ working group, the cohort Metadata group and the Biological samples group. New metadata data section of questionnaire to be created including all types of metadata.
My internet connection became very poor from about the middle of the call so I did not quite get what the next steps are to move things forward with the defined scope of the new working group.
Is there a plan to meet before the next steering committee meeting?
Regards,
Chifundo
- Show quoted text -From: Rachel Miles <***@***.***>
Sent: 07 May 2020 14:52
To: Mary De Silva <***@***.***>; Bruna Galobardes <***@***.***>; Kobus Herbst <***@***.***>; Alison Price <***@***.***>; John Chambers (IMPERIAL) <***@***.***>; ***@***.*** <***@***.***>; ***@***.*** <***@***.***>; ***@***.*** <***@***.***>; Emma Slaymaker <***@***.***>; Jim Todd <***@***.***>; ***@***.*** <***@***.***>; Mia Crampin <***@***.***>; Chifundo Kanjala <***@***.***>; Ian Goon <***@***.***>; Kirsty Le Doare <***@***.***>; ***@***.*** <***@***.***>; Connolly, John J <***@***.***>; Malay Kanti Mridha <***@***.***>; Novella, Rafael <***@***.***>; Ian Goon <***@***.***>
Subject: LMIC LPS Covid - Steering Group - Minutes & Actions
Dear All,
Many thanks for joining the steering group call yesterday, please see collated actions below and key deadlines (attendee list at the end of this email, for information).
ACTIONS LIST
1. Co-ordinating functions:
Action: IHCC will take over the coordination of this work going forwards. Wellcome and IHCC to meet to discuss what is feasible and IHCC to feedback to the Steering Group.
2. Finalising the questionnaire:
NB for all cohorts: Questions will need to be monitored and adjusted according to context and targets i.e. individual/household. Each cohort will need to each write their own preface and add their own questions to correctly identify participants as appropriate.
Action: Bruna will make all agreed changes to the questionnaire discussed on the call, including making a meta-data section to be completed at the cohort rather than participant level. DEADLINE – Thursday 7thMay
Action: Mary De Silva to link Kirsty Le Doare to the WHO Maternal and Child Health COVID co-ordinating group to ensure that WHO is aware of this work and to harmonise questions with the WHO is possible
Action: All working groups to reconvene offline, to narrow down the list of core questions to make the questionnaire shorter. Also, check your section against others to avoid duplications. Should be aiming for a telephone conversation of 30 minutes maximum, with 15 – 20 minutes of that used to address core questions. This will allow cohorts to include any other questions they need to.
DEADLINE – Thursday 14th May
Control measures: Agreed that the control measures matrix needs to be pilot tested in different contexts to finalise wording.
Action: Cohorts to volunteer to test how well the matrix captures different ‘control’ scenarios so that it can be used internationally (Mia and Kirsty have already volunteered).
Actions: New ‘Meta-data’ working group to be formed, including member(s) of the ‘control measures’ working group, the cohort Metadata group and the Biological samples group. New metadata data section of questionnaire to be created including all types of metadata.
3. Piloting the final questionnaire:
Action: Cohorts who are interested in piloting the core questionnaire to refine the questions to email Rachel (Secretariat-IHCC)
4. Agree co-ordinating functions for steering group and secretariat
Proposed functions and tasks:
• Coordinate piloting the questionnaire
• Coordinate publication of Core Questionnaire
• Promote use of questionnaire in other cohorts
• Support ethics approvals: Collect evidence from cohorts as they obtain ethics approval to help setting precedent (if this helps at the international level, it is useful in the UK)
• Keep track of use of questionnaire
• Coordinate platform to administer core questionnaire
• Coordinate website/shared space for documentation (IHCC)
• Convene topic-specific working groups to conduct cross-cohort analysis:
• Seroprevalence WG
• Mental Health WG
• Comms
It is not feasible for IHCC to take on all the coordination tasks so key tasks will be priorities. Active participation of the steering group is essential to this initiative, and will need to continue. It is also noted that these tasks can, and should, be expanded beyond the steering group and IHCC, to include colleagues who have the local expertise and skill-sets and ensure appropriate regional representation of this initiative.
Action: IHCC and Wellcome to meet to discuss what co-ordination activities IHCC could provide. IHCC will then take over the co-ordination and liaise with the Steering Group on the best way forward.
Best wishes,
Mary & Bruna
Attendees
Alison Price - Economic Impact
Kobus Herbst - Knowledge & Behaviour
Rafael Novella - Economic Impact
Mia Crampin - Knowledge & Behaviour
Emma Slaymaker - Social Impact
Malay Mridha - Knowledge & Behaviour
Eveline Geubbels - Social Impact
Michele Ramsay - Biological Samples
Ian Goon - (SAB) - Metadata
Kirsty Le Doare - Biological Samples
Chifundo Kanjala - Metadata
John Connolly - IHCC
John Chambers - Health Questions
Teri Manolio - IHCC
Robert Stewart - Health Questions
Mary De Silva - Wellcome (Chair)
Jim Todd - Environmental Impact
Bruna Galobardes - Wellcome

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