Volume 12 Issue 10, October 2011

Advances in sequencing technologies, assembly algorithms and computing power are making it feasible to assemble the entire transcriptome from short RNA reads. The article reviews the transcriptome assembly strategies, their advantages and limitations and how to apply them effectively.

This Review presents the growing evidence that mutations that do not cause a change in amino acid sequence — synonymous mutations — contribute to human disease. Such mutations may act at different stages of gene expression, including mRNA processing, translation initiation and elongation or protein folding.

There is a growing appreciation of the role of orphan genes — which lack homologues in other lineages — in creating evolutionary innovations. Orphan genes arise continuously in most genomes, mostlyde novo, and assume functions that are relevant for lineage-specific adaptations.

The authors review the experimental and computational approaches for determining haplotype phase, focusing on statistical methods, the factors that influence the strategy used and the value of using information on identity-by-descent.

Recent transcriptomics studies have revealed extensive mRNA diversity generated by alternative splicing. An emerging theme is the existence of regulatory networks through which splicing promotes dynamic remodelling of the transcriptome to promote physiological changes, involving robust and coordinated alternative splicing transitions.

Meta-analyses that use data from several genome-wide association studies are revealing more disease-associated genetic variants, but how can the privacy of study participants be protected when data are shared? This article considers ways to evaluate the risk of loss of privacy.