7,895 results match your criteria Nature Genetics [Journal]


Author Correction: Transposable elements drive widespread expression of oncogenes in human cancers.

Nat Genet 2019 Apr 16. Epub 2019 Apr 16.

Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.

In the version of this article initially published, grant PF-17-201-01-TBG from the American Cancer Society to author Erica C. Pehrsson was not included in the Acknowledgements. The error has been corrected in the HTML and PDF versions of the article. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0416-9DOI Listing

Author Correction: An atlas of genetic influences on osteoporosis in humans and mice.

Nat Genet 2019 Apr 15. Epub 2019 Apr 15.

Department of Human Genetics, McGill University, Montréal, Québec, Canada.

In the version of this article initially published, in Fig. 5a, the data in the right column of 'DAAM2 gRNA1' were incorrectly plotted as circles indicating 'untreated' rather than as squares indicating 'treated'. The error has been corrected in the HTML and PDF versions of the article. Read More

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0415-x
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0415-xDOI Listing
April 2019
2 Reads

Detecting the mutational signature of homologous recombination deficiency in clinical samples.

Nat Genet 2019 Apr 15. Epub 2019 Apr 15.

Department of Biomedical Informatics and Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.

Mutations in BRCA1 and/or BRCA2 (BRCA1/2) are the most common indication of deficiency in the homologous recombination (HR) DNA repair pathway. However, recent genome-wide analyses have shown that the same pattern of mutations found in BRCA1/2-mutant tumors is also present in several other tumors. Here, we present a new computational tool called Signature Multivariate Analysis (SigMA), which can be used to accurately detect the mutational signature associated with HR deficiency from targeted gene panels. Read More

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0390-2
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0390-2DOI Listing
April 2019
4 Reads

A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity.

Nat Genet 2019 Apr 15. Epub 2019 Apr 15.

Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA.

BMP/SMAD signaling is a crucial regulator of intestinal differentiation. However, the molecular underpinnings of the BMP pathway in this context are unknown. Here, we characterize the mechanism by which BMP/SMAD signaling drives enterocyte differentiation. Read More

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0384-0
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0384-0DOI Listing
April 2019
3 Reads

Evolution of buffering in a genetic circuit controlling plant stem cell proliferation.

Nat Genet 2019 Apr 15. Epub 2019 Apr 15.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

Precise control of plant stem cell proliferation is necessary for the continuous and reproducible development of plant organs. The peptide ligand CLAVATA3 (CLV3) and its receptor protein kinase CLAVATA1 (CLV1) maintain stem cell homeostasis within a deeply conserved negative feedback circuit. In Arabidopsis, CLV1 paralogs also contribute to homeostasis, by compensating for the loss of CLV1 through transcriptional upregulation. Read More

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0389-8
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0389-8DOI Listing
April 2019
1 Read

Durum wheat genome highlights past domestication signatures and future improvement targets.

Nat Genet 2019 Apr 8. Epub 2019 Apr 8.

CREA-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0381-3DOI Listing
April 2019
29.352 Impact Factor

Measuring intolerance to mutation in human genetics.

Nat Genet 2019 Apr 8. Epub 2019 Apr 8.

Department of Biological Sciences, Columbia University, New York, NY, USA.

In numerous applications, from working with animal models to mapping the genetic basis of human disease susceptibility, knowing whether a single disrupting mutation in a gene is likely to be deleterious is useful. With this goal in mind, a number of measures have been developed to identify genes in which protein-truncating variants (PTVs), or other types of mutations, are absent or kept at very low frequency in large population samples-genes that appear 'intolerant' to mutation. One measure in particular, the probability of being loss-of-function intolerant (pLI), has been widely adopted. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0383-1DOI Listing
April 2019
1 Read

Publisher Correction: Fgf10 is essential for limb and lung formation.

Nat Genet 2019 Apr 4. Epub 2019 Apr 4.

Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.

In the version of the paper initially published, Fig. 5a was inadvertently duplicated and presented as both Fig. 5a and 5f, and the correct image for Fig. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0396-9DOI Listing
April 2019
1 Read

Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids.

Authors:
Amy R Bentley Yun J Sung Michael R Brown Thomas W Winkler Aldi T Kraja Ioanna Ntalla Karen Schwander Daniel I Chasman Elise Lim Xuan Deng Xiuqing Guo Jingmin Liu Yingchang Lu Ching-Yu Cheng Xueling Sim Dina Vojinovic Jennifer E Huffman Solomon K Musani Changwei Li Mary F Feitosa Melissa A Richard Raymond Noordam Jenna Baker Guanjie Chen Hugues Aschard Traci M Bartz Jingzhong Ding Rajkumar Dorajoo Alisa K Manning Tuomo Rankinen Albert V Smith Salman M Tajuddin Wei Zhao Mariaelisa Graff Maris Alver Mathilde Boissel Jin Fang Chai Xu Chen Jasmin Divers Evangelos Evangelou Chuan Gao Anuj Goel Yanick Hagemeijer Sarah E Harris Fernando P Hartwig Meian He Andrea R V R Horimoto Fang-Chi Hsu Yi-Jen Hung Anne U Jackson Anuradhani Kasturiratne Pirjo Komulainen Brigitte Kühnel Karin Leander Keng-Hung Lin Jian'an Luan Leo-Pekka Lyytikäinen Nana Matoba Ilja M Nolte Maik Pietzner Bram Prins Muhammad Riaz Antonietta Robino M Abdullah Said Nicole Schupf Robert A Scott Tamar Sofer Alena Stancáková Fumihiko Takeuchi Bamidele O Tayo Peter J van der Most Tibor V Varga Tzung-Dau Wang Yajuan Wang Erin B Ware Wanqing Wen Yong-Bing Xiang Lisa R Yanek Weihua Zhang Jing Hua Zhao Adebowale Adeyemo Saima Afaq Najaf Amin Marzyeh Amini Dan E Arking Zorayr Arzumanyan Tin Aung Christie Ballantyne R Graham Barr Lawrence F Bielak Eric Boerwinkle Erwin P Bottinger Ulrich Broeckel Morris Brown Brian E Cade Archie Campbell Mickaël Canouil Sabanayagam Charumathi Yii-Der Ida Chen Kaare Christensen Maria Pina Concas John M Connell Lisa de Las Fuentes H Janaka de Silva Paul S de Vries Ayo Doumatey Qing Duan Charles B Eaton Ruben N Eppinga Jessica D Faul James S Floyd Nita G Forouhi Terrence Forrester Yechiel Friedlander Ilaria Gandin He Gao Mohsen Ghanbari Sina A Gharib Bruna Gigante Franco Giulianini Hans J Grabe C Charles Gu Tamara B Harris Sami Heikkinen Chew-Kiat Heng Makoto Hirata James E Hixson M Arfan Ikram Yucheng Jia Roby Joehanes Craig Johnson Jost Bruno Jonas Anne E Justice Tomohiro Katsuya Chiea Chuen Khor Tuomas O Kilpeläinen Woon-Puay Koh Ivana Kolcic Charles Kooperberg Jose E Krieger Stephen B Kritchevsky Michiaki Kubo Johanna Kuusisto Timo A Lakka Carl D Langefeld Claudia Langenberg Lenore J Launer Benjamin Lehne Cora E Lewis Yize Li Jingjing Liang Shiow Lin Ching-Ti Liu Jianjun Liu Kiang Liu Marie Loh Kurt K Lohman Tin Louie Anna Luzzi Reedik Mägi Anubha Mahajan Ani W Manichaikul Colin A McKenzie Thomas Meitinger Andres Metspalu Yuri Milaneschi Lili Milani Karen L Mohlke Yukihide Momozawa Andrew P Morris Alison D Murray Mike A Nalls Matthias Nauck Christopher P Nelson Kari E North Jeffrey R O'Connell Nicholette D Palmer George J Papanicolau Nancy L Pedersen Annette Peters Patricia A Peyser Ozren Polasek Neil Poulter Olli T Raitakari Alex P Reiner Frida Renström Treva K Rice Stephen S Rich Jennifer G Robinson Lynda M Rose Frits R Rosendaal Igor Rudan Carsten O Schmidt Pamela J Schreiner William R Scott Peter Sever Yuan Shi Stephen Sidney Mario Sims Jennifer A Smith Harold Snieder John M Starr Konstantin Strauch Heather M Stringham Nicholas Y Q Tan Hua Tang Kent D Taylor Yik Ying Teo Yih Chung Tham Henning Tiemeier Stephen T Turner André G Uitterlinden Diana van Heemst Melanie Waldenberger Heming Wang Lan Wang Lihua Wang Wen Bin Wei Christine A Williams Gregory Wilson Mary K Wojczynski Jie Yao Kristin Young Caizheng Yu Jian-Min Yuan Jie Zhou Alan B Zonderman Diane M Becker Michael Boehnke Donald W Bowden John C Chambers Richard S Cooper Ulf de Faire Ian J Deary Paul Elliott Tõnu Esko Martin Farrall Paul W Franks Barry I Freedman Philippe Froguel Paolo Gasparini Christian Gieger Bernardo L Horta Jyh-Ming Jimmy Juang Yoichiro Kamatani Candace M Kammerer Norihiro Kato Jaspal S Kooner Markku Laakso Cathy C Laurie I-Te Lee Terho Lehtimäki Patrik K E Magnusson Albertine J Oldehinkel Brenda W J H Penninx Alexandre C Pereira Rainer Rauramaa Susan Redline Nilesh J Samani James Scott Xiao-Ou Shu Pim van der Harst Lynne E Wagenknecht Jun-Sing Wang Ya Xing Wang Nicholas J Wareham Hugh Watkins David R Weir Ananda R Wickremasinghe Tangchun Wu Eleftheria Zeggini Wei Zheng Claude Bouchard Michele K Evans Vilmundur Gudnason Sharon L R Kardia Yongmei Liu Bruce M Psaty Paul M Ridker Rob M van Dam Dennis O Mook-Kanamori Myriam Fornage Michael A Province Tanika N Kelly Ervin R Fox Caroline Hayward Cornelia M van Duijn E Shyong Tai Tien Yin Wong Ruth J F Loos Nora Franceschini Jerome I Rotter Xiaofeng Zhu Laura J Bierut W James Gauderman Kenneth Rice Patricia B Munroe Alanna C Morrison Dabeeru C Rao Charles N Rotimi L Adrienne Cupples

Nat Genet 2019 04 29;51(4):636-648. Epub 2019 Mar 29.

Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.

The concentrations of high- and low-density-lipoprotein cholesterol and triglycerides are influenced by smoking, but it is unknown whether genetic associations with lipids may be modified by smoking. We conducted a multi-ancestry genome-wide gene-smoking interaction study in 133,805 individuals with follow-up in an additional 253,467 individuals. Combined meta-analyses identified 13 new loci associated with lipids, some of which were detected only because association differed by smoking status. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0378-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467258PMC
April 2019
10 Reads
29.352 Impact Factor

Biallelic expansion of an intronic repeat in RFC1 is a common cause of late-onset ataxia.

Nat Genet 2019 04 29;51(4):649-658. Epub 2019 Mar 29.

Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK.

Late-onset ataxia is common, often idiopathic, and can result from cerebellar, proprioceptive, or vestibular impairment; when in combination, it is also termed cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS). We used non-parametric linkage analysis and genome sequencing to identify a biallelic intronic AAGGG repeat expansion in the replication factor C subunit 1 (RFC1) gene as the cause of familial CANVAS and a frequent cause of late-onset ataxia, particularly if sensory neuronopathy and bilateral vestibular areflexia coexist. The expansion, which occurs in the poly(A) tail of an AluSx3 element and differs in both size and nucleotide sequence from the reference (AAAAG) allele, does not affect RFC1 expression in patient peripheral and brain tissue, suggesting no overt loss of function. Read More

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0372-4
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0372-4DOI Listing
April 2019
6 Reads

Genomic subtyping and therapeutic targeting of acute erythroleukemia.

Nat Genet 2019 04 29;51(4):694-704. Epub 2019 Mar 29.

Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Acute erythroid leukemia (AEL) is a high-risk leukemia of poorly understood genetic basis, with controversy regarding diagnosis in the spectrum of myelodysplasia and myeloid leukemia. We compared genomic features of 159 childhood and adult AEL cases with non-AEL myeloid disorders and defined five age-related subgroups with distinct transcriptional profiles: adult, TP53 mutated; NPM1 mutated; KMT2A mutated/rearranged; adult, DDX41 mutated; and pediatric, NUP98 rearranged. Genomic features influenced outcome, with NPM1 mutations and HOXB9 overexpression being associated with a favorable prognosis and TP53, FLT3 or RB1 alterations associated with poor survival. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0375-1DOI Listing
April 2019
1 Read
29.352 Impact Factor

Probabilistic fine-mapping of transcriptome-wide association studies.

Nat Genet 2019 04 29;51(4):675-682. Epub 2019 Mar 29.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.

Transcriptome-wide association studies using predicted expression have identified thousands of genes whose locally regulated expression is associated with complex traits and diseases. In this work, we show that linkage disequilibrium induces significant gene-trait associations at non-causal genes as a function of the expression quantitative trait loci weights used in expression prediction. We introduce a probabilistic framework that models correlation among transcriptome-wide association study signals to assign a probability for every gene in the risk region to explain the observed association signal. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0367-1DOI Listing

Transposable elements drive widespread expression of oncogenes in human cancers.

Nat Genet 2019 04 29;51(4):611-617. Epub 2019 Mar 29.

Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.

Transposable elements (TEs) are an abundant and rich genetic resource of regulatory sequences. Cryptic regulatory elements within TEs can be epigenetically reactivated in cancer to influence oncogenesis in a process termed onco-exaptation. However, the prevalence and impact of TE onco-exaptation events across cancer types are poorly characterized. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0373-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443099PMC

Opportunities and challenges for transcriptome-wide association studies.

Nat Genet 2019 04 29;51(4):592-599. Epub 2019 Mar 29.

Department of Computer Science, Stanford University, Stanford, CA, USA.

Transcriptome-wide association studies (TWAS) integrate genome-wide association studies (GWAS) and gene expression datasets to identify gene-trait associations. In this Perspective, we explore properties of TWAS as a potential approach to prioritize causal genes at GWAS loci, by using simulations and case studies of literature-curated candidate causal genes for schizophrenia, low-density-lipoprotein cholesterol and Crohn's disease. We explore risk loci where TWAS accurately prioritizes the likely causal gene as well as loci where TWAS prioritizes multiple genes, some likely to be non-causal, owing to sharing of expression quantitative trait loci (eQTL). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0385-zDOI Listing
April 2019
4 Reads

Genetics for all.

Authors:

Nat Genet 2019 04;51(4):579

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0394-yDOI Listing

Clinical use of current polygenic risk scores may exacerbate health disparities.

Nat Genet 2019 04 29;51(4):584-591. Epub 2019 Mar 29.

Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.

Polygenic risk scores (PRS) are poised to improve biomedical outcomes via precision medicine. However, the major ethical and scientific challenge surrounding clinical implementation of PRS is that those available today are several times more accurate in individuals of European ancestry than other ancestries. This disparity is an inescapable consequence of Eurocentric biases in genome-wide association studies, thus highlighting that-unlike clinical biomarkers and prescription drugs, which may individually work better in some populations but do not ubiquitously perform far better in European populations-clinical uses of PRS today would systematically afford greater improvement for European-descent populations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0379-xDOI Listing

Expanding the genetic basis of ataxia.

Nat Genet 2019 04;51(4):580-581

Department of Neurology, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0387-xDOI Listing

Resolving variant-to-function relationships in hematopoiesis.

Nat Genet 2019 04;51(4):581-583

Human Genetics, Wellcome Sanger Institute, Hinxton, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0386-yDOI Listing

Author Correction: Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Nat Genet 2019 04;51(4):766

Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.

In the version of this article initially published, in the graph keys in Fig. 1i, the colors indicating 'Ob' and 'Ad' were red and blue, respectively, but should have been blue and red, respectively; the shapes indicating 'MUS' and 'BM' were a triangle and a square, respectively, but should have been a square and a triangle, respectively. The errors have been corrected in the HTML and PDF versions of the article. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0400-4DOI Listing

Gene expression imputation across multiple brain regions provides insights into schizophrenia risk.

Nat Genet 2019 04 25;51(4):659-674. Epub 2019 Mar 25.

Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0364-4DOI Listing
April 2019
1 Read
29.352 Impact Factor

A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis.

Nat Genet 2019 04 18;51(4):627-635. Epub 2019 Mar 18.

Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0370-6DOI Listing
April 2019
1 Read

Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.

Nat Genet 2019 04 18;51(4):739-748. Epub 2019 Mar 18.

Institute of Crop Science, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0371-5DOI Listing
April 2019
2 Reads

Linked-read analysis identifies mutations in single-cell DNA-sequencing data.

Nat Genet 2019 04 18;51(4):749-754. Epub 2019 Mar 18.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Whole-genome sequencing of DNA from single cells has the potential to reshape our understanding of mutational heterogeneity in normal and diseased tissues. However, a major difficulty is distinguishing amplification artifacts from biologically derived somatic mutations. Here, we describe linked-read analysis (LiRA), a method that accurately identifies somatic single-nucleotide variants (sSNVs) by using read-level phasing with nearby germline heterozygous polymorphisms, thereby enabling the characterization of mutational signatures and estimation of somatic mutation rates in single cells. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0366-2DOI Listing

The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting.

Nat Genet 2019 04 11;51(4):618-626. Epub 2019 Mar 11.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Perturbations to mammalian switch/sucrose non-fermentable (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events in cancer. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits in small cell carcinoma of the ovary, hypercalcemic type (SCCOHT), SMARCA4-deficient thoracic sarcomas and dedifferentiated endometrial carcinomas. However, the consequences of dual ATPase subunit loss on mSWI/SNF complex subunit composition, chromatin targeting, DNA accessibility and gene expression remain unknown. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0363-5DOI Listing
April 2019
1 Read

Interrogation of human hematopoiesis at single-cell and single-variant resolution.

Nat Genet 2019 04 11;51(4):683-693. Epub 2019 Mar 11.

Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.

Widespread linkage disequilibrium and incomplete annotation of cell-to-cell state variation represent substantial challenges to elucidating mechanisms of trait-associated genetic variation. Here we perform genetic fine-mapping for blood cell traits in the UK Biobank to identify putative causal variants. These variants are enriched in genes encoding proteins in trait-relevant biological pathways and in accessible chromatin of hematopoietic progenitors. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0362-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441389PMC

Author Correction: Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction.

Nat Genet 2019 04;51(4):766

The State Key Laboratory of Cell Biology, CAS Center for Excellence on Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.

In the version of this article initially published, the following grant numbers and recipients were missing from the Acknowledgements: XDB19000000 to H.J. and B. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0388-9DOI Listing
April 2019
2 Reads
29.352 Impact Factor

Author Correction: Origin and evolution of the octoploid strawberry genome.

Nat Genet 2019 04;51(4):765

Department of Plant Sciences, University of California-Davis, Davis, CA, USA.

In the version of this article originally published, author Joshua R. Puzey was incorrectly listed as having affiliation 7 (School of Plant Sciences, University of Arizona, Tucson, AZ, USA); affiliation 6 (Department of Biology, College of William and Mary, Williamsburg, VA, USA) is the correct affiliation. The error has been corrected in the HTML and PDF versions of the article. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0380-4DOI Listing
April 2019
14 Reads

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Nat Genet 2019 04 4;51(4):716-727. Epub 2019 Mar 4.

Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.

Mesenchymal (stromal) stem cells (MSCs) constitute populations of mesodermal multipotent cells involved in tissue regeneration and homeostasis in many different organs. Here we performed comprehensive characterization of the transcriptional and epigenomic changes associated with osteoblast and adipocyte differentiation of human MSCs. We demonstrate that adipogenesis is driven by considerable remodeling of the chromatin landscape and de novo activation of enhancers, whereas osteogenesis involves activation of preestablished enhancers. Read More

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0359-1
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0359-1DOI Listing

Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements.

Nat Genet 2019 04 4;51(4):705-715. Epub 2019 Mar 4.

Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.

Cancer genomes are frequently characterized by numerical and structural chromosomal abnormalities. Here we integrated a centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy termed CEN-SELECT, to systematically interrogate the structural landscape of mis-segregated chromosomes. We show that single-chromosome mis-segregation into a micronucleus can directly trigger a broad spectrum of genomic rearrangement types. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0360-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441390PMC
April 2019
4 Reads

Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing.

Authors:
Brian W Kunkle Benjamin Grenier-Boley Rebecca Sims Joshua C Bis Vincent Damotte Adam C Naj Anne Boland Maria Vronskaya Sven J van der Lee Alexandre Amlie-Wolf Céline Bellenguez Aura Frizatti Vincent Chouraki Eden R Martin Kristel Sleegers Nandini Badarinarayan Johanna Jakobsdottir Kara L Hamilton-Nelson Sonia Moreno-Grau Robert Olaso Rachel Raybould Yuning Chen Amanda B Kuzma Mikko Hiltunen Taniesha Morgan Shahzad Ahmad Badri N Vardarajan Jacques Epelbaum Per Hoffmann Merce Boada Gary W Beecham Jean-Guillaume Garnier Denise Harold Annette L Fitzpatrick Otto Valladares Marie-Laure Moutet Amy Gerrish Albert V Smith Liming Qu Delphine Bacq Nicola Denning Xueqiu Jian Yi Zhao Maria Del Zompo Nick C Fox Seung-Hoan Choi Ignacio Mateo Joseph T Hughes Hieab H Adams John Malamon Florentino Sanchez-Garcia Yogen Patel Jennifer A Brody Beth A Dombroski Maria Candida Deniz Naranjo Makrina Daniilidou Gudny Eiriksdottir Shubhabrata Mukherjee David Wallon James Uphill Thor Aspelund Laura B Cantwell Fabienne Garzia Daniela Galimberti Edith Hofer Mariusz Butkiewicz Bertrand Fin Elio Scarpini Chloe Sarnowski Will S Bush Stéphane Meslage Johannes Kornhuber Charles C White Yuenjoo Song Robert C Barber Sebastiaan Engelborghs Sabrina Sordon Dina Voijnovic Perrie M Adams Rik Vandenberghe Manuel Mayhaus L Adrienne Cupples Marilyn S Albert Peter P De Deyn Wei Gu Jayanadra J Himali Duane Beekly Alessio Squassina Annette M Hartmann Adelina Orellana Deborah Blacker Eloy Rodriguez-Rodriguez Simon Lovestone Melissa E Garcia Rachelle S Doody Carmen Munoz-Fernadez Rebecca Sussams Honghuang Lin Thomas J Fairchild Yolanda A Benito Clive Holmes Hata Karamujić-Čomić Matthew P Frosch Hakan Thonberg Wolfgang Maier Gena Roschupkin Bernardino Ghetti Vilmantas Giedraitis Amit Kawalia Shuo Li Ryan M Huebinger Lena Kilander Susanne Moebus Isabel Hernández M Ilyas Kamboh RoseMarie Brundin James Turton Qiong Yang Mindy J Katz Letizia Concari Jenny Lord Alexa S Beiser C Dirk Keene Seppo Helisalmi Iwona Kloszewska Walter A Kukull Anne Maria Koivisto Aoibhinn Lynch Lluís Tarraga Eric B Larson Annakaisa Haapasalo Brian Lawlor Thomas H Mosley Richard B Lipton Vincenzo Solfrizzi Michael Gill W T Longstreth Thomas J Montine Vincenza Frisardi Monica Diez-Fairen Fernando Rivadeneira Ronald C Petersen Vincent Deramecourt Ignacio Alvarez Francesca Salani Antonio Ciaramella Eric Boerwinkle Eric M Reiman Nathalie Fievet Jerome I Rotter Joan S Reisch Olivier Hanon Chiara Cupidi A G Andre Uitterlinden Donald R Royall Carole Dufouil Raffaele Giovanni Maletta Itziar de Rojas Mary Sano Alexis Brice Roberta Cecchetti Peter St George-Hyslop Karen Ritchie Magda Tsolaki Debby W Tsuang Bruno Dubois David Craig Chuang-Kuo Wu Hilkka Soininen Despoina Avramidou Roger L Albin Laura Fratiglioni Antonia Germanou Liana G Apostolova Lina Keller Maria Koutroumani Steven E Arnold Francesco Panza Olymbia Gkatzima Sanjay Asthana Didier Hannequin Patrice Whitehead Craig S Atwood Paolo Caffarra Harald Hampel Inés Quintela Ángel Carracedo Lars Lannfelt David C Rubinsztein Lisa L Barnes Florence Pasquier Lutz Frölich Sandra Barral Bernadette McGuinness Thomas G Beach Janet A Johnston James T Becker Peter Passmore Eileen H Bigio Jonathan M Schott Thomas D Bird Jason D Warren Bradley F Boeve Michelle K Lupton James D Bowen Petra Proitsi Adam Boxer John F Powell James R Burke John S K Kauwe Jeffrey M Burns Michelangelo Mancuso Joseph D Buxbaum Ubaldo Bonuccelli Nigel J Cairns Andrew McQuillin Chuanhai Cao Gill Livingston Chris S Carlson Nicholas J Bass Cynthia M Carlsson John Hardy Regina M Carney Jose Bras Minerva M Carrasquillo Rita Guerreiro Mariet Allen Helena C Chui Elizabeth Fisher Carlo Masullo Elizabeth A Crocco Charles DeCarli Gina Bisceglio Malcolm Dick Li Ma Ranjan Duara Neill R Graff-Radford Denis A Evans Angela Hodges Kelley M Faber Martin Scherer Kenneth B Fallon Matthias Riemenschneider David W Fardo Reinhard Heun Martin R Farlow Heike Kölsch Steven Ferris Markus Leber Tatiana M Foroud Isabella Heuser Douglas R Galasko Ina Giegling Marla Gearing Michael Hüll Daniel H Geschwind John R Gilbert John Morris Robert C Green Kevin Mayo John H Growdon Thomas Feulner Ronald L Hamilton Lindy E Harrell Dmitriy Drichel Lawrence S Honig Thomas D Cushion Matthew J Huentelman Paul Hollingworth Christine M Hulette Bradley T Hyman Rachel Marshall Gail P Jarvik Alun Meggy Erin Abner Georgina E Menzies Lee-Way Jin Ganna Leonenko Luis M Real Gyungah R Jun Clinton T Baldwin Detelina Grozeva Anna Karydas Giancarlo Russo Jeffrey A Kaye Ronald Kim Frank Jessen Neil W Kowall Bruno Vellas Joel H Kramer Emma Vardy Frank M LaFerla Karl-Heinz Jöckel James J Lah Martin Dichgans James B Leverenz David Mann Allan I Levey Stuart Pickering-Brown Andrew P Lieberman Norman Klopp Kathryn L Lunetta H-Erich Wichmann Constantine G Lyketsos Kevin Morgan Daniel C Marson Kristelle Brown Frank Martiniuk Christopher Medway Deborah C Mash Markus M Nöthen Eliezer Masliah Nigel M Hooper Wayne C McCormick Antonio Daniele Susan M McCurry Anthony Bayer Andrew N McDavid John Gallacher Ann C McKee Hendrik van den Bussche Marsel Mesulam Carol Brayne Bruce L Miller Steffi Riedel-Heller Carol A Miller Joshua W Miller Ammar Al-Chalabi John C Morris Christopher E Shaw Amanda J Myers Jens Wiltfang Sid O'Bryant John M Olichney Victoria Alvarez Joseph E Parisi Andrew B Singleton Henry L Paulson John Collinge William R Perry Simon Mead Elaine Peskind David H Cribbs Martin Rossor Aimee Pierce Natalie S Ryan Wayne W Poon Benedetta Nacmias Huntington Potter Sandro Sorbi Joseph F Quinn Eleonora Sacchinelli Ashok Raj Gianfranco Spalletta Murray Raskind Carlo Caltagirone Paola Bossù Maria Donata Orfei Barry Reisberg Robert Clarke Christiane Reitz A David Smith John M Ringman Donald Warden Erik D Roberson Gordon Wilcock Ekaterina Rogaeva Amalia Cecilia Bruni Howard J Rosen Maura Gallo Roger N Rosenberg Yoav Ben-Shlomo Mark A Sager Patrizia Mecocci Andrew J Saykin Pau Pastor Michael L Cuccaro Jeffery M Vance Julie A Schneider Lori S Schneider Susan Slifer William W Seeley Amanda G Smith Joshua A Sonnen Salvatore Spina Robert A Stern Russell H Swerdlow Mitchell Tang Rudolph E Tanzi John Q Trojanowski Juan C Troncoso Vivianna M Van Deerlin Linda J Van Eldik Harry V Vinters Jean Paul Vonsattel Sandra Weintraub Kathleen A Welsh-Bohmer Kirk C Wilhelmsen Jennifer Williamson Thomas S Wingo Randall L Woltjer Clinton B Wright Chang-En Yu Lei Yu Yasaman Saba Alberto Pilotto Maria J Bullido Oliver Peters Paul K Crane David Bennett Paola Bosco Eliecer Coto Virginia Boccardi Phil L De Jager Alberto Lleo Nick Warner Oscar L Lopez Martin Ingelsson Panagiotis Deloukas Carlos Cruchaga Caroline Graff Rhian Gwilliam Myriam Fornage Alison M Goate Pascual Sanchez-Juan Patrick G Kehoe Najaf Amin Nilifur Ertekin-Taner Claudine Berr Stéphanie Debette Seth Love Lenore J Launer Steven G Younkin Jean-Francois Dartigues Chris Corcoran M Arfan Ikram Dennis W Dickson Gael Nicolas Dominique Campion JoAnn Tschanz Helena Schmidt Hakon Hakonarson Jordi Clarimon Ron Munger Reinhold Schmidt Lindsay A Farrer Christine Van Broeckhoven Michael C O'Donovan Anita L DeStefano Lesley Jones Jonathan L Haines Jean-Francois Deleuze Michael J Owen Vilmundur Gudnason Richard Mayeux Valentina Escott-Price Bruce M Psaty Alfredo Ramirez Li-San Wang Agustin Ruiz Cornelia M van Duijn Peter A Holmans Sudha Seshadri Julie Williams Phillippe Amouyel Gerard D Schellenberg Jean-Charles Lambert Margaret A Pericak-Vance

Nat Genet 2019 03 28;51(3):414-430. Epub 2019 Feb 28.

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.

Risk for late-onset Alzheimer's disease (LOAD), the most prevalent dementia, is partially driven by genetics. To identify LOAD risk loci, we performed a large genome-wide association meta-analysis of clinically diagnosed LOAD (94,437 individuals). We confirm 20 previous LOAD risk loci and identify five new genome-wide loci (IQCK, ACE, ADAM10, ADAMTS1, and WWOX), two of which (ADAM10, ACE) were identified in a recent genome-wide association (GWAS)-by-familial-proxy of Alzheimer's or dementia. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0358-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463297PMC
March 2019
15 Reads
29.352 Impact Factor

Brave new dialogue.

Authors:

Nat Genet 2019 03;51(3):365

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0374-2DOI Listing

The origin and evolution of a favorite fruit.

Authors:
David J Bertioli

Nat Genet 2019 03;51(3):372-373

Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0365-3
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0365-3DOI Listing
March 2019
13 Reads

Author Correction: The copy number variation landscape of congenital anomalies of the kidney and urinary tract.

Nat Genet 2019 04;51(4):764

Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.

In the version of this article initially published, affiliation 38 incorrectly read "ICNU-Nephrology and Urology Department, Barcelona, Spain"; "Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain" is the correct affiliation. The error has been corrected in the HTML and PDF versions of the article. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0376-0DOI Listing
April 2019
3 Reads

Author Correction: Repurposing large health insurance claims data to estimate genetic and environmental contributions in 560 phenotypes.

Nat Genet 2019 04;51(4):764-765

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

In the version of this article initially published, in Fig. 4b, the shared environmental variance (c) values for all MaTCH functional domains except 'all traits' were erroneously estimated because of a coding error. Figure 4 has been revised to include corrected c estimates in the data in panel b as well as the number of phenotypes in CaTCH and MaTCH functional domains in the y axes of panels a and b; the Fig. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0377-zDOI Listing
April 2019
29.352 Impact Factor

Biological and clinical insights from genetics of insomnia symptoms.

Nat Genet 2019 03 25;51(3):387-393. Epub 2019 Feb 25.

Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.

Insomnia is a common disorder linked with adverse long-term medical and psychiatric outcomes. The underlying pathophysiological processes and causal relationships of insomnia with disease are poorly understood. Here we identified 57 loci for self-reported insomnia symptoms in the UK Biobank (n = 453,379) and confirmed their effects on self-reported insomnia symptoms in the HUNT Study (n = 14,923 cases and 47,610 controls), physician-diagnosed insomnia in the Partners Biobank (n = 2,217 cases and 14,240 controls), and accelerometer-derived measures of sleep efficiency and sleep duration in the UK Biobank (n = 83,726). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0361-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415688PMC
March 2019
3 Reads

Genome-wide analysis of insomnia in 1,331,010 individuals identifies new risk loci and functional pathways.

Nat Genet 2019 03 25;51(3):394-403. Epub 2019 Feb 25.

Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands.

Insomnia is the second most prevalent mental disorder, with no sufficient treatment available. Despite substantial heritability, insight into the associated genes and neurobiological pathways remains limited. Here, we use a large genetic association sample (n = 1,331,010) to detect novel loci and gain insight into the pathways, tissue and cell types involved in insomnia complaints. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-018-0333-3DOI Listing
March 2019
1 Read
29.352 Impact Factor

Reconciling disparate estimates of viral genetic diversity during human influenza infections.

Nat Genet 2019 Feb 25. Epub 2019 Feb 25.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0349-3DOI Listing
February 2019

A statistical framework for cross-tissue transcriptome-wide association analysis.

Nat Genet 2019 03 25;51(3):568-576. Epub 2019 Feb 25.

Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA.

Transcriptome-wide association analysis is a powerful approach to studying the genetic architecture of complex traits. A key component of this approach is to build a model to impute gene expression levels from genotypes by using samples with matched genotypes and gene expression data in a given tissue. However, it is challenging to develop robust and accurate imputation models with a limited sample size for any single tissue. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0345-7DOI Listing
March 2019
1 Read

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing.

Nat Genet 2019 04 25;51(4):755-763. Epub 2019 Feb 25.

Department of Computer Science, Stanford University, Stanford, CA, USA.

Exome analysis of patients with a likely monogenic disease does not identify a causal variant in over half of cases. Splice-disrupting mutations make up the second largest class of known disease-causing mutations. Each individual (singleton) exome harbors over 500 rare variants of unknown significance (VUS) in the splicing region. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0348-4DOI Listing

Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations.

Nat Genet 2019 03 25;51(3):494-505. Epub 2019 Feb 25.

Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.

Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-018-0342-2DOI Listing
March 2019
1 Read
29.352 Impact Factor

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Authors:
Nick Shrine Anna L Guyatt A Mesut Erzurumluoglu Victoria E Jackson Brian D Hobbs Carl A Melbourne Chiara Batini Katherine A Fawcett Kijoung Song Phuwanat Sakornsakolpat Xingnan Li Ruth Boxall Nicola F Reeve Ma'en Obeidat Jing Hua Zhao Matthias Wielscher Stefan Weiss Katherine A Kentistou James P Cook Benjamin B Sun Jian Zhou Jennie Hui Stefan Karrasch Medea Imboden Sarah E Harris Jonathan Marten Stefan Enroth Shona M Kerr Ida Surakka Veronique Vitart Terho Lehtimäki Richard J Allen Per S Bakke Terri H Beaty Eugene R Bleecker Yohan Bossé Corry-Anke Brandsma Zhengming Chen James D Crapo John Danesh Dawn L DeMeo Frank Dudbridge Ralf Ewert Christian Gieger Amund Gulsvik Anna L Hansell Ke Hao Joshua D Hoffman John E Hokanson Georg Homuth Peter K Joshi Philippe Joubert Claudia Langenberg Xuan Li Liming Li Kuang Lin Lars Lind Nicholas Locantore Jian'an Luan Anubha Mahajan Joseph C Maranville Alison Murray David C Nickle Richard Packer Margaret M Parker Megan L Paynton David J Porteous Dmitry Prokopenko Dandi Qiao Rajesh Rawal Heiko Runz Ian Sayers Don D Sin Blair H Smith María Soler Artigas David Sparrow Ruth Tal-Singer Paul R H J Timmers Maarten Van den Berge John C Whittaker Prescott G Woodruff Laura M Yerges-Armstrong Olga G Troyanskaya Olli T Raitakari Mika Kähönen Ozren Polašek Ulf Gyllensten Igor Rudan Ian J Deary Nicole M Probst-Hensch Holger Schulz Alan L James James F Wilson Beate Stubbe Eleftheria Zeggini Marjo-Riitta Jarvelin Nick Wareham Edwin K Silverman Caroline Hayward Andrew P Morris Adam S Butterworth Robert A Scott Robin G Walters Deborah A Meyers Michael H Cho David P Strachan Ian P Hall Martin D Tobin Louise V Wain

Nat Genet 2019 03 25;51(3):481-493. Epub 2019 Feb 25.

Department of Health Sciences, University of Leicester, Leicester, UK.

Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent populations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-018-0321-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397078PMC
March 2019
4 Reads
29.352 Impact Factor

Genome-wide stability of the DNA replication program in single mammalian cells.

Nat Genet 2019 03 25;51(3):529-540. Epub 2019 Feb 25.

Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.

Here, we report a single-cell DNA replication sequencing method, scRepli-seq, a genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication-domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct profiles, which were also conserved among cells. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0347-5DOI Listing

Identification of common genetic risk variants for autism spectrum disorder.

Nat Genet 2019 03 25;51(3):431-444. Epub 2019 Feb 25.

The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.

Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample-size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 individuals with ASD and 27,969 controls that identified five genome-wide-significant loci. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0344-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454898PMC
March 2019
4 Reads
29.352 Impact Factor

Origin and evolution of the octoploid strawberry genome.

Nat Genet 2019 03 25;51(3):541-547. Epub 2019 Feb 25.

Department of Plant Sciences, University of California-Davis, Davis, California, USA.

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. Read More

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-019-0356-4
Publisher Site
http://dx.doi.org/10.1038/s41588-019-0356-4DOI Listing
March 2019
16 Reads

Reply to 'TMEM230 variants in Parkinson's disease' and 'Doubts about TMEM230 as a gene for parkinsonism'.

Nat Genet 2019 03;51(3):369-371

Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0355-5DOI Listing

TMEM230 variants in Parkinson's disease.

Nat Genet 2019 03;51(3):366

Department of Neurology, Oslo University Hospital, Oslo, Norway.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0353-7DOI Listing
March 2019
29.352 Impact Factor

Doubts about TMEM230 as a gene for parkinsonism.

Authors:
Matt J Farrer

Nat Genet 2019 03;51(3):367-368

Centre for Applied Neurogenetics, University of British Columbia, Vancouver, British Columbia, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0354-6DOI Listing

Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences.

Nat Genet 2019 03;51(3):577

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

In the version of this article initially published, in the Methods section 'Statistics and data analysis', subsection 'Measuring entropy with INSIGHT', the equation for the maximized log likelihood incorrectly duplicated the equation for entropy; the equation read but should have read. The error has been corrected in the HTML and PDF versions of the article. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-019-0369-zDOI Listing

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.

Authors:
Anne E Justice Tugce Karaderi Heather M Highland Kristin L Young Mariaelisa Graff Yingchang Lu Valérie Turcot Paul L Auer Rebecca S Fine Xiuqing Guo Claudia Schurmann Adelheid Lempradl Eirini Marouli Anubha Mahajan Thomas W Winkler Adam E Locke Carolina Medina-Gomez Tõnu Esko Sailaja Vedantam Ayush Giri Ken Sin Lo Tamuno Alfred Poorva Mudgal Maggie C Y Ng Nancy L Heard-Costa Mary F Feitosa Alisa K Manning Sara M Willems Suthesh Sivapalaratnam Goncalo Abecasis Dewan S Alam Matthew Allison Philippe Amouyel Zorayr Arzumanyan Beverley Balkau Lisa Bastarache Sven Bergmann Lawrence F Bielak Matthias Blüher Michael Boehnke Heiner Boeing Eric Boerwinkle Carsten A Böger Jette Bork-Jensen Erwin P Bottinger Donald W Bowden Ivan Brandslund Linda Broer Amber A Burt Adam S Butterworth Mark J Caulfield Giancarlo Cesana John C Chambers Daniel I Chasman Yii-Der Ida Chen Rajiv Chowdhury Cramer Christensen Audrey Y Chu Francis S Collins James P Cook Amanda J Cox David S Crosslin John Danesh Paul I W de Bakker Simon de Denus Renée de Mutsert George Dedoussis Ellen W Demerath Joe G Dennis Josh C Denny Emanuele Di Angelantonio Marcus Dörr Fotios Drenos Marie-Pierre Dubé Alison M Dunning Douglas F Easton Paul Elliott Evangelos Evangelou Aliki-Eleni Farmaki Shuang Feng Ele Ferrannini Jean Ferrieres Jose C Florez Myriam Fornage Caroline S Fox Paul W Franks Nele Friedrich Wei Gan Ilaria Gandin Paolo Gasparini Vilmantas Giedraitis Giorgia Girotto Mathias Gorski Harald Grallert Niels Grarup Megan L Grove Stefan Gustafsson Jeff Haessler Torben Hansen Andrew T Hattersley Caroline Hayward Iris M Heid Oddgeir L Holmen G Kees Hovingh Joanna M M Howson Yao Hu Yi-Jen Hung Kristian Hveem M Arfan Ikram Erik Ingelsson Anne U Jackson Gail P Jarvik Yucheng Jia Torben Jørgensen Pekka Jousilahti Johanne M Justesen Bratati Kahali Maria Karaleftheri Sharon L R Kardia Fredrik Karpe Frank Kee Hidetoshi Kitajima Pirjo Komulainen Jaspal S Kooner Peter Kovacs Bernhard K Krämer Kari Kuulasmaa Johanna Kuusisto Markku Laakso Timo A Lakka David Lamparter Leslie A Lange Claudia Langenberg Eric B Larson Nanette R Lee Wen-Jane Lee Terho Lehtimäki Cora E Lewis Huaixing Li Jin Li Ruifang Li-Gao Li-An Lin Xu Lin Lars Lind Jaana Lindström Allan Linneberg Ching-Ti Liu Dajiang J Liu Jian'an Luan Leo-Pekka Lyytikäinen Stuart MacGregor Reedik Mägi Satu Männistö Gaëlle Marenne Jonathan Marten Nicholas G D Masca Mark I McCarthy Karina Meidtner Evelin Mihailov Leena Moilanen Marie Moitry Dennis O Mook-Kanamori Anna Morgan Andrew P Morris Martina Müller-Nurasyid Patricia B Munroe Narisu Narisu Christopher P Nelson Matt Neville Ioanna Ntalla Jeffrey R O'Connell Katharine R Owen Oluf Pedersen Gina M Peloso Craig E Pennell Markus Perola James A Perry John R B Perry Tune H Pers Ailith Ewing Ozren Polasek Olli T Raitakari Asif Rasheed Chelsea K Raulerson Rainer Rauramaa Dermot F Reilly Alex P Reiner Paul M Ridker Manuel A Rivas Neil R Robertson Antonietta Robino Igor Rudan Katherine S Ruth Danish Saleheen Veikko Salomaa Nilesh J Samani Pamela J Schreiner Matthias B Schulze Robert A Scott Marcelo Segura-Lepe Xueling Sim Andrew J Slater Kerrin S Small Blair H Smith Jennifer A Smith Lorraine Southam Timothy D Spector Elizabeth K Speliotes Kari Stefansson Valgerdur Steinthorsdottir Kathleen E Stirrups Konstantin Strauch Heather M Stringham Michael Stumvoll Liang Sun Praveen Surendran Karin M A Swart Jean-Claude Tardif Kent D Taylor Alexander Teumer Deborah J Thompson Gudmar Thorleifsson Unnur Thorsteinsdottir Betina H Thuesen Anke Tönjes Mina Torres Emmanouil Tsafantakis Jaakko Tuomilehto André G Uitterlinden Matti Uusitupa Cornelia M van Duijn Mauno Vanhala Rohit Varma Sita H Vermeulen Henrik Vestergaard Veronique Vitart Thomas F Vogt Dragana Vuckovic Lynne E Wagenknecht Mark Walker Lars Wallentin Feijie Wang Carol A Wang Shuai Wang Nicholas J Wareham Helen R Warren Dawn M Waterworth Jennifer Wessel Harvey D White Cristen J Willer James G Wilson Andrew R Wood Ying Wu Hanieh Yaghootkar Jie Yao Laura M Yerges-Armstrong Robin Young Eleftheria Zeggini Xiaowei Zhan Weihua Zhang Jing Hua Zhao Wei Zhao He Zheng Wei Zhou M Carola Zillikens Fernando Rivadeneira Ingrid B Borecki J Andrew Pospisilik Panos Deloukas Timothy M Frayling Guillaume Lettre Karen L Mohlke Jerome I Rotter Zoltán Kutalik Joel N Hirschhorn L Adrienne Cupples Ruth J F Loos Kari E North Cecilia M Lindgren

Nat Genet 2019 03 18;51(3):452-469. Epub 2019 Feb 18.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

Body-fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body-fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF ≥5%) and nine low-frequency or rare (MAF <5%) coding novel variants. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-018-0334-2DOI Listing
March 2019
12 Reads
29.352 Impact Factor