A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

American Association for the Advancement of Science (AAAS) - Tập 335 Số 6070 - Trang 823-828 - 2012
Daniel G. MacArthur1,2, Suganthi Balasubramanian3,4, Adam Frankish2, Ni Huang2, James A. Morris2, Klaudia Walter2, Luke Jostins2, Lukas Habegger3,4, Ilaria Gandin5, Stephen B. Montgomery6, Cornelis A. Albers7,2, Zhengdong D. Zhang8, Donald F. Conrad9, Gerton Lunter10, Hancheng Zheng11, Qasim Ayub2, Mark A. DePristo12, Eric Banks12, Min Hu2, Robert E. Handsaker13,12, Jeffrey Rosenfeld14, Menachem Fromer12, Mike Jin4, Xinmeng Jasmine Mu3,4, Ekta Khurana3,4, Kai Ye15, Mike Kay2, Gary Saunders2, Marie‐Marthe Suner2, Toby Hunt2, If Barnes2, Clara Amid16,2, Denise Carvalho‐Silva2, Alexandra Bignell2, Catherine Snow2, Bryndís Yngvadóttir2, Anna F. Dominiczak2, D.N. Cooper17, Yali Xue2, Irene Gallego Romero5,2, Jun Wang11, Yingrui Li11, Richard A. Gibbs18, Steven A. McCarroll13,12, Emmanouil T. Dermitzakis6, Jonathan K. Pritchard5,19, Jeffrey C. Barrett2, Jennifer Harrow2, Matthew E. Hurles2, Mark Gerstein20,3,4, Chris Tyler‐Smith2
1Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW 2006, Australia
2Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
3Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA
4Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
5Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
6Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva 4, Switzerland
7Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge CB2 0PT, UK.
8Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
9Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
10Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
11BGI-Shenzhen, Shenzhen 518083, China
12Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
13Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
14IST/High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA.
15Molecular Epidemiology Section, Leiden University Medical Center, 2300 RC Leiden, Netherlands.
16The European Nucleotide Archive, European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton CB10 1SD, UK.
17Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
18Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
19Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
20Department of Computer Science, Yale University, New Haven, CT, USA

Tóm tắt

Defective Gene Detective

Identifying genes that give rise to diseases is one of the major goals of sequencing human genomes. However, putative loss-of-function genes, which are often some of the first identified targets of genome and exome sequencing, have often turned out to be sequencing errors rather than true genetic variants. In order to identify the true scope of loss-of-function genes within the human genome, MacArthur et al. (p. 823 ; see the Perspective by Quintana-Murci ) extensively validated the genomes from the 1000 Genomes Project, as well as an additional European individual, and found that the average person has about 100 true loss-of-function alleles of which approximately 20 have two copies within an individual. Because many known disease-causing genes were identified in “normal” individuals, the process of clinical sequencing needs to reassess how to identify likely causative alleles.

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