Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing.

Forward genetic screens in zebrafish have identified >9000 mutants, many of which are potential disease models. Most mutants remain molecularly uncharacterized because of the high cost, time and labor investment required for positional cloning. These costs limit the benefit of previous genetic screens and discourage future screens. Drastic improvements in DNA sequencing technology could dramatically improve the efficiency of positional cloning in zebrafish and other model organisms, but the best strategy for cloning by sequencing has yet to be established. Using four zebrafish inner ear mutants, we developed and compared two approaches for 'cloning by sequencing': one based on bulk segregant linkage (BSFseq) and one based on homozygosity mapping (HMFseq). Using BSFseq we discovered that mutations in lmx1b and jagged1b cause abnormal ear morphogenesis. With HMFseq we validated that the disruption of cdh23 abolishes the ear's sensory functions and identified a candidate lesion in lhfpl5a predicted to cause nonsyndromic deafness. The success of HMFseq shows that the high intrastrain polymorphism rate in zebrafish eliminates the need for time-consuming map crosses. Additionally, we analyzed diversity in zebrafish laboratory strains to find areas of elevated diversity and areas of fixed homozygosity, reinforcing recent findings that genome diversity is clustered. We present a database of >15 million sequence variants that provides much of this approach's power. In our four test cases, only a single candidate single nucleotide polymorphism (SNP) remained after subtracting all database SNPs from a mutant's critical region. The saturation of the common SNP database and our open source analysis pipeline MegaMapper will improve the pace at which the zebrafish community makes unique discoveries relevant to human health.

Joint spatial-angular sparse coding for dMRI with separable dictionaries.

Diffusion MRI (dMRI) provides the ability to reconstruct neuronal fibers in the brain, in vivo, by measuring water diffusion along angular gradient directions in q-space. High angular resolution diffusion imaging (HARDI) can produce better estimates of fiber orientation than the popularly used diffusion tensor imaging, but the high number of samples needed to estimate diffusivity requires longer patient scan times. To accelerate dMRI, compressed sensing (CS) has been utilized by exploiting a sparse dictionary representation of the data, discovered through sparse coding. The sparser the representation, the fewer samples are needed to reconstruct a high resolution signal with limited information loss, and so an important area of research has focused on finding the sparsest possible representation of dMRI. Current reconstruction methods however, rely on an angular representation per voxel with added spatial regularization, and so, for non-zero signals, one is required to have at least one non-zero coefficient per voxel. This means that the global level of sparsity must be greater than the number of voxels. In contrast, we propose a joint spatial-angular representation of dMRI that will allow us to achieve levels of global sparsity that are below the number of voxels. A major challenge, however, is the computational complexity of solving a global sparse coding problem over large-scale dMRI. In this work, we present novel adaptations of popular sparse coding algorithms that become better suited for solving large-scale problems by exploiting spatial-angular separability. Our experiments show that our method achieves significantly sparser representations of HARDI than is possible by the state of the art.

Rotation invariant features for HARDI.

Reducing the amount of information stored in diffusion MRI (dMRI) data to a set of meaningful and representative scalar values is a goal of much interest in medical imaging. Such features can have far reaching applications in segmentation, registration, and statistical characterization of regions of interest in the brain, as in comparing features between control and diseased patients. Currently, however, the number of biologically relevant features in dMRI is very limited. Moreover, existing features discard much of the information inherent in dMRI and embody several theoretical shortcomings. This paper proposes a new family of rotation invariant scalar features for dMRI based on the spherical harmonic (SH) representation of high angular resolution diffusion images (HARDI). These features describe the shape of the orientation distribution function extracted from HARDI data and are applicable to any reconstruction method that represents HARDI signals in terms of an SH basis. We further illustrate their significance in white matter characterization of synthetic, phantom and real HARDI brain datasets.

Estimation of non-negative ODFs using the eigenvalue distribution of spherical functions.

Current methods in high angular resolution diffusion imaging (HARDI) estimate the probability density function of water diffusion as a continuous-valued orientation distribution function (ODF) on the sphere. However, such methods could produce an ODF with negative values, because they enforce non-negativity only at finitely many directions. In this paper, we propose to enforce non-negativity on the continuous domain by enforcing the positive semi-definiteness of Toeplitz-like matrices constructed from the spherical harmonic representation of the ODF. We study the distribution of the eigenvalues of these matrices and use it to derive an iterative semi-definite program that enforces non-negativity on the continuous domain. We illustrate the performance of our method and compare it to the state-of-the-art with experiments on synthetic and real data.