eusurvey - survey x

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1+MG - Survey on accessible genomes - July 2020

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You are invited to participate in this survey because according to our information or your indication of interest, your dataset may be eligible for participation in the European 1+ Million Genomes initiative (1+MG).

The 1+MG is based upon the commitment of 20 European Union Member States and Norway to establish a cross-border federated network of national genome collections associated with phenotypic data, consented for advancing health and medicine practice and research across Europe.

To prepare the framework for the 1+MG we have developed the questionnaire below. Our goal is to understand what existing genomic datasets and corresponding phenotypic/clinical information are effectively available for participation in the 1+MG. Also, we would like to know what are the challenges and bottlenecks for sharing, and how they may be overcome by development of technical or policy solutions. We will use your answers to make recommendations for design of a European framework for sharing genomic and associated clinical data, develop solutions to overcome challenges, and also to provide guidance for participation in the 1+MG initiative.

The information you will provide in this survey will be accessed and analysed by members of the 1+MG Coordination Group, the 1+MG Working Group leaders and the European Commission staff members supporting the 1+MG initiative. They will have access to the full replies to the survey, including your contact data. The results of this analysis will be presented in the form of a summary report that will be published in the 1+MG Interest Group on CIRCABC. Your identity will not be published in this summary report. Moreover, full replies to the survey, including your contact data, will be made available by e-mail to the appointed 1+MG representatives of the country indicated by you in the reply as country where the relevant dataset is located. Finally, for the follow-up of the survey, your contact details may be made available to other experts within the 1+MG initiative and the Coordination and Support

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Action “Beyond 1 Million Genomes" (‘B1MG’).

If you have any questions regarding this survey, please use the contact point indicated on the right. Thank you very much for your support!

1+MG Coordination team and Working Group leaders

I understand the objectives of the survey and accept the above terms of my participation.

A. GENERAL QUESTIONS

1. Dataset name and reference webpage:(If available)

2. Main institution:

3. Country where the dataset is stored:AT - AustriaBE - BelgiumBG - BulgariaHR - CroatiaCY - CyprusCZ - CzechiaDK - DenmarkEE - EstoniaFI - FinlandFR - FranceDE - GermanyEL - GreeceHU - HungaryIE - IrelandIR - ItalyLV - LatviaLT - LithuaniaLU - LuxembourgMT - MaltaNL - NetherlandsPL - Poland

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PT - PortugalRO - RomaniaSK - Slovak RepublicSI - SloveniaES - SpainSE - Sweden

Indicate the country, if none of the above mentioned applies (i.e. not an EU Member State):

4. What is the level of access to this dataset:InstitutionalRegionalNationalInternational

5. What is the question being addressed with this data collection:Rare DiseasesCancerGeneral population/complex diseasesHost susceptibility to infectious disease (e.g. Covid19-related)

B1. SPECIFICALLY REGARDING RARE DISEASES

1. What was the main purpose for data collection?ClinicalResearchAnother purpose (e.g. biobanking, epidemiology, surveillance)

Please specify the kind of clinical work:DiagnosticsTreatmentOther (e.g. clinical trial)

Diagnostics: Data source description.

Diagnostics: Criteria for population selection.

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Treatment: Data source description.

Treatment: Criteria for population selection.

Other: Please specify.(e.g. clinical trial)

Other: Data source description.

Other: Criteria for population selection.

Please specify the kind of study:(Please select all that apply.)

Population based studySample based studyProject with start and end data (with follow-up)Project with start and end data (without follow-up)Cohort

Another purpose: Please specify.(e.g. biobanking, epidemiology, surveillance)

2. What type of genetic data was collected?(Please select all that apply.)

Whole Genome Sequencing (WGS)Whole Exome Sequencing (WES)Clinical exomeArrays

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WGS: How many whole genomes with a genome-wide coverage >30x?

WGS: Are there relatives with the same genomic information?YesNo

WGS: Please specify.ParentsSiblingsExtended family

WES: How many whole exomes with more than 20.000 genes captured with coverage >60x?

WES: Are there relatives with the same genomic information?YesNo

WES: Please specify.ParentsSiblingsExtended family

Clinical exome: How many clinical exomes with more than 5.000 genes captured with coverage >60x?

Clinical exome: Are there relatives with the same genomic information?YesNo

Clinical exome: Please specify.ParentsSiblingsExtended family

Arrays: Please specify the type of array.

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SNP arrayaCGH

SNP array: How many subjects have array data?

aCGH: How many subjects have array data?

SNP: Are there relatives with the same genomic information?YesNo

SNP: Please specify.ParentsSiblingsExtended family

aCGH: Are there relatives with the same genomic information?YesNo

aCGH: Please specify.ParentsSiblingsExtended family

3. What phenotypic/clinical data is available?(Please select all that apply.)

Clinical informationTreatmentTreatment responseLifestyle (questionnaires)Social-economic status informationNone of the above

Clinical information:(Please describe key content)

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Treatment:(Please describe key content)

Treatment response:(Please describe key content)

Lifestyle (questionnaires):(Please describe key content)

Social-economic status information:(Please describe key content)

Please specify:(Please describe key content)

C1. CLINICAL AND PHENOTYPIC DATA (Rare diseases)

1. Is the clinical/phenotypic data:Centralised (collected and stored at a central location)Federated in local systems like Electronic Health Records (hospital information systems) or Electronic Data Capture (EDC) systems

Data location:

Please specify the system/tool in which the data is stored.(E.g. name of Electronic Health care system, type and name/brand of database, name of Electronic Data Capture (EDC) system, Excel, …)

Please specify which:

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2. Please specify how each subject or participant in the phenotypic/clinical dataset is uniquely identified.

(Include the variable(s) or methods used to uniquely identify each subject/participant)

3. Is the phenotypic data linked to:(Please select all that apply)

WGS dataWES dataClinical exome dataArray dataOther

Other: Please specify.

WGS data:For all subjectsFor part of the collection

WGS: Please specify how many.

WES data:For all subjectsFor part of the collection

WES: Please specify how many.

Clinical exome data:For all subjectsFor part of the collection

Clinical exome: Please specify how many.

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Arrays: Please specify the type of array.SNP arrayaCGH

SNP array:For all subjectsFor part of the collection

SNP array: Please specify how many.

aCGH:For all subjectsFor part of the collection

aCGH: Please specify how many.

4. Data structure and format:(Please select all that apply)

Free textStructured dataDate fields

Free text: Which language?(Please specify)

Structured data: Is there a codebook available?(Please select all that apply)

Yes, with clear descriptions of the codes being used.Yes, using the following (inter)national coding systems:Yes, a combination of both above.Yes, but other:No.

The following (inter)national coding systems:(Please select all that apply)

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SNOMED-CTLOINCICD10Other

Please specify the (inter)national coding systems.

Please specify the kind of codebook.

Date fields: Which date format?(For instance YYYY-MM-DD [e.g. 2020-05-31] or DD MMMM YYYY [e.g. 31 May 20209])

5. Regarding data quality:

Is a metadataset available?YesNo

Is a technical support document available?YesNo

What are the data governance procedures?(Responsibilities and scope)

What are the quality audit procedures for data lifecycle?

6. Under which conditions can this clinical/phenotypic data be shared?(select all that apply)

Institutional approval or national/international approvalResearch agreementEuropean Reference Networks or other international registry membership approval

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D1. ETHICAL AND LEGAL ISSUES (Rare diseases)

For your data collection, we need to know for how many subjects you observe the following:

1. General Data Protection Regulation (GDPR) Authorisation: Under the GDPR, does the data collection have a consensual basis (i.e. specific consent following Art. 6(1)a with 9(2)a) or non-consensual basis (e.g. statutory basis such as public interest based on Art. 6(1)e with Art. 9(2)g,h,i or j), as implemented in your country, that would allow to contribute this data in a cross-border genome initiative like the 1+MG?

NoNo, but re-consenting is possibleYesDon’t know

For how many subjects?For all subjectsFor part of the collection

Please specify how many:

State the legal basis under Art. 6 and the legitimation under Art. 9.

Please specify, if possible, what leads to the uncertainty.

Please upload an example of a consent document.The maximum file size is 1 MB

2. Ethical and legal legitimacy. Can the data be used for the following purposes? (Please note that, typically, ethical clearance comprises either informed consent or a waiver of informed consent and approval by an ethics committee.)

a) The use in future (not yet defined) research projects?

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(Irrespective of conditional restrictions)

NoYesDon’t know

Is the use in future research covered by the data subject information as required by Art. 13 of the GDPR?

YesNo

If ‘Yes’:For all subjectsFor part of the collection



b) The use in healthcare for the benefit of other patients?(E.g. the data would be used by doctors of independent hospitals to find the most appropriate therapy for their patients)

YesNoDon’t know

Is the use in healthcare covered by the data subject information as required by Art. 13 GDPR?YesNo




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c) The use in policy development for health?(E.g. optimising the quality of care by other hospitals, doing health technology assessment, defining governmental reimbursement strategies)

YesNoDon’t know

Is the use for policy development covered by the data subject information as required by Art. 13 GDPR?

YesNo




d) The independent use of data by researchers for their own projects in other/all EU/EEA countries possible?

YesNoDon’t know

Is the use by external researchers covered by the data subject information as required by Art. 13 GDPR?

YesNo


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3. Intellectual Property Rights.

a) Are existing intellectual property rights in the data collection limiting their use?YesNoDon’t know


Please specify how many/type of genetic data:


b) Will the use of the data impact the intellectual property rights of the users in the results of their research?

YesNoDon’t know



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4. We realise there may be restrictions we are not fully covering in the present questionnaire. Are there any limitations for the use of data as specified above that are not covered by the questions?

B2. SPECIFICALLY REGARDING CANCER

1. What was the main purpose for data collection?ClinicalResearchOther (e.g. biobanking, epidemiology, surveillance)


Please specify:(e.g. clinical trial)





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Please specify:(e.g. biobanking, epidemiology, surveillance)

Please specify:(Please select all that apply.)


2. What type of collection?(Please select all that apply.)

Tumour samplesGermline samplesTumour with normal tissueOther

Please specify:



WGS: How many cancer whole genomes with a genome-wide coverage >30x?

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WGS: How many corresponding germline whole genomes with a genome-wide coverage >30x?

WES: How many cancer whole exomes with more than 20.000 genes captured with coverage >60x?

WES: How many corresponding germline whole exomes with a genome-wide coverage >60x?

Clinical exome: How many germline clinical exomes with more than 5.000 genes with a genome-wide coverage >60x?

Arrays: How many cancer arrays?

Arrays: Please specify the type of cancer array.

Arrays: How many corresponding germline arrays?

Arrays: Please specify the type of germline array.


Clinical informationTreatmentTreatment responseLifestyle (questionnaires)Social-economic status informationFamily dataNone of the above

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Family data:(Please describe key content)


C2. CLINICAL AND PHENOTYPIC DATA (Cancer)


Data location:

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Yes, with clear descriptions of the codes being used.Yes, using the following (inter)national coding systems:

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Yes, a combination of both above.Yes, but other:No.











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Institutional approval or national/international approvalResearch agreementEuropean Reference Networks or other international registry membership approvalNone

D2. ETHICAL AND LEGAL ISSUES (Cancer)









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a) The use in future (not yet defined) research projects?(Irrespective of conditional restrictions)

NoYesDon’t know


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YesNoDon’t know



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YesNoDon’t know


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YesNoDon’t know


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B3. SPECIFICALLY REGARDING GENERAL POPULATION/COMMON & COMPLEX DISEASES COLLECTIONS

1. What type of collection?General populationComplex disease dataset

Please indicate the sample size:

How is the genetic heterogeneity ensured?

Is the dataset representative of the population (i.e. using simple, stratified, cluster, or systematic random sampling)?

YesNo

Please specify the disease:

Please indicate the sample size:

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Population based studySample based study

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Project with start and end data (with follow-up)Project with start and end data (without follow-up)Cohort








Clinical Exome: How many clinical exomes with at least 5000 genes captured with coverage >60x?



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C3. CLINICAL AND PHENOTYPIC DATA (Common & complex diseases)


Data location:








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Is a metadataset available?

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YesNo






D3. ETHICAL AND LEGAL ISSUES (Common & complex diseases)





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NoYesDon’t know


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YesNoDon’t know






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YesNo



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YesNoDon’t know


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YesNoDon’t know





B4. SPECIFICALLY REGARDING HOST SUSCEPTIBILITY TO INFECTIOUS DISEASE (e.g. COVID-19–RELATED)


Please specify the kind of clinical work:Diagnostics

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TreatmentOther (e.g. clinical trial)











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Clinical exome: How many clinical exomes with at least 5000 genes captured with coverage >60x?




3. Is the virus genome sequence available?NoNo, but viral samples are available

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For how many subjects?

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C4. CLINICAL AND PHENOTYPIC DATA (Host susceptibility to infectious disease)


Data location:






WGS dataWES dataClinical exome data

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Array dataOther











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Date fields: Which date format?

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(For instance YYYY-MM-DD [e.g. 2020-05-31] or DD MMMM YYYY [e.g. 31 May 20209])








D4. ETHICAL AND LEGAL ISSUES (Host susceptibility to infectious disease)



No

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No, but re-consenting is possibleYesDon’t know








NoYesDon’t know


YesNo

If ‘Yes’:For all subjects

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For part of the collection




YesNoDon’t know






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YesNoDon’t know


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a) Are existing intellectual property rights in the data collection limiting their use?Yes

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NoDon’t know





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Filled in by / contact point:

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Name:

E-mail:

THANK YOU VERY MUCH FOR YOUR CONTRIBUTION!

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