Correcting CRISPR for copy number
Nature Genetics 49, 1674 (2017).
doi:10.1038/ng.3994
Authors: John Paul Shen & Trey Ideker
The CRISPR–Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high copy number. A new study describes a computational approach to correct for this copy number effect, increasing the specificity of CRIPSR screens to identify essential genes. (Source: Nature Genetics)
Source: Nature Genetics - November 29, 2017 Category: Genetics & Stem Cells Authors: John Paul Shen Trey Ideker Tags: News and Views Source Type: research
Mismatch repair prefers exons
Nature Genetics 49, 1673 (2017).
doi:10.1038/ng.3993
Authors: Dashiell J Massey & Amnon Koren
A new analysis of cancer genomes identifies a decrease in the mutation burden of exons, but not introns, as compared to expectation. This difference can be explained by preferential recruitment of the DNA mismatch repair machinery to a protein modification that marks exons. (Source: Nature Genetics)
Source: Nature Genetics - November 29, 2017 Category: Genetics & Stem Cells Authors: Dashiell J Massey Amnon Koren Tags: News and Views Source Type: research
Evolutionary insights from wild vervet genomes
Nature Genetics 49, 1671 (2017).
doi:10.1038/ng.3992
Author: Ellen M Leffler
A new study reports genome-wide variation in 163 vervet monkeys from across their taxonomic and geographic ranges. The analysis suggests a complex history of admixture and identifies signals of repeated evolutionary selection, some of which may be linked to response to simian immunodeficiency virus. (Source: Nature Genetics)
Source: Nature Genetics - November 29, 2017 Category: Genetics & Stem Cells Authors: Ellen M Leffler Tags: News and Views Source Type: research
The hammer of reason
Nature Genetics 49, 1663 (2017).
doi:10.1038/ng.3996
In the motivation, conduct and reporting of science, there is no substitute for reason, and it must prevail whenever scientific methods are used. Similarly, scientific recommendations can only be useful if they meet with rational decision-making. Because people come to decisions from diverse viewpoints and values, listening to the values and views of scientists and non-scientists—while explicitly refraining from debate and persuasion—may point the way to determining when and where scientific ideas are of interest and likely to be adopted. (Source: Nature Genetics)
Source: Nature Genetics - November 29, 2017 Category: Genetics & Stem Cells Tags: Editorial Source Type: research
Bayesian inference of negative and positive selection in human cancers
Nature Genetics 49, 1785 (2017).
doi:10.1038/ng.3987
Authors: Donate Weghorn & Shamil Sunyaev
Cancer genomics efforts have identified genes and regulatory elements driving cancer development and neoplastic progression. From a microevolution standpoint, these are subject to positive selection. Although elusive in current studies, genes whose wild-type coding sequences are needed for tumor growth are also of key interest. They are expected to experience negative selection and stay intact under pressure of incessant mutation. The detection of significantly mutated (or undermutated) genes is completely confounded b...
Source: Nature Genetics - November 6, 2017 Category: Genetics & Stem Cells Authors: Donate Weghorn Shamil Sunyaev Tags: Letter Source Type: research
High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Nature Genetics 49, 1731 (2017).
doi:10.1038/ng.3988
Authors: Julien Lagarde, Barbara Uszczynska-Ratajczak, Silvia Carbonell, Sílvia Pérez-Lluch, Amaya Abad, Carrie Davis, Thomas R Gingeras, Adam Frankish, Jennifer Harrow, Roderic Guigo & Rory Johnson (Source: Nature Genetics)
Source: Nature Genetics - November 6, 2017 Category: Genetics & Stem Cells Authors: Julien Lagarde Barbara Uszczynska-Ratajczak Silvia Carbonell S í lvia P é rez-Lluch Amaya Abad Carrie Davis Thomas R Gingeras Adam Frankish Jennifer Harrow Roderic Guigo Rory Johnson Tags: Article Source Type: research
Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers
Nature Genetics 49, 1693 (2017).
doi:10.1038/ng.3990
Authors: Collin M Blakely, Thomas B K Watkins, Wei Wu, Beatrice Gini, Jacob J Chabon, Caroline E McCoach, Nicholas McGranahan, Gareth A Wilson, Nicolai J Birkbak, Victor R Olivas, Julia Rotow, Ashley Maynard, Victoria Wang, Matthew A Gubens, Kimberly C Banks, Richard B Lanman, Aleah F Caulin, John St John, Anibal R Cordero, Petros Giannikopoulos, Andrew D Simmons, Philip C Mack, David R Gandara, Hatim Husain, Robert C Doebele, Jonathan W Riess, Maximilian Diehn, Charles Swanton & Trever G Bivona (Source: Nature Genetics)
Source: Nature Genetics - November 6, 2017 Category: Genetics & Stem Cells Authors: Collin M Blakely Thomas B K Watkins Wei Wu Beatrice Gini Jacob J Chabon Caroline E McCoach Nicholas McGranahan Gareth A Wilson Nicolai J Birkbak Victor R Olivas Julia Rotow Ashley Maynard Victoria Wang Matthew A Gubens Kimberly C Banks Richard B Lanman Al Tags: Article Source Type: research
Reduced mutation rate in exons due to differential mismatch repair
Nature Genetics 49, 1684 (2017).
doi:10.1038/ng.3991
Authors: Joan Frigola, Radhakrishnan Sabarinathan, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez & Núria López-Bigas (Source: Nature Genetics)
Source: Nature Genetics - November 6, 2017 Category: Genetics & Stem Cells Authors: Joan Frigola Radhakrishnan Sabarinathan Loris Mularoni Ferran Mui ñ os Abel Gonzalez-Perez N ú ria L ó pez-Bigas Tags: Analysis Source Type: research
Computational correction of copy number effect improves specificity of CRISPR – Cas9 essentiality screens in cancer cells
Nature Genetics 49, 1779 (2017).
doi:10.1038/ng.3984
Authors: Robin M Meyers, Jordan G Bryan, James M McFarland, Barbara A Weir, Ann E Sizemore, Han Xu, Neekesh V Dharia, Phillip G Montgomery, Glenn S Cowley, Sasha Pantel, Amy Goodale, Yenarae Lee, Levi D Ali, Guozhi Jiang, Rakela Lubonja, William F Harrington, Matthew Strickland, Ting Wu, Derek C Hawes, Victor A Zhivich, Meghan R Wyatt, Zohra Kalani, Jaime J Chang, Michael Okamoto, Kimberly Stegmaier, Todd R Golub, Jesse S Boehm, Francisca Vazquez, David E Root, William C Hahn & Aviad Tsherniak
The CRISPR–Cas9 system has revolutionized gene editing both ...
Source: Nature Genetics - October 30, 2017 Category: Genetics & Stem Cells Authors: Robin M Meyers Jordan G Bryan James M McFarland Barbara A Weir Ann E Sizemore Han Xu Neekesh V Dharia Phillip G Montgomery Glenn S Cowley Sasha Pantel Amy Goodale Yenarae Lee Levi D Ali Guozhi Jiang Rakela Lubonja William F Harrington Matthew Strickland T Tags: Letter Source Type: research
Exome-wide association study of plasma lipids in > 300,000 individuals
Nature Genetics 49, 1758 (2017).
doi:10.1038/ng.3977
Authors: Dajiang J Liu, Gina M Peloso, Haojie Yu, Adam S Butterworth, Xiao Wang, Anubha Mahajan, Danish Saleheen, Connor Emdin, Dewan Alam, Alexessander Couto Alves, Philippe Amouyel, Emanuele Di Angelantonio, Dominique Arveiler, Themistocles L Assimes, Paul L Auer, Usman Baber, Christie M Ballantyne, Lia E Bang, Marianne Benn, Joshua C Bis, Michael Boehnke, Eric Boerwinkle, Jette Bork-Jensen, Erwin P Bottinger, Ivan Brandslund, Morris Brown, Fabio Busonero, Mark J Caulfield, John C Chambers, Daniel I Chasman, Y Eugene Chen, Yii-Der Ida Chen, Rajiv Chowdhury, Cra...
Source: Nature Genetics - October 30, 2017 Category: Genetics & Stem Cells Authors: Dajiang J Liu Gina M Peloso Haojie Yu Adam S Butterworth Xiao Wang Anubha Mahajan Danish Saleheen Connor Emdin Dewan Alam Alexessander Couto Alves Philippe Amouyel Emanuele Di Angelantonio Dominique Arveiler Themistocles L Assimes Paul L Auer Usman Baber Tags: Letter Source Type: research
Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology
Nature Genetics 49, 1752 (2017).
doi:10.1038/ng.3985
Authors: Manuel A Ferreira, Judith M Vonk, Hansjörg Baurecht, Ingo Marenholz, Chao Tian, Joshua D Hoffman, Quinta Helmer, Annika Tillander, Vilhelmina Ullemar, Jenny van Dongen, Yi Lu, Franz Rüschendorf, Jorge Esparza-Gordillo, Chris W Medway, Edward Mountjoy, Kimberley Burrows, Oliver Hummel, Sarah Grosche, Ben M Brumpton, John S Witte, Jouke-Jan Hottenga, Gonneke Willemsen, Jie Zheng, Elke Rodríguez, Melanie Hotze, Andre Franke, Joana A Revez, Jonathan Beesley, Melanie C Matheson, Shyamali C Dharmage, Lisa M Bain, Lars G Fritsche, Maiken E Gabrie...
Source: Nature Genetics - October 30, 2017 Category: Genetics & Stem Cells Authors: Manuel A Ferreira Judith M Vonk Hansj ö rg Baurecht Ingo Marenholz Chao Tian Joshua D Hoffman Quinta Helmer Annika Tillander Vilhelmina Ullemar Jenny van Dongen Yi Lu Franz R ü schendorf Jorge Esparza-Gordillo Chris W Medway Edward Mountjoy Kimberley Bu Tags: Letter Source Type: research
Exome chip meta-analysis identifies novel loci and East Asian – specific coding variants that contribute to lipid levels and coronary artery disease
Nature Genetics 49, 1722 (2017).
doi:10.1038/ng.3978
Authors: Xiangfeng Lu, Gina M Peloso, Dajiang J Liu, Ying Wu, He Zhang, Wei Zhou, Jun Li, Clara Sze-man Tang, Rajkumar Dorajoo, Huaixing Li, Jirong Long, Xiuqing Guo, Ming Xu, Cassandra N Spracklen, Yang Chen, Xuezhen Liu, Yan Zhang, Chiea Chuen Khor, Jianjun Liu, Liang Sun, Laiyuan Wang, Yu-Tang Gao, Yao Hu, Kuai Yu, Yiqin Wang, Chloe Yu Yan Cheung, Feijie Wang, Jianfeng Huang, Qiao Fan, Qiuyin Cai, Shufeng Chen, Jinxiu Shi, Xueli Yang, Wanting Zhao, Wayne H-H Sheu, Stacey Shawn Cherny, Meian He, Alan B Feranil, Linda S Adair, Penny Gordon-Larsen, Shufa Du, Rohi...
Source: Nature Genetics - October 30, 2017 Category: Genetics & Stem Cells Authors: Xiangfeng Lu Gina M Peloso Dajiang J Liu Ying Wu He Zhang Wei Zhou Jun Li Clara Sze-man Tang Rajkumar Dorajoo Huaixing Li Jirong Long Xiuqing Guo Ming Xu Cassandra N Spracklen Yang Chen Xuezhen Liu Yan Zhang Chiea Chuen Khor Jianjun Liu Liang Sun Laiyuan Tags: Article Source Type: research
Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate
Nature Genetics 49, 1714 (2017).
doi:10.1038/ng.3959
Authors: Anna J Jasinska, Ivette Zelaya, Susan K Service, Christine B Peterson, Rita M Cantor, Oi-Wa Choi, Joseph DeYoung, Eleazar Eskin, Lynn A Fairbanks, Scott Fears, Allison E Furterer, Yu S Huang, Vasily Ramensky, Christopher A Schmitt, Hannes Svardal, Matthew J Jorgensen, Jay R Kaplan, Diego Villar, Bronwen L Aken, Paul Flicek, Rishi Nag, Emily S Wong, John Blangero, Thomas D Dyer, Marina Bogomolov, Yoav Benjamini, George M Weinstock, Ken Dewar, Chiara Sabatti, Richard K Wilson, J David Jentsch, Wesley Warren, Giovanni Coppola, Roger P Woods & Nelson B F...
Source: Nature Genetics - October 30, 2017 Category: Genetics & Stem Cells Authors: Anna J Jasinska Ivette Zelaya Susan K Service Christine B Peterson Rita M Cantor Oi-Wa Choi Joseph DeYoung Eleazar Eskin Lynn A Fairbanks Scott Fears Allison E Furterer Yu S Huang Vasily Ramensky Christopher A Schmitt Hannes Svardal Matthew J Jorgensen Ja Tags: Article Source Type: research
Ancient hybridization and strong adaptation to viruses across African vervet monkey populations
Nature Genetics 49, 1705 (2017).
doi:10.1038/ng.3980
Authors: Hannes Svardal, Anna J Jasinska, Cristian Apetrei, Giovanni Coppola, Yu Huang, Christopher A Schmitt, Beatrice Jacquelin, Vasily Ramensky, Michaela Müller-Trutwin, Martin Antonio, George Weinstock, J Paul Grobler, Ken Dewar, Richard K Wilson, Trudy R Turner, Wesley C Warren, Nelson B Freimer & Magnus Nordborg (Source: Nature Genetics)
Source: Nature Genetics - October 30, 2017 Category: Genetics & Stem Cells Authors: Hannes Svardal Anna J Jasinska Cristian Apetrei Giovanni Coppola Yu Huang Christopher A Schmitt Beatrice Jacquelin Vasily Ramensky Michaela M ü ller-Trutwin Martin Antonio George Weinstock J Paul Grobler Ken Dewar Richard K Wilson Trudy R Turner Wesley C Tags: Article Source Type: research
Corrigendum: Germline hypomorphic CARD11 mutations in severe atopic disease
Nature Genetics 49, 1661 (2017).
doi:10.1038/ng1117-1661b
Author: Chi A Ma, Jeffrey R Stinson, Yuan Zhang, Jordan K Abbott, Michael A Weinreich, Pia J Hauk, Paul R Reynolds, Jonathan J Lyons, Celeste G Nelson, Elisa Ruffo, Batsukh Dorjbal, Salomé Glauzy, Natsuko Yamakawa, Swadhinya Arjunaraja, Kelsey Voss, Jennifer Stoddard, Julie Niemela, Yu Zhang, Sergio D Rosenzweig, Joshua J McElwee, Thomas DiMaggio, Helen F Matthews, Nina Jones, Kelly D Stone, Alejandro Palma, Matías Oleastro, Emma Prieto, Andrea R Bernasconi, Geronimo Dubra, Silvia Danielian, Jonathan Zaiat, Marcelo A Marti, Brian Kim, Megan A Coope...
Source: Nature Genetics - October 27, 2017 Category: Genetics & Stem Cells Authors: Chi A Ma Jeffrey R Stinson Yuan Zhang Jordan K Abbott Michael A Weinreich Pia J Hauk Paul R Reynolds Jonathan J Lyons Celeste G Nelson Elisa Ruffo Batsukh Dorjbal Salom é Glauzy Natsuko Yamakawa Swadhinya Arjunaraja Kelsey Voss Jennifer Stoddard Julie N Tags: Corrigendum Source Type: research
