Disease gene identification strategies for exome sequencing

被引：318

作者：

Gilissen, Christian ^{[1
,2
]}

Hoischen, Alexander ^{[1
,2
]}

Brunner, Han G. ^{[1
,2
]}

Veltman, Joris A. ^{[1
,2
]}

机构：

[1] Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, Nijmegen Ctr Mol Life Sci, NL-6500 HB Nijmegen, Netherlands

[2] Radboud Univ Nijmegen, Med Ctr, Inst Genet & Metab Disorders, NL-6500 HB Nijmegen, Netherlands

来源：

EUROPEAN JOURNAL OF HUMAN GENETICS | 2012年 / 20卷 / 05期

关键词：

Mendelian disease; gene identification; strategies; next generation sequencing; exome sequencing; HEARING-LOSS; MENTAL-RETARDATION; CAUSATIVE GENE; NOTCH2; CAUSE; MUTATIONS; REVEALS; CELL; PRIORITIZATION; MALFORMATIONS; DEFICIENCY;

D O I：

10.1038/ejhg.2011.258

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Next generation sequencing can be used to search for Mendelian disease genes in an unbiased manner by sequencing the entire protein-coding sequence, known as the exome, or even the entire human genome. Identifying the pathogenic mutation amongst thousands to millions of genomic variants is a major challenge, and novel variant prioritization strategies are required. The choice of these strategies depends on the availability of well-phenotyped patients and family members, the mode of inheritance, the severity of the disease and its population frequency. In this review, we discuss the current strategies for Mendelian disease gene identification by exome resequencing. We conclude that exome strategies are successful and identify new Mendelian disease genes in approximately 60% of the projects. Improvements in bioinformatics as well as in sequencing technology will likely increase the success rate even further. Exome sequencing is likely to become the most commonly used tool for Mendelian disease gene identification for the coming years. European Journal of Human Genetics (2012) 20, 490-497; doi:10.1038/ejhg.2011.258; published online 18 January 2012

引用

页码：490 / 497

页数：8

共 82 条

[21] Exome Sequencing Reveals a Homozygous SYT14 Mutation in Adult-Onset, Autosomal-Recessive Spinocerebellar Ataxia with Psychomotor Retardation [J].

Doi, Hiroshi ;

Yoshida, Kunihiro ;

Yasuda, Takao ;

Fukuda, Mitsunori ;

Fukuda, Yoko ;

Morita, Hiroshi ;

Ikeda, Shu-ichi ;

Kato, Rumiko ;

Tsurusaki, Yoshinori ;

Miyake, Noriko ;

Saitsu, Hirotomo ;

Sakai, Haruya ;

Miyatake, Satoko ;

Shiina, Masaaki ;

Nukina, Nobuyuki ;

Koyano, Shigeru ;

Tsuji, Shoji ;

Kuroiwa, Yoshiyuki ;

Matsumoto, Naomichi .

AMERICAN JOURNAL OF HUMAN GENETICS, 2011, 89 (02) :320-327

[22] A genome-wide association study identifies IL23R as an inflammatory bowel disease gene [J].

Duerr, Richard H. ;

Taylor, Kent D. ;

Brant, Steven R. ;

Rioux, John D. ;

Silverberg, Mark S. ;

Daly, Mark J. ;

Steinhart, A. Hillary ;

Abraham, Clara ;

Regueiro, Miguel ;

Griffiths, Anne ;

Dassopoulos, Themistocles ;

Bitton, Alain ;

Yang, Huiying ;

Targan, Stephan ;

Datta, Lisa Wu ;

Kistner, Emily O. ;

Schumm, L. Philip ;

Lee, Annette T. ;

Gregersen, Peter K. ;

Barmada, M. Michael ;

Rotter, Jerome I. ;

Nicolae, Dan L. ;

Cho, Judy H. .

SCIENCE, 2006, 314 (5804) :1461-1463

[23] Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis [J].

Erlich, Yaniv ;

Edvardson, Simon ;

Hodges, Emily ;

Zenvirt, Shamir ;

Thekkat, Pramod ;

Shaag, Avraham ;

Dor, Talya ;

Hannon, Gregory J. ;

Elpeleg, Orly .

GENOME RESEARCH, 2011, 21 (05) :658-664

[24] Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes [J].

Franke, Lude ;

van Bakel, Harm ;

Fokkens, Like ;

de Jong, Edwin D. ;

Egmont-Petersen, Michael ;

Wijmenga, Cisca .

AMERICAN JOURNAL OF HUMAN GENETICS, 2006, 78 (06) :1011-1025

[25] Exome Sequencing Identifies WDR35 Variants Involved in Sensenbrenner Syndrome [J].

Gilissen, Christian ;

Arts, Heleen H. ;

Hoischen, Alexander ;

Spruijt, Liesbeth ;

Mans, Dorus A. ;

Arts, Peer ;

van Lier, Bart ;

Steehouwer, Marloes ;

van Reeuwijk, Jeroen ;

Kant, Sarina G. ;

Roepman, Ronald ;

Knoers, Nine V. A. M. ;

Veltman, Joris A. ;

Brunner, Han G. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2010, 87 (03) :418-423

[26] Increased exonic de novo mutation rate in individuals with schizophrenia [J].

Girard, Simon L. ;

Gauthier, Julie ;

Noreau, Anne ;

Xiong, Lan ;

Zhou, Sirui ;

Jouan, Loubna ;

Dionne-Laporte, Alexandre ;

Spiegelman, Dan ;

Henrion, Edouard ;

Diallo, Ousmane ;

Thibodeau, Pascale ;

Bachand, Isabelle ;

Bao, Jessie Y. J. ;

Tong, Amy Hin Yan ;

Lin, Chi-Ho ;

Millet, Bruno ;

Jaafari, Nematollah ;

Joober, Ridha ;

Dion, Patrick A. ;

Lok, Si ;

Krebs, Marie-Odile ;

Rouleau, Guy A. .

NATURE GENETICS, 2011, 43 (09) :860-U65

[27] Whole-Exome Re-Sequencing in a Family Quartet Identifies POP1 Mutations As the Cause of a Novel Skeletal Dysplasia [J].

Glazov, Evgeny A. ;

Zankl, Andreas ;

Donskoi, Marina ;

Kenna, Tony J. ;

Thomas, Gethin P. ;

Clark, Graeme R. ;

Duncan, Emma L. ;

Brown, Matthew A. .

PLOS GENETICS, 2011, 7 (03)

[28] Exome Sequencing Identifies Mitochondrial Alanyl-tRNA Synthetase Mutations in Infantile Mitochondrial Cardiomyopathy [J].

Gotz, Alexandra ;

Tyynismaa, Henna ;

Euro, Liliya ;

Ellonen, Pekka ;

Hyotylainen, Tuulia ;

Ojala, Tiina ;

Hamalainen, Riikka H. ;

Tommiska, Johanna ;

Raivio, Taneli ;

Oresic, Matej ;

Karikoski, Riitta ;

Tammela, Outi ;

Simola, Kalle O. J. ;

Paetau, Anders ;

Tyni, Tiina ;

Suomalainen, Anu .

AMERICAN JOURNAL OF HUMAN GENETICS, 2011, 88 (05) :635-642

[29] NBEAL2 is mutated in gray platelet syndrome and is required for biogenesis of platelet α-granules [J].

Gunay-Aygun, Meral ;

Falik-Zaccai, Tzipora C. ;

Vilboux, Thierry ;

Zivony-Elboum, Yifat ;

Gumruk, Fatma ;

Cetin, Mualla ;

Khayat, Morad ;

Boerkoel, Cornelius F. ;

Kfir, Nehama ;

Huang, Yan ;

Maynard, Dawn ;

Dorward, Heidi ;

Berger, Katherine ;

Kleta, Robert ;

Anikster, Yair ;

Arat, Mutlu ;

Freiberg, Andrew S. ;

Kehrel, Beate E. ;

Jurk, Kerstin ;

Cruz, Pedro ;

Mullikin, Jim C. ;

White, James G. ;

Huizing, Marjan ;

Gahl, William A. .

NATURE GENETICS, 2011, 43 (08) :732-734

[30] Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency [J].

Haack, Tobias B. ;

Danhauser, Katharina ;

Haberberger, Birgit ;

Hoser, Jonathan ;

Strecker, Valentina ;

Boehm, Detlef ;

Uziel, Graziella ;

Lamantea, Eleonora ;

Invernizzi, Federica ;

Poulton, Joanna ;

Rolinski, Boris ;

Iuso, Arcangela ;

Biskup, Saskia ;

Schmidt, Thorsten ;

Mewes, Hans-Werner ;

Wittig, Ilka ;

Meitinger, Thomas ;

Zeviani, Massimo ;

Prokisch, Holger .

NATURE GENETICS, 2010, 42 (12) :1131-+

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