Publications

While genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternative isoform usage. By analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to influenza infection and type 1 interferon stimulation. We identified more than a thousand quantitative trait loci (QTLs) associated with alternate isoform usage (isoQTLs), many of which are independent of expression QTLs (eQTLs) for the same gene. Compared with eQTLs, isoQTLs are enriched for splice sites and untranslated regions, but depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs explain a significant proportion of the disease heritability attributed to common genetic variants. At the locus, we shed light on the function of the gene and how two frequent, highly differentiated haplotypes with intermediate frequencies could be maintained by balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with low expression caused by nonsense-mediated decay, while the minor haplotype, known to increase Crohn's disease risk, is associated with high expression. In response to influenza infection, we found two uncharacterized isoforms expressed from the major haplotype, likely the result of multiple perfectly linked variants affecting the transcription and splicing at the locus. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in innate immune responses and, in the case of , may confer a historical fitness advantage in response to virus.

MOTIVATION

The structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many sub-populations, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states. We showed that our approximation provides unbiased migration rate and population size estimates across a wide parameter range.

RESULTS

We extend this approach by providing a new algorithm to calculate the probability of the state of internal nodes that includes the information from the full phylogenetic tree. We show that this algorithm is able to increase the probability attributed to the true sub-population of a node. Furthermore we use improved integration techniques, such that our method is now able to analyse larger datasets, including a H3N2 dataset with 433 sequences sampled from five different locations.

AVAILABILITY AND IMPLEMENTATION

The presented methods are part of the BEAST2 package MASCOT, the Marginal Approximation of the Structured COalescenT. This package can be downloaded via the BEAUti package manager. The source code is available at https://github.com/nicfel/Mascot.git.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.