New genomic resources and databases

4 August 2009

Recently researchers from The Children’s Hospital in Philadelphia have created a database of copy number variations detected in disease-free individuals in order to aid the diagnosis and identification of genetic diseases [Shaikh TH et al. (2009) Genome Res Epub]. Changes to DNA structure as a result of differences in the number of copies of a particular gene or segment of DNA, are referred to as copy number variations (CNVs). These variations can be found across the human genome and have been implicated in a number of genetic disorders and it has also been suggested that they may influence susceptibility and resistance to disease (see previous news). However, a large number of CNVs are also found in healthy individuals and differentiating between those CNVs which represent normal variation and those which contribute to disease can be a problem.

The database and high-resolution CNV map was generated following analysis of DNA from 2026 healthy children and their parents. The study catalogued 54,462 CNVs using a uniform array and computational platform. 77.8% of the CNVs were classified as non-unique as they detected in more than one un-related individual and 22.2% were detected in just one individual. Researchers can search the database produced by Shaikh et al which is available via the hospital’s website and compare specific CNVs to those collected in public repositories. The strengths of the database lie in the large number of individuals that were used in the study as well as the uniform analysis techniques that were used. In addition, DNA from both Caucasians and African-Americans were analysed, allowing for CNVs that differ between these ethnic groups to be identified.

Other resources aimed at harnessing the potential of genomics for clinical research and health include ClinSeq and the Human Connectome Project. ClinSeq is a pilot project aimed at investigating the use of large scale medical sequencing in a clinical research setting. The pilot project aims to recruit 1000 participants in the initial phase and use Sanger-based sequencing to target regions of the genome [Biesecker et al (2009) Genome Res Epub]. Initially, they plan to sequence 300-400 genes relevant to atherosclerosis and analyse the data for high-penetrance variants associated with specific clinical traits. Along with assessing the use of large-scale sequencing, the project will also provide insight into the implementation of genomic technology, informed consent, disclosure of genetic information, and archiving, analysing, and displaying sequence data. The Human Connectome Project aims to map the circuitry of the brain using brain imaging technology as well as DNA, behavioural and demographic information (see press release). It is hoped that this initiative will gather data which can be used by neuroscientists to aid our understanding of mental health and disease.

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