Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease

PURPOSE:To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD).DESIGN:Case series.PARTICIPANTS:A total of 562 patients diagnosed with IRD.METHODS:We performed a direct comparative analysis of current molecular diagnostics with WGS. We retrospectively reviewed the findings from a diagnostic NGS DNA test for 562 patients with IRD. A subset of 46 of 562 patients (encompassing potential clinical outcomes of diagnostic analysis) also underwent WGS, and we compared mutation detection rates and molecular diagnostic yields. In addition, we compared the sensitivity and specificity of the 2 techniques to identify known single nucleotide variants (SNVs) using 6 control samples with publically available genotype data.MAIN OUTCOME MEASURES:Diagnostic yield of genomic testing.RESULTS:Across known disease-causing genes, targeted NGS and WGS achieved similar levels of sensitivity and specificity for SNV detection. However, WGS also identified 14 clinically relevant genetic variants through WGS that had not been identified by NGS diagnostic testing for the 46 individuals with IRD. These variants included large deletions and variants in noncoding regions of the genome. Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing. Weighted estimates, accounting for population structure, suggest that WGS methods could result in an overall 29% (95% confidence interval, 15-45) uplift in diagnostic yield.CONCLUSIONS:We show that WGS methods can detect disease-causing genetic variants missed by current NGS diagnostic methodologies for IRD and thereby demonstrate the clinical utility and additional value of WGS.Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved

Eight Genome Sequences of Cluster BE1 Phages That Infect Streptomyces Species

This article reports eight newly isolated Streptomyces bacteriophages recovered using either direct plating or enrichment on three Streptomyces hosts

Tales of diversity: Genomic and morphological characteristics of forty-six <i>Arthrobacter</i> phages

<div><p>The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single <i>Arthrobacter</i> sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45–68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these <i>Arthrobacter</i> phages are primarily lytic, and only the singleton Galaxy is likely temperate.</p></div

Genome organization of <i>Arthrobacter</i> phage Laroye, Cluster AL.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180517#pone.0180517.g005" target="_blank">Fig 5</a> for details.</p

Genome organization of <i>Arthrobacter</i> phage Gordon, Cluster AU.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180517#pone.0180517.g005" target="_blank">Fig 5</a> for details.</p

Genome organization of <i>Arthrobacter</i> phage Amigo, Cluster AQ.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180517#pone.0180517.g005" target="_blank">Fig 5</a> for details.</p

Genome organization of <i>Arthrobacter</i> phage Jawnski, Cluster AO.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180517#pone.0180517.g005" target="_blank">Fig 5</a> for details.</p

Nucleotide sequence comparison of <i>Arthrobacter</i> phages.

<p>Dot Plot of <i>Arthrobacter</i> phage genomes displayed using Gepard [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180517#pone.0180517.ref035" target="_blank">35</a>]. Individual genome sequences were concatenated into a single file arranged such that related genomes were adjacent to each other. The assignment of clusters is shown along both the left and bottom.</p

Splitstree representation of <i>Arthrobacter</i> phages and average nucleotide comparisons of Cluster AO <i>Arthrobacter</i> phages.

<p>All <i>Arthrobacter</i> phage predicted proteins were assorted into 1052 phams according to shared amino acid sequence similarities. Each genome was then assigned a value reflecting the presence or absence of a pham member, and the genomes were compared and displayed using Splitstree [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180517#pone.0180517.ref036" target="_blank">36</a>]. Cluster and subcluster assignments derived from the dot plot and ANI analyses are annotated. The scale bar indicates 0.001 substitutions/site.</p

Genome organization of <i>Arthrobacter</i> phage Maggie, Cluster AN.

<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180517#pone.0180517.g005" target="_blank">Fig 5</a> for details.</p