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Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish

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NATURE COMMUNICATIONS 2019年第1期10卷 1-15页

作者： Siekierska, Aleksandra Stamberger, Hannah Deconinck, Tine Oprescu, Stephanie N. Partoens, Michele Zhang, Yifan Sourbron, Jo Adriaenssens, Elias Mullen, Patrick Wiencek, Patrick Hardies, Katia Lee, Jeong-Soo Giong, Hoi-Khoanh Distelmaier, Felix Elpeleg, Orly Helbig, Katherine L. Hersh, Joseph Isikay, Sedat Jordan, Elizabeth Karaca, Ender Kecskes, Angela Lupski, James R. Kovacs-Nagy, Reka May, Patrick Narayanan, Vinodh Pendziwiat, Manuela Ramsey, Keri Rangasamy, Sampathkumar Shinde, Deepali N. Spiegel, Ronen Timmerman, Vincent von Spiczak, Sarah Helbig, Ingo Balak, Chris Belnap, Newell Claasen, Ana Courtright, Amanda de Both, Matt Huentelman, Matthew J. Naymik, Marcus Richholt, Ryan Siniard, Ashley L. Szelinger, Szabolcs Craig, David W. schrauwen, isabelle Afawi, Zaid Balling, Rudi Baulac, Stephanie Barisic, Nina Caglayan, Hande S. Craiu, Dana Guerrero-Lopez, Rosa Guerrini, Renzo Hjalgrim, Helle Jahn, Johanna Klein, Karl Martin Leguern, Eric Lemke, Johannes R. Lerche, Holger Marini, Carla Moller, Rikke S. Muhle, Hiltrud Rosenow, Felix Serratosa, Jose Suls, Arvid Stephani, Ulrich Sterbova, Katalin Striano, Pasquale Zara, Federico Weckhuysen, Sarah Francklyn, Christopher Antonellis, Anthony de Witte, Peter De Jonghe, Peter Katholieke Univ Leuven Dept Pharmaceut & Pharmacol Sci Lab Mol Biodiscovery B-3000 Louvain Belgium Univ Antwerp VIB Ctr Mol Neurol Neurogenet Grp B-2610 Antwerp Belgium Univ Antwerp Inst Born Bunge B-2610 Antwerp Belgium Antwerp Univ Hosp Dept Neurol B-2650 Antwerp Belgium Univ Michigan Dept Human Genet Ann Arbor MI 48109 USA Univ Antwerp Dept Biomed Sci Peripheral Neuropathy Res Grp B-2610 Antwerp Belgium Univ Vermont Dept Biochem Burlington VT 05405 USA Korea Res Inst Biosci & Biotechnol Dis Target Struct Res Ctr Daejeon 34141 South Korea Univ Sci & Technol KRIBB Sch Daejeon 34141 South Korea Korea Inst Sci & Technol Dementia DTC R&D Convergence Program Seoul 02792 South Korea Heinrich Heine Univ Dusseldorf Univ Childrens Hosp Dept Gen Pediat Neonatol & Pediat Cardiol D-40225 Dusseldorf Germany Hadassah Hebrew Univ Med Ctr Monique & Jacques Roboh Dept Genet Res IL-01120 Jerusalem Israel Childrens Hosp Philadelphia Div Neurol Philadelphia PA 19104 USA Univ Louisville Sch Med Dept Pediat 571S Floyd St Louisville KY 40202 USA Hasan Kalyoncu Univ Sch Hlth Sci Dept Physiotherapy & Rehabil TR-27410 Gaziantep Turkey Ohio State Univ Dept Internal Med Div Human Genet 460 W 12th Ave Columbus OH 43210 USA Baylor Coll Med Dept Mol & Human Genet Houston TX 77030 USA Baylor Coll Med Human Genome Sequencing Ctr Houston TX 77030 USA Baylor Coll Med Dept Pediat Houston TX 77030 USA Texas Childrens Hosp Houston TX 77030 USA Tech Univ Munich Inst Human Genet D-81675 Munich Germany Univ Luxembourg Luxembourg Ctr Syst Biomed Esch Alzette 4365 Luxembourg Luxembourg Translat Genom Res Inst Ctr Rare Childhood Disorders Phoenix AZ 85004 USA Christian Albrechts Univ Kiel Dept Neuropediat Campus Kiel D-24105 Kiel Germany Univ Hosp Schleswig Holstein Campus Kiel D-24105 Kiel Germany Ambry Genet Div Clin Genom Aliso Viejo CA 92656 USA Emek Med Ctr Pediat Dept B IL-1834111 Afula Israel Technion Rappaport Sch Med IL-3200003 Haifa Israel Northern G

Aminoacyl tRNA synthetases (ARSs) link specific amino acids with their cognate transfer RNAs in a critical early step of protein translation. Mutations in ARSs have emerged as a cause of recessive, often complex neurological disease traits. Here we report an allelic series consisting of seven novel and two previously reported biallelic variants in valyl-tRNA synthetase (VARS) in ten patients with a developmental encephalopathy with microcephaly, often associated with early-onset epilepsy. In silico, in vitro, and yeast complementation assays demonstrate that the underlying pathomechanism of these mutations is most likely a loss of protein function. Zebrafish modeling accurately recapitulated some of the key neurological disease traits. These results provide both genetic and biological insights into neurodevelopmental disease and pave the way for further in-depth research on ARS related recessive disorders and precision therapies.

关键词： Disease genetics Encephalopathy Epilepsy Neurodevelopmental disorders

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Advances in Molecular Genetics and the Molecular Biology of Deafness

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BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 5629093-5629093页

作者： Nishio, Shin-ya schrauwen, isabelle Moteki, Hideaki Azaiez, Hela Shinshu Univ Sch Med Matsumoto Nagano 3908621 Japan Translat Genom Res Inst Phoenix AZ 85004 USA Univ Iowa Dept Otolaryngol Iowa City IA 52246 USA

Shin-ya Nishio 1 and isabelle schrauwen 2 and Hideaki Moteki 1 and Hela Azaiez 3 1, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan 2, Translational Genomics Research Institute, Phoenix, AZ 85004, USA 3, Department of Otolaryngology, University of Iowa, Iowa City, IA 52246, USA Received 9 June 2016; Accepted 13 June 2016; 20 July 2016 This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In addition to NGS, recent progress in genome editing, embryonic stem cells, and induced pluripotent stem cells has opened a new gate to a fast and thorough characterization and understanding of the precise functions and mechanisms involved in the biology of hearing and deafness.

关键词： GENETICS of deafness COCHLEAR implants DEAFNESS GENETICS MOLECULAR biology

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A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear

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HEARING RESEARCH 2016年 333卷 266-274页

作者： schrauwen, isabelle Hasin-Brumshtein, Yehudit Corneveaux, Jason J. Ohmen, Jeffrey White, Cory Allen, April N. Lusis, Aldons J. Van Camp, Guy Huentelman, Matthew J. Friedman, Rick A. Univ Antwerp Dept Med Genet B-2610 Antwerp Belgium Translat Genom Res Inst Neurogen Div 445 N 5th St Phoenix AZ 85004 USA Translat Genom Res Inst Dorrance Ctr Rare Childhood Disorders 445 N 5th St Phoenix AZ 85004 USA Univ Calif Los Angeles David Geffen Sch Med Dept Med Div Cardiol Los Angeles CA 90095 USA House Ear Res Inst Los Angeles CA 90057 USA Univ So Calif Keck Sch Med Los Angeles CA 90033 USA

The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://***/home/research/research-divisions/neurogen

关键词： Hearing Balance Cochlea Vestibule RNA-Seq Transcriptome

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Exploring genome-wide DNA methylation patterns in Aicardi syndrome

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Epigenomics 2017年第11期9卷 1373-1386页

作者： Ignazio S Piras Gabrielle Mills Lorida Llaci Marcus Naymik Keri Ramsey Newell Belnap Chris D Balak Wayne M Jepsen Szabolcs Szelinger Ashley L Siniard Candace R Lewis Madison LaFleur Ryan F Richholt Matt D De Both Kristiina Avela Sampathkumar Rangasamy David W Craig Vinodh Narayanan Irma Järvelä Matthew J Huentelman isabelle schrauwen 1 Center for Rare Childhood Disorders Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA2 Neurogenomics Division Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA 1 Center for Rare Childhood Disorders Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA2 Neurogenomics Division Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA3 Department of Pathology & Laboratory Medicine David Geffen School of Medicine University of California 10833 Le Conte Ave Los Angeles CA90095 USA 4 Department of Clinical Genetics Helsinki University Hospital Meilahdentie 2 FI-00029 Helsinki Finland 1 Center for Rare Childhood Disorders Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA2 Neurogenomics Division Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA5 University of Southern California Keck School of Medicine Department of Translational Genomics Los Angeles NRT 1450 Biggy Street CA90033 USA 6 Department of Medical Genetics University of Helsinki Haartmaninkatu 8 00251 Helsinki Finland 1 Center for Rare Childhood Disorders Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA2 Neurogenomics Division Translational Genomics Research Institute 445 N 5th Street Phoenix AZ USA7 Center for Statistical Genetics Department of Molecular & Human Genetics Baylor College of Medicine One Baylor Plaza Houston TX77030 USA

Aim:To explore differential DNA methylation (DNAm) in Aicardi syndrome (AIC), a severe neurodevelopmental disorder with largely unknown *** & methods:We characterized DNAm in AIC female patients and parents using the Illumina 450 K array. Differential DNAm was assessed using the local outlier factor algorithm, and results were validated via qPCR in a larger set of AIC female patients, parents and unrelated young female controls. Functional epigenetic modules analysis was used to detect pathways integrating both genome-wide DNAm and RNA-seq *** & conclusion:We detected differential methylation patterns in AIC patients in several neurodevelopmental and/or neuroimmunological networks. These networks may be part of the underlying pathogenic mechanisms involved in the disease.

关键词： Aicardi syndrome DNA methylation KCNAB3

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A Syndromic Intellectual Disability Disorder Caused by Variants in TELO2, a Gene Encoding a Component of the TTT Complex

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AMERICAN JOURNAL OF HUMAN GENETICS 2016年第5期98卷 909-918页

作者： You, Jing Sobreira, Nara L. Gable, Dustin L. Jurgens, Julie Grange, Dorothy K. Belnap, Newell Siniard, Ashley Szelinger, Szabolcs schrauwen, isabelle Richholt, Ryan F. Vallee, Stephanie E. Dinulos, Mary Beth P. Valle, David Armanios, Mary Hoover-Fong, Julie Johns Hopkins Univ Sch Med Predoctoral Training Program Human Genet Baltimore MD 21205 USA Johns Hopkins Univ Sch Med McKusick Nathans Inst Genet Med Baltimore MD 21205 USA Johns Hopkins Univ Sch Med Dept Pediat Baltimore MD 21205 USA Washington Univ Sch Med Dept Pediat St Louis MO 63110 USA Johns Hopkins Univ Sch Med Med Scientist Training Program Baltimore MD 21205 USA Johns Hopkins Univ Sch Med Dept Oncol Baltimore MD 21205 USA Ctr Rare Childhood Disorders Translat Genom Res Inst TGen Phoenix AZ 85004 USA Translat Genom Res Inst TGen Neurogen Div Phoenix AZ 85004 USA Dartmouth Hitchcock Med Ctr 1 Med Ctr Dr Lebanon NH 03756 USA Geisel Sch Med Dartmouth Pediat & Pathol Dept 1 Med Ctr Dr Lebanon NH 03756 USA Johns Hopkins Univ Sch Med McKusick Nathans Inst Genet Med Greenberg Ctr Skeletal Dysplasias Baltimore MD 21287 USA

The proteins encoded by TELO2, TTI1, and TTI2 interact to form the TTT complex, a co-chaperone for maturation of the phosphatidylinositol 3-kinase-related protein kinases (PIKKs). Here we report six affected individuals from four families with intellectual disability (ID) and neurological and other congenital abnormalities associated with compound heterozygous variants in TELO2. Although their fibroblasts showed reduced steady-state levels of TELO2 and the other components of the TTT complex, PIKK functions were normal in cellular assays. Our results suggest that these TELO2 missense variants result in loss of function, perturb TTT complex stability, and cause an autosomal-recessive syndromic form of ID.

关键词： variants IDAHO OPERATIONS OFFICE vif Genes Fibroblast Congenital Abnormalities Intellectual Disability

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DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System

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HUMAN MUTATION 2016年第8期37卷 812-819页

作者： Sommen, Manou schrauwen, isabelle Vandeweyer, Geert Boeckx, Nele Corneveaux, Jason J. van den Ende, Jenneke Boudewyns, An De Leenheer, Els Janssens, Sandra Claes, Kathleen Verstreken, Margriet Strenzke, Nicola Predoehl, Friederike Wuyts, Wim Mortier, Geert Bitner-Glindzicz, Maria Moser, Tobias Coucke, Paul Huentelman, Matthew J. Van Camp, Guy Univ Antwerp Dept Med Genet Univ Pl 1 B-2610 Antwerp Belgium Translat Genom Res Inst Neurogen Div Phoenix AZ USA Univ Antwerp Hosp Antwerp Belgium Univ Antwerp Hosp Dept Otorhinolaryngol Head & Neck Surg Antwerp Belgium Univ Ghent Ctr Med Genet Ghent Belgium St Augustinus Hosp Univ Dept Otolaryngol Antwerp Belgium Univ Med Ctr Gottingen Dept Otolaryngol Inner Ear Lab Gottingen Germany UCL Inst Child Hlth Clin & Mol Genet Unit London England Great Ormond St Hosp NHS Trust London England Univ Med Ctr Gottingen Inst Auditory Neurosci Gottingen Germany Univ Med Ctr Gottingen InnerEarLab Gottingen Germany

Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.

关键词： targeted resequencing mutation classification system hereditary hearing loss

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Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment

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EUROPEAN JOURNAL OF HUMAN GENETICS 2015年第1期23卷 110-115页

作者： Fransen, Erik Bonneux, Sarah Corneveaux, Jason J. schrauwen, isabelle Di Berardino, Federica White, Cory H. Ohmen, Jeffrey D. Van de Heyning, Paul Ambrosetti, Umberto Huentelman, Matthew J. Van Camp, Guy Friedman, Rick A. Univ Antwerp Ctr Med Genet B-2610 Antwerp Belgium Univ Antwerp StatUa Ctr Stat B-2610 Antwerp Belgium Translat Genom Res Inst Neurogen Div Phoenix AZ USA Univ Milan Dept Clin Sci & Community Hlth Audiol Unit Milan Italy Fdn IRCCS Ca Granda Osped Maggiore Policlin Milan Italy House Res Inst Cell Biol & Genet Div Los Angeles CA USA Univ Antwerp Hosp Dept Otolaryngol Edegem Belgium

We performed a genome-wide association study (GWAS) to identify the genes responsible for age-related hearing impairment (ARHI), the most common form of hearing impairment in the elderly. Analysis of common variants, with and without adjustment for stratification and environmental covariates, rare variants and interactions, as well as gene-set enrichment analysis, showed no variants with genome-wide significance. No evidence for replication of any previously reported genes was found. A study of the genetic architecture indicates for the first time that ARHI is highly polygenic in nature, with probably no major genes involved. The phenotype depends on the aggregated effect of a large number of SNPs, of which the individual effects are undetectable in a modestly powered GWAS. We estimated that 22% of the variance in our data set can be explained by the collective effect of all genotyped SNPs. A score analysis showed a modest enrichment in causative SNPs among the SNPs with a P-value below 0.01.

关键词： GENOMES HEARING disorders DISEASES in older people HEARING impaired GENOMICS GENETICS

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Genome-wide analysis reveals a novel autosomal-recessive hearing loss locus DFNB80 on chromosome 2p16.1-p21

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JOURNAL OF HUMAN GENETICS 2013年第2期58卷 98-101页

作者： Mosrati, Mohamed Ali schrauwen, isabelle Ben Saiid, Mariem Aifa-Hmani, Mounira Fransen, Erik Mneja, Malek Ghorbel, Abdelmonem Van Camp, Guy Masmoudi, Saber Sfax Univ Ctr Biotechnol Sfax Microorganisms & Biomol Lab Sfax 3018 Tunisia Univ Antwerp Dept Med Genet B-2020 Antwerp Belgium CHU Habib Bourguiba Dept Otolaryngol Head & Neck Surg Sfax Tunisia

Hearing impairment (HI) is the decreased ability to hear and discriminate among sounds. It is one of the most common birth defects. Epidemiological data show that more than one child in 1000 is born with HI, whereas more than 50% of prelingual HI cases are found to be hereditary. So far, 95 published autosomal-recessive nonsyndromic HI (ARNSHI) loci have been mapped, and 41 ARNSHI genes have been identified. In this study, we performed a genome-wide linkage study in a consanguineous Tunisian family, and report the mapping of a novel ARNSHI locus DFNB80 to chromosome 2p16.1-p21 between the two single-nucleotide polymorphisms rs10191091 and rs2193485 with a maximum multipoint logarithm of odds score of 4.1. The screening of seven candidate genes, failed to reveal any disease-causing mutations. Journal of Human Genetics (2013) 58, 98-101;doi:10.1038/jhg.2012.141;published online 13 December 2012

关键词： hearing impairment autosomal recessive locus candidate gene

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A sensitive and specific diagnostic test for hearing loss using a microdroplet PCR-based approach and next generation sequencing

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AMERICAN JOURNAL OF MEDICAL GENETICS PART A 2013年第1期161A卷 145-152页

作者： schrauwen, isabelle Sommen, Manou Corneveaux, Jason J. Reiman, Rebecca A. Hackett, Nicole J. Claes, Charlotte Claes, Kathleen Bitner-Glindzicz, Maria Coucke, Paul Van Camp, Guy Huentelman, Matthew J. Univ Antwerp Dept Med Genet B-2020 Antwerp Belgium Translat Genom Res Inst Neurogen Div Phoenix AZ USA Univ Ghent Ctr Med Genet B-9000 Ghent Belgium UCL Inst Child Hlth Clin & Mol Genet Unit London England Great Ormond St Hosp Sick Children London WC1N 3JH England

Implementing DNA diagnostics in clinical practice for extremely heterogeneous diseases such as hearing loss is challenging, especially when attempting to reach high sensitivity and specificity in a cost-effective fashion. Next generation sequencing has enabled the development of such a test, but the most commonly used genomic target enrichment methods such as hybridization-based capture suffer from restrictions. In this study, we have adopted a new flexible approach using microdroplet PCR-based technology for target enrichment, in combination with massive parallel sequencing to develop a DNA diagnostic test for autosomal recessive hereditary hearing loss. This approach enabled us to identify the genetic basis of hearing loss in 9 of 24 patients, a success rate of 37.5%. Our method also proved to have high sensitivity and specificity. Currently, routine molecular genetic diagnostic testing for deafness is in most cases only performed for the GJB2 gene and a positive result is typically only obtained in 1020% of deaf children. Individuals with mutations in GJB2 had already been excluded in our selected set of 24 patients. Therefore, we anticipate that our deafness test may lead to a genetic diagnosis in roughly 50% of unscreened autosomal recessive deafness cases. We propose that this diagnostic testing approach represents a significant improvement in clinical practice as a standard diagnostic tool for children with hearing loss. (c) 2012 Wiley Periodicals, Inc.

关键词： hearing loss deafness microdroplet PCR diagnostics

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Genome wide analysis in a family with sensorineural hearing loss, autism and mental retardation

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GENE 2012年第2期510卷 102-106页

作者： Mosrati, Mohamed Ali schrauwen, isabelle Kamoun, Hassen Charfeddine, Ilhem Fransen, Erik Ghorbel, Abdelmonem Van Camp, Guy Masmoudi, Saber Sfax Univ Ctr Biotechnol Sfax Microorganisms & Biomol Lab Sfax 3018 Tunisia Univ Antwerp Dept Med Genet B-2610 Antwerp Belgium Sfax Univ Human Mol Genet Lab Fac Med Sfax Sfax 3018 Tunisia Habib Bourguiba Sfax Dept CHU Sfax Tunisia

Hearing loss is a common congenital anomaly with an incidence of 1 in 1000 live births. It has been described together with several other clinical features as fortuitous association or commune genetic syndrome. In this study, we investigated a consanguineous Tunisian family with moderate to profound congenital hearing loss, mental retardation and autistic behaviors. We performed a genome wide microarray analysis study using approximately 300,000 SNPs in a common set of 7 invidious of this family. We identified regions of suggestive linkage with hearing loss on chromosomes 6p12 and 7q34. In addition, we identified a deletion on chromosome 8p in the two autistic individuals. This report presents an illustration of how consanguinity could increase familial clustering of multiple hereditary diseases within the same family. The application of next generation sequencing for this family seems to be a good strategy for further analysis leading to the identification of candidate genes. (C) 2012 Elsevier B.V. All rights reserved.

关键词： Hearing loss Mental retardation Autism Linkage Candidate gene

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