Archive by category | Genetics & Genomics

Method of the Year 2016

As is our tradition every year we have chosen a method, or in this case a set of methods, that have experienced rapid growth in the last years. This year’s choice of epitranscriptome analysis does not comprise a single technique but is based on advances in detecting, enriching and profiling base modifications on all RNA species.  Read more

Understanding and documenting variation in human genomes

To understand disease one needs to understand the genetic variations that underlie it. Many tools exist that predict the deleteriousness of variants in the human genome; PolyPhen2, SIFT or CADD (combined annotation dependent depletion), to name only a few examples.  On page 109 of our March issue Yuval Itan et al. present the mutation significance cutoff (MSC) to replace a global threshold for calling variants deleterious, often used for CADD scores, with a gene-level threshold. For MSC, as for any other variant prediction tool, it was important to validate the quality of the predictions with variants known to be deleterious. Established mutation databases are often used as ground truth to test the quality of prediction tools.  MSC, for example, was validated against variants found in two large databases, HGMD and ClinVar.  Read more

Testing times for metagenomics

An Article in the June issue of Nature Methods uses simulated data sets to evaluate programs used for metagenomics data analysis. The author of a News & Views argues that although the results indicate existing programs do work, new algorithms are needed as well as model metagenomics systems for use as test beds.  Read more