Genetics Archives

The 1000 Genomes Project is a consortium of researchers from more than 75 universities and companies around the world, which aims to map the variation in genomes from people across all continents. From the article in Nature:

The aim of the 1000 Genomes Project is to discover, genotype and provide accurate haplotype information on all forms of human DNA polymorphism in multiple human populations. Specifically, the goal is to characterize over 95% of variants that are in genomic regions accessible to current high-throughput sequencing technologies and that have allele frequency of 1% or higher (the classical definition of polymorphism) in each of five major population groups (populations in or with ancestry from Europe, East Asia, South Asia, West Africa and the Americas).

In a pilot study, they started with low-coverage sequencing of 179 individuals; deep sequencing of six individuals in two trios; and exon sequencing in 697 individuals. In total 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants were found. Together these account for over 95% of all variation found in all humans. On average, each individual had 250 to 300 loss-of-function variants of genes and 50 to 100 which have previously been linked to inherited disorders. In the next phase results will be explored further and a total of 2,500 individual genomes will be sequenced.
NatureNews: 1000 Genomes Project reveals human variation…
Article: A map of human genome variation from population-scale sequencing…

Amsterdam Molecular Therapeutics is developing one of the first commercial genetic therapies, Glybera, for patients with lipoprotein lipase deficiency (LPLD). Glybera has been submitted to the European Medicines Agency and a decision on the approval is expected mid-2011. However, before therapy comes diagnosis. In collaboration with AMT, Progenika Biopharma has developed the LPLchip which detects mutations in the LPL gene, and has now received CE approval. The chip can detect 120 different mutations in a sample of blood or saliva, enabling identification of patients who may benefit from gene therapy. So far, the picture for Glybera is looking good, with three studies showing a decrease in the incidence of pancreatitis, one of the most important complications of LPLD, in patients undergoing treatment. Expect to hear more about this in the future.
Press release: Progenika Receives CE Mark for First DNA Chip to Detect Mutations in Lipoprotein Lipase (LPL) Gene…

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An MIT research team with help from English and Korean scientists have identified a synthetic material that is effective in promoting the growth of pluripotent stem cells on its surface. Using this new technology, scientists should hopefully be able to overcome the challenge of farming enough stem cells for effective research and future therapeutic needs.

Previous studies had suggested that several chemical and physical properties of surfaces — including roughness, stiffness and affinity for water — might play a role in stem-cell growth. The researchers created about 500 polymers (long chains of repeating molecules) that varied in those traits, grew stem cells on them and analyzed each polymer’s performance. After correlating surface characteristics with performance, they found that there was an optimal range of surface hydrophobicity (water-repelling behavior), but varying roughness and stiffness did not have much effect on cell growth.

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Currently, when a pharmaceutical company wants to test the toxicity of drug candidate chemicals, they turn to in vivo tests on living animals. However, a new study performed by Roche Pharma and Roche Applied Science details a method for testing hepatotoxicity which could potentially reduce the cost of cytotoxicity testing and spare many animal lives in the future. This new method uses Roche’s xCELLigence system, which can determine the toxicity of a compound through biochemical assays and gene expression analysis. Unlike in vivo testing, the xCELLigence system can also provide quantitative cell analysis in real time.
From the xCELLigence product page:

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