The "Setting Normative Function: Identification of areas where Standards and Guidelines are required" session at the 4th Biennial Meeting of the Human Variome Project Consortium fell within the context of a larger discussion of gene/disease specific databases. The session aimed to stimulate discussion amongst the Consortium about what specific standards and guidelines are required for gene/disease specific databases.

1. SETTING NORMATIVE FUNCTION: IDENTIFICATION OF AREAS
WHERE STANDARDS AND GUIDELINES ARE REQUIRED
Standards:
systems, procedures, technologies that HVP determined shall be used
Guidelines:
systems, procedures, technologies that HVP determined to be beneficial to adopt
Raymond Arleen Finlay Mauno Mireille
DALGLEISH AUERBACH MACRAY VIHINEN CLAUSTRES

2. DATABASE QUALITY AND DATA QUALITY/RELIABILITY
How to ensure data accuracy?
How to avoid data redundancy?
How to ensure nomenclature checking?
How to ensure quality assurance (to organize EQC?)
What is the role of the HVP in database quality?
What is the role of biomedical journals in ensuring variant reporting standards?
SYSTEMATICS of DATABASES
Logical database checks (e.g. dates)
Ontologies, nomenclatures, vocabularies...
The role of the CURATOR: towards a new concept of a profession with a career
structure (ex. a core health service?)

3. PATHOGENICITY ASSESSMENT (PA) and REPORTING
Familial segregation of variants and associated phenotype?
Annotation (functional significance: in vitro, in vivo and in silico analyses?)
How much phenotype must be attached to data? define a clinical form?
How to accommodate incomplete or variable penetrance in PA?
How to assess polyvariant mutants (modifiers of mutations)?
How to establish the frequency of variants in patients and controls?
(ex. 2 patients in a family: how many times the allele is reported?)
Integration of sometimes discrepant information?
Updating pathogenicity (may change with time)/state of knowledge of VUS

4. ETHICAL AND LEGAL ISSUES
Country-specific framework approval?
Signed Consent Forms (autonomy protection) (PROSPECTIVE)?
Capacity of an individual to consent for submission of the family pedigree data?
Anonymisation (privacy protection) vs. medical and scientific interest?
ETHNIC QUALIFICATIONS
Should they be population definitions or geographical locations?
Founder effects?
INTELLECTUAL PROPERTY RIGHTS
How to protect curators and submitters against misuse?
Need to define clarity of data use policy with respect to diagnostic vs. research?
LINKS WITH INDUSTRY AND PRIVATE LABS
Conditions of access and commercialisation

5. CORE DESCRIPTION (HVP recommendations already published)
Database name
Patient/family ID (anonymous/encrypted)
URL resource
Sex
Contact information (e-mail)
Ethnicity/geographic location
Date resource established
Gene/variant/protein
Conditions of use (free or type of license)
Clinical Phenotype
Curation policy and curator’s identity
Case-control (number of affected/unaffected
Standards used (gene/symbol/chr. location/
carriers and controls
link to RefSeq, ontologies, vocabularies)
Frequency of the variant in the population(s)
Data formats
Co-segregation with disease
Data accessibility/output options
Allelic status (homozygous, heterozygous, hemizygous)
Data release policy and frequency
Co-occurring variants
Data submission policy
Detection technique and year of testing
Documentation available
Testing coverage (which genes/exons were tested)
Relevant publications
Nomenclature
Tools available
Disclaimer

6. CORE DESCRIPTION :
additional HVP recommendations to be formulated ?
Scope: purposes of the DB and data types captured
QMS (quality management system?)
Country-specific framework approval obtained
Nature and source of financing or funding
GOVERNANCE and MANAGEMENT
Oversight roles and responsibilities
Charter to regulate relationship with third parties?
Medical/legal responsibilities?
Dispute resolution?
Sustainability and funding
STANDARDS COMPLIANCE and DATA EXCHANGE
Interaction between Country Nodes and gene/disease-
specific databases (LSDBs)