24 research outputs found
Analysis of Rare, Exonic Variation amongst Subjects with Autism Spectrum Disorders and Population Controls
We report on results from whole-exome sequencing (WES) of 1,039 subjects diagnosed with autism spectrum disorders (ASD) and 870 controls selected from the NIMH repository to be of similar ancestry to cases. The WES data came from two centers using different methods to produce sequence and to call variants from it. Therefore, an initial goal was to ensure the distribution of rare variation was similar for data from different centers. This proved straightforward by filtering called variants by fraction of missing data, read depth, and balance of alternative to reference reads. Results were evaluated using seven samples sequenced at both centers and by results from the association study. Next we addressed how the data and/or results from the centers should be combined. Gene-based analyses of association was an obvious choice, but should statistics for association be combined across centers (meta-analysis) or should data be combined and then analyzed (mega-analysis)? Because of the nature of many gene-based tests, we showed by theory and simulations that mega-analysis has better power than meta-analysis. Finally, before analyzing the data for association, we explored the impact of population structure on rare variant analysis in these data. Like other recent studies, we found evidence that population structure can confound case-control studies by the clustering of rare variants in ancestry space; yet, unlike some recent studies, for these data we found that principal component-based analyses were sufficient to control for ancestry and produce test statistics with appropriate distributions. After using a variety of gene-based tests and both meta- and mega-analysis, we found no new risk genes for ASD in this sample. Our results suggest that standard gene-based tests will require much larger samples of cases and controls before being effective for gene discovery, even for a disorder like ASD. © 2013 Liu et al
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants
Abstract Functional characterization of the noncoding genome is essential for biological understanding of gene regulation and disease. Here, we introduce the computational framework PINES (Phenotype-Informed Noncoding Element Scoring), which predicts the functional impact of noncoding variants by integrating epigenetic annotations in a phenotype-dependent manner. PINES enables analyses to be customized towards genomic annotations from cell types of the highest relevance given the phenotype of interest. We illustrate that PINES identifies functional noncoding variation more accurately than methods that do not use phenotype-weighted knowledge, while at the same time being flexible and easy to use via a dedicated web portal
25 MUTATIONS IN STXBP3 CONTRIBUTE TO VERY EARLY ONSET OF IBD, IMMUNODEFICIENCY AND HEARING LOSS
PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants
Distribution of doubletons as a function of the eigen-map.
<p>The first eigen-vector versus second eigen-vector for (A) Baylor and (B) Broad samples. Eigen-vectors are obtained by applying PCA to all common variants. For each individual, we count the number of doubletons. To indicate the relative number of doubletons per individual, points are color-coded as follows: black (bottom : fewest doubletons), blue (next 25), green (next 25), and orange (top 25: most doubletons) within the Baylor and Broad samples, respectively.</p
Counts of non-synonymous variants in Baylor and Broad before filtering.
<p>Note: Single: count of singletons; Double: count of doubletons; RVs: count of variants with MAF and not singletons or doubletons; LFVs: count of variants with MAF ; CVs: count of variants with MAF .</p