Literature DB >> 25852444

Whole-Exome Sequencing in the Clinic: Lessons from Six Consecutive Cases from the Clinician's Perspective.

Amber Volk1, Erin Conboy2, Beverly Wical3, Marc Patterson4, Salman Kirmani5.   

Abstract

Whole-exome sequencing (WES) is being used clinically to diagnose rare Mendelian disorders, especially when standard tests have failed. The diagnostic yield from WES is reported to be ∼15-30%; however, data regarding the clinical utility and interpretative challenges from the clinician's perspective are lacking. Here, we present a series of the first 6 unselected consecutive cases seen over a period of 6 months where WES was employed in clinical labs via trio-based testing (proband and parents). While we do not discount the value of WES in the clinical setting, our cases and experience illustrate the significant clinical challenges of WES, even when a diagnosis may be achieved.

Entities:  

Keywords:  Diagnostic odyssey; Schinzel-Giedion syndrome; Whole-exome sequencing

Year:  2015        PMID: 25852444      PMCID: PMC4369115          DOI: 10.1159/000371598

Source DB:  PubMed          Journal:  Mol Syndromol        ISSN: 1661-8769


  14 in total

1.  Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability.

Authors:  Fadi F Hamdan; Julie Gauthier; Yoichi Araki; Da-Ting Lin; Yuhki Yoshizawa; Kyohei Higashi; A-Reum Park; Dan Spiegelman; Sylvia Dobrzeniecka; Amélie Piton; Hideyuki Tomitori; Hussein Daoud; Christine Massicotte; Edouard Henrion; Ousmane Diallo; Masoud Shekarabi; Claude Marineau; Michael Shevell; Bruno Maranda; Grant Mitchell; Amélie Nadeau; Guy D'Anjou; Michel Vanasse; Myriam Srour; Ronald G Lafrenière; Pierre Drapeau; Jean Claude Lacaille; Eunjoon Kim; Jae-Ran Lee; Kazuei Igarashi; Richard L Huganir; Guy A Rouleau; Jacques L Michaud
Journal:  Am J Hum Genet       Date:  2011-03-03       Impact factor: 11.025

Review 2.  Exome sequencing as a tool for Mendelian disease gene discovery.

Authors:  Michael J Bamshad; Sarah B Ng; Abigail W Bigham; Holly K Tabor; Mary J Emond; Deborah A Nickerson; Jay Shendure
Journal:  Nat Rev Genet       Date:  2011-09-27       Impact factor: 53.242

3.  An evaluation of copy number variation detection tools from whole-exome sequencing data.

Authors:  Renjie Tan; Yadong Wang; Sarah E Kleinstein; Yongzhuang Liu; Xiaolin Zhu; Hongzhe Guo; Qinghua Jiang; Andrew S Allen; Mingfu Zhu
Journal:  Hum Mutat       Date:  2014-05-01       Impact factor: 4.878

4.  Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis.

Authors:  Yaniv Erlich; Simon Edvardson; Emily Hodges; Shamir Zenvirt; Pramod Thekkat; Avraham Shaag; Talya Dor; Gregory J Hannon; Orly Elpeleg
Journal:  Genome Res       Date:  2011-04-12       Impact factor: 9.043

5.  Performance of mutation pathogenicity prediction methods on missense variants.

Authors:  Janita Thusberg; Ayodeji Olatubosun; Mauno Vihinen
Journal:  Hum Mutat       Date:  2011-02-22       Impact factor: 4.878

6.  Diagnostic exome sequencing in persons with severe intellectual disability.

Authors:  Joep de Ligt; Marjolein H Willemsen; Bregje W M van Bon; Tjitske Kleefstra; Helger G Yntema; Thessa Kroes; Anneke T Vulto-van Silfhout; David A Koolen; Petra de Vries; Christian Gilissen; Marisol del Rosario; Alexander Hoischen; Hans Scheffer; Bert B A de Vries; Han G Brunner; Joris A Veltman; Lisenka E L M Vissers
Journal:  N Engl J Med       Date:  2012-10-03       Impact factor: 91.245

7.  Application of whole exome sequencing to identify disease-causing variants in inherited human diseases.

Authors:  Gerald Goh; Murim Choi
Journal:  Genomics Inform       Date:  2012-12-31

8.  Points to consider in the clinical application of genomic sequencing.

Authors: 
Journal:  Genet Med       Date:  2012-08       Impact factor: 8.822

9.  ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Authors:  C Sue Richards; Sherri Bale; Daniel B Bellissimo; Soma Das; Wayne W Grody; Madhuri R Hegde; Elaine Lyon; Brian E Ward
Journal:  Genet Med       Date:  2008-04       Impact factor: 8.822

10.  KIF1A, an axonal transporter of synaptic vesicles, is mutated in hereditary sensory and autonomic neuropathy type 2.

Authors:  Jean-Baptiste Rivière; Siriram Ramalingam; Valérie Lavastre; Masoud Shekarabi; Sébastien Holbert; Julie Lafontaine; Myriam Srour; Nancy Merner; Daniel Rochefort; Pascale Hince; Rébecca Gaudet; Anne-Marie Mes-Masson; Jonathan Baets; Henry Houlden; Bernard Brais; Garth A Nicholson; Hilde Van Esch; Shahriar Nafissi; Peter De Jonghe; Mary M Reilly; Vincent Timmerman; Patrick A Dion; Guy A Rouleau
Journal:  Am J Hum Genet       Date:  2011-08-04       Impact factor: 11.025

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  14 in total

Review 1.  Clinical and genetic findings in a family with NMNAT1-associated Leber congenital amaurosis: case report and review of the literature.

Authors:  A Hedergott; A E Volk; P Herkenrath; H Thiele; J Fricke; J Altmüller; P Nürnberg; C Kubisch; A Neugebauer
Journal:  Graefes Arch Clin Exp Ophthalmol       Date:  2015-10-13       Impact factor: 3.117

Review 2.  Schinzel-Giedion syndrome: a novel case, review and revised diagnostic criteria.

Authors:  Wei-Liang Liu; Zhi-Xu He; Fang Li; Rong Ai; Hong-Wei Ma
Journal:  J Genet       Date:  2018-03       Impact factor: 1.166

3.  Monoallelic KIF1A-related disorders: a multicenter cross sectional study and systematic literature review.

Authors:  Stefania Della Vecchia; Alessandra Tessa; Claudia Dosi; Jacopo Baldacci; Rosa Pasquariello; Antonella Antenora; Guja Astrea; Maria Teresa Bassi; Roberta Battini; Carlo Casali; Ettore Cioffi; Greta Conti; Giovanna De Michele; Anna Rita Ferrari; Alessandro Filla; Chiara Fiorillo; Carlo Fusco; Salvatore Gallone; Chiara Germiniasi; Renzo Guerrini; Shalom Haggiag; Diego Lopergolo; Andrea Martinuzzi; Federico Melani; Andrea Mignarri; Elena Panzeri; Antonella Pini; Anna Maria Pinto; Francesca Pochiero; Guido Primiano; Elena Procopio; Alessandra Renieri; Romina Romaniello; Cristina Sancricca; Serenella Servidei; Carlotta Spagnoli; Chiara Ticci; Anna Rubegni; Filippo Maria Santorelli
Journal:  J Neurol       Date:  2021-09-06       Impact factor: 4.849

4.  X-Linked Candidate Genes for a Ciliopathy-Like Disorder.

Authors:  Ashleigh R Pavey; Thierry Vilboux; Holly E Babcock; Margot Ahronovich; Benjamin D Solomon
Journal:  Mol Syndromol       Date:  2016-03-16

5.  TBX5 variant with the novel phenotype of mixed‑type total anomalous pulmonary venous return in Holt‑Oram Syndrome and variable intrafamilial heart defects.

Authors:  Bilal Azab; Dunia Aburizeg; Weizhen Ji; Lauren Jeffries; Nooredeen Jamal Isbeih; Amal Saleh Al-Akily; Hashim Mohammad; Yousef Abu Osba; Mohammad A Shahin; Zain Dardas; Ma'mon M Hatmal; Iyad Al-Ammouri; Saquib Lakhani
Journal:  Mol Med Rep       Date:  2022-05-06       Impact factor: 3.423

6.  Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies.

Authors:  Rocio Acuna-Hidalgo; Pelagia Deriziotis; Marloes Steehouwer; Christian Gilissen; Sarah A Graham; Sipko van Dam; Julie Hoover-Fong; Aida B Telegrafi; Anne Destree; Robert Smigiel; Lindsday A Lambie; Hülya Kayserili; Umut Altunoglu; Elisabetta Lapi; Maria Luisa Uzielli; Mariana Aracena; Banu G Nur; Ercan Mihci; Lilia M A Moreira; Viviane Borges Ferreira; Dafne D G Horovitz; Katia M da Rocha; Aleksandra Jezela-Stanek; Alice S Brooks; Heiko Reutter; Julie S Cohen; Ali Fatemi; Martin Smitka; Theresa A Grebe; Nataliya Di Donato; Charu Deshpande; Anthony Vandersteen; Charles Marques Lourenço; Andreas Dufke; Eva Rossier; Gwenaelle Andre; Alessandra Baumer; Careni Spencer; Julie McGaughran; Lude Franke; Joris A Veltman; Bert B A De Vries; Albert Schinzel; Simon E Fisher; Alexander Hoischen; Bregje W van Bon
Journal:  PLoS Genet       Date:  2017-03-27       Impact factor: 5.917

Review 7.  Analysis of Downs syndrome with molecular techniques for future diagnoses.

Authors:  May Salem Al-Nbaheen
Journal:  Saudi J Biol Sci       Date:  2016-02-03       Impact factor: 4.219

8.  Utility of trio-based exome sequencing in the elucidation of the genetic basis of isolated syndromic intellectual disability: illustrative cases.

Authors:  Thaise Nr Carneiro; Ana Cv Krepischi; Silvia S Costa; Israel Tojal da Silva; Angela M Vianna-Morgante; Renan Valieris; Suzana Am Ezquina; Debora R Bertola; Paulo A Otto; Carla Rosenberg
Journal:  Appl Clin Genet       Date:  2018-08-22

Review 9.  SETBP1 dysregulation in congenital disorders and myeloid neoplasms.

Authors:  Nicoletta Coccaro; Giuseppina Tota; Antonella Zagaria; Luisa Anelli; Giorgina Specchia; Francesco Albano
Journal:  Oncotarget       Date:  2017-04-19

10.  The recurrent SETBP1 c.2608G > A, p.(Gly870Ser) variant in a patient with Schinzel-Giedion syndrome: an illustrative case of the utility of whole exome sequencing in a critically ill neonate.

Authors:  Maria Pia Leone; Pietro Palumbo; Orazio Palumbo; Ester Di Muro; Massimiliano Chetta; Nicola Laforgia; Nicoletta Resta; Alessandro Stella; Stefano Castellana; Tommaso Mazza; Marco Castori; Massimo Carella; Nenad Bukvic
Journal:  Ital J Pediatr       Date:  2020-05-27       Impact factor: 2.638

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