Predicted genetic burden and frequency of phenotype-associated variants in the horse

Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.

Genetic Variation and the Distribution of Variant Types in the Horse

Genetic variation is a key contributor to health and disease. Understanding the link between an individual's genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.

Smoothness-constrained quantization for wavelet image compression

Uniform quantization of wavelet coefficients introduces perceptually disturbing artifacts by decreasing the visual smoothness. In this paper, the local Holder regularity is used to quantify these changes in visual smoothness. A modified uniform quantization scheme that constrains local regularity reduction is proposed. The quantizer modification is applicable to any uniform quantization scheme and requires no additional side information to be transmitted to the decoder, unlike standard deadzone quantizers. The reconstructed images show a noticeable perceptual improvement as well as an increased PSNR relative to uniform quantization.

Regularity-preserving image interpolation

Assumptions about image continuity lead to oversmoothed edges in common image interpolation algorithms. A wavelet-based interpolation method that imposes no continuity constraints is introduced. The algorithm estimates the regularity of edges by measuring the decay of wavelet transform coefficients across scales and preserves the underlying regularity by extrapolating a new subband to be used in image resynthesis. The algorithm produces visibly sharper edges than traditional techniques and exhibits an average peak signal-to-noise ratio (PSNR) improvement of 2.5 dB over bilinear and bicubic techniques.