Literature DB >> 23346032

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

Gerald Goh1, Murim Choi.   

Abstract

The recent advent of next-generation sequencing technologies has dramatically changed the nature of biomedical research. Human genetics is no exception-it has never been easier to interrogate human patient genomes at the nucleotide level to identify disease-associated variants. To further facilitate the efficiency of this approach, whole exome sequencing (WES) was first developed in 2009. Over the past three years, multiple groups have demonstrated the power of WES through robust disease-associated variant discoveries across a diverse spectrum of human diseases. Here, we review the application of WES to different types of inherited human diseases and discuss analytical challenges and possible solutions, with the aim of providing a practical guide for the effective use of this technology.

Entities:  

Keywords:  discovery of disease-causing variants; inherited human disease; next-generation sequencing; whole exome sequencing

Year:  2012        PMID: 23346032      PMCID: PMC3543920          DOI: 10.5808/GI.2012.10.4.214

Source DB:  PubMed          Journal:  Genomics Inform        ISSN: 1598-866X


  19 in total

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Authors:  R P Lifton; A G Gharavi; D S Geller
Journal:  Cell       Date:  2001-02-23       Impact factor: 41.582

2.  Recent segmental duplications in the human genome.

Authors:  Jeffrey A Bailey; Zhiping Gu; Royden A Clark; Knut Reinert; Rhea V Samonte; Stuart Schwartz; Mark D Adams; Eugene W Myers; Peter W Li; Evan E Eichler
Journal:  Science       Date:  2002-08-09       Impact factor: 47.728

3.  De novo mutations revealed by whole-exome sequencing are strongly associated with autism.

Authors:  Stephan J Sanders; Michael T Murtha; Abha R Gupta; John D Murdoch; Melanie J Raubeson; A Jeremy Willsey; A Gulhan Ercan-Sencicek; Nicholas M DiLullo; Neelroop N Parikshak; Jason L Stein; Michael F Walker; Gordon T Ober; Nicole A Teran; Youeun Song; Paul El-Fishawy; Ryan C Murtha; Murim Choi; John D Overton; Robert D Bjornson; Nicholas J Carriero; Kyle A Meyer; Kaya Bilguvar; Shrikant M Mane; Nenad Sestan; Richard P Lifton; Murat Günel; Kathryn Roeder; Daniel H Geschwind; Bernie Devlin; Matthew W State
Journal:  Nature       Date:  2012-04-04       Impact factor: 49.962

Review 4.  Rare and common variants: twenty arguments.

Authors:  Greg Gibson
Journal:  Nat Rev Genet       Date:  2012-01-18       Impact factor: 53.242

5.  A map of human genome variation from population-scale sequencing.

Authors:  Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal:  Nature       Date:  2010-10-28       Impact factor: 49.962

6.  Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.

Authors:  Murim Choi; Ute I Scholl; Weizhen Ji; Tiewen Liu; Irina R Tikhonova; Paul Zumbo; Ahmet Nayir; Ayşin Bakkaloğlu; Seza Ozen; Sami Sanjad; Carol Nelson-Williams; Anita Farhi; Shrikant Mane; Richard P Lifton
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-27       Impact factor: 11.205

7.  Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Authors:  Benjamin M Neale; Yan Kou; Li Liu; Avi Ma'ayan; Kaitlin E Samocha; Aniko Sabo; Chiao-Feng Lin; Christine Stevens; Li-San Wang; Vladimir Makarov; Paz Polak; Seungtai Yoon; Jared Maguire; Emily L Crawford; Nicholas G Campbell; Evan T Geller; Otto Valladares; Chad Schafer; Han Liu; Tuo Zhao; Guiqing Cai; Jayon Lihm; Ruth Dannenfelser; Omar Jabado; Zuleyma Peralta; Uma Nagaswamy; Donna Muzny; Jeffrey G Reid; Irene Newsham; Yuanqing Wu; Lora Lewis; Yi Han; Benjamin F Voight; Elaine Lim; Elizabeth Rossin; Andrew Kirby; Jason Flannick; Menachem Fromer; Khalid Shakir; Tim Fennell; Kiran Garimella; Eric Banks; Ryan Poplin; Stacey Gabriel; Mark DePristo; Jack R Wimbish; Braden E Boone; Shawn E Levy; Catalina Betancur; Shamil Sunyaev; Eric Boerwinkle; Joseph D Buxbaum; Edwin H Cook; Bernie Devlin; Richard A Gibbs; Kathryn Roeder; Gerard D Schellenberg; James S Sutcliffe; Mark J Daly
Journal:  Nature       Date:  2012-04-04       Impact factor: 49.962

8.  Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.

Authors:  Brian J O'Roak; Laura Vives; Santhosh Girirajan; Emre Karakoc; Niklas Krumm; Bradley P Coe; Roie Levy; Arthur Ko; Choli Lee; Joshua D Smith; Emily H Turner; Ian B Stanaway; Benjamin Vernot; Maika Malig; Carl Baker; Beau Reilly; Joshua M Akey; Elhanan Borenstein; Mark J Rieder; Deborah A Nickerson; Raphael Bernier; Jay Shendure; Evan E Eichler
Journal:  Nature       Date:  2012-04-04       Impact factor: 49.962

9.  Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations.

Authors:  Kaya Bilgüvar; Ali Kemal Oztürk; Angeliki Louvi; Kenneth Y Kwan; Murim Choi; Burak Tatli; Dilek Yalnizoğlu; Beyhan Tüysüz; Ahmet Okay Cağlayan; Sarenur Gökben; Hande Kaymakçalan; Tanyeri Barak; Mehmet Bakircioğlu; Katsuhito Yasuno; Winson Ho; Stephan Sanders; Ying Zhu; Sanem Yilmaz; Alp Dinçer; Michele H Johnson; Richard A Bronen; Naci Koçer; Hüseyin Per; Shrikant Mane; Mehmet Necmettin Pamir; Cengiz Yalçinkaya; Sefer Kumandaş; Meral Topçu; Meral Ozmen; Nenad Sestan; Richard P Lifton; Matthew W State; Murat Günel
Journal:  Nature       Date:  2010-08-22       Impact factor: 49.962

10.  Performance comparison of exome DNA sequencing technologies.

Authors:  Michael J Clark; Rui Chen; Hugo Y K Lam; Konrad J Karczewski; Rong Chen; Ghia Euskirchen; Atul J Butte; Michael Snyder
Journal:  Nat Biotechnol       Date:  2011-09-25       Impact factor: 68.164

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  26 in total

Review 1.  Whole-Exome Sequencing in the Clinic: Lessons from Six Consecutive Cases from the Clinician's Perspective.

Authors:  Amber Volk; Erin Conboy; Beverly Wical; Marc Patterson; Salman Kirmani
Journal:  Mol Syndromol       Date:  2015-02-03

2.  Rare cases of congenital arthrogryposis multiplex caused by novel recurrent CHRNG mutations.

Authors:  Jieun Seo; In-Ho Choi; Je Sang Lee; Yongjin Yoo; Nayoung K D Kim; Murim Choi; Jung Min Ko; Yong Beom Shin
Journal:  J Hum Genet       Date:  2015-01-22       Impact factor: 3.172

Review 3.  Primary Mitochondrial Disease and Secondary Mitochondrial Dysfunction: Importance of Distinction for Diagnosis and Treatment.

Authors:  Dmitriy M Niyazov; Stephan G Kahler; Richard E Frye
Journal:  Mol Syndromol       Date:  2016-06-03

4.  Whole Exome Sequencing Reveals a Mutation in CRYBB2 in a Large Mexican Family with Autosomal Dominant Pulverulent Cataract.

Authors:  Olga Messina-Baas; Manuel L Gonzalez-Garay; Luz M González-Huerta; Jaime Toral-López; Sergio A Cuevas-Covarrubias
Journal:  Mol Syndromol       Date:  2016-04-14

5.  SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes.

Authors:  Yue Xing; Alan R Dabney; Xiao Li; Guosong Wang; Clare A Gill; Claudio Casola
Journal:  Front Genet       Date:  2020-02-21       Impact factor: 4.599

Review 6.  Techniques and Approaches to Genetic Analyses in Nephrological Disorders.

Authors:  Laurel K Willig
Journal:  J Pediatr Genet       Date:  2015-08-13

Review 7.  SOFT syndrome caused by compound heterozygous mutations of POC1A and its skeletal manifestation.

Authors:  Jung Min Ko; Soyoon Jung; Jieun Seo; Choong Ho Shin; Hae Il Cheong; Murim Choi; Ok-Hwa Kim; Tae-Joon Cho
Journal:  J Hum Genet       Date:  2016-01-21       Impact factor: 3.172

8.  Identification of two novel mutations in FAM136A and DTNA genes in autosomal-dominant familial Meniere's disease.

Authors:  Teresa Requena; Sonia Cabrera; Carmen Martín-Sierra; Steven D Price; Anna Lysakowski; José A Lopez-Escamez
Journal:  Hum Mol Genet       Date:  2014-10-09       Impact factor: 6.150

9.  Identification of a novel SBF2 frameshift mutation in charcot-marie-tooth disease type 4B2 using whole-exome sequencing.

Authors:  Meiyan Chen; Jing Wu; Ning Liang; Lihui Tang; Yanhua Chen; Huishuang Chen; Wei Wei; Tianying Wei; Hui Huang; Xin Yi; Ming Qi
Journal:  Genomics Proteomics Bioinformatics       Date:  2014-10-28       Impact factor: 7.691

10.  Genetic testing for inherited eye conditions in over 6,000 individuals through the eyeGENE network.

Authors:  Kerry E Goetz; Melissa J Reeves; Shaina Gagadam; Delphine Blain; Chelsea Bender; Cara Lwin; Amelia Naik; Santa J Tumminia; Robert B Hufnagel
Journal:  Am J Med Genet C Semin Med Genet       Date:  2020-09-07       Impact factor: 3.359

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