Ethical Guidelines for LSDB curators

Curators of databases are continually worried about being ethically correct even though there is no legal requirement to be so. To allow curators to be able to simply adhere to world standards laid down by WHO, HUGO, OECD, etc. R. Cotton, with the aid of world authorities of ethics of genetics, initiated a process to finally develop a “standard operating procedure” for curators based on world guidelines to avoid curator concerns. This process is being finalised by Dr. Sue Povey appropriately an LSDB curator and clinical geneticist.

Contact: S. Povey ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) London, U.K.

Visualising information in variant databases

Display of data in databases has ranged from simple flat file tables to maps of the gene with mutations superimposed, sometimes in an ungainly manner. Few had interactive possibilities with the maps. Tim Smith developed two varieties of software that allowed both display of variation contained in the database, one in a novel format, and access to contained data by clicking the variant (BMC Bioinformatics 9: 206). This has now been fitted to a LSDB (http://www.goldenhelix.org/a1atvar). This software needs extending where needed and also the extent of its application explored e.g. for NCBI. This work is being supplemented by a review of current interfaces and access (see below).

Contact: T. Smith ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia.

Reviews of interfaces, portals and browsers of variation data and their classification

Those needing to access mutations and any data concerning them, particularly phenotype need to do so rapidly, ideally with two clicks. Systematic documentation of procedure and times to access genotype/phenotype information is required of key databases. These include: dbSNP, OMIM, HGMD, LOVD, UMD, some non-LOVD/UMD databases, DECIHPER, IDbases (MUTbase software) CNV (Scherer), etc. Documentation will include clicks from home page to variant, clicks from variant to phenotype and or other data. The click type and numbers will be documented. This research is required to inform access developments, possibly VariVis and any modifications required (see above).

Contact: E. Webb ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia.

Review variation collection and communication and publication mechanisms

Much mutation information and its phenotype is published but beyond say 50 mutations in a gene it is difficult to do so in scientific journals due to policy. This has led to many mutations never being released from clinic records even though the 75th mutation in a gene and its effect may be vital information for prognosis of a patient on the other side of the world. The WayStation (http://www.centralmutations.org) was set up to publish such cases but has not been fully progressed due to the lack of funds this work may however be useful when integrating the global systems. Nevertheless mutation is submitted without the reward of publication directly to LSDBs and can be done at dbSNP/dbGaP so at least the data is public and available (see also microattribution above). Details of submission by various mechanisms other than publication need to be assessed. Thus details such as ease and steps of use, data required, expert reviewing, time to acceptance, etc, need to be reviewed in such databases as HGMD, dbSNP, dbGaP, LOVD, UMD, DECIPHER, IDbases, CNV, some non-LOVD/UMD databases, e.g. InSiGHT. This may be examined with a novel HNPCC mutation as a pilot submission.

Contact: R. Cotton ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia.

HVP Consortium formation

Despite 60% of all humans being affected in a lifetime and 71% of admissions of a major US Paediatric hospital being genetically based, inherited disease is invisible to Governments and funders as it is split between 2,000 (at present) – 20,000 (eventually) genes, 100-200 countries and 10 or so professions. Thus to have an impact on funders all involved individuals need to have a voice through a consortium. Such a consortium has been initiated and intends to include not only clinicians, counsellors and diagnosticians, but also support groups, patients and instrument and supply companies. We aim for 1,000 members in Australia alone, but 10 or 100 times that should be involved globally.

Contact: L. Hardman ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia.

Student/Volunteer Network

Student volunteers played a major role in the LSDB prototype PAHdb for Charles Scriver and they were rewarded in many ways such as publication, conference attendance, etc. We have initiated a listing of students willing to assist with some of the documentation tasks especially some from the Arab world after R. Cottons visits and have made contact with the University of Melbourne Medical Student Association.

Contact: R. Cotton ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia.

Evidence Based Genetic Medicine (EBGM)

Due to the rarity of genetic disease, EBGM had not been popular but it is clearly necessary for each faulty gene. It is made difficult by the dozens of excellent authoritative sources about each disease worldwide. We intend to develop a search engine to search multiple sources to assist clinicians.

Contact: T. Harrison ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia.

Cost of Genetic Healthcare

The nature of genetic healthcare, being not routine is hard to cost. However, it needs to be costed to ensure it is properly funded to give appropriate care. This project has been initiated with a MSc student.

Contact: A. Hsueh ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia; J. Halliday ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Melbourne, Australia. David Quin Melbourne, Australia

Incentives for data collection

Currently there is no incentive for diagnostic labs to submit mutations anywhere despite the fact that they rely heavily on mutations in publications and databases when they have to decide on the pathogenicity of mutations they are dealing with. There have been suggestions that not only education of the professionals involved should occur, but that QA, best practice and licensing could logically be used to enhance mutation submission. Desirée du Sart is a key member of HGSA and Australia regulatory committees and will pilot this approach through her official capacity.

Contact: D. du Sart ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).