A structured simple form for ordering genetic tests is needed to ensure coupling of clinical detail (phenotype) with DNA variants (genotype) to ensure utility in publication and databases

Abstract

Communicated by Garry R. CuttingResearchers and clinicians ideally need instant access to all the variation in their gene/locus of interest to efficiently conduct their research and genetic healthcare to the highest standards. Currently much key data resides in the laboratory books or patient records around the world, as there are many impediments to submitting this data. It would be ideal therefore if a semiautomated pathway was available, with a minimum of effort, to make the deidentified data publicly available for others to use. The Human Variome Project (HVP) meeting listed 96 recommendations to work toward this situation. This article is planned to initiate a strategy to enhance the collection of phenotype and genotype data from the clinician/diagnostic laboratory nexus. Thus, the aim is to develop universally applicable forms that people can use when investigating patients for each inherited disease, to assist in satisfying many of the recommendations of the HVP Meeting [Cotton et al., 2007]. We call for comment and collaboration in this article. Hum Mutat 28(10), [931][932] 2007. KEY WORDS: mutation; variome; recommendations; phenotype; genotype Communities of those caring for patients with inherited diseases have identified several important problems that impede the generation and flow of useful genotype/phenotype information to assist them in genetic research and healthcare. Most importantly, there is the problem that clinical details (phenotype) are often disconnected from the mutation found (genotype). Ideally, clinical phenotype information would be passed from the clinician to the diagnostician and back, and then in a suitably anonymized form in the public arena where it could be used by others, as it is important for diagnostic and therapeutic decisions. This proposal is particularly aimed at those who assess the patients and order the tests.

The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease

“…They can help patients understand that accurate, complete and current data improve our understanding of their disease, its course and complications, and that a database benefits themselves, their families, and others who are also affected. Providing complete and accurate clinical information with any request for a genetic test is important since this may be transferred directly to a database [31]. Physicians can also update their patients' data throughout the course of their illness and, sometimes, encourage the patients to do so themselves.…”

Guidelines for establishing locus specific databases

“…Recommendations have been made, for example, for LSDB content [Claustres et al, 2002;Horaitis and Cotton, 2005;Scriver et al, 1999Scriver et al, , 2000, ethics Povey et al, 2010], data collection [Cotton et al, 2007, somatic variations [Olivier et al, 2009], interpretation and reporting of variants [Plon et al, 2008;Richards et al, 2008], curation [Cotton et al, 2008;Celli et al, 2011] data sharing , and nomenclature, [den Dunnen and Antonarakis, 2000;Taschner and den Dunnen, 2011]. These instructions have been useful, however, some of them are already partly outdated and others are scattered throughout a number of publications.…”

Curating gene variant databases (LSDBs): Toward a universal standard

“…Recommendations have been made covering many aspects of gene variant databases, including the description of variants [den Dunnen and Antonorakis, 2000], LSDB content [Claustres et al, 2002;Mitropoulou et al, 2010], data collection [Cotton at al., 2007], data sharing [den Dunnen et al, 2009], and ethics [Povey et al, 2010]. These recommendations have been very useful and helped to accomplish basic standardization.…”

“…While literature on gene variant databases is extensive [Claustres et al, 2002;Cotton et al, 2007;den Dunnen and Antonorakis, 2000;den Dunnen et al, 2009;Mitropoulou et al, 2010;Povey et al, 2010], little is available on the process of database curation. Here, we discuss the subject of database curation, based on our extensive experience with the LSDBs hosted at the Leiden Muscular Dystrophy pages (http://www.DMD.nl), the Osteogenesis Imperfecta Variant Database (https://oi.gene.le.ac.uk), the EhlersDanlos Syndrome Variant Database (https://eds.gene.le.ac.uk), the Immuno Deficiency databases (http://bioinf.uta.fi/IDbases), and on our contributions to several database curation courses of the Human Genome Variation Society (HGVS)/Human Variome Project (HVP) and the GEN2PHEN project.…”