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Exome sequencing, hearing loss

John Patton, Carmen Brewer, Wade Chien, Jennifer J Johnston, Andrew J Griffith, Leslie G Biesecker
Variants in the unconventional myosin gene, MYO1A, have been reported to cause non-syndromic sensorineural hearing loss with a pattern of autosomal dominant inheritance. Others have challenged this association. We used a genotypic ascertainment study design to test the association of MYO1A variants with hearing loss. We evaluated MYO1A variants from a cohort of 951 individuals with exome sequencing who were not ascertained for hearing loss. Five individuals had one of two variants claimed to be associated with sensorineural hearing loss in a prior study and 33 individuals had one of 13 predicted deleterious variants...
October 19, 2016: European Journal of Human Genetics: EJHG
Flavia Palombo, Nadia Al-Wardy, Guido Alberto Gnecchi Ruscone, Manuela Oppo, Mohammed Nasser Al Kindi, Andrea Angius, Khalsa Al Lamki, Giorgia Girotto, Tania Giangregorio, Matteo Benelli, Alberto Magi, Marco Seri, Paolo Gasparini, Francesco Cucca, Marco Sazzini, Mazin Al Khabori, Tommaso Pippucci, Giovanni Romeo
The increased risk for autosomal recessive disorders is one of the most well-known medical implications of consanguinity. In the Sultanate of Oman, a country characterized by one of the highest rates of consanguineous marriages worldwide, prevalence of genetic hearing loss (GHL) is estimated to be 6/10 000. Families of GHL patients have higher consanguinity rates than the general Omani population, indicating a major role for recessive forms. Mutations in GJB2, the most commonly mutated GHL gene, have been sporadically described...
October 13, 2016: Journal of Human Genetics
Karen Low, Tazeen Ashraf, Natalie Canham, Jill Clayton-Smith, Charu Deshpande, Alan Donaldson, Richard Fisher, Frances Flinter, Nicola Foulds, Alan Fryer, Kate Gibson, Ian Hayes, Alison Hills, Susan Holder, Melita Irving, Shelagh Joss, Emma Kivuva, Kathryn Lachlan, Alex Magee, Vivienne McConnell, Meriel McEntagart, Kay Metcalfe, Tara Montgomery, Ruth Newbury-Ecob, Fiona Stewart, Peter Turnpenny, Julie Vogt, David Fitzpatrick, Maggie Williams, Sarah Smithson
KBG syndrome is characterized by short stature, distinctive facial features, and developmental/cognitive delay and is caused by mutations in ANKRD11, one of the ankyrin repeat-containing cofactors. We describe 32 KBG patients aged 2-47 years from 27 families ascertained via two pathways: targeted ANKRD11 sequencing (TS) in a group who had a clinical diagnosis of KBG and whole exome sequencing (ES) in a second group in whom the diagnosis was unknown. Speech delay and learning difficulties were almost universal and variable behavioral problems frequent...
November 2016: American Journal of Medical Genetics. Part A
Hikaru Kanemasa, Ryoko Fukai, Yasunari Sakai, Michiko Torio, Noriko Miyake, Sooyoung Lee, Hiroaki Ono, Satoshi Akamine, Kei Nishiyama, Masafumi Sanefuji, Yoshito Ishizaki, Hiroyuki Torisu, Hirotomo Saitsu, Naomichi Matsumoto, Toshiro Hara
BACKGROUND: Alternating hemiplegia of childhood (AHC) is a rare neurological disorder that manifests recurrent attacks of hemiplegia, oculogyric, and choreoathetotic involuntary movements. De novo mutations in ATP1A3 cause three types of neurological diseases: AHC; rapid-onset dystonia-Parkinsonism (RDP); and cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss (CAPOS) syndromes. It remains to be determined whether or not a rare mutation in ATP1A3 may cause atypical phenotypes...
2016: BMC Neurology
Rabia Faridi, Atteeq U Rehman, Robert J Morell, Penelope L Friedman, Leigh Demain, Sana Zahra, Asma Ali Khan, Dalia Tohlob, Muhammad Zaman Assir, Glenda Beaman, Shaheen N Khan, William G Newman, Sheikh Riazuddin, Thomas B Friedman
Perrault syndrome (PS) is a genetically heterogeneous disorder characterized by primary ovarian insufficiency (POI) in females and sensorineural hearing loss in males and females. In many PS subjects, causative variants have not been found in the five reported PS genes. The objective of this study was to identify the genetic cause of PS in an extended consanguineous family with six deaf individuals. Whole exome sequencing (WES) was completed on four affected members of a large family, and variants and co-segregation was confirmed by Sanger sequencing...
September 15, 2016: Clinical Genetics
Qing Fu, Mingchu Xu, Xue Chen, Xunlun Sheng, Zhisheng Yuan, Yani Liu, Huajin Li, Zixi Sun, Huiping Li, Lizhu Yang, Keqing Wang, Fangxia Zhang, Yumei Li, Chen Zhao, Ruifang Sui, Rui Chen
BACKGROUND: Usher syndrome is a genetically heterogeneous disorder featured by combined visual impairment and hearing loss. Despite a dozen of genes involved in Usher syndrome having been identified, the genetic basis remains unknown in 20-30% of patients. In this study, we aimed to identify the novel disease-causing gene of a distinct subtype of Usher syndrome. METHODS: Ophthalmic examinations and hearing tests were performed on patients with Usher syndrome in two consanguineous families...
September 14, 2016: Journal of Medical Genetics
Karin Weiss, Paulien A Terhal, Lior Cohen, Michael Bruccoleri, Melita Irving, Ariel F Martinez, Jill A Rosenfeld, Keren Machol, Yaping Yang, Pengfei Liu, Magdalena Walkiewicz, Joke Beuten, Natalia Gomez-Ospina, Katrina Haude, Chin-To Fong, Gregory M Enns, Jonathan A Bernstein, Judith Fan, Garrett Gotway, Mohammad Ghorbani, Koen van Gassen, Glen R Monroe, Gijs van Haaften, Lina Basel-Vanagaite, Xiang-Jiao Yang, Philippe M Campeau, Maximilian Muenke
Chromodomain helicase DNA-binding protein 4 (CHD4) is an ATP-dependent chromatin remodeler involved in epigenetic regulation of gene transcription, DNA repair, and cell cycle progression. Also known as Mi2β, CHD4 is an integral subunit of a well-characterized histone deacetylase complex. Here we report five individuals with de novo missense substitutions in CHD4 identified through whole-exome sequencing and web-based gene matching. These individuals have overlapping phenotypes including developmental delay, intellectual disability, hearing loss, macrocephaly, distinct facial dysmorphisms, palatal abnormalities, ventriculomegaly, and hypogonadism as well as additional findings such as bone fusions...
October 6, 2016: American Journal of Human Genetics
Prasanthi Namburi, Rinki Ratnapriya, Samer Khateb, Csilla H Lazar, Yael Kinarty, Alexey Obolensky, Inbar Erdinest, Devorah Marks-Ohana, Eran Pras, Tamar Ben-Yosef, Hadas Newman, Menachem Gross, Anand Swaroop, Eyal Banin, Dror Sharon
Inherited retinal diseases (IRDs) are a diverse group of genetically and clinically heterogeneous retinal abnormalities. The present study was designed to identify genetic defects in individuals with an uncommon combination of autosomal recessive progressive cone-rod degeneration accompanied by sensorineural hearing loss (arCRD-SNHL). Homozygosity mapping followed by whole-exome sequencing (WES) and founder mutation screening revealed two truncating rare variants (c.893-1G>A and c.534delT) in CEP78, which encodes centrosomal protein 78, in six individuals of Jewish ancestry with CRD and SNHL...
September 1, 2016: American Journal of Human Genetics
S Naz, A Imtiaz, G Mujtaba, A Maqsood, R Bashir, I Bukhari, M R Khan, M Ramzan, A Fatima, A U Rehman, M Iqbal, T Chaudhry, M Lund, C C Brewer, R J Morell, T B Friedman
The genetic underpinnings of recessively inherited moderate to severe sensorineural hearing loss are not well understood, despite its higher prevalence in comparison to profound deafness. We recruited 92 consanguineous families segregating stable or progressive, recessively inherited moderate or severe hearing loss. We utilized homozygosity mapping, Sanger sequencing, targeted capture of known deafness genes with massively parallel sequencing and whole exome sequencing to identify the molecular basis of hearing loss in these families...
October 6, 2016: Clinical Genetics
G Bademci, F B Cengiz, J Foster Ii, D Duman, L Sennaroglu, O Diaz-Horta, T Atik, T Kirazli, L Olgun, H Alper, I Menendez, I Loclar, G Sennaroglu, S Tokgoz-Yilmaz, S Guo, Y Olgun, N Mahdieh, M Bonyadi, N Bozan, A Ayral, F Ozkinay, M Yildirim-Baylan, S H Blanton, M Tekin
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)...
2016: Scientific Reports
Sarah B Pierce, Suleyman Gulsuner, Gail A Stapleton, Tom Walsh, Ming K Lee, Jessica B Mandell, Augusto Morales, Rachel E Klevit, Mary-Claire King, R Curtis Rogers
Mutations in nuclear genes required for the replication and maintenance of mitochondrial DNA cause progressive multisystemic neuromuscular disorders with overlapping phenotypes. Biallelic mutations in C10orf2, encoding the Twinkle mitochondrial DNA helicase, lead to infantile-onset cerebellar ataxia (IOSCA), as well as milder and more severe phenotypes. We present a 13-year-old girl with ataxia, severe hearing loss, optic atrophy, peripheral neuropathy, and hypergonadotropic hypogonadism. Whole-exome sequencing revealed that the patient is compound heterozygous for previously unreported variants in the C10orf2 gene: a paternally inherited frameshift variant (c...
July 2016: Cold Spring Harbor Molecular Case Studies
Xin Zhang Cai, Ying Li, Lu Xia, Yu Peng, Chu Feng He, Lu Jiang, Yong Feng, Kun Xia, Xue Zhong Liu, Ling Yun Mei, Zheng Mao Hu
Hearing impairment, or deafness (in its most severe form), is one of the most common human sensory disorders. There have been several reports of autosomal dominant mutations in the POU4F3 gene, which is associated with non-syndromic hearing loss. In this study, we identified a novel heterozygous mutation (c.602delT, p.L201fs) in the gene POU4F3 by taking advantage of whole-exome sequencing, which was validated by Sanger sequencing and completely co-segregated within a large hearing impaired Chinese family. We have focused on this pedigree since 2002, and we have mapped a deafness locus named DFNA42 (which has been renamed DFNA52, OMIM entry 607683) via a genome-wide scan...
August 18, 2016: Journal of Human Genetics
Taraka R Donti, Ruchi Masand, Daryl A Scott, William J Craigen, Brett H Graham
Deficiency of the TCA cycle enzyme Succinyl-CoA Synthetase/Ligase (SCS), due to pathogenic variants in subunits encoded by SUCLG1 and SUCLA2, causes mitochondrial encephalomyopathy, methylmalonic acidemia, and mitochondrial DNA (mtDNA) depletion. In this study, we report an 11year old patient who presented with truncal ataxia, chorea, hypotonia, bilateral sensorineural hearing loss and preserved cognition. Whole exome sequencing identified a heterozygous known pathogenic variant and a heterozygous novel missense variant of uncertain clinical significance (VUS) in SUCLG1...
September 2016: Molecular Genetics and Metabolism
Konstanze Hörtnagel, Inge Krägeloh-Mann, Antje Bornemann, Miriam Döcker, Saskia Biskup, Heidi Mayrhofer, Florian Battke, Gabriele du Bois, Klaus Harzer
Vesicular protein sorting-associated proteins (VPS, including VPS11) are indispensable in the endocytic network, in particular the endosome-lysosome biogenesis. Exome sequencing revealed the homozygous variant p.Leu387_ Gly395del in the VPS11 gene in two siblings. On immunoblotting, the mutant VPS11 protein showed a distinctly reduced immunostaining intensity. The children presented with primary and severe developmental delay associated with myoclonic seizures, spastic tetraplegia, trunk and neck hypotonia, blindness, hearing loss, and microcephaly...
November 2016: Journal of Inherited Metabolic Disease
Sarah Hull, Aeesha N J Malik, Gavin Arno, Donna S Mackay, Vincent Plagnol, Michel Michaelides, Sahar Mansour, Assunta Albanese, Katrina Tatton Brown, Graham E Holder, Andrew R Webster, Paul T Heath, Anthony T Moore
IMPORTANCE: A multiorgan syndromic disorder characterized by sideroblastic anemia, immunodeficiency, periodic fever, and developmental delay with an uncharacterized retinal dystrophy is caused by TRNT1. This report of a family with a homozygous mutation in TRNT1 expands the ocular phenotype to include cataract and inner retinal dysfunction and details a mild systemic phenotype. OBSERVATIONS: A consanguineous family with 3 affected children was investigated. Key clinical features comprised hypogammaglobulinemia, short stature with microcephaly, cataract, and inner retinal dysfunction without sideroblastic anemia or developmental delay...
September 1, 2016: JAMA Ophthalmology
Neil J Ingham, Francesca Carlisle, Selina Pearson, Morag A Lewis, Annalisa Buniello, Jing Chen, Rivka L Isaacson, Johanna Pass, Jacqueline K White, Sally J Dawson, Karen P Steel
Progressive hearing loss is very common in the population but we still know little about the underlying pathology. A new spontaneous mouse mutation (stonedeaf, stdf ) leading to recessive, early-onset progressive hearing loss was detected and exome sequencing revealed a Thr289Arg substitution in Sphingosine-1-Phosphate Receptor-2 (S1pr2). Mutants aged 2 weeks had normal hearing sensitivity, but at 4 weeks most showed variable degrees of hearing impairment, which became severe or profound in all mutants by 14 weeks...
2016: Scientific Reports
Christina L Runge, Amit Indap, Yifan Zhou, Jack W Kent, Ericka King, Christy B Erbe, Regina Cole, Jack Littrell, Kate Merath, Roland James, Franz Rüschendorf, Joseph E Kerschner, Gabor Marth, Norbert Hübner, Harald H H Göring, David R Friedland, Wai-Meng Kwok, Michael Olivier
IMPORTANCE: Sensorineural hearing loss (SNHL) is commonly caused by conditions that affect cochlear structures or the auditory nerve, and the genes identified as causing SNHL to date only explain a fraction of the overall genetic risk for this debilitating disorder. It is likely that other genes and mutations also cause SNHL. OBJECTIVE: To identify a candidate gene that causes bilateral, symmetric, progressive SNHL in a large multigeneration family of Northern European descent...
September 1, 2016: JAMA Otolaryngology—Head & Neck Surgery
Hirofumi Kurata, Hiroshi Terashima, Mitsuko Nakashima, Tetsuya Okazaki, Wataru Matsumura, Koyo Ohno, Yoshiaki Saito, Yoshihiro Maegaki, Masaya Kubota, Eiji Nanba, Hirotomo Saitsu, Naomichi Matsumoto, Mitsuhiro Kato
Mutations in SPATA5 have recently been shown to result in a phenotype of microcephaly, intellectual disability, seizures, and hearing loss in childhood. Our aim in this report is to delineate the SPATA5 syndrome as a clinical entity, including the facial appearance, neurophysiological, and neuroimaging findings. Using whole exome sequencing and Sanger sequencing, we identified three children with SPATA5 mutations from two families. Two siblings carried compound heterozygous mutations, c.989_991del (p.Thr330del) and c...
June 1, 2016: Clinical Genetics
Eyal Reinstein, Shay Tzur, Concetta Bormans, Doron M Behar
Whole-exome sequencing for clinical applications is now an integral part of medical genetics practice. Though most studies are performed in order to establish diagnoses in individuals with rare and clinically unrecognizable disorders, due to the constantly decreasing costs and commercial availability, whole-exome sequencing has gradually become the initial tool to study patients with clinically recognized disorders when more than one gene is responsible for the phenotype or in complex phenotypes, when variants in more than one gene can be the cause for the disease...
2016: Genetics Research
Markus Vogel, Eunike Velleuer, Leon F Schmidt-Jiménez, Ertan Mayatepek, Arndt Borkhardt, Malik Alawi, Kerstin Kutsche, Fanny Kortüm
Hereditary congenital facial paresis (HCFP) belongs to the congenital cranial dysinnervation disorders. HCFP is characterized by the isolated dysfunction of the seventh cranial nerve and can be associated with hearing loss, strabismus, and orofacial anomalies. Möbius syndrome shares facial palsy with HCFP, but is additionally characterized by limited abduction of the eye(s). Genetic heterogeneity has been documented for HCFP as one locus mapped to chromosome 3q21-q22 (HCFP1) and a second to 10q21.3-q22.1 (HCFP2)...
July 2016: American Journal of Medical Genetics. Part A
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