The anatomical distribution of genetic associations

Alan B Wells, Nathan Kopp, Xiaoxiao Xu, David R O’Brien, Wei Yang, Arye Nehorai, Tracy L. Adair-Kirk, Raphael Kopan, Joseph D Dougherty
doi: http://dx.doi.org/10.1101/021824

Deeper understanding of the anatomical intermediaries for disease and other complex genetic traits is essential to understanding mechanisms and developing new interventions. Existing ontology tools provide functional annotations for many genes in the genome and they are widely used to develop mechanistic hypotheses based on genetic and transcriptomic data. Yet, information about where a set of genes is expressed may be equally useful in interpreting results and forming novel mechanistic hypotheses for a trait. Therefore, we developed a framework for statistically testing the relationship between gene expression across the body and sets of candidate genes from across the genome. We validated this tool and tested its utility on three applications. First, using thousands of loci identified by GWA studies, our framework identifies the number of disease-associated genes that have enriched expression in the disease-affected tissue. Second, we experimentally confirmed an underappreciated prediction highlighted by our tool: variation in skin expressed genes are a major quantitative genetic modulator of white blood cell count – a trait considered to be a feature of the immune system. Finally, using gene lists derived from sequencing data, we show that human genes under constrained selective pressure are disproportionately expressed in nervous system tissues.

Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment

Rob Patro, Geet Duggal, Carl Kingsford
doi: http://dx.doi.org/10.1101/021592

Transcript quantification is a central task in the analysis of RNA-seq data. Accurate computational methods for the quantification of transcript abundances are essential for downstream analysis. However, most existing approaches are much slower than is necessary for their degree of accuracy. We introduce Salmon, a novel method and software tool for transcript quantification that exhibits state-of-the-art accuracy while being significantly faster than most other tools. Salmon achieves this through the combined application of a two-phase inference procedure, a reduced data representation, and a novel lightweight read alignment algorithm. Salmon is written in C++11, and is available under the GPL v3 license as open-source software at https://combine-lab.github.io/salmon.

TransRate: reference free quality assessment of de-novo transcriptome assemblies

Richard D Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly
doi: http://dx.doi.org/10.1101/021626

TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only sequenced reads as the input, TransRate measures the quality of individual contigs and whole assemblies, enabling assembly optimization and comparison. TransRate can accurately evaluate assemblies of conserved and novel RNA molecules of any kind in any species. We show that it is more accurate than comparable methods and demonstrate its use on a variety of data.

SSCM: A method to analyze and predict the pathogenicity of sequence variants

Sharad Vikram, Matthew D Rasmussen, Eric A Evans, Imran S Haque
doi: http://dx.doi.org/10.1101/021527

The advent of cost-effective DNA sequencing has provided clinics with high-resolution information about patients’ genetic variants, which has resulted in the need for efficient interpretation of this genomic data. Traditionally, variant interpretation has been dominated by many manual, time-consuming processes due to the disparate forms of relevant information in clinical databases and literature. Computational techniques promise to automate much of this, and while they currently play only a supporting role, their continued improvement for variant interpretation is necessary to tackle the problem of scaling genetic sequencing to ever larger populations. Here, we present SSCM-Pathogenic, a genome-wide, allele-specific score for predicting variant pathogenicity. The score, generated by a semi-supervised clustering algorithm, shows predictive power on clinically relevant mutations, while also displaying predictive ability in noncoding regions of the genome.

CARGO: Effective format-free compressed storage of genomic information

Łukasz Roguski, Paolo Ribeca
(Submitted on 17 Jun 2015)

The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats, sometimes inheriting from them suboptimal design choices; this hinders flexible and effective data sharing. Here we present CARGO (Compressed ARchiving for GenOmics), a high-level framework to automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of our approach to FASTQ and SAM archives require a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors, and scale well to multi-TB datasets.

Dynamics of transcription factor binding site evolution

Murat Tuğrul, Tiago Paixão, Nicholas H. Barton, Gašper Tkačik
(Submitted on 16 Jun 2015)

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ~10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genetics.

Excess False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

David M Rocke, Luyao Ruan, Yilun Zhang, J. Jared Gossett, Blythe Durbin-Johnson, Sharon Aviran
doi: http://dx.doi.org/10.1101/020784

Motivation: An important property of a valid method for testing for differential expression is that the false positive rate should at least roughly correspond to the p-value cutoff, so that if 10,000 genes are tested at a p-value cutoff of 10−4, and if all the null hypotheses are true, then there should be only about 1 gene declared to be significantly differentially expressed. We tested this by resampling from existing RNA-Seq data sets and also by matched negative binomial simulations. Results: Methods we examined, which rely strongly on a negative binomial model, such as edgeR, DESeq, and DESeq2, show large numbers of false positives in both the resampled real-data case and in the simulated negative binomial case. This also occurs with a negative binomial generalized linear model function in R. Methods that use only the variance function, such as limma-voom, do not show excessive false positives, as is also the case with a variance stabilizing transformation followed by linear model analysis with limma. The excess false positives are likely caused by apparently small biases in estimation of negative binomial dispersion and, perhaps surprisingly, occur mostly when the mean and/or the dis-persion is high, rather than for low-count genes.

Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between alleles

Lindsay V Clark, Andrea Drauch Schreier
doi: http://dx.doi.org/10.1101/020610

A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite dataset from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.4.

Are Genetic Interactions Influencing Gene Expression Evidence for Biological Epistasis or Statistical Artifacts?

Alexandra Fish, John A. Capra, William S Bush
doi: http://dx.doi.org/10.1101/020479

Interactions between genetic variants, also called epistasis, are pervasive in model organisms; however, their importance in humans remains unclear because statistical interactions in observational studies can be explained by processes other than biological epistasis. Using statistical modeling, we identified 1,093 interactions between pairs of cis-regulatory variants impacting gene expression in lymphoblastoid cell lines. Factors known to confound these analyses (ceiling/floor effects, population stratification, haplotype effects, or single variants tagged through linkage disequilibrium) explained most of these interactions. However, we found 15 interactions robust to these explanations, and we further show that despite potential confounding, interacting variants were enriched in numerous regulatory regions suggesting potential biological importance. While genetic interactions may not be the true underlying mechanism of all our statistical models, our analyses discover new signals undetected in standard single-marker analyses. Ultimately, we identified new complex genetic architectures regulating 23 genes, suggesting that single-variant analyses may miss important modifiers.

The weighting is the hardest part: on the behavior of the likelihood ratio test and score test under weight misspecification in rare variant association studies

Camelia Claudia Minica, Giulio Genovese, Dorret I. Boomsma, Christina M. Hultman, René Pool, Jacqueline M. Vink, Conor V. Dolan, Benjamin M. Neale
doi: http://dx.doi.org/10.1101/020198

Rare variant association studies are gaining importance in human genetic research with the increasing availability of exome/genome sequence data. One important test of association between a target set of rare variants (RVs) and a given phenotype is the sequence kernel association test (SKAT). Assignment of weights reflecting the hypothesized contribution of the RVs to the trait variance is embedded within any set-based test. Since the true weights are generally unknown, it is important to establish the effect of weight misspecification in SKAT. We used simulated and real data to characterize the behavior of the likelihood ratio test (LRT) and score test under weight misspecification. Results revealed that LRT is generally more robust to weight misspecification, and more powerful than score test in such a circumstance. For instance, when the rare variants within the target were simulated to have larger betas than the more common ones, incorrect assignment of equal weights reduced the power of the LRT by ~5% while the power of score test dropped by ~30%. Furthermore, LRT was more robust to the inclusion of weighed neutral variation in the test. To optimize weighting we proposed the use of a data-driven weighting scheme. With this approach and the LRT we detected significant enrichment of case mutations with MAF below 5% (P-value=7E-04) of a set of highly constrained genes in the Swedish schizophrenia case-control cohort of 4,940 individuals with observed exome-sequencing data. The score test is currently widely used in sequence kernel association studies for both its computational efficiency and power. Indeed, assuming correct specification, in some circumstances the score test is the most powerful test. However, our results showed that LRT has the compelling qualities of being generally more robust and more powerful under weight misspecification. This is a paramount result, given that, arguably, misspecified models are likely to be the rule rather than the exception in the weighting-based approaches.