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Nature Genetics Contents: March 2017 pp 319 - 480

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Nature Genetics

TABLE OF CONTENTS

March 2017 Volume 49, Issue 3

Editorial
News and Views
Analysis
Articles
Letters
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Editorial

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The creativity of immigrants   p319
doi:10.1038/ng.3814

News and Views

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The road to precision oncology   pp320 - 321
Andrew V Biankin
doi:10.1038/ng.3796
The ultimate goal of precision medicine is to use population-based molecular, clinical and other data to make individually tailored clinical decisions for patients, although the path to achieving this goal is not entirely clear. A new study shows how knowledge banks of patient data can be used to make individual treatment decisions in acute myeloid leukemia.

See also: Analysis by Gerstung et al.

Convergence and divergence in sex-chromosome evolution   pp321 - 322
Catherine L Peichel
doi:10.1038/ng.3797
A sequence assembly of the chicken W chromosome enables reconstruction of the gene content of the W chromosome across 14 bird species and shows striking similarities in the maintenance of broadly expressed and dosage-sensitive genes on highly degenerate sex chromosomes in both birds and mammals. However, the chicken W chromosome is not enriched for genes with expression in female-specific tissues, providing an intriguing contrast to the acquisition and amplification of genes with testis-specific expression on mammalian Y chromosomes and suggesting that the inheritance of chromosomes solely through females or males can lead to different evolutionary outcomes.

See also: Article by Bellott et al.

Untangling the genetics from the epigenetics in pancreatic cancer metastasis   pp323 - 324
Christopher R Vakoc & David A Tuveson
doi:10.1038/ng.3798
Comparative genomic analyses of primary tumors and metastases within individuals with pancreatic cancer have exposed the complex clonal dynamics that underlie the dissemination of cancer cells to distant sites. Recent studies implicate non-genetic mechanisms in this process, particularly fluctuations in chromatin states and metabolism, which can endow rare cells within a primary tumor with metastatic potential.

See also: Article by Makohon-Moore et al. | Article by McDonald et al.

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Analysis

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Case-control association mapping by proxy using family history of disease   pp325 - 331
Jimmy Z Liu, Yaniv Erlich & Joseph K Pickrell
doi:10.1038/ng.3766
Jimmy Liu and colleagues perform genome-wide association by proxy (GWAX) in a large population cohort by replacing cases with their first-degree relatives. They apply GWAX to 12 common diseases and show its utility by identifying new risk loci for Alzheimer's disease, coronary artery disease and type 2 diabetes.

Precision oncology for acute myeloid leukemia using a knowledge bank approach   pp332 - 340
Moritz Gerstung, Elli Papaemmanuil, Inigo Martincorena, Lars Bullinger, Verena I Gaidzik, Peter Paschka, Michael Heuser, Felicitas Thol, Niccolo Bolli, Peter Ganly, Arnold Ganser, Ultan McDermott, Konstanze Döhner, Richard F Schlenk, Hartmut Döhner & Peter J Campbell
doi:10.1038/ng.3756
Peter Campbell, Hartmut Döhner and colleagues present an analysis of genetic mutations and clinical information from 1,540 patients with acute myeloid leukemia, demonstrating the utility of clinical knowledge banks for personalized medicine. They show that use of their approach could reduce the number of hematopoietic cell transplants in patients with AML by up to 25% while maintaining survival rates.

See also: News and Views by Biankin

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers   pp341 - 348
Dominik Glodzik, Sandro Morganella, Helen Davies, Peter T Simpson, Yilong Li, Xueqing Zou, Javier Diez-Perez, Johan Staaf, Ludmil B Alexandrov, Marcel Smid, Arie B Brinkman, Inga Hansine Rye, Hege Russnes, Keiran Raine, Colin A Purdie, Sunil R Lakhani, Alastair M Thompson, Ewan Birney, Hendrik G Stunnenberg, Marc J van de Vijver, John W M Martens, Anne-Lise Børresen-Dale, Andrea L Richardson, Gu Kong, Alain Viari, Douglas Easton, Gerard Evan, Peter J Campbell, Michael R Stratton & Serena Nik-Zainal
doi:10.1038/ng.3771
Serena Nik-Zainal and colleagues present a detailed analysis of somatic rearrangements in 560 breast cancers. They highlight 33 rearrangement hotspots characterized mainly by large tandem duplications and show that these hotspots are enriched in breast cancer germline susceptibility loci and breast-specific super-enhancer elements.

Systematic analysis of telomere length and somatic alterations in 31 cancer types   pp349 - 357
Floris P Barthel, Wei Wei, Ming Tang, Emmanuel Martinez-Ledesma, Xin Hu, Samirkumar B Amin, Kadir C Akdemir, Sahil Seth, Xingzhi Song, Qianghu Wang, Tara Lichtenberg, Jian Hu, Jianhua Zhang, Siyuan Zheng & Roel G W Verhaak
doi:10.1038/ng.3781
Siyuan Zheng, Roel Verhaak and colleagues report an analysis of telomere lengths and somatic alterations in telomere-related pathways across 31 cancer types. Their study provides an overview of the molecular mechanisms driving TERT expression and activation of the ALT pathway, and identifies a subset of tumors with neither detectable TERT expression nor somatic alterations in ATRX or DAXX.

Articles

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Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer   pp358 - 366
Alvin P Makohon-Moore, Ming Zhang, Johannes G Reiter, Ivana Bozic, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, Fay Wong, Yuchen Jiao, Zachary A Kohutek, Jungeui Hong, Marc Attiyeh, Breanna Javier, Laura D Wood, Ralph H Hruban, Martin A Nowak, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein & Christine A Iacobuzio-Donahue
doi:10.1038/ng.3764
Christine Iacobuzio-Donahue and colleagues report a detailed analysis of whole-genome sequencing data from primary and metastatic tumors in four patients with pancreatic cancer. They find that in each patient primary tumors and metastases have identical mutations in known driver genes.

See also: News and Views by Vakoc & Tuveson | Article by McDonald et al.

Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis   pp367 - 376
Oliver G McDonald, Xin Li, Tyler Saunders, Rakel Tryggvadottir, Samantha J Mentch, Marc O Warmoes, Anna E Word, Alessandro Carrer, Tal H Salz, Sonoko Natsume, Kimberly M Stauffer, Alvin Makohon-Moore, Yi Zhong, Hao Wu, Kathryn E Wellen, Jason W Locasale, Christine A Iacobuzio-Donahue & Andrew P Feinberg
doi:10.1038/ng.3753
Andrew Feinberg, Christine Iacobuzio-Donahue and colleagues describe the epigenomic reprogramming that occurs during pancreatic cancer progression. They also show that hematogenous metastases co-evolve a dependence on the oxidative branch of the pentose phosphate pathway (oxPPP) and that oxPPP inhibition reverses chromatin reprogramming and blocks tumorigenic potential.

See also: News and Views by Vakoc & Tuveson | Article by Makohon-Moore et al.

Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells   pp377 - 386
Jin Xu, Ava C Carter, Anne-Valerie Gendrel, Mikael Attia, Joshua Loftus, William J Greenleaf, Robert Tibshirani, Edith Heard & Howard Y Chang
doi:10.1038/ng.3769
Howard Chang and colleagues use allele-specific ATAC-seq to profile active regulatory DNA across the genome in mouse embryonic stem cells and neural progenitor cells. They find that monoallelic DNA accessibility across autosomes is pervasive, developmentally programmed and composed of several patterns.

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators   pp387 - 394
Daniel W Bellott, Helen Skaletsky, Ting-Jan Cho, Laura Brown, Devin Locke, Nancy Chen, Svetlana Galkina, Tatyana Pyntikova, Natalia Koutseva, Tina Graves, Colin Kremitzki, Wesley C Warren, Andrew G Clark, Elena Gaginskaya, Richard K Wilson & David C Page
doi:10.1038/ng.3778
David Page and colleagues report the sequence of the chicken W sex chromosome and compare ancestral W-linked genes across bird species. They find that the W chromosome did not acquire genes expressed exclusively in reproductive tissue, but retained genes through selection to maintain appropriate dosage levels of broadly expressed genes.

See also: News and Views by Peichel

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance   pp395 - 402
Abigail L Manson, Keira A Cohen, Thomas Abeel, Christopher A Desjardins, Derek T Armstrong, Clifton E Barry III, Jeannette Brand, TBResist Global Genome Consortium, Sinéad B Chapman, Sang-Nae Cho, Andrei Gabrielian, James Gomez, Andreea M Jodals, Moses Joloba, Pontus Jureen, Jong Seok Lee, Lesibana Malinga, Mamoudou Maiga, Dale Nordenberg, Ecaterina Noroc, Elena Romancenco, Alex Salazar, Willy Ssengooba, A A Velayati, Kathryn Winglee, Aksana Zalutskaya, Laura E Via, Gail H Cassell, Susan E Dorman, Jerrold Ellner, Parissa Farnia, James E Galagan, Alex Rosenthal, Valeriu Crudu, Daniela Homorodean, Po-Ren Hsueh, Sujatha Narayanan, Alexander S Pym, Alena Skrahina, Soumya Swaminathan, Martie Van der Walt, David Alland, William R Bishai, Ted Cohen, Sven Hoffner, Bruce W Birren & Ashlee M Earl
doi:10.1038/ng.3767
Ashlee Earl and colleagues analyze whole-genome sequences from 5,310 Mycobacterium tuberculosis isolates from five continents. They find that resistance to isoniazid arises before rifampicin resistance across all of the lineages, geographical regions and time periods.

Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk   pp403 - 415
Helen R Warren, Evangelos Evangelou, Claudia P Cabrera, He Gao, Meixia Ren, Borbala Mifsud, Ioanna Ntalla, Praveen Surendran, Chunyu Liu, James P Cook, Aldi T Kraja, Fotios Drenos, Marie Loh, Niek Verweij, Jonathan Marten, Ibrahim Karaman, Marcelo P Segura Lepe, Paul F O'Reilly, Joanne Knight, Harold Snieder, Norihiro Kato, Jiang He, E Shyong Tai, M Abdullah Said, David Porteous, Maris Alver, Neil Poulter, Martin Farrall, Ron T Gansevoort, Sandosh Padmanabhan, Reedik Mägi, Alice Stanton, John Connell, Stephan J L Bakker, Andres Metspalu, Denis C Shields, Simon Thom, Morris Brown, Peter Sever, Tõnu Esko, Caroline Hayward, Pim van der Harst, Danish Saleheen, Rajiv Chowdhury, John C Chambers, Daniel I Chasman, Aravinda Chakravarti, Christopher Newton-Cheh, Cecilia M Lindgren, Daniel Levy, Jaspal S Kooner, Bernard Keavney, Maciej Tomaszewski, Nilesh J Samani, Joanna M M Howson, Martin D Tobin, Patricia B Munroe, Georg B Ehret, Louise V Wain, Louise V Wain, Ahmad Vaez, Rick Jansen, Roby Joehanes, Peter J van der Most, A Mesut Erzurumluoglu, Paul O'Reilly, Claudia P Cabrera, Helen R Warren, Lynda M Rose, Germaine C Verwoert, Jouke-Jan Hottenga, Rona J Strawbridge, Tonu Esko, Dan E Arking, Shih-Jen Hwang, Xiuqing Guo, Zoltan Kutalik, Stella Trompet, Nick Shrine, Alexander Teumer, Janina S Ried, Joshua C Bis, Albert V Smith, Najaf Amin, Ilja M Nolte, Leo-Pekka Lyytikäinen, Anubha Mahajan, Nicholas J Wareham, Edith Hofer, Peter K Joshi, Kati Kristiansson, Michela Traglia, Aki S Havulinna, Anuj Goel, Mike A Nalls, Siim Sõber, Dragana Vuckovic, Jian'an Luan, Fabiola Del Greco M, Kristin L Ayers, Jaume Marrugat, Daniela Ruggiero, Lorna M Lopez, Teemu Niiranen, Stefan Enroth, Anne U Jackson, Christopher P Nelson, Jennifer E Huffman, Weihua Zhang, Jonathan Marten, Ilaria Gandin, Sarah E Harris, Tatijana Zemonik, Yingchang Lu, Evangelos Evangelou, Nabi Shah, Martin H de Borst, Massimo Mangino, Bram P Prins, Archie Campbell, Ruifang Li-Gao, Ganesh Chauhan, Christopher Oldmeadow, Gonçalo Abecasis, Maryam Abedi, Caterina M Barbieri, Michael R Barnes, Chiara Batini, BIOS Consortium, Tineka Blake, Michael Boehnke, Erwin P Bottinger, Peter S Braund, Morris Brown, Marco Brumat, Harry Campbell, John C Chambers, Massimiliano Cocca, Francis Collins, John Connell, Heather J Cordell, Jeffrey J Damman, Gail Davies, Eco J de Geus, Renée de Mutsert, Joris Deelen, Yusuf Demirkale, Alex S F Doney, Marcus Dörr, Martin Farrall, Teresa Ferreira, Mattias Frånberg, He Gao, Vilmantas Giedraitis, Christian Gieger, Franco Giulianini, Alan J Gow, Anders Hamsten, Tamara B Harris, Albert Hofman, Elizabeth G Holliday, Marjo-Riitta Jarvelin, Åsa Johansson, Andrew D Johnson, Pekka Jousilahti, Antti Jula, Mika Kähönen, Sekar Kathiresan, Kay-Tee Khaw, Ivana Kolcic, Seppo Koskinen, Claudia Langenberg, Marty Larson, Lenore J Launer, Benjamin Lehne, David C M Liewald, Lifelines Cohort Study, Li Lin, Lars Lind, François Mach, Chrysovalanto Mamasoula, Cristina Menni, Borbala Mifsud, Yuri Milaneschi, Anna Morgan, Andrew D Morris, Alanna C Morrison, Peter J Munson, Priyanka Nandakumar, Quang Tri Nguyen, Teresa Nutile, Albertine J Oldehinkel, Ben A Oostra, Elin Org, Sandosh Padmanabhan, Aarno Palotie, Guillaume Paré, Alison Pattie, Brenda W J H Penninx, Neil Poulter, Peter P Pramstaller, Olli T Raitakari, Meixia Ren, Kenneth Rice, Paul M Ridker, Harriëtte Riese, Samuli Ripatti, Antonietta Robino, Jerome I Rotter, Igor Rudan, Yasaman Saba, Aude Saint Pierre, Cinzia F Sala, Antti-Pekka Sarin, Reinhold Schmidt, Rodney Scott, Marc A Seelen, Denis C Shields, David Siscovick, Rossella Sorice, Alice Stanton, David J Stott, Johan Sundström, Morris Swertz, Kent D Taylor, Simon Thom, Ioanna Tzoulaki, Christophe Tzourio, André G Uitterlinden, Understanding Society Scientific group, Uwe Völker, Peter Vollenweider, Sarah Wild, Gonneke Willemsen, Alan F Wright, Jie Yao, Sébastien Thériault, David Conen, Attia John, Peter Sever, Stéphanie Debette, Dennis O Mook-Kanamori, Eleftheria Zeggini, Tim D Spector, Pim van der Harst, Colin N A Palmer, Anne-Claire Vergnaud, Ruth J F Loos, Ozren Polasek, John M Starr, Giorgia Girotto, Caroline Hayward, Jaspal S Kooner, Cecila M Lindgren, Veronique Vitart, Nilesh J Samani, Jaakko Tuomilehto, Ulf Gyllensten, Paul Knekt, Ian J Deary, Marina Ciullo, Roberto Elosua, Bernard D Keavney, Andrew A Hicks, Robert A Scott, Paolo Gasparini, Maris Laan, YongMei Liu, Hugh Watkins, Catharina A Hartman, Veikko Salomaa, Daniela Toniolo, Markus Perola, James F Wilson, Helena Schmidt, Jing Hua Zhao, Terho Lehtimäki, Cornelia M van Duijn, Vilmundur Gudnason, Bruce M Psaty, Annette Peters, Rainer Rettig, Alan James, J Wouter Jukema, David P Strachan, Walter Palmas, Andres Metspalu, Erik Ingelsson, Dorret I Boomsma, Oscar H Franco, Murielle Bochud, Christopher Newton-Cheh, Patricia B Munroe, Paul Elliott, Daniel I Chasman, Aravinda Chakravarti, Joanne Knight, Andrew P Morris, Daniel Levy, Martin D Tobin, Harold Snieder, Mark J Caulfield & Georg B Ehret for The International Consortium of Blood Pressure (ICBP) 1000G Analyses, The CHD Exome+ Consortium, The ExomeBP Consortium, The T2D-GENES Consortium, The GoT2DGenes Consortium, The Cohorts for Heart and Ageing Research in Genome Epidemiology (CHARGE) BP Exome Consortium, The International Genomics of Blood Pressure (iGEN-BP) Consortium & Michael R Barnes, Ioanna Tzoulaki, Mark J Caulfield & Paul Elliott for The UK Biobank CardioMetabolic Consortium BP working group
doi:10.1038/ng.3768
Mark Caulfield, Paul Elliott and colleagues use data from the UK Biobank to perform genome-wide association analysis for blood pressure traits. They identify and validate 107 novel loci and highlight new biological pathways for potential therapeutic intervention for hypertension.

Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets   pp416 - 425
Louise V Wain, Nick Shrine, María Soler Artigas, A Mesut Erzurumluoglu, Boris Noyvert, Lara Bossini-Castillo, Ma'en Obeidat, Amanda P Henry, Michael A Portelli, Robert J Hall, Charlotte K Billington, Tracy L Rimington, Anthony G Fenech, Catherine John, Tineka Blake, Victoria E Jackson, Richard J Allen, Bram P Prins, Understanding Society Scientific Group, Archie Campbell, David J Porteous, Marjo-Riitta Jarvelin, Matthias Wielscher, Alan L James, Jennie Hui, Nicholas J Wareham, Jing Hua Zhao, James F Wilson, Peter K Joshi, Beate Stubbe, Rajesh Rawal, Holger Schulz, Medea Imboden, Nicole M Probst-Hensch, Stefan Karrasch, Christian Gieger, Ian J Deary, Sarah E Harris, Jonathan Marten, Igor Rudan, Stefan Enroth, Ulf Gyllensten, Shona M Kerr, Ozren Polasek, Mika Kähönen, Ida Surakka, Veronique Vitart, Caroline Hayward, Terho Lehtimäki, Olli T Raitakari, David M Evans, A John Henderson, Craig E Pennell, Carol A Wang, Peter D Sly, Emily S Wan, Robert Busch, Brian D Hobbs, Augusto A Litonjua, David W Sparrow, Amund Gulsvik, Per S Bakke, James D Crapo, Terri H Beaty, Nadia N Hansel, Rasika A Mathias, Ingo Ruczinski, Kathleen C Barnes, Yohan Bossé, Philippe Joubert, Maarten van den Berge, Corry-Anke Brandsma, Peter D Paré, Don D Sin, David C Nickle, Ke Hao, Omri Gottesman, Frederick E Dewey, Shannon E Bruse, David J Carey, H Lester Kirchner, Geisinger-Regeneron DiscovEHR Collaboration, Stefan Jonsson, Gudmar Thorleifsson, Ingileif Jonsdottir, Thorarinn Gislason, Kari Stefansson, Claudia Schurmann, Girish Nadkarni, Erwin P Bottinger, Ruth J F Loos, Robin G Walters, Zhengming Chen, Iona Y Millwood, Julien Vaucher, Om P Kurmi, Liming Li, Anna L Hansell, Chris Brightling, Eleftheria Zeggini, Michael H Cho, Edwin K Silverman, Ian Sayers, Gosia Trynka, Andrew P Morris, David P Strachan, Ian P Hall & Martin D Tobin
doi:10.1038/ng.3787
Louise Wain, Ian Hall, Martin Tobin and colleagues report genome-wide association analyses of lung function, identifying 43 new signals associated with one or more lung function traits. A genetic risk score derived from these results was significantly associated with risk for chronic obstructive pulmonary disease in independent populations.

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Nature Insight Frontiers in Biology

This year's Frontiers in Biology Insight features Reviews on how genomics is helping to uncover the peopling of the world, the interplay between morphogens and morphogenesis in determining organismal shape, the factors that influence the immune response to cancer, advances in single-cell genomics, and the effects of base modifications in messenger RNA.
 

Letters

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Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis   pp426 - 432
Brian D Hobbs, Kim de Jong, Maxime Lamontagne, Yohan Bossé, Nick Shrine, María Soler Artigas, Louise V Wain, Ian P Hall, Victoria E Jackson, Annah B Wyss, Stephanie J London, Kari E North, Nora Franceschini, David P Strachan, Terri H Beaty, John E Hokanson, James D Crapo, Peter J Castaldi, Robert P Chase, Traci M Bartz, Susan R Heckbert, Bruce M Psaty, Sina A Gharib, Pieter Zanen, Jan W Lammers, Matthijs Oudkerk, H J Groen, Nicholas Locantore, Ruth Tal-Singer, Stephen I Rennard, Jørgen Vestbo, Wim Timens, Peter D Paré, Jeanne C Latourelle, Josée Dupuis, George T O'Connor, Jemma B Wilk, Woo Jin Kim, Mi Kyeong Lee, Yeon-Mok Oh, Judith M Vonk, Harry J de Koning, Shuguang Leng, Steven A Belinsky, Yohannes Tesfaigzi, Ani Manichaikul, Xin-Qun Wang, Stephen S Rich, R Graham Barr, David Sparrow, Augusto A Litonjua, Per Bakke, Amund Gulsvik, Lies Lahousse, Guy G Brusselle, Bruno H Stricker, André G Uitterlinden, Elizabeth J Ampleford, Eugene R Bleecker, Prescott G Woodruff, Deborah A Meyers, Dandi Qiao, David A Lomas, Jae-Joon Yim, Deog Kyeom Kim, Iwona Hawrylkiewicz, Pawel Sliwinski, Megan Hardin, Tasha E Fingerlin, David A Schwartz, Dirkje S Postma, William MacNee, Martin D Tobin, Edwin K Silverman, H Marike Boezen, Michael H Cho, COPDGene Investigators, ECLIPSE Investigators, LifeLines Investigators, SPIROMICS Research Group, International COPD Genetics Network Investigators, UK BiLEVE Investigators & International COPD Genetics Consortium
doi:10.1038/ng.3752
Michael Cho and colleagues report a genome-wide association study of risk for chronic obstructive pulmonary disease (COPD) in a large, multi-ancestry cohort. They identify 22 genome-wide significant loci, including 13 not previously associated with COPD and 4 not previously associated with any lung function trait.

A missense variant in NCF1 is associated with susceptibility to multiple autoimmune diseases   pp433 - 437
Jian Zhao, Jianyang Ma, Yun Deng, Jennifer A Kelly, Kwangwoo Kim, So-Young Bang, Hye-Soon Lee, Quan-Zhen Li, Edward K Wakeland, Rong Qiu, Mengru Liu, Jianping Guo, Zhanguo Li, Wenfeng Tan, Astrid Rasmussen, Christopher J Lessard, Kathy L Sivils, Bevra H Hahn, Jennifer M Grossman, Diane L Kamen, Gary S Gilkeson, Sang-Cheol Bae, Patrick M Gaffney, Nan Shen & Betty P Tsao
doi:10.1038/ng.3782
Betty Tsao, Jian Zhao, Nan Shen and colleagues show that a common missense variant in NCF1 confers susceptibility to multiple autoimmune diseases. This variant, which leads to reduced production of reactive oxygen species, accounts for the strong association signal previously identified in the GTF2IRD1-GTF2I region at 7q11.23.

Dense genotyping of immune-related loci implicates host responses to microbial exposure in Behcet's disease susceptibility   pp438 - 443
Masaki Takeuchi, Nobuhisa Mizuki, Akira Meguro, Michael J Ombrello, Yohei Kirino, Colleen Satorius, Julie Le, Mary Blake, Burak Erer, Tatsukata Kawagoe, Duran Ustek, Ilknur Tugal-Tutkun, Emire Seyahi, Yilmaz Ozyazgan, Inês Sousa, Fereydoun Davatchi, Vânia Francisco, Farhad Shahram, Bahar Sadeghi Abdollahi, Abdolhadi Nadji, Niloofar Mojarad Shafiee, Fahmida Ghaderibarmi, Shigeaki Ohno, Atsuhisa Ueda, Yoshiaki Ishigatsubo, Massimo Gadina, Sofia A Oliveira, Ahmet Gül, Daniel L Kastner & Elaine F Remmers
doi:10.1038/ng.3786
Daniel Kastner, Elaine Remmers and colleagues perform an association study of Behcet's disease based on dense genotyping of immune-related loci. They identify new association signals near genes involved in host response to microbial exposure and extend evidence for shared susceptibility loci with Crohn's disease and leprosy.

Acquired CYP19A1 amplification is an early specific mechanism of aromatase inhibitor resistance in ERα metastatic breast cancer   pp444 - 450
Luca Magnani, Gianmaria Frigè, Raffaella Maria Gadaleta, Giacomo Corleone, Sonia Fabris, Hermannus Kempe, Pernette J Verschure, Iros Barozzi, Valentina Vircillo, Sung-Pil Hong, Ylenia Perone, Massimo Saini, Andreas Trumpp, Giuseppe Viale, Antonino Neri, Simak Ali, Marco Angelo Colleoni, Giancarlo Pruneri & Saverio Minucci
doi:10.1038/ng.3773
Saverio Minucci, Giancarlo Pruneri, Luca Magnani and colleagues identify acquired CYP19A1 amplification as a mechanism of resistance to aromatase inhibitors in ERα metastatic breast cancer. Mechanistically, they show that CYP19A1 amplification results in increased aromatase activity and estrogen-independent ERα binding to target genes.

Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes   pp451 - 456
Jasmijn D E de Rooij, Cristyn Branstetter, Jing Ma, Yongjin Li, Michael P Walsh, Jinjun Cheng, Askar Obulkasim, Jinjun Dang, John Easton, Lonneke J Verboon, Heather L Mulder, Martin Zimmermann, Cary Koss, Pankaj Gupta, Michael Edmonson, Michael Rusch, Joshua Yew Suang Lim, Katarina Reinhardt, Martina Pigazzi, Guangchun Song, Allen Eng Juh Yeoh, Lee-Yung Shih, Der-Cherng Liang, Stephanie Halene, Diane S Krause, Jinghui Zhang, James R Downing, Franco Locatelli, Dirk Reinhardt, Marry M van den Heuvel-Eibrink, C Michel Zwaan, Maarten Fornerod & Tanja A Gruber
doi:10.1038/ng.3772
Franco Locatelli, Dirk Reinhardt, Marry van den Heuvel-Eibrink, C Michel Zwaan, Maarten Fornerod, Tanja Gruber and colleagues report whole-exome and transcriptome sequencing of acute megakaryoblastic leukemia from pediatric and adult patients without Down syndrome (non-DS-AMKL). They find that pediatric non-DS-AMKL can be divided into seven subgroups characterized by chimeric oncogenes with cooperating mutations in epigenetic and kinase signaling genes.

Biallelic mutations in the 3′ exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing   pp457 - 464
Rea M Lardelli, Ashleigh E Schaffer, Veerle R C Eggens, Maha S Zaki, Stephanie Grainger, Shashank Sathe, Eric L Van Nostrand, Zinayida Schlachetzki, Basak Rosti, Naiara Akizu, Eric Scott, Jennifer L Silhavy, Laura Dean Heckman, Rasim Ozgur Rosti, Esra Dikoglu, Anne Gregor, Alicia Guemez-Gamboa, Damir Musaev, Rohit Mande, Ari Widjaja, Tim L Shaw, Sebastian Markmiller, Isaac Marin-Valencia, Justin H Davies, Linda de Meirleir, Hulya Kayserili, Umut Altunoglu, Mary Louise Freckmann, Linda Warwick, David Chitayat, Susan Blaser, Ahmet Okay Çağlayan, Kaya Bilguvar, Huseyin Per, Christina Fagerberg, Henrik T Christesen, Maria Kibaek, Kimberly A Aldinger, David Manchester, Naomichi Matsumoto, Kazuhiro Muramatsu, Hirotomo Saitsu, Masaaki Shiina, Kazuhiro Ogata, Nicola Foulds, William B Dobyns, Neil C Chi, David Traver, Luigina Spaccini, Stefania Maria Bova, Stacey B Gabriel, Murat Gunel, Enza Maria Valente, Marie-Cecile Nassogne, Eric J Bennett, Gene W Yeo, Frank Baas, Jens Lykke-Andersen & Joseph G Gleeson
doi:10.1038/ng.3762
Jens Lykke-Andersen, Frank Baas, Joseph Gleeson and colleagues report that mutations in the 3′ exonuclease TOE1 cause pontocerebellar hypoplasia type 7. They further show that these mutations result in the accumulation of incompletely processed small nuclear RNAs, leading to severe, early-onset neurodegeneration.

Divergent effects of intrinsically active MEK variants on developmental Ras signaling   pp465 - 469
Yogesh Goyal, Granton A Jindal, José L Pelliccia, Kei Yamaya, Eyan Yeung, Alan S Futran, Rebecca D Burdine, Trudi Schüpbach & Stanislav Y Shvartsman
doi:10.1038/ng.3780
Stanislav Shvartsman and colleagues quantify signaling changes caused by disease-associated mutations in MAP2K1 (encoding MEK) in fruit fly and zebrafish embryos. They find that intrinsically active MEK variants can both increase and reduce the levels of pathway activation depending on cellular context.

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks   pp470 - 475
Ivica Medugorac, Alexander Graf, Cécile Grohs, Sophie Rothammer, Yondon Zagdsuren, Elena Gladyr, Natalia Zinovieva, Johanna Barbieri, Doris Seichter, Ingolf Russ, André Eggen, Garrett Hellenthal, Gottfried Brem, Helmut Blum, Stefan Krebs & Aurélien Capitan
doi:10.1038/ng.3775
Ivica Medugorac, Aurélien Capitan and colleagues use high-density SNP genotyping and whole-genome sequencing to infer bovine haplotypes in the genomes of 76 Mongolian yaks. They show that these introgressed regions are enriched for genes involved in nervous system development and function, supporting the idea that introgressive hybridization contributed to the improvement of yak management and breeding.

A study of allelic diversity underlying flowering-time adaptation in maize landraces   pp476 - 480
J Alberto Romero Navarro, Martha Willcox, Juan Burgueño, Cinta Romay, Kelly Swarts, Samuel Trachsel, Ernesto Preciado, Arturo Terron, Humberto Vallejo Delgado, Victor Vidal, Alejandro Ortega, Armando Espinoza Banda, Noel Orlando Gómez Montiel, Ivan Ortiz-Monasterio, Félix San Vicente, Armando Guadarrama Espinoza, Gary Atlin, Peter Wenzl, Sarah Hearne & Edward S Buckler
doi:10.1038/ng.3784
Edward Buckler, Sarah Hearne and colleagues integrate two approaches to characterize the genetic diversity of a large number of geographically distributed maize landraces. They examine flowering time and adaptation to altitude and find that the majority of the associated SNPs overlap both traits.

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