High-throughput sequencing (HTS) of three pear trees (Pyrus communis) resulted in the identification of two isolates of a Tepovirus species and one isolate of a Robigovirus species, both genera from the family Betaflexiviridae and never reported in pears. Their complete genomes were fully characterized, revealing genomes of about 6.8 kb (Tepovirus) and 8.4 kb (Robigovirus). According to the species demarcation criteria in the family Betaflexiviridae, the tepovirus isolates reported here are divergent isolates of Prunus Virus T (PrVT). The robigovirus isolate had enough difference in pairwise comparison with its closer related species, cherry virus Turkey (CVTR) and it should be considered a new species of this genus, tentatively named as pomes virus Greece (PVGR). A survey was conducted using specific primers designed for each of the viruses and one additional pear accession tested positive to PrVT. Furthermore, both viruses were successfully graft-transmissible to Malus domestica or Malus micromalus, suggesting their potential to be transmitted to Malus species. This study expands the list of viruses infecting pome fruit trees and augments our knowledge on the molecular diversity and host range evolution of betaflexiviruses.

In the present study we report the identification of a novel partitivirus recovered from Miscanthus sinensis, for which the provisional name "silvergrass cryptic virus 1" (SgCV-1) is proposed. High-throughput sequencing (HTS) and rapid amplification of cDNA ends (RACE) allowed the assembly of the complete sequence of each double-stranded RNA genome segment of this novel virus. The largest dsRNA segment, dsRNA1 (1699 bp), was predicted to encode a viral RNA-dependent RNA polymerase protein (RdRp) with 478 aa, and dsRNA2 (1490 bp) and dsRNA3 (1508 bp) were predicted to encode putative capsid proteins (CPs) with 347 and 348 aa, respectively. SgCV-1 has the highest amino acid sequence identity (≤ 70.80% in RdPp and ≤ 34.5% in CPs) to members of the genus Deltapartitivirus, family Partitiviridae, especially to unclassified viruses related to members of this genus. Its genome segment and protein lengths are also within the range of those of deltapartitiviruses. Moreover, phylogenetic analysis based on RdRp amino acid sequences also showed clustering of this novel virus with the related unclassified deltapartitiviruses. An RT-PCR survey of 94 imported M. sinensis samples held in quarantine identified seven additional samples carrying SgCV-1. This new virus fulfils all ICTV criteria to be considered a new member of the genus Deltapartitivirus.

Eriophyid mites are commonly found on the leaf surface of different plant species. In the present study, a novel virus associated with an eriophyid mite species was detected using high-throughput sequencing (HTS) of total RNA from fruit tree leaves, primarily growing under greenhouse conditions. The complete genome sequence was characterized using rapid amplification of cDNA ends followed by Sanger sequencing, revealing a genome of 8885 nucleotides in length. The single positive-stranded RNA genome was predicted to encode typical conserved domains of members of the genus Iflavirus in the family Iflaviridae. Phylogenetic analysis showed this virus to be closely related to the unclassified iflavirus tomato matilda associated virus (TMaV), with a maximum amino acid sequence identity of 59% in the RNA-dependent RNA polymerase domain. This low identity value justifies the recognition of the novel virus as a potential novel iflavirus. In addition to a lack of graft-transmissibility evidence, RT-PCR and HTS detection of this virus in the putative host plants were not consistent through different years and growing seasons, raising the possibility that rather than a plant virus, this was a virus infecting an organism associated with fruit tree leaves. Identification of Tetra pinnatifidae HTS-derived contigs in all fruit tree samples carrying the novel virus suggested this mite as the most likely host of the new virus (p-value < 1e-11), which is tentatively named “eriophyid mite-associated virus” (EMaV). This study highlights the importance of a careful biological study before assigning a new virus to a particular plant host when using metagenomics data.

Introduction: Usher syndrome (USH) is the most common cause of hereditary deaf-blindness. Three clinical subtypes have been classified. USH type I is the most severe subtype characterized by congenital severe-to-profound hearing loss, retinitis pigmentosa and vestibular dysfunction. Methods: One family was analyzed and the analysis included the combination of a custom capture/next-generation sequencing panel of 180 known deafness gene, Sanger sequencing and bioinformatics approaches. Results: Compound heterozygous mutations in the MYO7A gene: a known missense mutation c.494C > T (p.Thr165Met) and a novel missense mutation c.6113G > A (p.Gly2038Glu) were identified in a proband. This Chinese hearing-impaired child was misdiagnosed as non-syndromic hearing loss which was later changed to the diagnosis of USH type I after comprehensive audiometric, vestibular and ophthalmological examinations at 9 years old. Conclusions: Due to the features of genetic heterogeneity and variation in clinical manifestation, molecular diagnosis and ophthalmological examinations by skilled ophthalmologists with knowledge of USH should be suggested as a routine assessment which may improve the accuracy and reliability of etiological diagnosis for hearing loss.

Objectives: The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. Despite this heterogeneity, DNA variants found within SLC26A4 have been reported to be the second most common contributor after those of GJB2 in many populations. Methods: Whole exome sequencing and/or Sanger sequencing of SLC26A4 in 117 individuals with sensorineural hearing loss with or without inner ear anomalies but not with goiter from Turkey, Iran, and Mexico were performed. Results: We identified 27 unique SLC26A4 variants in 31 probands. The variants c.1673A > G (p.N558S), c.1708-1G > A, c.1952C > T (p.P651L), and c.2090-1G > A have not been previously reported. The p.N558S variant was detected in two unrelated Mexican families. Conclusion: A range of SLC26A4 variants without a common recurrent mutation underlies SLC26A4-related hearing loss in Turkey, Iran, and Mexico. (C) 2017 Elsevier B.V. All rights reserved.

Introduction: Branchio-oto-renal (BOR) syndrome is an autosomal dominant genetic disorder characterized by second branchial arch anomalies, hearing impairment, and renal malformations. Pathogenic mutations have been discovered in several genes such as EYA1, SIX5, and SIXI. However, nearly half of those affected reveal no pathogenic variant by traditional genetic testing.Methods and materials: Whole Exome sequencing and/or Sanger sequencing performed in 10 unrelated families from Turkey, Iran, Ecuador, and USA with BOR syndrome in this study.Results: We identified causative DNA variants in six families including novel c.525delT, c.979T > C, and c.1768deIG and a previously reported c.1779A > T variants in EYA1. Two large heterozygous deletions involving EYA1 were detected in additional two families. Whole exome sequencing did not reveal a causative variant in the remaining four families.Conclusions: A variety of DNA changes including large deletions underlie BOR syndrome in different populations, which can be detected with comprehensive genetic testing. (C) 2017 Elsevier B.V. All rights reserved.

Key Clinical MessageOur report clarifies the role of ATP6V1B2 in patients with deafness and onycho‐osteodystrophy and confirms that a recurring ATP6V1B2 c.1516C>T [p.(Arg506*)], variant causes dominant deafness–onychodystrophy (DDOD) syndrome.

Patients with unclear patterns of developmental and cognitive delay may go years without a definitive diagnosis despite extensive testing due to overlapping phenotypes of many genetic disorders. In this study, we identified causative variants in DYRK1A, KARS, or KAT6A in four individuals with global developmental delay and various findings including microcephaly and sensorineural hearing loss using whole exome sequencing. We present the cognitive, neurologic, and physical findings of four individuals to expand the clinical knowledge of possible features of the phenotypes of three rare genetic disorders. Through this process, we provide support for the use of whole exome sequencing in the setting of severe, intellectual disability or in those in whom a genetic disorder is suspected despite initial negative testing.

CLINICAL DESCRIPTION:KBG syndrome is characterized by macrodontia of upper central incisors, distinctive craniofacial features such as triangular face, prominent nasal bridge, thin upper lip and synophrys; skeletal findings including short stature, delayed bone age, and costovertebral anomalies; and developmental delay/intellectual disability sometimes associated with seizures and EEG abnormalities. The condition was named KBG syndrome after the initials of the last names of three original families reported in 1975.EPIDEMIOLOGY:The prevalence of KBG syndrome is not established. There are over 100 patients reported in the literature. It is likely that KBG syndrome is underreported due to incomplete recognition and very mild presentations of the disorder in some individuals. KBG syndrome is typically milder in females.ETIOLOGY:Causative variants in ANKRD11 have been identified in affected individuals. The vast majority of identified variants are loss of function, which include nonsense and frameshift variants and larger deletions at 16q24.3. Haploinsufficiency appears to be the mechanism of pathogenicity.GENETIC COUNSELING:Familial and de novo cases have been reported. Causative de novo variants occur approximately one third of the time. Transmission follows an autosomal dominant pattern. The syndrome displays inter- and intra-familial variability.

Significance The inner ear is a vertebrate organ of delicate and complex architecture that translates sound into electrical signals deciphered by the brain. This study utilizes a genetic approach to associate a mutation of ROR1 (receptor tyrosine kinase-like orphan receptor 1) with inner ear anomalies and deafness in humans. Characterization of Ror1 mutant mice reveals fasciculation deficiencies of spiral ganglion axons and disruption of sensory hair cell synapses and peripheral innervations. The molecular basis of this phenotype involves alterations of the NF-κB pathway. Thus, we present ROR1 as a previously unrecognized gene that is essential for the development of the inner ear and hearing in humans and mice.

Despite the risk of permanent ototoxic effects, aminoglycosides remain commonly utilized antibiotics worldwide due to low cost and efficiency in treating severe infections. Over the last two decades, mitochondrial mutations have been shown to enhance the likelihood of ototoxic injury. In particular the 1555A>G mutation in the mitochondrial gene MTRNR1 has been strongly associated with the onset of aminoglycoside-induced deafness; though pinning down the exact mechanism of action has thus far been elusive. Clinically aminoglycoside-induced deafness has been characterized by variation in the degree of hearing loss, which has prompted an investigation into genetic modifiers. To date, several putative mutations have been categorized as contributing factors to the onset of deafness with no single variation being sufficient to bring about hearing loss. Meanwhile current methods to mitigate the risk of ototoxic injury are in various stages of development. Efforts to alter the molecular structure of aminoglycosides have shown a potential path to reducing ototoxicity while preserving antibacterial properties, but these drugs are not clinically available. On the other hand, application of preemptive audiometry provides the most readily available method to both monitor and reduce the extent of aminoglycoside-induced deafness.

The genetics of both syndromic (SHL) and non-syndromic hearing loss (NSHL) is characterized by a high degree of genetic heterogeneity. We analyzed whole exome sequencing data of 102 unrelated probands with apparently NSHL without a causative variant in known NSHL genes. We detected five causative variants in different SHL genes ( SOX10, MITF , PTPN11 , CHD7 , and KMT2D ) in five (4.9%) probands. Clinical re-evaluation of these probands shows that some of them have subtle syndromic findings, while none of them meets clinical criteria for the diagnosis of the associated syndrome (Waardenburg ( SOX10 and MITF ), Kallmann ( CHD7 and SOX10 ), Noonan/LEOPARD ( PTPN11 ), CHARGE ( CHD7 ), or Kabuki ( KMT2D ). This study demonstrates that individuals who are evaluated for NSHL can have pathogenic variants in SHL genes that are not usually considered for etiologic studies.

Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil. Haplotype analysis of this variant was consistent with a single founder. No other cases with this variant were detected among 105 simplex cases from other cities of northeastern Brazil, suggesting that this variant is confined to a geographical region. This study suggests that it is feasible to develop population-specific screening for deafness variants once causative variants are identified in different geographical groups.

Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.

Extreme genetic heterogeneity along with remarkable variation in the distribution of causative variants across in different ethnicities makes single gene testing inefficient for hearing loss. We developed a custom capture/next-generation sequencing gene panel of 146 known deafness genes with a total target size of approximately 1 MB. The genes were identified by searching databases including Hereditary Hearing Loss Homepage, the Human Genome Mutation Database (HGMD), Online Mendelian Inheritance in Man (OMIM) and most recent peer-reviewed publications related to the genetics of deafness. The design covered all coding exons, UTRs and 25 bases of intronic flanking sequences for each exon. To validate our panel, we used 6 positive controls with variants in known deafness genes and 8 unsolved samples from individuals with hearing loss. Mean coverage of the targeted exons was 697X. On average, each sample had 99.8%, 96.2% and 92.7% of the targeted region coverage of 1X, 50X and 100X reads, respectively. Analysis detected all known variants in nuclear genes. These results prove the accuracy and reliability of the custom capture experiment.

We report a child with hypoinsulinemic hypoglycemia and distinctive facies, with a diagnosis of the previously described MORFAN (Mental retardation, pre- and post-natal Overgrowth, Remarkable Face, and Acanthosis Nigricans) syndrome of unknown etiology. Whole-exome sequencing revealed a de novo AKT2 mutation. Although AKT2 has been implicated in four patients with hypoinsulinemic hypoglycemia, our report expands phenotypic spectrum to include MORFAN syndrome characteristics.

Mutations in ANKRD11 have recently been reported to cause KBG syndrome, an autosomal dominant condition characterized by intellectual disability (ID), behavioral problems, and macrodontia. To understand the pathogenic mechanism that relates ANKRD11 mutations with the phenotype of KBG syndrome, we studied the cellular characteristics of wild-type ANKRD11 and the effects of mutations in humans and mice. We show that the abundance of wild-type ANKRD11 is tightly regulated during the cell cycle, and that the ANKRD11 C-terminus is required for the degradation of the protein. Analysis of 11 pathogenic ANKRD11 variants in humans, including six reported in this study, and one reported in the Ankrd11 Yod/+ mouse, shows that all mutations affect the C-terminal regions and that the mutant proteins accumulate aberrantly. In silico analysis shows the presence of D-box sequences that are signals for proteasome degradation. We suggest that ANKRD11 C-terminus plays an important role in regulating the abundance of the protein, and a disturbance of the protein abundance due to the mutations leads to KBG syndrome.

Purpose: Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES).Methods: After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes.Results: We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared-haplotypes, suggesting founder effects.Conclusion: We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining-families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.

Background: 3MC1 syndrome is a rare autosomal recessive disorder characterized by intellectual disability, short stature and distinct craniofacial, umbilical, and sacral anomalies. Five mutations in MASP1, encoding lectin complement pathway enzymes MASP-1 and MASP-3, have thus far been reported to cause 3MC1 syndrome. Only one previously reported mutation affects both MASP-1 and MASP-3, while the other mutations affect only MASP-3.Methods: We evaluated six unrelated individuals with 3MC1 syndrome and performed Sanger sequencing for all coding exons of MASP1. We also measured complement lectin and alternative pathway activities in an affected individual's serum.Results: We found two novel splice site mutations, c.1012-2A > G in one and c.891 + 1G > T in two probands, and three novel missense mutations, c.1451G > A (p.G484E), c.1657G > A (p.D553N), and c.1987G > T (p.D663Y). Missense mutations affect only MASP-3, while splice site mutations affect both MASP-1 and MASP-3. In a proband who is homozygous for c.891 + 1G > T, we detected a total lack of lectin complement pathway activity and a 2.5-fold lower alternative pathway activity. The phenotype observed in patients whose both MASP-1 and MASP-3 are affected and in those whose only MASP-3 is affected does not appear to be different. We observed structural brain abnormalities, neonatal tooth, a vascular anomaly and a solid lesion in liver as novel phenotypic features of 3MC1 syndrome.Conclusion: Novel mutations and additional phenotypic features expand the genotypic and phenotypic spectrum of 3MC1 syndrome. Although patients with MASP-1 dysfunction in addition to disrupted MASP-3 have an altered complement system, their disease phenotype is not different from those having only MASP-3 dysfunction.

Hearing loss (HL) is a major public health issue. It is clinically and genetically heterogeneous.The identification of the causal mutation is important for early diagnosis, clinical follow-up, and genetic counseling. HL due to mutations in COL11A2 , encoding collagen type XI alpha-2, can be non-syndromic autosomal-dominant or autosomal-recessive, and also syndromic as in Otospondylomegaepiphyseal Dysplasia, Stickler syndrome type III, and Weissenbacher–Zweymuller syndrome. However, thus far only one mutation co-segregating with autosomal recessive non-syndromic hearing loss (ARNSHL) in a single family has been reported. In this study, whole exome sequencing of two consanguineous families with ARNSHL from Tunisia and Turkey revealed two novel causative COL11A2 mutations, c.109G > T (p.Ala37Ser) and c.2662C > A (p.Pro888Thr). The variants identified co-segregated with deafness in both families. All homozygous individuals in those families had early onset profound hearing loss across all frequencies without syndromic findings. The variants are predicted to be damaging the protein function. The p.Pro888Thr mutation affects a -Gly-X–Y- triplet repeat motif. The novel p.Ala37Ser is the first missense mutation located in the NC4 domain of the COL11A2 protein. Structural model suggests that this mutation will likely obliterate, or at least partially compromise, the ability of NC4 domain to interact with its cognate ligands. In conclusion, we confirm that COL11A2 mutations cause ARNSHL and broaden the mutation spectrum that may shed new light on genotype–phenotype correlation for the associated phenotypes and clinical follow-up.