Nature Genetics Contents: October 2018 Volume 50 Number 10

TABLE OF CONTENTS October 2018 Volume 50, Issue 10 Editorial Correspondence News & Views Perspectives Letters Articles Analysis Advertisement Meet the shortlist! The shortlist for this year's Nature Research Awards for Inspiring Science and Innovating Science has been announced. These Awards showcase exceptional achievements of leading women in science and of those who have encouraged girls and women to engage with STEM subjects.  See more about our shortlisted nominees > In partnership with The Estée Lauder Companies. Editorial The measure of a healthy society    p1345 doi:10.1038/s41588-018-0249-y Correspondence Mutations in RECQL are not associated with breast cancer risk in an Australian population    pp1346 - 1348 Na Li, Simone M. Rowley, David L. Goode, Kaushalya C. Amarasinghe, Simone McInerny et al. doi:10.1038/s41588-018-0206-9 Reply to 'Mutations in RECQL are not associated with breast cancer risk in an Australian population'    pp1348 - 1349 Humayun Ahmed, Jordan Lerner-Ellis, Cezary Cybulski, Kelly Metcalfe, Jan Lubiński et al. doi:10.1038/s41588-018-0233-6 News & Views Cancer cell lines as patient avatars for drug response prediction    pp1350 - 1351 Ultan McDermott doi:10.1038/s41588-018-0245-2 Genetics EVENT The Genetics of Heart and Vascular Disease 12.10.18 Hilton Head Island, USA More science events from Perspectives Challenges and guidelines toward 4D nucleome data and model standards    pp1352 - 1358 Marc A. Marti-Renom, Genevieve Almouzni, Wendy A. Bickmore, Kerstin Bystricky, Giacomo Cavalli et al. doi:10.1038/s41588-018-0236-3 Letters Genome-wide association analyses identify 39 new susceptibility loci for diverticular disease    pp1359 - 1365 Lillias H. Maguire, Samuel K. Handelman, Xiaomeng Du, Yanhua Chen, Tune H. Pers et al. doi:10.1038/s41588-018-0203-z Genome-wide analyses identify 42 risk loci for diverticular disease, 39 of which are new. Genes in associated regions are enriched for expression in connective tissue cell types and are coexpressed with genes involved in vascular and mesenchymal biology. Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes    pp1366 - 1374 Harm-Jan Westra, Marta Martínez-Bonet, Suna Onengut-Gumuscu, Annette Lee, Yang Luo et al. doi:10.1038/s41588-018-0216-7 Fine-mapping and functional studies highlight potential causal risk variants for rheumatoid arthritis and type 1 diabetes, including missense variants at DNASE1L3, PTPN22, SH2B3, and TYK2, and noncoding variants at MEG3, CD28–CTLA4, and IL2RA. Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer    pp1375 - 1380 Giulia Orlando, Philip J. Law, Alex J. Cornish, Sara E. Dobbins, Daniel Chubb et al. doi:10.1038/s41588-018-0211-z Promoter capture Hi-C in colorectal cancer cells integrated with cancer genome and expression data identifies a noncoding, cis-regulatory element that is recurrently mutated in cancer, affecting ETV1 expression, cell viability and patient survival. Mutational processes shape the landscape of TP53 mutations in human cancer    pp1381 - 1387 Andrew O. Giacomelli, Xiaoping Yang, Robert E. Lintner, James M. McFarland, Marc Duby et al. doi:10.1038/s41588-018-0204-y Large-scale loss-of-function screens and TP53 saturation mutagenesis screens in human cancer cell lines suggest that mutational processes combine with phenotypic selection to shape the landscape of somatic mutations at the TP53 locus. Articles Integrative detection and analysis of structural variation in cancer genomes    pp1388 - 1398 Jesse R. Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song et al. doi:10.1038/s41588-018-0195-8 The authors present an integrative framework for identifying structural variants (SVs) in cancer that applies optical mapping, Hi-C, and whole-genome sequencing. They find SVs affecting distal regulatory sequences, DNA replication, and three-dimensional chromatin structure. Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy    pp1399 - 1411 Jin-Ku Lee, Zhaoqi Liu, Jason K. Sa, Sang Shin, Jiguang Wang et al. doi:10.1038/s41588-018-0209-6 Analysis of genomic and transcriptomic data from 462 patient-derived tumor cell (PDC) samples across 14 cancer types, along with pharmacological responses to 60 agents, indicates that PDC-derived drug sensitivities might be predictive of clinical response to targeted therapies. Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits    pp1412 - 1425 Evangelos Evangelou, Helen R. Warren, David Mosen-Ansorena, Borbala Mifsud, Raha Pazoki et al. doi:10.1038/s41588-018-0205-x Association analyses in over 1 million individuals identify 535 new loci influencing blood pressure traits. The results provide new insights into blood pressure regulation and highlight shared genetic architecture between blood pressure and lifestyle exposures. Genomic history of the Sardinian population    pp1426 - 1434 Charleston W. K. Chiang, Joseph H. Marcus, Carlo Sidore, Arjun Biddanda, Hussein Al-Asadi et al. doi:10.1038/s41588-018-0215-8 Analyses of 3,514 whole-genome-sequenced individuals from Sardinia indicate that within-island substructure and sex-biased processes have impacted the genetic history of Sardinia, providing new insight into the demography of ancestral Sardinians. Parallel selection on a dormancy gene during domestication of crops from multiple families    pp1435 - 1441 Min Wang, Wenzhen Li, Chao Fang, Fan Xu, Yucheng Liu et al. doi:10.1038/s41588-018-0229-2 The stay-green G gene, which controls seed dormancy, shows evidence of selection in soybean, rice and tomato. G interacts with NCED3 and PSY and modulates abscisic acid synthesis. De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation    pp1442 - 1451 M. Felicia Basilicata, Ange-Line Bruel, Giuseppe Semplicio, Claudia Isabelle Keller Valsecchi, Tuğçe Aktaş et al. doi:10.1038/s41588-018-0220-y De novo mutations in MSL3 cause an X-linked syndrome affecting both males and females. MSL3 mutations reduce H4K16ac levels and lead to misregulation of cellular pathways involved in morphogenesis, cellular shape, and cell migration. Promoter bivalency favors an open chromatin architecture in embryonic stem cells    pp1452 - 1462 Glòria Mas, Enrique Blanco, Cecilia Ballaré, Miriam Sansó, Yannick G. Spill et al. doi:10.1038/s41588-018-0218-5 Analysis of bivalent promoters in embryonic stem cells (ESCs) shows that deletion of MLL2 in ESCs leads to increased Polycomb occupancy, reduced promoter accessibility, redistribution of long-range chromatin interactions, and failure to differentiate. Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis    pp1463 - 1473 Bjørt K. Kragesteen, Malte Spielmann, Christina Paliou, Verena Heinrich, Robert Schöpflin et al. doi:10.1038/s41588-018-0221-x A Pitx1 enhancer shows activity in forelimbs and hindlimbs but only interacts with Pitx1 in hindlimbs because of its three-dimensional configuration. Structural variants that affect three-dimensional conformation induce Pitx1 expression in forelimbs and cause partial arm-to-leg transformation in mice and humans. Functional classification of long non-coding RNAs by k-mer content    pp1474 - 1482 Jessime M. Kirk, Susan O. Kim, Kaoru Inoue, Matthew J. Smola, David M. Lee et al. doi:10.1038/s41588-018-0207-8 SEEKR is a method that deconstructs linear sequence relationships between lncRNAs and evaluates similarity on the basis of abundance of short motifs called k-mers. LncRNAs of related function often have similar k-mer profiles despite lacking linear homology. Analysis Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk    pp1483 - 1493 Yakir A. Reshef, Hilary K. Finucane, David R. Kelley, Alexander Gusev, Dylan Kotliar et al. doi:10.1038/s41588-018-0196-7 Signed linkage disequilibrium profile regression is a new method for detecting directional effects of genomic annotations on disease risk. The results implicate new causal disease genes and can suggest mechanisms underlying the effects of causal genes on disease. Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. With Nature Briefing, we'll keep you updated on the latest research, so you can focus on yours. Click here to sign up.   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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