Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast

Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a segregating population are combined, genomic variants can be used to orient the direction of causality between gene expression traits. Instrumental variable methods use a local expression quantitative trait locus (eQTL) as a randomized instrument for a gene’s expression level, and assign target genes based on distal eQTL associations. Mediation-based methods additionally require that distal eQTL associations are mediated by the source gene. A detailed comparison between these methods has not yet been conducted, due to the lack of a standardized implementation of different methods, the limited sample size of most multi-omics datasets, and the absence of ground-truth networks for most organisms. Here we used Findr, a software package providing uniform implementations of instrumental variable, mediation, and coexpression-based methods, a recent dataset of 1,012 segregants from a cross between two budding yeast strains, and the YEASTRACT database of known transcriptional interactions to compare causal gene network inference methods. We found that causal inference methods result in a significant overlap with the ground-truth, whereas coexpression did not perform better than random. A subsampling analysis revealed that the performance of mediation saturates at large sample sizes, due to a loss of sensitivity when residual correlations become significant. Instrumental variable methods on the other hand contain false positive predictions, due to genomic linkage between eQTL instruments. Instrumental variable and mediation-based methods also have complementary roles for identifying causal genes underlying transcriptional hotspots. Instrumental variable methods correctly predicted STB5 targets for a hotspot centred on the transcription factor STB5, whereas mediation failed due to Stb5p auto-regulating its own expression. Mediation suggests a new candidate gene, DNM1, for a hotspot on Chr XII, whereas instrumental variable methods could not distinguish between multiple genes located within the hotspot. In conclusion, causal inference from genomics and transcriptomics data is a powerful approach for reconstructing causal gene networks, which could be further improved by the development of methods to control for residual correlations in mediation analyses and genomic linkage and pleiotropic effects from transcriptional hotspots in instrumental variable analyses.

Mitochondrial DNA SNPs associated with Schizophrenia exhibit Highly Variable Inter-allelic Haplogroup Affiliation and Nuclear Genogeographic Affinity: Bi-Genomic Linkage Disequilibrium raises Major Concerns for Link to Disease

Mitochondria play a significant role in human diseases. However, disease associations with mitochondrial DNA (mtDNA) SNPs have proven difficult to replicate. A reanalysis of eight schizophrenia-associated mtDNA SNPs, in 23,743 normal Danes and 2,538 schizophrenia patients, revealed marked inter-allelic differences in haplogroup affiliation and nuclear ancestry, genogeophraphic affinity (GGA). This bi-genomic linkage disequilibrium (2GLD) could entail population stratification. Only two mitochondrial SNPs, m. 15043A and m. 15218G, were significantly associated with schizophrenia. However, these associations disappeared when corrected for haplogroup affiliation. The extensive 2GLD documented is a major concern when interpreting historic as well as designing future mtDNA association studies.

Phenotyping ripe rot resistance in the Actinidia chinensis (kiwifruit) mapping population

Resistance to ripe rot (Cryptosporiopsis actinidiae) in kiwifruit is likely to be controlled by quantitative trait loci (QTL) Accurate phenotyping of ripe rot resistance is crucial to locating QTL on the kiwifruit genomic linkage map and may facilitate identification of candidate genes for breeding A detached fruit assay was developed to compare resistance to ripe rot in the mapping population Fruit at or near eating ripeness were inoculated by inserting mycelial plugs (3 mm diameter) under shallow skin flaps and then lesion development was monitored at 20C Results suggested that resistance was quantitative Assay variability was reduced by pipetting spore inoculum into uniform wounds (5 mm) in the fruit surface Preliminary analysis using single marker ttests showed that marker Ke316 which may be involved in acyl lipid metabolism/transfer was associated with ripe rot susceptibility The association weakened as more genotypes were tested and more analyses are necessary to determine whether Ke316 detects an actual QTL and/or if further QTLs are detectable